bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of fractional flow reserve and atherosclerotic plaque characteristics on coronary non-contrast T1-weighted magnetic resonance imaging
Authors: Sugane Hiroki , Asaumi Yasuhide , Ogata Soshiro , Kimura Michito , Kanaya Tomoaki , Hoshi Tomoya , Sato Akira , Miura Hiroyuki , Tomishima Yoshiyuki , Morita Yoshiaki , Nakao Kazuhiro , Otsuka Fumiyuku , Kataoka Yu , Kawasaki Tomohiro , Nishimura Kunihiro , Narula Jagat , Yasuda Satoshi , Noguchi Teruo
Published: August 2023

Background

The relationship between high-risk coronary plaque characteristics regardless of the severity of lesion stenosis and myocardial ischemia remains unsettled. High-intensity plaques (HIPs) on non-contrast T1-weighted magnetic resonance imaging (T1WI) have been characterized as high-risk coronary plaques. We sought to elucidate whether the presence of coronary HIPs on T1WI influences fractional flow reserve (FFR) in the distal segment of the vessel.

Methods

We retrospectively analyzed 232 vessels in 190 patients with chronic stable coronary syndrome who underwent both invasive FFR measurement and coronary T1WI using a multicenter registry. The plaque-to-myocardial signal intensity ratio (PMR) of the most stenotic lesion was evaluated; a coronary plaque with PMR >1.4 was defined as a HIP.

Results

The median PMR of coronary plaques on T1WI in vessels with FFR ≤0.80 was significantly higher than that of plaques with FFR >0.80 (1.18 [interquartile range (IQR): 0.96–1.45] vs. 0.97 [IQR: 0.85–1.12]; p<0.001)). Multivariable analysis showed that an increase in PMR of the most stenotic segment is associated with lower FFR (beta-coefficient, –0.051; p<0.001). The presence of coronary HIPs was an independent predictor of FFR ≤0.80 (odds ratio, 5.54; 95% confidence interval, 1.50–20.5; p=0.010).

Conclusions

Coronary plaques with high PMR are associated with low FFR in the corresponding vessel, indicating that plaque morphology might influence the degree of myocardial ischemia.

Trial registration

UMIN 000029246

Clinical Perspective

What is new?

Incremental of coronary plaque to myocardial signal intensity ratio on T1-weithted magnetic resonance imaging (T1WI), which is represented as instability of coronary plaques was associated with low factional flow reserve (FFR) value in patients with chronic coronary syndrome (CCS).

The presence of a coronary high-intensity plaque (HIP) detected with T1WI is a strong predictor of low fractional flow reserve (FFR) even after adjusting age, gender, proximal left anterior descending artery, the severity of stenosis in the most stenotic lesion and variables related to plaque volume evaluated on computed tomography angiography.

What are the clinical implications?

Non-contrast T1WI without contrast media is an anatomy-based, but not ischemia-based, screening method for predicting future coronary events.

The presence of a coronary HIP on T1WI, which represents a complicated atheroma, is an additional determinant of coronary physiology.
Tetherin restricts SARS-CoV-2 replication despite antagonistic effects of Spike and ORF7a
Authors: Hagelauer Elena , Lotke Rishikesh , Kmiec Dorota , Hu Dan , Hohner Mirjam , Stopper Sophie , Layer Mirjam , Nchioua Rayhane , Kirchhoff Frank , Sauter Daniel , Schindler Michael
Published: August 2023

SARS-CoV-2 infection induces interferon-stimulated genes, one of which encodes Tetherin, a transmembrane protein inhibiting the release of various enveloped viruses from infected cells. Previous studies revealed that SARS-CoV encodes two Tetherin antagonists: the Spike protein (S) inducing lysosomal degradation of Tetherin, and ORF7a altering its glycosylation. SARS-CoV-2 ORF7a has also been shown to antagonize Tetherin. Therefore, we here investigated whether SARS-CoV-2 S is also a Tetherin antagonist and compared the abilities and mechanisms of S and ORF7a in counteracting Tetherin. SARS-CoV and SARS-CoV-2 S reduced Tetherin cell surface levels in a cell type-dependent manner, possibly related to the basal protein levels of Tetherin. In HEK293T cells, under conditions of high exogenous Tetherin expression, SARS-CoV-2 S and ORF7a reduced total Tetherin levels much more efficiently than the respective counterparts derived from SARS-CoV. Nevertheless, ORF7a from both strains was able to alter Tetherin glycosylation. The ability to decrease total protein levels of Tetherin was conserved among S proteins from different SARS-CoV-2 variants (D614G, Cluster 5, α, γ, δ, ο). While SARS-CoV-2 S and ORF7a both colocalized with Tetherin, only ORF7a directly interacted with the restriction factor. Despite the presence of two Tetherin antagonists, however, SARS-CoV-2 replication in Caco-2 cells was further enhanced upon Tetherin knockout. Altogether, our data show that endogenous Tetherin restricts SARS-CoV-2 replication, and that the antiviral activity of Tetherin is partially counteracted by two viral antagonists with differential and complementary modes of action, S and ORF7a.

IMPORTANCE

Viruses have adopted multiple strategies to cope with innate antiviral immunity. They blunt signaling and encode proteins that counteract antiviral host factors. One such factor is Tetherin, that tethers nascent virions to the cell membrane and interferes with virus release. For SARS-CoV, the viral glycoprotein Spike (S) and the accessory protein ORF7a are Tetherin antagonists. For pandemic SARS-CoV-2, such activity has only been shown for ORF7a. We therefore analyzed whether SARS-CoV-2 S is a Tetherin-counteracting protein and whether there are differences in the abilities of the viral proteins to antagonize Tetherin. Of note, the efficiency of Tetherin antagonism was more pronounced for S and ORF7a from SARS-CoV-2 compared to their SARS-CoV orthologs. Still, Tetherin was able to restrict SARS-CoV-2 replication. Our results highlight the fundamental importance of the innate immune response in the context of SARS-CoV-2 control and the evolutionary pressure on pathogenic viruses to withhold efficient Tetherin antagonism.
Multi-omic spatial effects on high-resolution AI-derived retinal thickness
Authors: Jackson VE , Wu Y , Bonelli R , Owen J , Farashi S , Kihara Y , Gantner ML , Egan C , Williams KM , Ansell BRE , Tufail A , Lee AY , Bahlo M
Published: August 2023

Retinal thickness is a marker of retinal health and more broadly, is seen as a promising biomarker for many systemic diseases. Retinal thickness measurements are procured from optical coherence tomography (OCT) as part of routine clinical eyecare. We processed the UK Biobank OCT images using a convolutional neural network to produce fine-scale retinal thickness measurements across >29,000 points in the macula, the part of the retina responsible for human central vision. The macula is disproportionately affected by high disease burden retinal disorders such as age-related macular degeneration and diabetic retinopathy, which both involve metabolic dysregulation. Analysis of common genomic variants, metabolomic, blood and immune biomarkers, ICD10 codes and polygenic risk scores across a fine-scale macular thickness grid, reveals multiple novel genetic loci-including four on the X chromosome; retinal thinning associated with many systemic disorders including multiple sclerosis; and multiple associations to correlated metabolites that cluster spatially in the retina. We highlight parafoveal thickness to be particularly susceptible to systemic insults. These results demonstrate the gains in discovery power and resolution achievable with AI-leveraged analysis. Results are accessible using a bespoke web interface that gives full control to pursue findings.

Graphical Abstract
Recommended distances for physical distancing during COVID-19 pandemics reveal cultural connections between countries
Authors: Chai Dongwoo , El Mossadeq Layla , Raymond Michel , Courtier-Orgogozo Virginie
Published: August 2023

During COVID-19 pandemic several public health measures were implemented by diverse countries to reduce the risk of COVID-19, including social distancing. Here we collected the minimal distance recommended by each country for physical distancing at the onset of the pandemic and aimed to examine whether it had an impact on the outbreak dynamics and how this specific value was chosen. Despite an absence of data on SARS-CoV-2 viral transmission at the beginning of the pandemic, we found that most countries recommended physical distancing with a precise minimal distance, between one meter/three feet and two meters/six feet. 45% of the countries advised one meter/three feet and 49% advised a higher minimal distance. The recommended minimal distance did not show a clear correlation with reproduction rate nor with the number of new cases per million, suggesting that the overall COVID-19 dynamics in each country depended on multiple interacting factors. Interestingly, the recommended minimal distance correlated with several cultural parameters: it was higher in countries with larger interpersonal distance between two interacting individuals in non-epidemic conditions, and it correlated with civil law systems, and with currency. This suggests that countries which share common conceptions such as civil law systems and currency unions tend to adopt the same public health measures.
Autoimmune inflammation triggers aberrant astrocytic calcium signaling to impair synaptic plasticity
Authors: Baraibar AM , Colomer T , Moreno-García A , Bernal-Chico A , Sánchez E , Utrilla C , Serrat R , Soria-Gómez E , Rodríguez-Antigüedad A , Araque A , Matute C , Marsicano G , Mato S
Published: August 2023

Cortical pathology involving inflammatory and neurodegenerative mechanisms is a hallmark of multiple sclerosis (MS) and a correlate of disease progression and cognitive decline. Astrocytes play a pivotal role in MS initiation and progression but astrocyte-neuronal network alterations contributing to gray matter pathology remain undefined. Here we measured astrocytic calcium in the experimental autoimmune encephalomyelitis (EAE) model of MS using fiber photometry in freely behaving mice and two-photon imagingex vivo. We identified the emergence of spontaneously hyperactive cortical astrocytes displaying calcium transients of increased duration as well as dysfunctional responses to cannabinoid, glutamate and purinoreceptor agonists during acute EAE disease. Deficits in astrocyte calcium responses are associated to abnormal signaling by Giand Gqprotein coupled receptors in the inflamed cortex and are partially mirrored in cells activated with pro-inflammatory factors bothin vitroandex vivothus suggesting cell-autonomous effects of the cortical neuroinflammatory environment. Finally, we show that deregulated astrocyte calcium activity is associated to an enhancement of glutamatergic gliotransmission and a shift of astrocyte-mediated short-term and long-term plasticity mechanisms towards synaptic potentiation. Overall our data identities astrocyte-neuronal network dysfunction as key pathological feature of the inflammatory gray matter that may contribute to MS symptomatology and clinical progression.
Central inhibition of Stearoyl-CoA Desaturase has minimal effects on the peripheral metabolic symptoms of the 3xTg Alzheimer’s disease mouse model
Authors: Hamilton Laura K. , Mbra Paule , Mailloux Sophia , Galoppin Manon , Aumont Anne , Fernandes Karl J.L.
Published: August 2023

Evidence from genetic and epidemiological studies point to lipid metabolism defects in both the brain and periphery being at the core of Alzheimer’s disease (AD) pathogenesis. Previously, we reported that central inhibition of the rate-limiting enzyme in monounsaturated fatty acid synthesis, Stearoyl-CoA Desaturase (SCD), improves brain structure and function in the 3xTg mouse model of AD (3xTg-AD). Here, we tested whether these beneficial central effects involve recovery of peripheral metabolic defects, such as fat accumulation and glucose and insulin handling. As early as 3 months of age, 3xTg-AD mice exhibited obesity-like phenotypes including increased body weight and visceral and subcutaneous white adipose tissue deposition, as well as diabetic-like peripheral gluco-regulatory abnormalities. Intracerebral infusion of an SCD inhibitor that normalizes brain fatty acid metabolism, synapse loss and learning and memory deficits in middle-aged symptomatic 3xTg-AD mice did not affect peripheral phenotypes. This suggests that the beneficial effects of central SCD inhibition on cognitive function are not mediated by recovery of peripheral metabolic abnormalities. Given the widespread side-effects of systemically administered SCD inhibitors, these data suggest that selective inhibition of SCD in the brain may represent a clinically safer and more effective strategy for AD.
Cell adhesion marker expression dynamics during fusion of the optic fissure
Authors: Hardy Holly , Rainger Joe
Published: August 2023

Tissue fusion is a critical process that is repeated in multiple contexts during embryonic development and shares common attributes to processes such as wound healing and metastases. Ocular coloboma is a developmental eye disorder that presents as a physical gap in the ventral eye, and is a major cause of childhood blindness. Coloboma results from fusion failure between opposing ventral retinal epithelia, but there are major knowledge gaps in our understanding of this process at the molecular and cell behavioural levels. Here we catalogue the expression of cell adhesion proteins: N-cadherin, E-cadherin, ZO-1, and the EMT transcriptional activator and cadherin regulator SNAI2. We find that fusion pioneer cells at the edges of the fusing optic fissure have unique and dynamic expression profiles for N-cad, E-cad and ZO-1, and that these are temporally preceded by expression of SNAI2. This highlights the unique properties of these cells and indicates that regulation of cell adhesion factors is a critical process in optic fissure closure.
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings
Authors: LeRoy Nathan J. , Smith Jason P. , Zheng Guangtao , Rymuza Julia , Gharavi Erfaneh , Brown Donald E. , Zhang Aidong , Sheffield Nathan C.
Published: August 2023

Motivation

Data from the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is now widely available. One major computational challenge is dealing with high dimensionality and inherent sparsity, which is typically addressed by producing lower-dimensional representations of single cells for downstream clustering tasks. Current approaches produce such individual cell embeddings directly through a one-step learning process. Here, we propose an alternative approach by building embedding models pre-trained on reference data. We argue that this provides a more flexible analysis workflow that also has computational performance advantages through transfer learning.

Results

We implemented our approach in scEmbed, an unsupervised machine learning framework that learns low-dimensional embeddings of genomic regulatory regions to represent and analyze scATAC-seq data. scEmbed performs well in terms of clustering ability and has the key advantage of learning patterns of region co-occurrence that can be transferred to other, unseen datasets. Moreover, pre-trained models on reference data can be exploited to build fast and accurate cell-type annotation systems without the need for other data modalities. scEmbed is implemented in Python and it is available to download from GitHub. We also make our pre-trained models available on huggingface for public use.

Availability

scEmbed is open source and available athttps://github.com/databio/geniml. Pre-trained models from this work can be obtained on huggingface:https://huggingface.co/databio.
Metabolic adjustments to winter severity in two geographically separated great tit (Parus major) populations
Authors: Pacioni Cesare , Bushuev Andrey , Sentís Marina , Kerimov Anvar , Ivankina Elena , Lens Luc , Strubbe Diederik
Published: August 2023

Understanding the potential limits placed on organisms by their ecophysiology is crucial for predicting their responses to varying environmental conditions. Studies to date have traditionally relied on between-species comparisons, however, recently, there has been a growing recognition of the importance of intraspecific variation in shaping an organism’s ecological and physiological responses. In this context, widely distributed resident bird species offer a well-suited study system to examine intraspecific geographical variation in ecophysiological traits. A main hypothesis for explaining avian thermoregulatory mechanisms is the aerobic capacity model, which posits a positive correlation between basal (BMR) and summit (Msum) metabolism, caused by the energetic maintenance costs associated with increased muscle mass for shivering thermogenesis and enhanced investment in digestive organs for food processing. Most evidence for this hypothesis, however, comes from interspecific comparisons only, and the ecophysiological underpinnings of avian thermoregulatory capacities hence remain controversial. Here, we focus on great tits (Parus major), measuring winter BMR and Msumin two populations from different climates, a maritime-temperate (Gontrode, Belgium) and a continental (Zvenigorod, Russia) one. We test for the presence of intraspecific geographical variation in metabolic rates and assess the predictions following the aerobic capacity model. We found that metabolic rates differed between populations, whereby the birds from the maritime-temperate climate (Gontrode) showed higher (whole-body and mass-independent) BMR whereas conversely, great tits from Zvenigorod showed higher levels of both (whole-body and mass-independent) Msum. Within each population, our data did not fully support the aerobic capacity model’s predictions. We argue that the decoupling of BMR and Msumobserved may be caused by different selective forces acting on these metabolic rates, with birds from the continental-climate Zvenigorod population facing the need to conserve energy for surviving long winter nights (by keeping their BMR at low levels) while simultaneously being able to generate more heat (i.e., a high Msum) to withstand cold spells. We argue that the coupling or uncoupling of basal and maximum metabolic rates at the intraspecific level is likely influenced by different selective pressures that shape local adaptations in response to different climate regimes.
Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling inDrosophila
Authors: Liu Andrew , O’Connell Jessica , Wall Farley , Carthew Richard W.
Published: August 2023

The atypical cadherins Fat and Dachsous (Ds) signal through the Hippo pathway to regulate growth of numerous organs, including theDrosophilawing. Here, we find that Ds-Fat signaling tunes a unique feature of cell proliferation found to control the rate of wing growth during the third instar larval phase. The duration of the cell cycle increases in direct proportion to the size of the wing, leading to linear-like growth during the third instar. Ds-Fat signaling enhances the rate at which the cell cycle lengthens with wing size, thus diminishing the rate of wing growth. We show that this results in a complex but stereotyped relative scaling of wing growth with body growth inDrosophila. Finally, we examine the dynamics of Fat and Ds protein distribution in the wing, observing graded distributions that change during growth. However, the significance of these dynamics is unclear since perturbations in expression have negligible impact on wing growth.
In silicoassessment of 18S rDNA metabarcoding markers for the characterization of nematode communities
Authors: Ficetola Gentile Francesco , Guerrieri Alessia , Cantera Isabel , Bonin Aurelie
Published: August 2023

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of their biodiversity. DNA metabarcoding is increasingly used to assess nematode biodiversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene.In-silicoanalyses have a great potential to assess key parameters of primers, including their taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we testedin-silicothe performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, as amplified most of sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Ourin-silicoanalyses provide new insights for the identification of most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.
Systematic characterization of therapeutic vulnerabilities in Multiple Myeloma with Amp1q reveals increased sensitivity to the combination of MCL1 and PI3K inhibitors
Authors: Sklavenitis-Pistofidis Romanos , Lightbody Elizabeth D. , Reidy Mairead , Tsuji Junko , Aranha Michelle P. , Heilpern-Mallory Daniel , Huynh Daisy , Chong Stephen J. F. , Hackett Liam , Haradhvala Nicholas J. , Wu Ting , Su Nang K. , Berrios Brianna , Alberge Jean-Baptiste , Dutta Ankit , Davids Matthew S. , Papaioannou Maria , Getz Gad , Ghobrial Irene M. , Manier Salomon
Published: August 2023

The development of targeted therapy for patients with Multiple Myeloma (MM) is hampered by the low frequency of actionable genetic abnormalities. Gain or amplification of chr1q (Amp1q) is the most frequent arm-level copy number gain in patients with MM, and it is associated with higher risk of progression and death despite recent advances in therapeutics. Thus, developing targeted therapy for patients with MM and Amp1q stands to benefit a large portion of patients in need of more effective management. Here, we employed large-scale dependency screens and drug screens to systematically characterize the therapeutic vulnerabilities of MM with Amp1q and showed increased sensitivity to the combination of MCL1 and PI3K inhibitors. Using single-cell RNA sequencing, we compared subclones with and without Amp1q within the same patient tumors and showed that Amp1q is associated with higher levels ofMCL1and the PI3K pathway. Furthermore, by isolating isogenic clones with different copy number for part of the chr1q arm, we showed increased sensitivity to MCL1 and PI3K inhibitors with arm-level gain. Lastly, we demonstrated synergy between MCL1 and PI3K inhibitors and dissected their mechanism of action in MM with Amp1q.
Combining video telemetry and wearable MEG for naturalistic imaging
Authors: O'Neill George C , Seymour Robert A , Mellor Stephanie , Alexander Nicholas , Tierney Tim M , Bernachot Lea , Fahimi Hnazee Mansoureh , Spedden Meaghan E , Timms Ryan C , Bush Daniel , Bestmann Sven , Brookes Matthew J , Barnes Gareth R
Published: August 2023

Neuroimaging studies have typically relied on rigorously controlled experimental paradigms to probe cognition, in which movement is restricted, primitive, an afterthought or merely used to indicate a subject's choice. Whilst powerful, these paradigms do not often resemble how we behave in everyday life, so a new generation of ecologically valid experiments are being developed. Magnetoencephalography (MEG) measures neural activity by sensing extracranial magnetic fields. It has recently been transformed from a large, static imaging modality to a wearable method where participants can move freely. This makes wearable MEG systems a prime candidate for naturalistic experiments going forward. However, these experiments will also require novel methods to capture and integrate information about complex behaviour executed during neuroimaging, and it is not yet clear how this could be achieved. Here we use video recordings of multi-limb dance moves, processed with open-source machine learning methods, to automatically identify analysis time windows of interest in concurrent wearable MEG data. In a first step, we compare a traditional, block-designed analysis of limb movements, where the times of interest are based on stimulus presentation, to an analysis pipeline based on hidden Markov model states derived from the video telemetry. Next, we show that it is possible to identify discrete modes of neuronal activity related to specific limbs and body posture by processing the participants' choreographed movement in a dancing paradigm. This demonstrates the potential of combing video telemetry with mobile neuroimaging for future studies of complex and naturalistic behaviours.
Plant-mediated effects of fire and fragmentation drive plant-pollinator interaction β-diversity in fire-dependent pine savannas
Authors: Moreno-García Pablo , Freeman Johanna E. , Campbell Joshua W. , Broadbent Eben N. , Almeyda Zambrano Angélica M. , Prata Gabriel , de Almeida Danilo R. A. , Gilb Scott , Baiser Benjamin
Published: August 2023

Interaction β-diversity is an essential measure to understand and conserve species interactions and ecosystem functioning. Interaction β-diversity explains the variation in species interactions across spatial and temporal gradients, resulting from species turnover or interaction rewiring. Each component of interaction β-diversity has different ecological implications and practical consequences. While interaction β-diversity due to species turnover is related to assembly processes and fragmentation, rewiring can support high biodiversity and confer resilience to ecological networks. Despite this, it is unclear whether both components respond to the same or different ecological drivers. Here, we assessed the ecological drivers of plant-pollinator interaction β-diversity and its components across 24 sites in 9 Longleaf Pine (LLP) savannas in north and central Florida. We evaluated the effects of flowering plant composition and flower abundance, vegetation, fire regime, soil moisture, terrain characteristics, climate, spatial context, and geographic location. We used path analysis to evaluate the drivers of spatial interaction β-diversity and its main components. We then used generalized linear mixed models to assess the temporal patterns of spatial β-diversity among sites within preserves. We found that plant-pollinator networks in LLP savannas are highly variable across space and time, mainly due to species turnover and possibly in response to abiotic gradients and dispersal boundaries. Flower abundance and flowering plant composition, geographic location, fire seasonality, soil moisture, and landscape context were the main drivers of plant-pollinator β-diversity, highlighting the role of fire management and habitat connectivity in preserving plant-pollinator networks.
Deep Learning-Enabled, Detection of Rare Circulating Tumor Cell Clusters in Whole Blood Using Label-free, Flow Cytometry
Authors: Vora Nilay , Shekar Prashant , Esmail Michael , Patra Abani , Georgakoudi Irene
Published: August 2023

Metastatic tumors have poor prognoses for progression-free and overall survival for all cancer patients. Rare circulating tumor cells (CTCs) and rarer circulating tumor cell clusters (CTCCs) are potential biomarkers of metastatic growth, with CTCCs representing an increased risk factor for metastasis. Current detection platforms are optimized forex vivodetection of CTCs only. Microfluidic chips and size exclusion methods have been proposed for CTCC detection; however, they lackin vivoutility and real-time monitoring capability. Confocal backscatter and fluorescence flow cytometry (BSFC) has been used for label-free detection of CTCCs in whole blood based on machine learning (ML) enabled peak classification. Here, we expand to a deep-learning (DL) -based, peak detection and classification model to detect CTCCs in whole blood data. We demonstrate that DL-based BSFC has a low false alarm rate of 0.78 events/min with a high Pearson correlation coefficient of 0.943 between detected events and expected events. DL-based BSFC of whole blood maintains a detection purity of 72% and a sensitivity of 35.3% for both homotypic and heterotypic CTCCs starting at a minimum size of two cells. We also demonstrate through artificial spiking studies that DL-based BSFC is sensitive to changes in the number of CTCCs present in the samples and does not add variability in detection beyond the expected variability from Poisson statistics. The performance established by DL-based BSFC motivates its use forin vivodetection of CTCCs. Further developments of label-free BSFC to enhance throughput could lead to critical applications in the clinical detection of CTCCs andex vivoisolation of CTCC from whole blood with minimal disruption and processing steps.
Genetic regulatory effects in response to a high cholesterol, high fat diet in baboons
Authors: Lin Wenhe , Wall Jeffrey D. , Li Ge , Newman Deborah , Yang Yunqi , Abney Mark , VandeBerg John L. , Olivier Michael , Gilad Yoav , Cox Laura A.
Published: August 2023

Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWAS), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using nonhuman primate models.
TNFR1/p38αMAPK signaling in Nex+ supraspinal neurons regulates sex-specific chronic neuropathic pain
Authors: Swanson Kathryn A. , Nguyen Kayla L. , Gupta Shruti , Ricard Jerome , Bethea John R.
Published: August 2023

Upregulation of soluble tumor necrosis factor (sTNF) cytokine signaling through TNF receptor 1 (TNFR1) and subsequent neuronal hyperexcitability are observed in both animal models and human chronic neuropathic pain (CNP) (Clark et al., 2013; Empl et al., 2001; Ji et al., 2018; Lindenlaub and Sommer, 2003). To test the hypothesis that supraspinal circuitry is critical to pain chronification, we studied the intersect between supraspinal TNFR1 mediated neuronal signaling and sex specificity by selectively removing TNFR1 in Nex+ neurons in adult mice (NexCreERT2::TNFR1f/f). We determined that following chronic constriction injury (CCI), pain resolves in males; however, female acute pain transitions to chronic. Subsequently, we investigated two downstream pathways, p38MAPK and NF-κB, important in TNFR1 signaling and injury response. We detected p38αMAPK and NF-κB activation in male cortical tissue; however, p38αMAPK phosphorylation was reduced in NexCreERT2::TNFR1f/fmales. We observed similar behavioral results following CCI in NexCreERT2::p38αMAPKf/fmice. Previously, we established estrogen’s ability to modulate sTNF/TNFR1 signaling in CNP, which may contribute to female prevalence of CNP (Bouhassira et al., 2008; Claiborne et al., 2006; de Mos et al., 2007; Del Rivero et al., 2019; Li et al., 2009). To explore the intersection between estrogen and inflammation in CNP we used a combination therapy of an estrogen receptor β (ER β) inhibitor with a sTNF/TNFR1 or general p38MAPK inhibitor. We determined both combination therapies lend “male-like” therapeutic relief to females following CCI. These data suggest that TNFR1/p38αMAPK signaling in Nex+ neurons in CNP is male-specific and lack of therapeutic efficacy following sTNF inhibition in females is due to ER β interference. These studies highlight sex-specific differences in pathways important to pain chronification and elucidate potential therapeutic strategies that would be effective in both sexes.
Visual Sequence Encoding is Enhanced by Predictable Music Pairing via Modulating Medial Temporal Lobe and Its Connectivity with Frontostriatal Loops
Authors: Ren Yiren , Brown Thackery
Published: August 2023

Listening to music during cognitive activities, such as reading and studying, is very common in human daily life. Therefore, it is important to understand how music interacts with concurrent cognitive functions, particularly memory. Current literature has presented mixed results for whether music can benefit learning in other modalities. Evidence is needed for what neural mechanisms music can tap into to enhance concurrent memory processing. This fMRI study aimed to begin filling this gap by investigating how music of varying predictability levels influences parallel visual sequence encoding performance. Behavioral results suggest that overall, predictable music enhances visual sequential encoding, and this effect increases with the structural regularity and familiarity of music. fMRI results indicate that during visual sequence encoding, music activates traditional music-processing and motor-related areas, but decreases parahippocampal and striatal engagement. This deactivation may indicate a more efficient encoding of visual information when music is present. By comparing music conditions of different structural predictability and familiarity, we probed how this occurs. We demonstrate improved encoding with increased syntactical regularity, which was associated with decreased activity in default mode network and increased activity in inferior temporal gyrus. Furthermore, the temporal schema provided by music familiarity may influence encoding through altered functional connectivity between the prefrontal cortex, medial temporal lobe and striatum. Overall, we propose that pairing music with learning might facilitate memory by reducing neural demands for visual encoding and simultaneously strengthening the connectivity between the medial temporal lobe and frontostriatal loops important for sequencing information.

Significance Statement

There is considerable interest in what mechanisms can be tapped to improve human memory. Music provides a potential modulator, but few studies have investigated music effects on encoding episodic memory. This study used a novel design to examine how music can influence concurrent visual item sequence encoding. We provided neural data to better understand mechanisms behind potential benefits of music for learning. Our results demonstrated predictable music may help guide parallel learning of sequences in another modality. We found that music might facilitate processing in neural systems associated with visual declarative long-term and working memory, and familiar music might modulate reward circuits and provide a temporal schema which facilitates better encoding of the temporal structure of new non-music information.
Acetic acid is a superior ion pairing modifier for sub-nanogram and single cell proteomics
Authors: Eberhard Colten D. , Orsburn Benjamin C.
Published: August 2023

A recent study demonstrated a substantial increase in peptide signal and corresponding proteome coverage when employing 0.5% acetic acid (AA) as the ion pairing modifier in place of the 0.1% formic acid traditionally used in shotgun proteomics. In this study, we investigated the effect of modifier in the context of sub-nanogram and single cell proteomics (SCP). We first evaluated a tryptic digest standard down to 20 picograms total load on column on a TIMSTOF SCP system. In line with the previous results, we observed a signal increase when using AA, leading to increased proteome coverage at every peptide load assessed. Relative improvements were more apparent at lower concentrations, with a 20 picogram peptide digest demonstrating a striking 1.8-fold increase to over 2,000 protein groups identified in a 30 minute analysis. Furthermore, we find that this increase in signal can be leveraged to reduce ramp times, leading to 1.7x more scans across each peak and improvements in quantification as measured by %CVs. When evaluating single cancer cells, approximately 13% more peptide groups were identified on average when employing AA in the place of FA. All vendor raw and processed data are available through ProteomeXchange as PXD046002 and PXD051590.

TOC Graphic
Oligo-PROTAC strategy for cell-selective and targeted degradation of activated STAT3
Authors: Hall Jeremy , Zhang Zhuoran , Wang Dongfang , Bhattacharya Supriyo , Alcantara Marice , Liang Yong , Swiderski Piotr , Forman Stephen , Kwak Larry , Vaidehi Nagarajan , Kortylewski Marcin
Published: August 2023

Decoy-oligodeoxynucleotides (D-ODNs) can target undruggable transcription factors, such as STAT3. However, challenges in D-ODN delivery and potency hampered their translation. To overcome these limitations, we conjugated STAT3-specific D-ODN to thalidomide (Tha), a known ligand to cereblon (CRBN, a component of E3 ubiquitin ligase) to generate a proteolysis-targeting chimera (STAT3DPROTAC). STAT3DPROTACdownregulated STAT3, but not STAT1 or STAT5, in target cells. Computational modeling of the STAT3DPROTACternary complex predicted two surface lysines on STAT3, K601 and K626 as potential ubiquitination sites for the PROTAC bound E3 ligase. Accordingly, K601/K626 point mutations in STAT3, as well as proteasome inhibitors, and CRBN deletion alleviated STAT3DPROTACeffect. Next, we conjugated STAT3DPROTACto a CpG ligand targeting Toll-like receptor 9 (TLR9) to generate myeloid/B-cell-selective C-STAT3DPROTACconjugate. Naked C-STAT3DPROTACwas spontaneously internalized by TLR9+myeloid cells, B cells as well as human Ly18 and mouse A20 lymphoma cells, but not by T cells. C-STAT3DPROTACdecreased STAT3 levels to 50% at 250 nM and over 85% at 2 µM dosing in myeloid cells. We also observed significantly improved downregulation of STAT3 target genes involved in lymphoma cell proliferation and/or survival (BCL2L1, CCND2, MYC). Finally, we assessed the antitumor efficacy of C-STAT3DPROTACcompared to C-STAT3D or scrambled control (C-SCR) against human lymphoma xenotransplants. Local C-STAT3DPROTACadministration triggered lymphoma regression while control treatments had limited effects. Our results underscore feasibility of using PROTAC strategy for cell-selective, decoy oligonucleotide-based targeting of STAT3 and potentially other tumorigenic transcription factors for cancer therapy.
Ophidian physique: the capacity of middle trunk vertebral shape for quantitative taxonomic delimitation in snakes
Authors: Jacisin John J. , Lawing A. Michelle
Published: August 2023

Skeletal specializations in snakes have resulted in incredible locomotive adaptability, including oft-overlooked vertebral complexity. Snake vertebrae are usually identified via qualitative descriptions of morphological traits; however, identifying and describing snake vertebrae in a scientifically replicable way has long hindered fossil snake research, where attempts to identify between or within snake groups can be onerous. Here, we build a framework of extant snake middle trunk vertebral shape using 2D geometric morphometrics (GMM) and quantitative methods to explore the viability of using these tools to assign and identify snake trunk vertebrae taxonomically and ecologically. We use 23 landmarks to evaluate anterior vertebral shape variation in 504 snake trunk vertebrae representing 189 species across 11 families for delimiting taxonomy and primary foraging habitat. We found that snake vertebral shape variation of overall proportions and articular surfaces contained statistically significant taxonomic and ecomorphological information useful for group assignment. Differences in primary foraging habitat also resulted in similar morphological trends within taxonomic groups in shape space. We then used linear discriminant functions to test the reliability of taxonomic assignments based on the shape captured by our landmark scheme. Analysis of the full dataset had high overall accuracy for family and subfamily, but only moderate success for genus, species, and primary foraging habitat. When applied to a single subfamily, overall accuracy greatly increased for genus and primary foraging habitat, implying that iterative application of this method may improve results. This study presents the framework for a new replicable method to supplement qualitative morphological descriptions of taxa. We recommend that GMM is best employed alongside qualitative descriptions for the optimal and reproducible delimitation of snake vertebrae. Finally, this method will allow non-expert diagnosticians to have more confidence in identifying fossil snake vertebrae, helping increase the number of snake fossils identified in museum collections.
Identification of Key Yeast Species and Microbe-Microbe Interactions Impacting Larval Growth ofDrosophilain the Wild
Authors: Mure Ayumi , Sugiura Yuki , Maeda Rae , Honda Kohei , Sakurai Nozomu , Takahashi Yuuki , Watada Masayoshi , Katoh Toshihiko , Gotoh Aina , Gotoh Yasuhiro , Taniguchi Itsuki , Nakamura Keiji , Hayashi Tetsuya , Katayama Takane , Uemura Tadashi , Hattori Yukako
Published: August 2023

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources ofDrosophilalarvae, and investigated their functions.Hanseniaspora uvarumis the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses,Acetobacter orientalisemerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.
Effect of percutaneous ventricular assisted device on post-cardiac arrest myocardial dysfunction in swine model with prolonged cardiac arrest
Authors: Nakashima Takahiro , Tiba Mohamad Hakam , Hsu Cindy H. , Gottula Adam L. , McCracken Brendan M. , Greer Nicholas L. , Cramer Traci A. , Sutton Nadia R. , Ward Kevin R. , Neumar Robert W
Published: August 2023

Background

Percutaneous left ventricular assist device (pLVAD) can provide hemodynamic support during and after cardiac arrest, but it remains unclear if pLVAD reduces post-cardiac arrest myocardial dysfunction.

Methods

This is an analysis of a subset of animals that achieved return of spontaneous circulation (ROSC) in a study comparing pLVAD, transient aortic occlusion (AO), or both during cardiopulmonary resuscitation (CPR) after prolonged cardiac arrest. pLVAD, AO, or both were initiated after 24 minutes of ventricular fibrillation cardiac arrest (8 min no-flow and 16 min mechanical CPR). AO was discontinued post-ROSC, and pLVAD support or standard care were continued. Beginning 60 minutes post-ROSC, pLVAD support was weaned to <1.0 L/min while maintaining a mean arterial pressure >70 mmHg, and subsequently removed at 240 minutes when feasible. The primary outcome was the recovery of cardiac index (CI), stroke volume index (SVI), and left ventricular ejection fraction (LVEF) at 240 minutes post-ROSC. Data are shown as mean (standard error).

Results

Seventeen animals achieved ROSC without complication and were included in this analysis (pLVAD group, n = 11 and standard care group, n = 6). For the primary outcome, the pLVAD group had significantly higher CI of 4.2(0.3) vs. 3.1(0.4) L/min/m2 (p=0.043) and LVEF 60(3) vs. 49(4) % (p=0.029) at 240 minutes after ROSC, respectively, when compared with the standard care group, while SVI was not significant difference (2[3] vs. 23[4] mL/min/m2,p=0.054). During the first 60 minutes after ROSC with maximum pLVAD flow, the pLVAD group had significantly higher coronary perfusion pressure (62[4] vs. 47[5] mmHg, p=0.019), lower LV stroke work index (3.9[3.0] vs. 14.9[4.4] cJ/m2, p=0.043), and lower total pulmonary resistance index (13.2[4.8] vs. 21.5[14.4] Wood Unit, p=0.001).

Conclusion

These results suggest that early pLVAD support after ROSC is associated with better recovery myocardial function compared to standard care after prolonged cardiac arrest.
Cine phase contrast magnetic resonance imaging of calf muscle contraction in pediatric patients with cerebral palsy and healthy children: comparison of voluntary motion and electrically evoked motion
Authors: Weidensteiner Claudia , Deligianni Xeni , Haas Tanja , Madoerin Philipp , Bieri Oliver , Garcia Meritxell , Romkes Jacqueline , Rutz Erich , Santini Francesco , Brunner Reinald
Published: August 2023

The aim of this study is to investigate the feasibility of phase contrast imaging for assessment of muscle function in children with cerebral palsy. Time-resolved cine phase contrast MRI at 3T was synchronized with (a) electrical muscle stimulation (EMS) of the calf muscle and (b) voluntary plantarflexion following visual instructions. Fourteen ambulatory pediatric patients with equinus and 13 normally developing, healthy children were scanned. Ten patients were scanned pre and post botulinum toxin treatment. Four patients and four healthy children performed voluntary plantarflexion additionally to EMS. The achieved force was higher for the voluntary task for both patients and healthy controls, but its periodicity was worse compared to the stimulated contraction in patients. Therefore, it was possible to acquire contraction velocity time courses showing two distinct velocity peaks – the first for voluntary muscle contraction and the second for release – in four out of four healthy controls but in none of the patients. During EMS, two distinct velocity peaks could be resolved if the tolerated current was high enough to evoke sufficient contraction. That was achieved in 21% of the scans in patients (15 out of 72 scans during EMS in total) compared to 82% (14 out of 17) in healthy children. Then, the data quality was sufficient to generate strain maps. However, it was not possible to detect an effect of botulinum toxin in these patients since we did not succeed in acquiring data with sufficient quality both pre- and post-treatment. In conclusion, both EMS and voluntary motion worked well in healthy, normally developing children. Compliance was higher for the voluntary task for both patients and healthy controls. In conclusion, it was necessary to use EMS for a successful measurement of contraction/release velocity and strain in CP patients and although in this cohort the results were inconclusive, in the future optimization of the stimulation protocol could increase the acceptance and improve the output.