bluuebunny/crossref_metadata_2025 huggingface dataset:
Accuracy of computed tomography in diagnosing temporomandibular joint osteoarthritis relative to histopathological findings – an ex–vivo study of 41 horses
Authors: Jasinski Tomasz , Zdrojkowski Łukasz , Turek Bernard , Kaczorowski Michał , Pawliński Bartosz , Brehm Walter , Domino Małgorzata
Published: November 2024

Computed tomography (CT) is commonly used for imaging the equine head, particularly when diseases of temporomandibular joint (TMJ), including osteoarthritis (OA), are suspected. However, certain CT findings have been proposed as ’anatomical variations’, and their clinical significance remains unknown. The objectives of this prospective descriptive cross-sectional study were to describe the CT and histopathological findings of TMJ OA in relation to horse age, evaluate the accuracy of TMJ OA diagnosis with regard to ’CT anatomical variations’, and explore the correlations between specific CT and histopathological findings. CT images and tissue samples from 41 heads (82 TMJs) were independently and simultaneously reviewed by two observers. Descriptive statistics on both findings, their age–related frequency, and accuracy of TMJ OA diagnosis were calculated. Based on histopathological assessment, TMJ OA was confirmed in 18% of joints in horses aged 1–4 years, 63% of joints in horses aged 5–15 years, and 83% of joints in horses over 15 years. Considering entire CT findings, TMJ OA was radiologically recognized in 76% of joints, with a sensitivity of 0.95 and a specificity of 0.37. When ’CT anatomical variations’ were excluded, TMJ OA was recognized in 30% of joints, with a sensitivity of 0.51 and a specificity of 0.88. Findings suggest that the equine TMJ may undergo both age–related and disease–related remodeling, detectable through CT and histopathology, and that the inclusion or exclusion of certain ’CT anatomical variations’ in the diagnostic protocol affects the sensitivity and specificity of CT–based TMJ OA recognition.
A Deep Attention-Based Encoder for the Prediction of Type 2 Diabetes Longitudinal Outcomes from Routinely Collected Health Care Data
Authors: Manzini Enrico , Vlacho Bogdan , Franch-Nadal Josep , Escudero Joan , Génova Ana , Reixach Elisenda , Andrés Erich , Pizarro Israel , Mauricio Dídac , Perera-Lluna Alexandre
Published: November 2024

Recent evidence indicates that Type 2 Diabetes Mellitus (T2DM) is a complex and highly heterogeneous disease involving various pathophysiological and genetic pathways, which presents clinicians with challenges in disease management. While deep learning models have made significant progress in helping practitioners manage T2DM treatments, several important limitations persist. In this paper we propose DARE, a model based on the transformer encoder, designed for analyzing longitudinal heterogeneous diabetes data. The model can be easily fine-tuned for various clinical prediction tasks, enabling a computational approach to assist clinicians in the management of the disease. We trained DARE using data from over 200,000 diabetic subjects from the primary healthcare SIDIAP database, which includes diagnosis and drug codes, along with various clinical and analytical measurements. After an unsupervised pre-training phase, we fine-tuned the model for predicting three specific clinical outcomes: i) occurrence of comorbidity, ii) achievement of target glycaemic control (defined as glycated hemoglobin<7%) and iii) changes in glucose-lowering treatment. In cross-validation, the embedding vectors generated by DARE outperformed those from baseline models (comorbidities prediction taskAUC= 0.88, treatment prediction taskAUC= 0.91, HbA1c target prediction taskAUC= 0.82). Our findings suggest that attention-based encoders improve results with respect to different deep learning and classical baseline models when used to predict different clinical relevant outcomes from T2DM longitudinal data.
Alu overexpression leads to increased double-stranded RNA in dermatomyositis
Authors: Najjar Rayan , Mammen Andrew , Mustelin Tomas
Published: November 2024

Dermatomyositis is an autoimmune condition characterized by a high interferon signature of unknown etiology. Because genes constitute only <2% of our genomes, there is a need to explore the role of the non-coding genome in disease pathogenesis. Our genomes include roughly 1.2 million Alu elements occupying about 10% of the genome and can form double-stranded (ds)RNA capable of triggering MDA5 leading to interferon production. We aligned muscle biopsy RNA sequencing data to the Telomere-to-Telomere reference genome and quantified short interspersed elements including Alus. Dermatomyositis muscle (n=39) showed a global elevation in Alu expression as well as an increased expression of unique Alu elements (n=557, p<0.05) compared to healthy controls (n=34), in a pattern not seen in other myositis types (n=81). The majority (75.3%) of these Alus originated from genomic regions outside genes, with a hot spot of expression on chromosome 19. A subset of the uniquely overexpressed Alus (n=167) correlated strongly with interferon stimulated genes and markers of myositis activity. Since Alu transcripts have a propensity to form dsRNA and are the major targets of both ADAR and MDA5, we quantified the A-to-I RNA editomes inside Alus and found a uniquely expanded Alu editome in dermatomyositis compared to other myositis types, reflecting an increase in dsRNA. Edited Alus clustered on chromosome 19, which is known to have the highest concentration of dsRNA. We hypothesize that overexpressed Alus in dermatomyositis form endogenous dsRNA that exceed the capacity of RNA editing enzymes and trigger dsRNA sensors leading to interferon production.
Emerging pathogens associated with acute respiratory infections in children before, during and after the COVID-19 pandemic in Hanoi, Vietnam
Authors: Ho Nhan Thi , Nguyen Hang Thi Thuy , Hoang Ha Thi , Pham Dung Van , Nguyen Quang Ngoc , Le Huong Thi Minh , Pham An Nhat , Doan Phuong Mai
Published: November 2024

The COVID-19 pandemic has caused changes in respiratory infectious disease patterns. We analyzed de-identified data of microbiology assays of nasopharyngeal samples and blood samples of children with acute respiratory infection (ARI) visited Vinmec Times City International hospital in Hanoi, Vietnam from January 2019 to December 2023 to examine the overall pattern of viral and bacterial emerging pathogens associated with ARI in children before, during and after the COVID-19 pandemic. The data was aggregated by month and time series analysis and visualization was done. Bacterial Polymerase Chain Reaction (PCR) panel was done for 4125 samples,Mycoplasma pneumonia(MP) IgM was done for 5049 samples, bacterial culture was done for 10280 samples and viral PCR or rapid test was done for 42041 samples. After the COVID-19 pandemic,Haemophilus influenzae(HI) andStreptococcus pneumoniae(SP) have re-emerged as epidemic pathogens associated with lower respiratory tract infection (LRI).Influenza type Aandtype Bhave reestablished regular cycles of peaks in winter-spring months after an early rebound together with an unprecedented newly emergence ofHuman Adenovirus(HAdV) soon after the relief of COVID-19 restriction. Late after the COVID-19 pandemic, from middle of 2023, atypical pneumonia pathogenMycoplasma pneumonia(MP) has emerged remarkably and becoming epidemic and there was also a small, brief emergence ofChlamydophila pneumoniae(CP) infection. Our data is useful to understand the influence of COVID-19 pandemic on the emergence or re-emergence of viral and bacterial respiratory infection pathogens in children and is useful for disease surveillance and public health intervention.
Post-stroke changes in brain structure and function can both influence acute upper limb function and subsequent recovery
Authors: Zich Catharina , Ward Nick S , Forss Nina , Bestmann Sven , Quinn Andrew J , Karhunen Eeva , Laaksonen Kristina
Published: November 2024

Improving outcomes after stroke depends on understanding both the causes of initial function/impairment and the mechanisms of recovery. Recovery in patients with initially low function/high impairment is variable, suggesting the factors relating to initial function/impairment are different to the factors important for subsequent recovery. Here we aimed to determine the contribution of altered brain structure and function to initial severity and subsequent recovery of the upper limb post-stroke.

The Nine-Hole Peg Test was recorded in week 1 and one-month post-stroke and used to divide 36 stroke patients (18 females, age: M = 66.56 years) into those with high/low initial function and high/low subsequent recovery. We determined differences in week 1 brain structure (Magnetic Resonance Imaging) and function (Magnetoencephalography, tactile stimulation) between high/low patients for both initial function and subsequent recovery. Lastly, we examined the relative contribution of changes in brain structure and function to recovery in patients with low levels of initial function.

Low initial function and low subsequent recovery are related to lower sensorimotor β power and greater lesion-induced disconnection of contralateral [ipsilesional] white-matter motor projection connections. Moreover, differences in intra-hemispheric connectivity (structural and functional) are unique to initial motor function, while differences in inter-hemispheric connectivity (structural and functional) are unique to subsequent motor recovery.

Function-related and recovery-related differences in brain function and structure after stroke are related, yet not identical. Separating out the factors that contribute to each process is key to identifying potential therapeutic targets for improving outcomes.
“In Situ Resistance Insulin – Localized Type 2 Diabetes Mellitus or Type 6 Diabetes Mellitus?”: A Scoping Review
Authors: de Oliveira Andrade Luís Jesuino , Matos de Oliveira Gabriela Correia , Nunes Carneiro Andrade João Cláudio , Vinhaes Bittencourt Alcina Maria , Matos de Oliveira Luís
Published: November 2024

In the context of type 2 diabetes mellitus (T2DM), the concept of organ-specific insulin resistance (IR) as a localized manifestation has garnered increasing attention. A scoping review was conducted to investigate the clinical relevance of IR confined to individual organs without systemic metabolic implications. Utilizing a methodological framework adapted from Arksey and O’Malley, a comprehensive search of PubMed was performed, focusing on the period between January 1990 and October 2024. The search strategy combined Medical Subject Headings terms and keywords related to IR and specific organs. Notably, while “insulin resistance” yielded a substantial number of results, the subset of “organ-specific insulin resistance” returned a more limited dataset, highlighting a gap in current literature. The systematic selection process encompassed identification, screening, eligibility, and inclusion stages to ensure robust inclusion criteria. This scoping review underscores the importance of exploring organ-specific IR in the diabetic milieu and sets the stage for further research to elucidate its role in the pathogenesis of T2DM. Conclusion: The findings suggest that investigating organ-specific IR in the context of T2DM is a promising avenue for future research to deepen our understanding of disease pathophysiology. Thus, this scoping review answers the following question “In Situ Resistance Insulin - Localized Type 2 Diabetes Mellitus or Type 6 Diabetes Mellitus?”, emphasizing the need for targeted investigations into localized manifestations of IR and their implications for DM management strategies.
Polymorphic tandem repeats shape single-cell gene expression across the immune landscape
Authors: Tanudisastro Hope A. , Cuomo Anna S.E. , Weisburd Ben , Welland Matthew , Spenceley Eleanor , Franklin Michael , Xue Angli , Bowen Blake , Wing Kristof , Tang Owen , Gray Michael , Reis Andre L.M. , Margoliash Jonathan , Kurtas Edibe Nehir , Pullin Jeffrey , Lee Arthur S. , Brand Harrison , Harper Michael , Bobowik Katalina , Silk Michael , Marshall John , Bakiris Vivian , Madala Bindu Swapna , Uren Caitlin , Bartie Caitlin , Senabouth Anne , Dashnow Harriet , Fearnley Liam , Dolzhenko Egor , Qiao Zhen , Grieve Stuart , Nguyen Tung , Talkowski Michael , Alexander Stephen I. , Siggs Owen M. , Gruenschloss Leonhard , Nicholas Hannah R. , Piscionere Jennifer , Simons Cas , Wallace Chris , Gymrek Melissa , Deveson Ira W. , Hewitt Alex W. , Figtree Gemma A. , de Lange Katrina M. , Powell Joseph E. , MacArthur Daniel G.
Published: November 2024

Tandem repeats (TRs) – highly polymorphic, repetitive sequences dispersed across the human genome – are crucial regulators of gene expression and diverse biological processes. Yet, due to historical challenges in their accurate calling and analysis, TRs have remained underexplored compared to single nucleotide variants (SNVs). Here, we introduce a cell type-specific resource exploring the impact of TR variation on human gene expression. Leveraging whole genome and single-cell RNA sequencing, we catalog over 1.7 million polymorphic TR loci and their associations with gene expression across more than 5 million blood-derived cells from 1,790 individuals. We identify over 58,000 single-cell expression quantitative trait TR loci (sc-eTRs), 16.6% of which are specific to one of 28 distinct immune cell types. Further fine-mapping uncovers 6,210 sc-eTRs as candidate causal drivers of gene expression in 21% of genes tested genome-wide. We show through colocalization that TRs are likely regulators of over 2,000 GWAS loci associated with immune-mediated and hematological traits, and further identify novel TRs warranting investigation in rare disease cohorts. TRs are pivotal, yet long-overlooked, contributors to cell type-specific gene expression, with promising implications for understanding rare disease pathogenesis and the genetic architecture of complex traits.
Computational modelling shows evidence in support of both sensory and frontal theories of consciousness
Authors: Bandara Kavindu H. , Rowe Elise G. , Garrido Marta I.
Published: November 2024

The role of the prefrontal cortex (PFC) in consciousness is hotly debated. Frontal theories argue that the PFC is necessary for consciousness, while sensory theories propose that consciousness arises from recurrent activity in the posterior cortex alone, with activity in the PFC resulting from the mere act of reporting. To resolve this dispute, we re-analysed an EEG dataset of 30 participants from a no-report inattentional blindness paradigm where faces are (un)consciously perceived. Dynamic causal modelling was used to estimate the effective connectivity between the key contended brain regions, the prefrontal and the posterior cortices. Then, a second-level parametric empirical Bayesian model was conducted to determine how connectivity was modulated by awareness and task-relevance. While an initial data-driven search could not corroborate neither sensory nor frontal theories of consciousness, a more directed hypothesis-driven analysis revealed strong evidence that both theories could explain the data, with a very slight preference for frontal theories. Specifically, a model with backward connections switched off within the posterior cortex explained awareness better (53%) than a model without backward connections from the PFC to sensory regions. Our findings provide some support for a subtle, yet crucial, contribution of the frontal cortex in consciousness, and highlight the need to revise current theories of consciousness.
Sleep Disruption Improves Performance in Simple Olfactory and Visual Decision-Making Tasks
Authors: Pflitsch Paula , Oury Nadine , Krishnan Kumaresh , Joo William , Lyons Declan G. , Capelle Maxim , Herrera Kristian J. , Bahl Armin , Rihel Jason , Engert Florian , Zwaka Hanna
Published: November 2024

Sleep disruption drastically impacts cognitive functions including decision-making and attention across many different species. In this study, we leveraged the small size and conserved vertebrate brain structure of larval zebrafish to investigate how sleep disruption modulates visual- and olfactory-decision-making. Strikingly, sleep disruption improved performance in both paradigms. Specifically, sleep disruption lengthens reaction times and increases correct decisions in a visual motion discrimination task, an effect that we attribute to longer integration periods in disrupted animals. Using a drift diffusion model, we predict specific circuit changes underlying these effects. Additionally, we demonstrate that sleep disruption heightens odor sensitivity in an olfactory decision-making task, likely mediated by cortisol. Our findings lay essential groundwork for investigating the brain circuit changes that arise from sleep disruption across species.
PM2.5 from Automobile Exhaust Induces Apoptosis in Male Rat Germ Cellsviathe ROS-UPRmtSignaling Pathway
Authors: Wang Cao , Zhao Yingchi , Liu Bin , Luo Zhen , Zhou Guangxu , Mao Kaiyi
Published: November 2024

Objective

To explore the underlying mechanism behind the fine particulate matter’s (PM2.5)-mediated regulation of reproductive function in male rats, and to determine the role of vitamins in this process.

Methods

In all, 32 male SD rats were randomized to a control cohort (normal saline), a Vit cohort (vitamin C at 100 mg/kg + vitamin E at 50 mg/kg), a PM2.5 cohort (PM2.5 10 mg/kg), and a PM2.5+Vit cohort (PM2.5 exposure + vitamin C at 100 mg/kg + vitamin E at 50 mg/kg), with eight rats in each cohort. After four weeks of exposure, mating experiments were carried out. Thereafter, rats were euthanized, and the testis and epididymis tissues were excised for hematoxylin-eosin (HE) staining and sperm quality analysis. Apoptosis of testis tissues was quantified via a terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay. Moreover, the testicular oxidative stress (OS)-, apoptosis- and mitochondrial unfolded protein response (UPRmt)-related essential protein expressions were measured via western blotting (WB).

Results

After PM2.5 exposure, the sperm count and motility decreased, while sperm abnormality and the apoptosis index increased. HE staining showed that the number of spermatogenic cells decreased. WB showed that the PM2.5 group had decreased expressions of superoxide dismutase (SOD), nuclear factor E2-related factor 2 (Nrf2), and B-cell lymphoma-2 (Bcl-2) (p< 0.05), increased expressions of malondialdehyde (MDA), Bcl-2 associated X protein (Bax), and Caspase3 (p< 0.05), and downregulated expressions of C/EBP homologous protein (CHOP), heat shock protein 60 (HSP60), and activating transcription factor 5 (ATF5) (p< 0.05). These were all reversed by vitamin intervention.

Conclusion

PM2.5 from automobile exhaust disrupts male reproductive function. A combination of vitamins may protect reproductive function via the reactive oxygen species (ROS)-UPRmtsignaling pathway.

Highlights

PM2.5 from vehicle exhaust can cause apoptosis of male germ cells.

PM2.5 from vehicle exhaust induces germ cell apoptosis through the ROS-UPRmt signaling pathway.

Combined vitamin C and E can enhance UPRmt activity to alleviate the germ cell apoptosis caused by PM2.5 from vehicle exhaust.

Graphical abstract
Cross-Kingdom Genomic Conservation of Human Sleep-Related Gene Orthologs: Phylogenomic Evidence fromChlamydomonas reinhardtii
Authors: Pandi-Perumal Seithikurippu R , Saravanan Konda Mani , Paul Sayan , Abraham George C. , Spence David Warren , Chidambaram Saravana Babu
Published: November 2024

Sleep is a widespread and evolutionarily conserved process observed in diverse organisms, from jellyfish to mammals, hinting at its origin as a life-supporting mechanism over 500 million years ago. Although its fundamental purpose and mechanisms remain unclear, the evolution and adaptive significance of sleep continue to be debated. This study explores the evolutionary origins of sleep using Chlamydomonas reinhardtii as a model organism, identifying 145 orthologs analogous to known sleep-related genes across species, highlighting the evolutionary conservation of sleep-regulating pathways. Additionally, discovering uncharacterized proteins with high sequence similarity and significant e-values suggests unexplored roles in sleep regulation, underscoring the potential of C. reinhardtii to reveal new insights into the molecular basis of sleep. This work provides a foundation for identifying previously unknown sleep-associated proteins, particularly within single-celled organisms, which may offer novel perspectives on the biological role of sleep. The study demonstrates that phylogenomic analysis of diverse model organisms can expand our understanding of the evolutionary trajectory of sleep and its fundamental function, paving the way for further research in sleep biology and its health implications. Overall, the fundamental functions of sleep observed in higher animal phyla originated from its primordial activities, demonstrating an evolutionary continuum wherein more specialized tasks were integrated with sleep’s essential restorative properties.
GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts
Authors: Schneider Kristen , Chowdhury Murad , Tepper Mariano , Khan Jawad ,   Colorado Center for Personalized Medicine, Shortt Jonathan A. , Gignoux Chris , Layer Ryan
Published: November 2024

Many patients do not experience optimal benefits from medical advances because clinical research does not adequately represent them. While the diversity of biomedical research cohorts is improving, ensuring that individual patients are adequately represented remains challenging. We propose a new approach, GenoSiS, which leverages machine learning-based similarity search to dynamically find patient-matched cohorts across different populations quickly. These cohorts could serve as reference cohorts to improve a range of clinical analyses, including disease risk score calculations and dosage decisions. While GenoSiS focuses on finding genetic similarity within a biobank, our similarity search architecture can be extended to represent other medically relevant patient characteristics and search other biobanks.
AnnSQL: A Python SQL-based package for large-scale single-cell genomics analysis on a laptop
Authors: Pavan Kenny , Saunders Arpiar
Published: November 2024

As single-cell genomics technologies continue to accelerate biological discovery, software tools that use elegant syntax and minimal computational resources to analyze atlas-scale datasets are increasingly needed. Here we introduce AnnSQL, a Python package that constructs an AnnData-inspired database using the in-process DuckDb engine, enabling orders-of-magnitude performance enhancements for parsing single-cell genomics datasets with the ease of SQL. We highlight AnnSQL functionality and demonstrate transformative runtime improvements by comparing AnnData or AnnSQL operations on a 4.4 million cell single-nucleus RNA-seq dataset: AnnSQL-based operations were executed in minutes on a laptop for which equivalent AnnData operations largely failed (or were ∼700x slower) on a high-performance computing cluster. AnnSQL lowers computational barriers for large-scale single-cell/nucleus RNA-seq analysis on a personal computer, while demonstrating a promising computational infrastructure extendable for complete single-cell workflows across various genome-wide measurements.

Availability and Implementation

AnnSQL is a pip installable package that can be accessed with usage documentation at:https://github.com/ArpiarSaundersLab/annsql.
Two ways to learn in visuomotor adaptation
Authors: Zhang Yifan , Jayaswal Sana , Schweighofer Nicolas
Published: November 2024

Previous research has demonstrated significant inter-individual variability in the recruitment of the fast-explicit and slow-implicit processes during motor adaptation. In addition, we previously identified qualitative individual differences in adaptation linked to the formation and updating of new memory processes. Here, we investigated quantitative and qualitative differences in visuomotor adaptation with a design incorporating repeated learning and forgetting blocks, allowing for precise estimation of individual learning and forgetting rates in fast-slow adaptation models. Participants engaged in a two-day online visuomotor adaptation task. They first adapted to a 30-degree perturbation to eight targets in three blocks separated by short blocks of no feedback trials. Approximately 24 hours later, they performed a no-feedback retention block and a relearning block. We clustered the participants into strong and weak learners based on adaptation levels at the end of day one and fitted a fast-slow system to the adaptation data. Strong learners exhibited a strong negative correlation between the estimated slow and fast processes, which predicted 24-hour retention and savings, respectively, supporting the engagement of a fast-slow system. The pronounced individual differences in the recruitment of the two processes were attributed to wide ranges of estimated learning rates. Conversely, weak learners exhibited a positive correlation between the two estimated processes, as well as retention but no savings, supporting the engagement of a single slow system. Finally, both during baseline and adaptation, reaction times were shorter for weak learners. Our findings thus revealed two distinct ways to learn in visuomotor adaptation and highlight the necessity of considering both quantitative and qualitative individual differences in studies of motor learning.
Island population demography: Breeding dynamics and drivers of Gotland’s iconic Golden Eagles
Authors: Singh Navinder J , Olofsson Robin , van der Meiden Aemilius Johannes , Lopez-Painado Andres , Månsson Johan
Published: November 2024

Raptor populations on islands are limited by resource availability and the dispersal possibilities for young birds, which are often determined by the size of the island. This leads to differences in population dynamics and viability compared to mainland populations. Human land use modifications on islands—such as agriculture, forestry, excessive hunting, and urban infrastructure development—may affect resource availability and increase risks to these populations, ultimately threatening their survival. Consequently, many island raptor populations have been dramatically reduced or driven to extinction and have never fully recovered. The conditions necessary for their long-term persistence remain uncertain.

Gotland, a large, human-dominated island located in the Baltic Sea, is home to one of the densest populations of Golden Eagles (Aquila chrysaetos) in the world. However, the drivers of population dynamics remain unknown, and many speculations exist that require empirical testing.

Approximately 86 Golden Eagle territories were identified and surveyed across Gotland, an island spanning approximately 3,200 km² (152 km long, 52 km wide, with an 800 km coastline). We investigated the spatial drivers of breeding dynamics in this eagle population, evaluating the effects of territorial habitat composition, overlap with White-tailed Eagles, prey density, and neighborhood effects on territorial productivity.

The average productivity was 0.41 fledglings per pair, which varied annually, with approximately 72% of territories occupied and 32% being successful. Despite significant variation in habitat composition across territories, spatial differences in productivity were primarily influenced by the proportion of coniferous forest (nesting habitat), access to coastal areas (greater prey diversity), the density of the main prey species (roe deer,Capreolus capreolus), and the reproductive status of neighboring territories in a year.

Several novel findings emerged: the role of roe deer as a potential prey species had been previously underappreciated, proximity to the coast was associated with increased productivity, and the variation in spatio-temporal reproductive dynamics across neighboring territories appears to influence overall population dynamics. This relationship warrants further study. We discuss the implications of these findings for the long-term conservation and persistence of this iconic island population and similar populations worldwide.
Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue
Authors: Chen Zeyuan Johnson , Das Sankha Subhra , Kar Asha , Lee Seung Hyuk T. , Abuhanna Kevin D. , Alvarez Marcus , Sukhatme Mihir G. , Gelev Kyla Z. , Heffel Matthew G. , Zhang Yi , Avram Oren , Rahmani Elior , Sankararaman Sriram , Heinonen Sini , Peltoniemi Hilkka , Halperin Eran , Pietiläinen Kirsi H. , Luo Chongyuan , Pajukanta Päivi
Published: November 2024

Human subcutaneous adipose tissue (SAT) contains a diverse array of cell-types; however, the epigenomic landscape among the SAT cell-types has remained elusive. Our integrative analysis of single-cell resolution DNA methylation and chromatin conformation profiles (snm3C-seq), coupled with matching RNA expression (snRNA-seq), systematically cataloged the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types. We discovered that the SAT CG methylation (mCG) landscape is characterized by pronounced hyper-methylation in myeloid cells and hypo-methylation in adipocytes and adipose stem and progenitor cells (ASPCs), driving nearly half of the 705,063 detected differentially methylated regions (DMRs). In addition to the enriched cell-type-specific transcription factor binding motifs, we identifiedTET1andDNMT3Aas plausible candidates for regulating cell-type level mCG profiles. Furthermore, we observed that global mCG profiles closely correspond to SAT lineage, which is also reflected in cell-type-specific chromosome compartmentalization. Adipocytes, in particular, display significantly more short-range chromosomal interactions, facilitating the formation of complex local 3D genomic structures that regulate downstream transcriptomic activity, including those associated with adipogenesis. Finally, we discovered that variants in cell-type level DMRs and A compartments significantly predict and are enriched for variance explained in abdominal obesity. Together, our multimodal study characterizes human SAT epigenomic landscape at the cell-type resolution and links partitioned polygenic risk of abdominal obesity to SAT epigenome.
Spatiotemporally restricted Hippo signalings instruct the fate and maturation of hepatobiliary cells
Authors: Wang Yebin , Zhong Zhenxing , Wang Yu , Zhu Ying , Guan Kun-Liang , Yu Fa-Xing
Published: November 2024

The Hippo pathway is an evolutionary conserved signaling cascade involved in organ size control and tumorigenesis, but its cellular functions and regulatory mechanisms are not fully understood. Recently, we have defined two independent modules (HPO1 and HPO2) in the Hippo signaling network. Here, by using spatially resolved transcriptomic and imaging analysis of mouse livers with defective Hippo signaling, we show that HPO1 and HPO2 operate in distinct cells at different developmental stages to regulate the fate and maturation of liver parenchymal cells. HPO1 controls the maturation of hepatocytes postnatally, and its perturbation leads to the expansion of immature hepatocytes (imHep). HPO2, on the other hand, regulates the maturation of cholangiocytes perinatally, and its ablation results in the accumulation of immature cholangiocytes (imCho2) identical to developing ductal plate cells. Moreover, the inactivation of HPO1 or HPO2 causes the conversion of hepatocytes into immature cholangiocytes (imCho1). These immature cells are also observed in regenerating livers following different damages. In contrast, deletion ofYap/Tazencoding downstream effectors of the Hippo pathway accelerates liver maturation and promotes cell death. These findings suggest that the spatiotemporally restricted Hippo signaling modules act as checkpoints in liver development and may coordinate cell proliferation and maturation to ensure proper liver size and function.
Investigate c-Fos changes in genetically identified amygdala neurons after mild footshock stress
Authors: Dong Hallie , Schlüter Oliver M. , Huang Xiaojie
Published: November 2024

The amygdala is a key brain region that processes stress-related inputs to reshape future behaviors. The lateral amygdala (LA), basolateral amygdala (BLA), and central amygdala (CeA) are important subregions that mediate different aspects of stress experiences from receiving sensory input to memory formation and behavioral responding. The principal neurons in these regions are glutamatergic pyramidal neurons, which are genetically separable into two subpopulations, protein phosphatase 1 regulatory subunit 1B-positive (Ppp1r1b, also known as DARPP-32) parvocellular neurons and R-spondin2-positive (Rspo2) magnocellular neurons. Recent studies show that these two subpopulations of amygdala neurons differentially regulate appetitive versus aversive behaviors. The research goal of this study is to explore whether amygdala Ppp1r1b and Rspo2 neurons are transcriptionally activated by moderate stress experience, such that persistent cellular changes are made to influence future functional output of these two subtypes of neurons. To test transcriptional activation, we focused on c-Fos, one of the early genes that are transiently expressed in response to cellular stimulations to regulate downstream gene transcription. Moderate stress was introduced through brief footshocks, with mice without footshock as controls. Between shocked and control mice, we observed similar numbers of Ppp1r1b or Rspo2 neurons per unit area that expressed c-Fos, which was consistent across LA-BLA and CeA. Moreover, in LA-BLA, Ppp1r1b/c-Fos cells consistently outnumber Rspo2/c-Fos cells across treatment conditions, and the reverse is true in CeA. These results suggest that moderate stress experience is not sufficient to induce robust transcriptional alterations in the two key subpopulations of amygdala neurons, and Ppp1r1b versus Rspo2 neuron activities, as measured by c-Fos expression levels, show differential dominance in amygdala subregions.
Prolonged low flows and non-native fish operate additively to alter insect emergence in mountain streams
Authors: Evangelista Charlotte , Buoro Mathieu , Leathers Kyle , Tronel Tatiana , Carlson Stephanie M. , Ruhi Albert
Published: November 2024

Climate-induced flow alteration is subjecting mountain streams to more frequent and severe low-flow periods due to lower snowpack and earlier snowmelt. Yet, anticipating how stream ecosystems respond to prolonged low flows remains challenging because trophic levels can respond differently, and non-native predators could dampen or amplify responses. Here, we conducted a large-scale experiment to examine how early, prolonged low flows projected by the end of the century in California’s Sierra Nevada will alter mountain stream food webs and emerging insect flux—a critical stream-to-land cross-ecosystem linkage. Additionally, we tested whether Brown trout (Salmo trutta), a widespread non-native top predator, would change food-web responses to low-flow conditions. We found that early low flows and non-native fish effects were additive rather than synergistic or antagonistic. Early low flows did not alter the overall rate of emerging insects but they did shift community structure and reduce the prevalence of small-sized individuals—possibly reflecting larger size at emergence and faster growth rates due to warming. In contrast, non-native fish presence increased seasonally-aggregated abundance of stream insects up to 12%, mainly by increasing abundance of Chironomidae and small-sized Ephemeroptera and Trichoptera. In channels with fish, benthic algal biomass doubled and scraper-grazer and collector-gatherer insects emerged 60% and 55% more than channels without fish, likely benefiting from trout keeping mesopredators at bay. This experiment illustrates that prolonged low flows and invasions can profoundly alter mountain river food webs even when operating additively; and shows how mesocosm-based research may help understand global-change driven disruption of cross-ecosystem linkages.
Synchronous activation of striatal cholinergic interneurons induces local serotonin release
Authors: Matityahu Lior , Hobel Zachary B. , Berkowitz Noa , Malgady Jeffrey M. , Gilin Naomi , Plotkin Joshua L. , Goldberg Joshua A.
Published: November 2024

Striatal cholinergic interneurons (CINs) activate nicotinic acetylcholine receptors on dopamine axons to extend the range of dopamine release. Here we show that synchronous activation of CINs induces and extends the range of local serotonin release via a similar mechanism. This process is exaggerated in the hypercholinergic striatum of a mouse model of OCD-like behavior, implicating CINs as critical regulators of serotonin levels in the healthy and pathological striatum.
Assessing the Biosecurity Risk of Footwear as a Fomite for Transmission of Adventitious Infectious Agents to Mice
Authors: Palillo Michael B , Mishkin Noah , Atmane Mohamad , Palillo Jack A , Carrasco Sebastian , Woods Cheryl , Henderson Kenneth S. , Lipman Neil S , Arbona Rodolfo J Ricart
Published: November 2024

The soles of staff shoes accessing vivaria can become contaminated on urban streets, potentially serving as a source of fomite-mediated transmission of adventitious agents to laboratory rodents. While shoe covers may mitigate this risk, donning them can lead to hand contamination. Staff accessing our vivaria use motor-driven shoe cleaners hundreds of times daily to remove and collect particulates via a vacuum collection system from the top, sole, and sides of shoes instead of shoe covers. Shoe cleaner debris (SCD) and contact media (CM) exposed to SCD from shoe cleaners in 5 vivaria were assessed by PCR for 84 adventitious agents. SCD and CM samples tested positive for 33 and 37 agents, respectively, and a combined 39 agents total. To assess SCD infectivity, NSG and Swiss outbred mice were housed for 7 days in direct contact with SCD and oronasally inoculated with a suspension created from SCD collected from each of the 5 vivaria. Mice were tested by PCR and serology 3-, 7-, 14- and 63-days post-inoculation. All mice remained healthy until the study’s end and tested negative for all agents found in SCD/CM except murine astrovirus 1,Staphyloccocus xylosusandCandidatus Savagella, agents known to be enzootic in the experimental mouse source colony. In a follow-up study, the soles of 27 staff street shoes were directly sampled using CM. Half of CM was used for PCR, while the other half was added as bedding material to a cage containing NSG and Swiss outbred mice. While CM tested positive for 11 agents, all mice were healthy 63 days post-exposure and again positive for only enzootic agents. These results suggest that shoe debris might not be a significant biosecurity risk to laboratory mice, questioning the need for shoe covers or cleaners when entering experimental barrier vivaria.
Planning and movement activities co-adapt in a motor-reference frame during 3D BCI-controlled reach adaptation in monkey frontal and parietal cortices
Authors: Ferrea E. , Morel P. , Gail A.
Published: November 2024

Perturbing visual feedback is a powerful tool for studying visuomotor adaptation. However, unperturbed proprioceptive signals in common paradigms inherently co-varies with physical movements and causes incongruency with the visual input. This can create challenges when interpreting underlying neurophysiological mechanisms. We employed a brain-computer interface (BCI) in rhesus monkeys to investigate spatial encoding in frontal and parietal areas during a 3D visuomotor rotation task where only visual feedback was movement-contingent. We found that both brain regions better reflected the adapted motor commands than the perturbed visual feedback during movement preparation and execution. This adaptive response was observed in both local and remote neurons, even when they did not directly contribute to the BCI input signals. The transfer of adaptive changes in planning activity to corresponding movement corrections was stronger in the frontal than in the parietal cortex. Our results suggest an integrated large-scale visuomotor adaptation mechanism in a motor-reference frame spanning across frontoparietal cortices.
PGR5 is needed for redox-dependent regulation of ATP synthase both in chloroplasts and in cyanobacteria
Authors: Nikkanen Lauri , Wey Laura T , Woodford Russell , Mustila Henna , Ermakova Maria , Rintamäki Eevi , Allahverdiyeva Yagut
Published: November 2024

Control of the proton motive force (pmf) via regulation of ATP synthase constitutes a key mechanism for photosynthetic organisms to maintain redox balance and induce photoprotective mechanisms under light fluctuations. Using time-resolved electrochromic shift measurements in various photosynthetic organisms, we found that ATP synthase is dynamically regulated during light fluctuations. While light-induced reduction of the CF1γ subunit is known to activate chloroplast ATP synthase, it did not account for the regulation in fluctuating light in Arabidopsis thaliana, suggesting alternative mechanisms. The PROTON GRADIENT REGULATION 5 (PGR5) protein is important for photoprotection in algal and plant chloroplasts. PGR5 has been proposed to facilitate cyclic electron transport around PSI (CET), but it also affects ATP synthase activity. The physiological role of cyanobacterial Pgr5 has remained elusive. We characterised a ∆pgr5 mutant of Synechocystis sp. PCC 6803 and investigated pmf dynamics in pgr5 mutants of Chlamydomonas reinhardtii, Arabidopsis, and the C4 grass Setaria viridis. While PGR5 was not required for CET in Synechocystis, it was needed for downregulating ATP synthase under high irradiance in all tested organisms via a thiol redox state dependent mechanism. As AtPGR5 interacted with AtCF1γ, PGR5 may have a conserved function as an inhibitor of ATP synthase.
Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models
Authors: Hayes Conor F. , Magana-Zook Steven A. , Gonçalves Andre , Solak Ahmet Can , Faissol Daniel , Landajuela Mikel
Published: November 2024

We propose a novel approach for antibody library design that combines deep learning and multi-objective linear programming with diversity constraints. Our method leverages recent advances in sequence and structure-based deep learning for protein engineering to predict the effects of mutations on antibody properties. These predictions are then used to seed a cascade of constrained integer linear programming problems, the solutions of which yield a diverse and high-performing antibody library. Operating in acold-startsetting, our approach creates designs without iterative feedback from wet laboratory experiments or computational simulations. We demonstrate the effectiveness of our method by designing antibody libraries for Trastuzumab in complex with the HER2 receptor, showing that it outperforms existing techniques in overall quality and diversity of the generated libraries. Our source code is available athttps://github.com/LLNL/protlib-designer.
A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliateZoothamnium niveum
Authors: Contarini PE , Emboule E , Jean-Louis P , Woyke T , Date SV , Gros O , Volland J-M
Published: November 2024

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliateZoothamnium niveumand its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup,Z. niveumholds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.
Evaluating Combined Neurotoxicity of Amyloid Beta and Tau Oligomers in Alzheimer’s Disease: A New Criterion
Authors: Kuznetsov Andrey V.
Published: November 2024

A criterion characterizing the combined neurotoxicity of amyloid beta and tau oligomers is suggested. A mathematical model that makes it possible to calculate a value of this criterion during senile plaque and NFT formation is proposed. Computations show that for physiologically relevant parameter values, the value of the criterion increases approximately linearly as time increases. Once the formation of neurofibrillary tangles starts in addition to the senile plaque formation, the slope characterizing the rate at which the criterion increases becomes larger. The critical value of the criterion upon reaching which the neuron dies is estimated. Computations predict that unless the production rates of amyloid beta and tau monomers are very large, in order for the accumulated toxicity to reach the critical value, the degradation machinery responsible for the degradation of amyloid beta and tau must become dysfunctional. The value of the criterion after 20 years of the aggregation process is strongly influenced by deposition rates of amyloid beta and tau oligomers into senile plaques and NFTs. This suggests that deposition of amyloid beta and tau oligomers into senile plaques and NFTs may reduce accumulated toxicity by sequestering more toxic oligomeric species into less toxic insoluble aggregates.