bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep in People Experiencing Homelessness Under Different Conditions and Seasons
Authors: Rice Alicia , Casiraghi Leandro P. , Gildee Cristina , Almquist Zack W. , Hagopian Amy , Martin Melanie A. , de la Iglesia Horacio O.
Published: January 2025

Poor sleep represents a central health disparity for people experiencing homelessness, and any intervention to alleviate the impacts of homelessness should aim to improve sleep. We measured actimetry-based sleep in homeless adults spending their nights in four types of shelters in Seattle, WA, during the summer and winter. Homeless participants experienced more sleepless nights than housed participants in both seasons. During the summer sleeping nights, homeless participants experienced sleep patterns similar to housed subjects, but during the winter, their sleep duration was up to 1.5 hours shorter. Similarly, sleep quality, determined through sleep variability index, activity during the night, and intraindividual variability of sleep parameters, was poorer during the winter in homeless than in housed participants. Our study demonstrates the feasibility of using objectively measured sleep as a proxy for assessing the value of specific interventions to improve living conditions in people experiencing homelessness. Given the bidirectional relationship between sleep and both physical and mental health, our study reveals the health inequities of chronic sleep disparity for those living outdoors.

Significance statement

Sleep disparities are central to the poor physical and mental health experienced by houseless people. Here we show that measured sleep through wrist actigraphy captures different aspects of this sleep disparity and represents a useful, objective metric of the impact of interventions to improve living conditions among people experiencing homelessness.
γδ T cells are the prime anti-tumoral T cells in pediatric neuroblastoma
Authors: Castenmiller Suzanne M. , Borst Anne L. , Wardak Leyma , Molenaar Jan J. , Papadopoulou Maria , de Krijger Ronald R. , van der Steeg Alida F. W. , Vermijlen David , de Groot Rosa , Wienke Judith , Wolkers Monika C.
Published: January 2025

High-risk pediatric neuroblastoma patients have a dismal survival rate despite intensive treatment regimens. New treatment options are thus required. Even though HLA expression in neuroblastoma is low and immune cell infiltrates are limited, the presence of tumor infiltrating lymphocytes (TILs) is indicative for better patient survival. Here, we show that most tumor lesions contain viable immune cell infiltrates after induction chemotherapy, with high percentages of CD3+T cells. We therefore expanded the TILs and tested their anti-tumoral activity. With sufficient starting material, TIL expansion was as efficient as for adult solid tumors. However, whereas TIL products from adult tumors almost exclusively contained αβ T cells, in neuroblastoma-derived TILs, γδ T cells expanded with similar efficacy as αβ T cells. Importantly, the anti-tumor responses in response to autologous tumor digest primarily originated from (Vδ1- and Vδ3-expressing) γδ T cells, and not from αβ T cells. In conclusion, this finding creates a window of opportunity for immunotherapy for neuroblastoma patients, with γδ T cells as potential prime responders.
Stability and Performance of Linear Combination Tests of Gene Set Enrichment for Multiple Covariance Estimators in Unbalanced Studies
Authors: Khademioureh Sara , Amini Payam , Ghasemi Erfan , Calistrate-Petre Paul , Pyne Saumyadipta , Dinu Irina
Published: January 2025

Gene set analysis (GSA) is essential for understanding coordinated gene expression changes within biological pathways, especially in high-dimensional data generated by platforms such as RNA-seq and microarrays. This study focuses on the linear combination test (LCT), a GSA method that combines multiple gene-level statistics into a powerful test statistic to assess the association between a gene set and outcomes of interest in a given set of samples. We evaluated the performance and stability of LCT using different covariance matrix estimators, including ridge, graphical lasso, and adaptive lasso, which are known for their effectiveness in high-dimensional data analysis. In addition, we assessed the robustness of LCT in the face of unbalanced study designs, which are typical in biomedical research due to limited sample availability and the high cost of data generation. We conducted a simulation study and applied LCT to publicly available gene expression datasets comparing patients with systemic lupus erythematosus (SLE) to healthy controls, where the number of controls is significantly lower than the number of cases. Our findings demonstrate that while LCT's default shrinkage estimator shows limitations in highly correlated and unbalanced designs, ridge estimation provides a more reliable alternative for unbalanced scenarios. Researchers can optimize LCT's performance by selecting appropriate covariance estimators based on their data structure. These results suggest that LCT is a reliable and powerful tool for GSA in unbalanced studies, identifying SLE-relevant gene sets more effectively than other GSA methods and showing validation against clinical phenotypes, offering valuable insights into the underlying mechanisms of complex diseases such as SLE.
Local Microenvironments of capsomer variants in the PBCV-1
Authors: Guo Wenhan , Alarcon Esther , Sanchez Jason E , Xiao Chuan , Li Lin
Published: January 2025

PBCV-1, a giant virus classified among the Nucleocytoviricota virus (NCV) whose structure has been determined to near atomic resolution. The majority capsomers forming the capsid of PBCV-1 are Type I capsomers while five other type of variants have been found in recent high resolution structure. Interestingly, some variants, such as Type V capsomers, are found at particular capsid locations whose roles are unclear. To reveal the roles of a Type V capsomer, we replaced the Type V capsomer by a Type I capsomer to compare the interaction among the two types of capsomer variant, especially the interactions between each of the Type V/Type I capsomer and its local capsid microenvironment. Our results revealed significant differences between Type V and Type I capsomers. Notably, the Type V capsomer demonstrated a stronger binding force to the surrounding capsomers than the Type I capsomer. Moreover, the identified salt bridges between Type V/I capsomers and their surrounding capsomers corroborate the results of electrostatic calculations, further highlighting the important residues involved in these interactions. Understanding these local capsid microenvironments will be essential to elucidate the mechanisms governing viral capsid assembly.
Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes
Authors: Rídl Jakub , Dedukh Dmitrij , Halenková Zuzana , Schlebusch Stephen A , Beneš Vladimír , Lopez Mireia Osuna , Osiejuk Tomasz S. , Ruiz-Ruano Francisco J , Suh Alexander , Albrecht Tomáš , Reif Jiří , Reifová Radka
Published: January 2025

Centromeres are an important part of chromosomes which direct chromosome segregation during cell division. Their modifications can therefore explain the unusual mitotic and meiotic behaviour of certain chromosomes, such as the germline-restricted chromosome (GRC) of songbirds. This chromosome is eliminated from somatic cells during early embryogenesis and later also from male germ cells during spermatogenesis. Although the mechanism of elimination is not yet known, it is possible that it involves a modification of the centromeric sequence on the GRC, resulting in problems with the attachment of this chromosome to the mitotic or meiotic spindle and its lagging during anaphase, which eventually leads to its elimination from the nucleus. However, the repetitive nature and rapid evolution of centromeres make their identification and comparative analysis across species and chromosomes challenging. Here, we used a combination of cytogenetic and genomic approaches to identify the centromeric sequence of two closely related songbird species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia). We found a 436-bp satellite repeat present in the centromeric regions of all regular chromosomes, making it a strong candidate for the centromeric repeat. This centromeric repeat was highly similar between the two nightingale species. Interestingly, hybridization of the probe to this satellite repeat on meiotic spreads suggested that this repeat is missing on the GRC. Our results indicate that the change of the centromeric sequence may underlie the unusual inheritance and programmed DNA elimination of the GRC in songbirds.
Ensemble docking for intrinsically disordered proteins
Authors: Dhar Anjali , Sisk Thomas R. , Robustelli Paul
Published: January 2025

Intrinsically disordered proteins (IDPs) are implicated in many human diseases and are increasingly being pursued as drug targets. Conventional structure-based drug design methods that rely on well-defined binding sites are however, largely unsuitable for IDPs. Here, we present computationally efficient ensemble docking approaches to predict the relative affinities of small molecules to IDPs and characterize their dynamic, heterogenous binding mechanisms at atomic resolution. We demonstrate that these ensemble docking protocols accurately predict the relative binding affinities of small molecule α-synuclein ligands measured by NMR spectroscopy and generate conformational ensembles of ligand binding modes in remarkable agreement with experimentally validated long-timescale molecular dynamics simulations. Our results display the potential of ensemble docking approaches for predicting small molecule binding to IDPs and suggest that these methods may be valuable tools for IDP drug discovery campaigns.
Human Genome Book:Words,Sentences and Paragraphs
Authors: Liang Wang
Published: January 2025

Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments that can be fully annotated and understood remain relatively limited. If we consider the genome as a book, constructing its equivalents of words, sentences, and paragraphs has been a long-standing and popular research direction. Recently, studies on transfer learning in large language models have provided a novel approach to this challenge. Multilingual transfer ability, which assesses how well models fine-tuned on a source language can be applied to other languages, has been extensively studied in multilingual pre-trained models. Similarly, the transfer of natural language capabilities to “DNA language” has also been validated. Building upon these findings, we first trained a foundational model capable of transferring linguistic capabilities from English to DNA sequences. Using this model, we constructed a vocabulary of DNA words and mapped DNA words to their English equivalents. Subsequently, we fine-tuned this model using English datasets for paragraphing and sentence segmentation to develop models capable of segmenting DNA sequences into sentences and paragraphs. Leveraging these models, we processed the GRCh38.p14 human genome by segmenting, tokenizing, and organizing it into a “book” comprised of genomic “words,” “sentences,” and “paragraphs.” Additionally, based on the DNA-to-English vocabulary mapping, we created an “English version” of the genomic book. This study offers a novel perspective for understanding the genome and provides exciting possibilities for developing innovative tools for DNA search, generation, and analysis.
Individual dopaminergic neurons induce unique, yet overlapping combinations of behavioural modulations including safety learning, memory retrieval and acute locomotion
Authors: Toshima Naoko , Behrad Arman , Behnke Franziska , Kaushik Gauri , Weiglein Aliće , Strauch Martin , Thoener Juliane , Kobler Oliver , Wang Maia Lisandra M. , Dörr Markus , Schleyer Michael
Published: January 2025

Two evolutionary highly conserved functions of dopamine are to carry “teaching” signals during associative learning and to control movement. In mammals and humans these functions are generally thought to be produced by different populations of neurons. Here, we investigated in the larva ofDrosophila melanogasterwhether both these functions can be induced by the same individual dopaminergic neurons in the central brain. Focusing on the dopaminergic neurons of the DL1-cluster, we asked whether the optogenetic activation of individual neurons established associative punishment and/or safety memories, controlled the retrieval of the established memories, and acutely modulated locomotion. We found that each neuron had a unique, yet overlapping set of behavioural effects. Several individual neurons both established a memory and modulated acute locomotion by increasing the animals’ bending and decreasing its velocity. Our results demonstrate that individual dopaminergic neurons can fulfil a surprisingly broad range of functions in different behavioural contexts. Given the highly conserved roles of the dopaminergic system across the animal kingdom, this study raises the question whether a similarly diverse functionality can be found also in other animals, including humans.
Metabolic alterations in human post-mortem frontal cortex and cerebrospinal fluid associated with high levels of nicotine metabolite cotinine
Authors: Masvosva Wadzanai , Lehtonen Marko , Martiskainen Mika , Tiihonen Jari , Karhunen Pekka J. , Hanhineva Kati , Rysä Jaana , Kok Eloise , Kärkkäinen Olli
Published: January 2025

Cigarette smoking is the single most significant cause of preventable death in the world. Tobacco smoking causes exposure to thousands of chemicals and disrupts biological pathways. It impacts several organs, including the brain, where its effects are mediated by nicotinic acetylcholine receptors. Women seem to be more susceptible to the negative health effects of smoking. In this study we focused on the changes in the metabolic profile of human postmortem frontal cortex and cerebrospinal fluid samples associated with high levels of the nicotine metabolite cotinine. We used non-targeted metabolomics to analyze post-mortem frontal cortex and cerebrospinal fluid (CSF) samples from the Tampere Sudden Death Study cohort. We identified 137 cases (24 females) with high cotinine levels, indicating nicotine exposure. For controls, we identified 82 subjects (20 females) with no cotinine in the frontal cortex or CSF samples and no known history of smoking based on medical records and autopsy reports. Cases had significantly higher levels of 1-methylhistamine (Cohen’s d=0.66, p<0.0001) and N-acetylputrescine (d=0.84, p<0.0001), and lower levels of aspartic acid (d=-0.53, p<0.001), 3-methylhistidine (d=-0.58, p=0.0004), and taurine (d=-0.47, p=0.0002) in the frontal cortex compared to controls. Compared to the frontal cortex, differences between cases and controls were smaller in the CSF samples. Most of the observed differences were similar in both sexes, with a few exceptions like low ergothioneine levels, observed especially in female cases. In conclusion, smoking or nicotine exposure is associated with alterations in metabolites linked to increased oxidative stress and neuroinflammation, as well as reduced neurotransmitter levels in the frontal cortex.
Binge Eating and Psychological Distress: Investigating Relationships with Depression, Anxiety, and Stress
Authors: Soares Marinho Ana Carolina , da Costa Julio Cezar Albuquerque , Fernandes Sheyla C.S
Published: January 2025

Binge eating (BE) involves the consumption of a greater amount of food than most people would under similar conditions, within a specified period and may be associated with various psychiatric disorders. This study aimed to compare the variables of Depression, Anxiety, and Stress among groups defined by the severity of binge eating symptoms. Participants were recruited through social media advertisements and responded online to the Depression, Anxiety, and Stress Scale (DASS-21) and the Binge Eating Scale (BES). It was observed that individuals with medium-high depressive symptoms showed a higher presence of binge eating symptoms, while those with moderate, severe, and extremely severe anxiety symptoms exhibited an increased occurrence of binge eating. The findings suggest a need for interventions addressing binge eating with comorbidities such as depression and anxiety, or binge eating as a comorbidity of these conditions.
Improving the accuracy of Respiratory Syncytial Virus (RSV) incidence among hospitalised adults in Bristol, UK
Authors: Lihou Katie , Challen Robert , Chatzilena Anastasia , Qian George , Oben Glenda , King Jade , McGuinness Serena , Morales-Aza Begonia , Duale Kaltun , Rodriguez Pereira Ainhoa , Healy William , Oliver Jennifer , Maskell Nick , Finn Adam , Danon Leon , Hyams Catherine
Published: January 2025

Respiratory Syncytial Virus (RSV) burden in adults is of interest due to recently-licensed vaccines, however, estimates are affected by test characteristics.

We conducted a prospective cohort study of adults with acute lower respiratory tract disease (aLRTD) hospitalised in Bristol from April 2022–March 2023. RSV was detected by RT-PCR at standard-of-care and by additional nasopharyngeal, saliva, and sputum samples. Latent class analysis quantified and adjusted for test error and multiple testing.

6906/11445 aLRTD cases (60%) were tested and 251 were positive (3.6%). Test-positivity peaked in December (7.9-12.7%). Among cases, 43% had pneumonia and 55% had non-pneumonic infection. Due to low positivity-rates and imperfect specificity, test-positivity (3.6%) overestimated true prevalence (2.3%). Adjusted adult population incidence/1000-person-years was 0.33 (0.21-0.49), and 2.02 (1.10-3.06) in ≥75-year-olds.

RSV vaccines could reduce morbidity of hospitalised adult aLRTD, including non-pneumonic infection. Adult RSV burden accuracy is improved by adjustment for test characteristics, particularly estimates out-of-season.
Mapping obesity-related traits with regional white matter microstructure highlights the importance of brainstem tracts and sex-related differences
Authors: Gurholt Tiril P. , Beck Dani , Voldsbekk Irene , Parker Nadine , Askeland-Gjerde Daniel E. , de Lange Ann-Marie G. , van der Meer Dennis , Tamnes Christian K. , Thompson Paul M. , Sønderby Ida E. , Maximov Ivan I. , Westlye Lars T. , Andreassen Ole A.
Published: January 2025

Background and aims

The relationships between obesity-related traits and the brain’s white matter characteristics and the context of sex- and age-related differences, remain unclear. This study aims to elucidate these body-brain connections using a large-scale dataset.

Methods

We analyzed data from 40,040 participants from the UK Biobank (52.2% female; ages 44-83 years) using multiple linear regression to evaluate associations between obesity-related traits (obesity, body anthropometrics) and white matter diffusion tensor imaging (DTI) metrics (fractional anisotropy, axial diffusivity, radial diffusivity, mean diffusivity). We also examined interactions with age and sex.

Results

Our analyses revealed significant associations between obesity-related traits and DTI metrics with partial correlation coefficient |r| effect sizes ranging from 0.02 to 0.20 for most regions of interest with largest effects in brainstem tracts. We observed more widespread sex-by-obesity-related than age-by-obesity-related interaction effects on DTI metrics.

Conclusions

Our results link obesity-related traits and white matter phenotypes, suggesting that shared body fat-related pathways linking physical and brain health that may vary based on sex and age. Understanding these relationships could enhance the development and evaluation of targeted, individualized, treatment strategies for conditions that co-occur with obesity, although further longitudinal studies are needed to map the dynamics of these associations.
A real-world cohort study of immune-related adverse events in patients receiving immune checkpoint inhibitors
Authors: Wang Yanfei , Guo Yi , Tan Aik Choon , Zhao Lili , Shi Xu , Chen Yong , Sun Ramon C , Liu Mei , Su Jing , George Thomas J , Bian Jiang , Song Qianqian
Published: January 2025

Background

Immune checkpoint inhibitors (ICIs) have significantly improved patient survival outcomes across various cancer types. However, their use is often associated with immune-related adverse events (irAEs), posing challenges in clinical management. Understanding the incidence, severity, and risk factors of irAEs is critical for optimizing ICI therapy and minimizing adverse outcomes.

Objective

This study aimed to identify and evaluate risk factors for immune-related adverse events (irAEs) among patients receiving ICIs, focusing on patient demographics, comorbidities, cancer types, and ICI regimens. Additionally, we sought to examine the incidence, severity, and organ-specific patterns of irAEs to guide personalized management strategies.

Methods

This retrospective cohort study utilized real-world data from the OneFlorida+ Clinical Research Network, including 9,193 adult patients who received ICIs between January 2018 and December 2022. Patients were categorized based on whether they developed irAEs within one year of initiating ICI therapy. Multivariable logistic regression was employed to identify risk factors for irAEs, adjusting for key covariates such as age, sex, cancer type, smoking status, and comorbidities. Kaplan-Meier survival analysis and cumulative incidence functions were applied to evaluate time to irAE event and overall incidence, stratified by irAE severity, cancer type, and ICI regimens.

Results

Of the 6,526 patients included in the final analysis, 56.2% developed irAEs within one year of ICI treatment, including 284 severe cases. Female and younger patients (ages 18-29) were at higher risk of developing irAEs, while comorbidities such as myocardial infarction, congestive heart failure, and renal disease significantly increased irAE risk. In contrast, dementia was associated with a reduced risk of irAEs. Patients treated with combined CTLA4+PD(L)1 inhibitors exhibited a 35% higher risk of irAEs compared to PD-1 inhibitors alone (OR: 1.35, 95% CI: 1.14–1.60, P < 0.001). Cancer type also influenced irAE risk, with breast cancer (OR: 2.36, 95% CI: 1.57–3.60, P < 0.001) and hematological cancer (OR: 2.61, 95% CI: 1.40–5.14, P = 0.004) associated with higher risk compared to melanoma, whereas brain cancer had a reduced risk (OR: 0.55, 95% CI: 0.32–0.92, P = 0.025). Survival analysis revealed that irAE severity significantly impacts both the timing of irAE onset (P = 0.038) and overall survival (P < 0.0001). While treatment regimens significantly influenced irAE-free survival in multi-site cancers (P = 0.02) and overall survival in kidney cancer (P = 0.0011), their effects were less pronounced in other cancer types.
Measuring Frailty: A Comparison of the Cumulative Deficit Model of Frailty in Survey and Routine Data
Authors: Johnson Lara , Guthrie Bruce , Anand Atul , Marshall Alan , Seth Sohan
Published: January 2025

Purpose

Frailty, a state of increased vulnerability to adverse health outcomes, impacts individuals and healthcare systems. The cumulative deficit model provides a flexible frailty measure but its application across diverse data remains underexplored. This study compares frailty indices derived from survey and routine data.

Methods

Frailty indices in the Clinical Practice Research Datalink (CPRD) Aurum (N = 1,625,677) and the English Longitudinal Study of Ageing (ELSA) (N = 5190) were compared for adults aged 65+ in England. Deficits were categorised as "one-to-one", "one-to-many", and "one-to-none". Age-sex-standardised deficit prevalence, frailty distribution and associations with demographics were analysed using summary statistics and regression.

Results

Mean frailty index scores were similar (CPRD: 0.13 ± 0.10; ELSA: 0.13 ± 0.12) but differences were observed in the capture of specific deficits. The majority of deficits had a “one-to-none” or “one-to-many” mapping. Among 14 comparable deficits, visual impairment, fractures and heart failure were more common in CPRD, while falls, sleep disturbance and arthritis were more frequent in ELSA. Severe frailty and greater fitness were more prevalent in ELSA than CPRD. Sex and age influenced frailty similarly in both datasets, with frailty index scores increasing more rapidly with age in CPRD.

Conclusion

Differences in the number and types of deficits measured offset each other overall, supporting the cumulative deficit model’s premise that including a sufficient range of deficits does not significantly alter population-level frailty measures. This interchangeability may alleviate concerns about deficit selection, supporting more flexible approaches to population frailty assessment across both survey and routine data.

KEY SUMMARY POINTS

Aim

We assess whether similar frailty prevalence is observed in survey and routine data despite differences in the number, types and prevalence of the individual deficits measured in frailty indices.

Findings

Frailty index calculations using established principles showed strong comparability between survey and routine data. Including a sufficient range of deficits does not significantly alter population-level frailty measures.

Message

The cumulative deficit model’s robustness to deficit selection supports flexible approaches to population frailty assessment across diverse data sources, such as survey and routine data.
In vitroantioxidant and anti-inflammatory activities, total phenolic and flavonoid contents ofAnadenanthera colubrinafrom Northern Peru
Authors: Samame-Caramutti Edert Abel , Salcedo-Valdez Luis , Suárez-Cunza Silvia
Published: January 2025

The antioxidant and anti-inflammatory activities of the hydroethanolic extract from bark ofAnadenanthera colubrina(ACE), as well as its total phenolic (TPC) and flavonoid (TFC) contents, were studiedin vitro. The ACE showed a high antioxidant activity both in the DPPH●radical scavenging (747.6mg Trolox equivalents/g dry extract) and in the FRAP (435.9mg FeSO4equivalents/g dry extract) chemical assays. The extract (50 to 1000μg/mL) inhibited the lipid peroxidation (formation of TBARS), hemolysis induced by H2O2, and egg albumin denaturation. No activity was observed in the hypotonicity-induced hemolysis assay. The TPC and TFC were 642.7mg GAE/g and 416.2mg CE/g dry extract, respectively. To the best of our knowledge, these activities were reported for the first time forA. colubrinafrom northern Peru, and suggest that the ACE has notable antioxidant and anti-inflammatory properties, and that the high TPC and TFC could be responsible, at least partially, for these activities.
Dual regulatory role of IS91-encoded Orf121 in IS91transposition
Authors: Fauconnier Aurélien , Da Re Sandra , Gaschet Margaux , Jové Thomas , Ploy Marie-Cécile , Pasternak Cécile
Published: January 2025

Prokaryotic insertion sequences (IS) are pivotal in the propagation of bacterial multidrug resistance, with IS91notably linked to virulence and antibiotic resistance genes. However, the precise mechanism by which IS91contributes to gene dissemination remains elusive. Unique among its family, IS91features a small open reading frame (orf) upstream of thetnpAtransposase gene, potentially encoding a 121-amino acid protein,orf121, which may be translationally coupled withtnpA.

Using a genetic system based on the mating-out assay inEscherichia coli, we explored the role oforf121in thein vivotransposition of IS91. Our findings indicate that the overlap betweenorf121andtnpAis crucial fortnpAtranscription, with both being primarily transcribed as bicistronic mRNAs from the Porf121promoter. Additionally, the expression oforf121(whetherin cisortrans) significantly reduces the frequency of IS91transposition and the rate of one-ended transposition. Furthermore, only the single-stranded DNA circles of IS91intermediates can integrate into new target sequences, and Orf121 negatively influences this insertion step.

In summary,orf121acts as a negative regulator of transposition while ensuring the expression oftnpA, thus providing insights into the complex mechanisms underlying IS91-mediated gene dissemination and its potential role in antibiotic resistance propagation.
CalciumNetExploreR: An R Package for Network Analysis of Calcium Imaging Data
Authors: Lenci Simone , Sieger Dirk
Published: January 2025

1

Analyzing calcium imaging data to understand complex functional networks can be challenging, often requiring multiple tools, custom scripts, and some coding expertise. To address these challenges, we present CalciumNetExploreR (CNER), an R package designed to streamline and standardize the analysis of time-series data from neuronal populations. While originally developed with calcium imaging in mind, CNER’s modular design also makes it adaptable to other sources of neural time-series data, such as fMRI or electrophysiological recordings.

CNER integrates essential steps—normalization, binarization, population activity visualization, network construction, degree distribution analysis, principal component analysis (PCA), power spectral density (PSD) evaluation, and event frequency calculations—into a single, cohesive pipeline. This comprehensive approach enables users to efficiently extract and compare network metrics, including clustering coefficients, global efficiency, community structures, and principal component variances. By offering a flexible and customizable framework, CNER simplifies the examination of functional connectivity and network topology, effectively providing the means to characterize a cellular functional network or analogous structures in other modalities.

Designed as a user-friendly package, CNER allows both experimental and computational neuroscientists to incorporate robust statistical and graphical analyses into their workflows without extensive coding knowledge. By unifying key analytical components into one pipeline, CNER reduces barriers associated with large-scale data analyses, ultimately facilitating deeper insights into the functional organization and dynamic properties of neuronal networks across diverse recording techniques.
Crossmodal pitch-luminance association in tortoises
Authors: Loconsole Maria , Malaman Beatrice , Stancher Gionata , Versace Elisabetta
Published: January 2025

If you think that high-pitched sounds match bright colours more than dark ones, you are not alone. Spontaneous associations between different sensory modalities —crossmodal associations— are widely observed in humans. More recently, crossmodal associations have been reported in chimpanzees, monkeys, dogs, chickens, and tortoises, indicating a general cognitive strategy that reflects natural correlations in the environment or similarities in the architecture of the nervous system. Alternatively, or complementarily, crossmodal associations may arise from learning of species-specific occurrences. Recent research on primates has tentatively linked human pitch-luminance associations to the evolution of language. While humans and chimpanzees spontaneously match a high-pitched sound with a white shape and a low-pitched sound with a black shape, baboons and chickens do not exhibit any preferential association. Identifying spontaneous pitch-luminance associations in species that do not rely on vocal communication, such as the solitary Hermann’s tortoises, would support the idea of a language-independent phenomenon. To test this idea, we studied tortoises for pitch-luminance associations in a spontaneous food-searching task. After hearing a high-pitched (700 Hz) vs low-pitched (450 Hz) sound, animals could choose to search for food behind either a light- or dark-coloured wall. When hearing the high-pitched sound, tortoises chose the white stimulus, whereas when hearing the low-pitched sound, they chose the black stimulus, similarly to what humans and chimpanzees do. These results demonstrate crossmodal pitch-luminance associations in tortoises. While showing this commonality in the perceptual organization of phylogenetically distant species, we shift the question on whether pitch-luminance associations reflect homology or convergent evolution.
ST-FFPE-mIF: Integrating Spatial Transcriptomics and Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tissues Using Stereo-seq
Authors: Zhang Xue , Zhang Meng , Xu Yuan , Song Yangyang , Yang Xinfeng , Wu Yanan , Zhao Xuelin , Ran Dongsheng , Liu Xin , Huang Huaqiang , Lei Wenxiao , Li Hongyan , Zhang Yongfen , Xi Feng , Li Guibo , Liu Xing , Xu Luohao , Chen Ao , Liao Sha , Zhang Jiajun
Published: January 2025

Stereo-seq is the state-of-the-art technique, which allows capturing of spatial transcriptomic data at sub-cellular resolution and in large scale of view. Stereo-seq FFPE technique is recently launched with the capability to obtain spatially resolved gene expression in FFPE tissue sections. However, the omic information is limited to transcriptome. To delineate spatial molecular hierarchy from transcriptome to phenome, we present the protocol that implements nine-plex immunofluorescence staining with detection of spatial transcriptomics in one FFPE tissue section (short for ST-FFPE-mIF). This protocol details the modified biochemistry procedure and also provides analytical framework to achieve single-cell resolution through nuclear or membrane staining-based cell segmentation. We demonstrated the application of ST-FFPE-mIF in colorectal cancer sample to illustrate how ST-FFPE-mIF facilitates a robust analysis of spatially resolved multi-omic data at the single-cell level.
Single-molecule mitochondrial DNA imaging reveals heteroplasmy dynamics shaped by developmental bottlenecks and selection in different organsin vivo
Authors: Chandrasegaram Rajini , Hynes-Allen Antony M. , Gao Beitong , Dhawanjewar Abhilesh , Frison Michele , Petridi Stavroula , Chinnery Patrick F. , Ma Hansong , van den Ameele Jelle
Published: January 2025

Mitochondrial DNA (mtDNA) occurs in many copies per cell, with cell-to-cell variability in mutation load, known as heteroplasmy. Developmental and age-related expansion of pathogenic mtDNA mutations contributes to mitochondrial and neurodegenerative disease pathogenesis. Here, we describe an approach forin situsequence-specific detection of single mtDNA molecules (mtDNA-smFISH). We apply this method to visualize and measurein situmtDNA and heteroplasmy levels at single-cell resolution in whole-mountDrosophilatissue and cultured human cells. InDrosophila, we identify a somatic mtDNA bottleneck during neurogenesis. This amplifies heteroplasmy variability between neurons, as predicted from a mathematical bottleneck model, predisposing individual neurons to a high mutation load and degeneration. However, both during neurogenesis and oogenesis, mtDNA segregation is accompanied by purifying selection, promoting wild-type over mutant mtDNA. mtDNA-smFISH thus elucidates novel mechanisms whereby developmental cell-fate transitions, accompanied by changes in cell morphology, behaviour and metabolism, will shape disease-relevant and tissue-specific transmission and selection of mtDNA mutations.
Tet3 Mediates O-GlcNAcylation-Induced Remyelination
Authors: Li Yawen , Li Pingping , Song Yixuan , Zhang Mingliang
Published: January 2025

The failure of oligodendrocyte precursor cells (OPCs) to generate mature oligodendrocytes represents a major hurdle impeding myelin repair. However, the cellular determinants for OPC differentiation and the pharmacological targets driving remyelination remain rudimentary. Here, we demonstrate that O-GlcNAcylation intrinsically drives remyelination, in which Tet3 is one downstream effector. Enhanced O-GlcNAcylation significantly promotes OPC differentiation, whereas conditional depletion of Ogt in OPCs seriously impairs myelin formation in the developing central nervous system (CNS). Intriguingly, O-GlcNAcylation in OPCs positively correlates with the myelin status, and enhanced O-GlcNAcylation dramatically accelerates remyelination. Proteomic analyses reveal a cohort of proteins uniquely O-GlcNAcylated in OPCs. Among these, Tet3 is exclusively O-GlcNAcylated in OPCs within CNS, which in turn modulates its demethylation activity, thereby regulating myelin gene expression and remyelination. Our findings highlight the crucial role of the Ogt-Tet3 axis in OPC differentiation and suggest O-GlcNAcylation as a druggable target for treating demyelinating diseases.
Misclassification in memory modification inAppNL-G-Fknock-in mouse model of Alzheimer’s disease
Authors: Huang Mei-Lun , Suzuki Yusuke , Sasaguri Hiroki , Saito Takashi , Saido Takaomi C , Imayoshi Itaru
Published: January 2025

Alzheimer’s disease (AD), the leading cause of dementia, could potentially be mitigated through early detection and interventions. However, it remains challenging to assess subtle cognitive changes in the early AD continuum. Computational modeling is a promising approach to explain a generative process underlying subtle behavioral changes with a number of putative variables. Nonetheless, internal models of the patient’s reasoning process remain underexplored in AD. Determining the states of an internal model between measurable pathological states and behavioral phenotypes would advance explanations about the generative process in earlier disease stages beyond assessing behavior alone. In this study, we assumed the latent cause model as an internal model and estimated internal states defined by the model parameters being in conjunction with measurable behavioral phenotypes. The 6- and 12-month-oldAppNL-G-Fknock-in AD model mice and the age-matched control mice underwent memory modification learning, which consisted of classical fear conditioning, extinction, and reinstatement. The results showed thatAppNL-G-Fmice exhibited a lower extent of reinstatement of fear memory. Computational modeling revealed that the deficit in theAppNL-G-Fmice would be due to their internal states being biased toward overgeneralization or overdifferentiation of their observations, and consequently the competing memories were not retained. This deficit was replicated in another type of memory modification learning in the reversal Barnes maze task. Following reversal learning,AppNL-G-Fmice, given spatial cues, failed to infer coexisting memories for two goal locations during the trial. We concluded that the altered internal states ofAppNL-G-Fmice illustrated their misclassification in the memory modification process. This novel approach highlights the potential of investigating internal states to precisely assess cognitive changes in early AD and multidimensionally evaluate how early interventions may work.
Neuroactive steroids activate membrane progesterone receptors to induce sex specific effects on protein kinase activity
Authors: Lemons Abigail H. S. , Murphy Briana , Dengler Jake S. , Salar Seda , Davies Paul A. , Smalley Joshua L. , Moss Stephen J.
Published: January 2025

Neuroactive steroids (NAS), which are synthesized in the brain from progesterone, exert potent effects on behavior and are used to treat postpartum depression, yet how these compounds induce sustained modifications in neuronal activity are ill-defined. Here, we examined the efficacy of NAS for membrane progesterone receptors (mPRs) δ and ε, members of a family of GPCRs for progestins that are expressed in the CNS. NAS increase PKC activity via Gqactivation of mPRδ with EC50s between 3-11nM. In contrast, they activate Gsvia mPRε to potentiate PKA activity with similar potencies. NAS also induced rapid internalization of only mPRδ. In the forebrain of female mice, mPRδ expression levels were 8-fold higher than males. Consistent with this, activation of PKC by NAS was evident in acute brain slices from female mice. Collectively, our results suggests that NAS may exert sex-specific effects on intracellular signaling in the brain via activation of mPRs.
Different artificial lighting spectra change the mating behavior of generalist predatorOrius insidiosus(Say), and photoperiod extension promotes its development
Authors: Canovas Morgane L. , Abram Paul K. , Labbé Roselyne , Cormier Jean-François , Galstian Tigran , Dorais Martine
Published: January 2025

In protected cropping systems such as greenhouses and indoor farming, augmentative biological control depends on release rates, establishment, and reproduction of natural enemies. Light-emitting diodes (LEDs) are widely used to enhance plant growth in these systems and are increasingly implemented in mass-rearing facilities for natural enemies. However, the impacts of LEDs on the life cycle of beneficial predators remain insufficiently explored. This study examined the mating behaviors and developmental performance of generalist predatorOrius insidiosusunder light spectra previously shown to support its predation of the pest thripsFrankliniella occidentalis. In laboratory experiments, predator pairs were exposed to artificial light sequences starting with a 12h base light condition simulating a cloudy winter day, supplemented by 8h photoperiod extensions (blue, blue-red, or blue-green-red spectra), and a control without extension. Mating occurred under all tested conditions, but blue light reduced mating probability, frequency, and duration. Photoperiod extension improved fecundity, fertility, and second-generation numbers ofO. insidiosusadults, with blue light favoring egg laying and hatching but not metamorphosis into adults. The second-generation sex ratio was unaffected by light sequence, maintaining population viability with a balanced proportion of females. Our findings demonstrate thatO. insidiosuscan successfully mate, reproduce, and develop under artificial lighting and highlight the potential of modulating light spectrum to optimize both mass-rearing and establishment in protected crops.

Highlights

Photoperiod extension enhances development of the predatory bugO. insidiosus.

Blue light reducesO. insidiosusmating probability, frequency, and duration.

Photoperiod extension with blue light favorsO. insidiosusfertility and fecundity.

Orius insidiosussex ratio is unaffected by photoperiod.

LEDs could enhance natural enemy establishment in protected crops.
Lambda N as a model substrate for studying the mechanism of Escherichia coli ATP-dependent protease Lon as a regulatory enzyme
Authors: Castro Marianita , Lee Sanghyuk , Lee Irene
Published: January 2025

As an ATP-dependent protease, the quality control functions of Lon have been extensively studied and reviewed in the literature. By contrast, very little research has been conducted to investigate Lon’s physiological functions and its mechanism as a regulatory protease. In this manuscript, we provided a survey of literature and data to convey that the lambda N (λN) protein is a suitable Escherichia coli Lon (ELon) substrate for studying the role played by Lon in regulating an RNA transcription process. For proof of principle, we demonstrated that the minimal component of the RNA transcription complex containing RNA polymerase (RNAP) and the σ factor can inhibit λN degradation by ELon through SDS-PAGE, and the carboxyl-terminal of λN is important for Lon competing with RNAP interaction. Using negative stain electron microscopy, we obtained structural evidence to show that λN lacking the carboxyl-terminal flanked by residues 99-107 interacted with ELon differently than full-length λN. Taken together, the activity and EM data provide a starting point for performing a physiological enzymology study on the contribution of ELon toward RNA transcription.
Customized feminine hygiene wash containing postbiotics fromLactobacillusspp. to treat Urinary Tract Infections (UTI)
Authors: Nair Veena G , Chellappan David Raj , Durai Remya Devi , Rajesh Y.B.R.D , Narbhavi Dhiviya , Anupriya A , Prabhusaran N , Nagarajan Saisubramanian
Published: January 2025

Abstract

The rising prevalence of antimicrobial resistance has intensified the search for innovative therapeutic strategies, particularly in the prevention of urinary tract infections (UTIs). This study presents the development and evaluation of a novel postbiotics vaginal wash formulated to prevent UTIs by utilizing metabolites derived from indigenous vaginal Lactobacillus spp. The primary objective was to create a cost-effective, stable, and non-invasive solution targeting uropathogenic bacteria. Key metabolites, including tryptamine, (-)-terpinen-4-ol, and itaconic anhydride, were identified from cell free supernatant of vaginalLactobacillusand incorporated into a poloxamer 407-based formulation.In vitroassays demonstrated significant bioactivity against uropathogenic bacteria, effectively inhibiting bacterial colonization and biofilm formation. Preclinical validation was conducted using BALB/c mice models to assess both the safety and efficacy of the vaginal wash. Results indicated a substantial reduction in infection rates among treated mice, with no observed adverse effects, confirming the formulation’s safety profile. In conclusion, this novel postbiotics vaginal wash represents a promising non-invasive therapeutic approach for UTI prevention. By harnessing bioactive metabolites from human vaginal Lactobacillus spp., the formulation offers a potential solution to combat antimicrobial resistance while improving women’s health outcomes. Further clinical studies are warranted to validate these findings and explore broader applications in clinical practice, paving the way for new strategies in managing UTIs and enhancing overall female health.
Fast turns are not sped up slow turns: How bluegill sunfish change their kinematics with turn speed
Authors: Clark Andrew , Tytell Eric
Published: January 2025

Fish turn extremely often, but this behavior is relatively understudied due to how challenging it can be to get fish to perform such an unsteady maneuver repeatedly. Specifically, little is known about whether fish control turns differently at different turning rates. Here we address the challenge of studying turning by developing a device that elicits turns repeatedly at specific speeds. Using this device, we compare the swimming kinematics of bluegill sunfish (Lepomis macrochirus) during fast and slow turns through 180 degrees. We find that the fish behave differently when turning quickly than when turning slowly: a fast turn is not a sped up slow turn, but is kinematically distinct. In particular, during fast turns, bluegill bend their bodies to minimize moment of inertia before they maximize torque, while in slow turns they maximize torque first, before they bend their bodies. In fast turns, they also beat their pectoral fins at a higher frequency, but take fewer pectoral fin strokes. Differences between the two speed turns may be due to initial momentum and how momentum is conserved throughout the turn, because fast turns have higher initial linear momentum that they can convert into angular momentum to turn around.

Summary statement

Bluegill change how they handle torque and moment of inertia when turning rapidly than when turning slowly. Tradeoffs between linear and angular momentum may play a key role.
Synthesizing unmodified, supercoiled circular DNA moleculesin vitro
Authors: Rezaei Sepideh , Moncada-Restrepo Monica , Leng Sophia , Chambers Jeremy W. , Leng Fenfei
Published: January 2025

Supercoiled (Sc) circular DNA, such as plasmids, has shown therapeutic potential since the 1990s, but is limited by bacterial modifications, unnecessary DNA sequences, and contaminations that may trigger harmful responses. To overcome these challenges, we have developed two novel scalable biochemical methods to synthesize unmodified Sc circular DNA. Linear DNA with two loxP sites in the same orientation is generated via PCR or rolling circle amplification. Cre recombinase then converts this linear DNA into relaxed circular DNA. After T5 exonuclease removes unwanted linear DNA, topoisomerases are employed to generate Sc circular DNA. We have synthesized EGFP-FL, a 2,002 bp mini-circular DNA carrying essential EGFP expression elements. EGFP-FL transfected human HeLa and mouse C2C12 cells with much higher efficiency thanE. coli-derived plasmids. These new biochemical methods can produce unmodified Sc circular DNA, in length from 196 base pairs to several kilobases and in quantities from micrograms to milligrams, providing a promising platform for diverse applications.