bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiles of testosterone and pre-androgens and sexual function in premenopausal women
Authors: Werner Marlene A , Van Lissa Caspar J , Both Stephanie , Skiba Marina A , Bell Robin J , Davis Susan R
Published: January 2025

Background

There is inconsistent evidence as to the role of testosterone and pre-androgens in premenopausal female sexual function, and reported associations between blood concentrations of these hormones and female sexual function vary in strength.

Aim

To examine the patterns of testosterone and pre-androgen concentrations and variations in sexual function in premenopausal eumenorrheic women.

Methods

This was a secondary analysis of a sample of 588 premenopausal eumenorrheic women from the Grollo-Ruzzene Foundation Young Women’s Health Study. Socio-demographics, health information, and questionnaire data were collected using online surveys. Eligible women were invited to provide a blood sample. We ran latent profile analysis (LPA) and subsequent analyses in R using RStudio.

Outcomes

Indicator variables in the LPA included sexual arousal and desire domains of the Profile of Female Sexual Function and testosterone, dehydroepiandrosterone (DHEA), and androstenedione, measured by liquid chromatography–tandem mass spectrometry.

Results

Analyses resulted in a pattern of 3 latent classes. Classes reporting relatively lower and higher sexual arousal (LPA-derived means and 95% CIs: -0.79 [-1.24; -0.34] and 0.62 [0.51; 0.72]) did not differ significantly in sex steroid concentrations (testosterone: -0.21 [-0.38; -0.03] and -0.33 [-0.47; -0.20]; DHEA: -0.47 [-0.57; -0.37] and -0.26 [-0.39; -0.13]; androstenedione: -0.36 [-0.50; -0.22] and -0.39 [-0.49; -0.29]), while the class reporting relatively medium arousal (-0.11 [-0.31; 0.08]) showed the highest testosterone, DHEA, and androstenedione concentrations (testosterone: 0.8 [0.60; 1.01]; DHEA: 0.99 [0.76; 1.23]; androstenedione: 1.08 [0.88; 1.29]). There were no significant differences in sexual desire between classes (-0.08 [-0.23; 0.06]; 0.00 [-0.13; 0.14]; 0.10 [-0.09; 0.30]) differing significantly in sex steroid concentrations (-0.69 [-0.80; -0.58], -0.04 [-0.15; 0.07], 0.94 [0.71; 1.16] for testosterone) nor associations between the sex steroid concentrations and degrees of sexual desire.

Clinical Implications

These findings cast further doubt on the utility of measuring sex steroids for diagnosing female sexual dysfunction in premenopausal eumenorrheic women, even when considered in combination.

Strengths and Limitations

We analyzed a large community sample and controlled for potentially biasing factors. We analyzed sex steroid concentrations determined with gold-standard methodology. Excluding women with early menopause and menstrual dysfunction might have resulted in finding 3, rather than more, latent classes.

Conclusion

Testosterone and pre-androgen profiles do not clearly identify premenopausal eumenorrheic women with low sexual arousal and desire.
Toys in the bedroom: use of sexual devices in partnered sexual activity is associated with higher female orgasmic intensity, arousal, and sexual satisfaction and is not related to psychopathologies
Authors: Sansone Andrea , Mollaioli Daniele , Colonnello Elena , Bandini Camilla , Morello Martina , Marinelli Ginevra , Ciocca Giacomo , Limoncin Erika , Jannini Emmanuele A
Published: January 2025

Background

Sex devices are tools that can improve the sexual health of users, but their effects on sexual outcomes in partnered intercourse have rarely been evaluated.

Aim

The aim of this study was to assess the relationship between partnered and solitary use of sex devices and different sexual health outcomes among sexually active women aged 18–35 in a heterosexual relationship.

Methods

The cross-sectional descriptive study was conducted with 361 participants between May and June 2023 recruited through a social media campaign. Female sexual function was measured with the Female Sexual Function Index and the Orgasmometer-F. The Generalized Anxiety Disorder scale, the Patient Health Questionnaire and the Dark Future Scale were used to investigate psychological health. Statistical analysis was performed with the statistical software R; the significance level for statistical analyses was set as P < 0.05.

Outcomes

The outcomes of the study include female sexual function and orgasmic intensity, as well as measures of symptoms of anxiety, depression, and uncertainty for the future.

Results

Compared to those who only used sex devices for solitary masturbation, women using sex devices in the context of partnered intercourse had higher arousal and satisfaction scores (P = 0.042 and P = 0.004, respectively), as well as higher subjective perception of orgasmic intensity over the last 6 months (P = 0.005) and in partnered sexual intercourse in the last 4 weeks (P = 0.002). Conversely, orgasmic intensity during masturbation in the last 4 weeks was higher among solitary users (P < 0.001). No significant difference was found between the two study groups for all other outcome measures.

Clinical Implications

The use of sex devices in the context of partnered intercourse is associated with increased sexual function and more intense orgasmic experience.

Strengths & Limitations

The study investigates a novel topic, on a large sample size, by using several validated instruments to measure sexual functioning of participants. However, a definite cause-effect relationship cannot be established due to the study design. Self-report bias and lack of clinical data on study participants are further limitations. Additionally, being a study limited to heterosexual, sexually active women involved in a relationship, results cannot be generalized to all women.

Conclusion

The study found an association between better sexual functioning and use of sex devices in partnered intercourse.
The PEBP genes FLOWERING LOCUS T and TERMINAL FLOWER 1 modulate seed dormancy and size
Authors: Nadal Bigas Judit , Fiers Martijn , van der Wal Froukje , Willems Leo A J , Willemsen Viola , Nijveen Harm , Angenent Gerco C , Immink Richard G H
Published: January 2025

The phosphatidylethanolamine-binding protein (PEBP) family members FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) are major regulators of plant reproduction. In Arabidopsis, the FT/TFL1 balance defines the timing of floral transition and the determination of inflorescence meristem identity. However, emerging studies have elucidated a plethora of previously unknown functions for these genes in various physiological processes. Here, we characterized potential roles in seed size and dormancy of FT and TFL1 in Arabidopsis thaliana using CRISPR mutants and reporter analysis. Our findings unveiled a role for TFL1 in seed dormancy while confirming the role of FT in regulating this trait. We showed that the interplay between these two genes in seed dormancy is antagonistic, mirroring their roles in flowering time and inflorescence architecture. Analysis of reporter lines demonstrated that FT and TFL1 are partly co-expressed in seeds. Finally, we showed that total seed yield is affected in these mutants. Together, our results highlight the versatility of these two genes beyond their canonical functions. The impact of FT and TFL1 on seed characteristics emphasizes the significance of approaching gene studies from various perspectives, enabling the identification of multifaceted molecular factors that could play a major role in shaping the future of agriculture.
Lyman-α forest power spectrum and its cross-correlation with dark matter haloes in different astrophysical models
Authors: Nakashima Koichiro , Nishizawa Atsushi J , Nagamine Kentaro , Oku Yuri , Shimizu Ikkoh
Published: January 2025

The $\mathrm{Ly}\,\alpha$ forest, a series of H i absorption lines in the quasar spectra, is a powerful tool for probing the large-scale structure of the intergalactic medium. Its three-dimensional (3D) correlation and cross-correlations with quasars allow precise measurements of the baryon acoustic oscillation feature and redshift space distortions at redshifts $z\gt 2$. Understanding small-scale astrophysical phenomena, such as star formation and feedback, is crucial for full-shape analyses. In this study, we measure the 3D auto-power spectrum of the $\mathrm{Ly}\,\alpha$ forest and its cross-power spectrum with haloes using hydrodynamic simulations from the gadget3-osaka code, which includes models for star formation and supernova feedback. Across five astrophysical models, we find $5{\!-\!}10~{{\ \rm per\ cent}}$ differences among them at $k\gt 2\, h\mathrm{Mpc}^{-1}$ in the $\mathrm{Ly}\,\alpha$ auto-power spectrum. The $\mathrm{Ly}\,\alpha \, \times \,$halo cross-power spectra show even larger deviations, exceeding $10~{{\ \rm per\ cent}}$. Using the fitting models presented by Arinyo-i-Prats et al. and Givans et al., we jointly fit the $\mathrm{Ly}\,\alpha$ auto- and $\mathrm{Ly}\,\alpha$$\times$ halo cross-power spectra, and assess the accuracy of the estimated $f\sigma _8$ parameter by comparing it with the ground truth from the simulations, varying the maximum wavenumber $k_\mathrm{max}$ and minimum halo mass $M_\mathrm{ h}$. Our results demonstrate that the extended model proposed by Givans et al. provides a good fit to the simulated data at $k_\mathrm{max}\le 3.0\, h\mathrm{Mpc}^{-1}$ for $M_\mathrm{ h}\gt 10^{10.5}\, \mathrm{ M}_\odot$. Furthermore, the model accurately reproduces the correct value of $f\sigma _8$, irrespective of the astrophysical models employed. This demonstrates its robustness against variations in astrophysical models.
How low education increases COVID-19 mortality: the mediating role of vaccination, distrust in science, and lack of preventative health behavior
Authors: Zhuo Jie , Harrigan Nicholas
Published: January 2025

Background

Previous research shows the significant correlation between low education and COVID-19 mortality in underprivileged communities, even when accounting for factors like poverty and race. The exact mechanisms by which low education gives rise to COVID-19 mortality, however, are less clear.

Methods

We propose that low education predicts COVID-19 morality because low education gives rise to a less engaged, less agentic approach to one’s own healthcare. We operationalize low engagement and low agentic behavior as four variables that mediate the effect of low education on COVID-19 mortality: (i) vaccination, (ii) distrust of science (Republican vote), (iii) poor health, and (iv) prevention. We model COVID-19 mortality in 3108 counties of the United States, using deaths across 60 fortnights.

Main Results

All four indicators of an agentic, engaged approach to health are statistically significant mediators of the relationship between low education and COVID-19 mortality: vaccination [IRR = 1.02; (1.02, 1.03)]; Republican vote [IRR: 1.07; (1.06, 1.09)]; poor health [IRR: 1.01; (1.01, 1.02)]; and prevention [IRR: 1.00, (1.001, 1.003)].

Discussion

These findings suggest that low level of formal education predicts mortality from COVID-19 because low levels of education gives rise to a less engaged and less agentic approach to one’s own health.
Clustering of obesogenic behaviours amongst 140 052 South American adolescents: a harmonized meta-analysis of national health surveys
Authors: Matias Thiago Sousa , de Oliveira Araujo Raphael Henrique , Tassitano Rafael Miranda , Ramírez-Vélez Robinson , Sadarangani Kabir P , Ywgne José , Gaia Jhonatan Wélington Pereira , de Jesus Gilmar Mercês , da Silva Danilo Rodrigues Pereira
Published: January 2025

Background

Physical activity, sedentary behaviour, and diet synergically coexist (in different ways) within adolescents’ lifestyles. Thus, understanding obesogenic behaviour patterns within populations is critical to promoting adolescents’ health. This study investigates clustering patterns of adolescents’ obesogenic behaviours across South American countries.

Methods

The present work is a harmonized analysis of 10 national representative cross-sectional health surveys investigating adolescents’ risk and protective factors for non-communicable diseases. The surveys used questionnaires, and three obesogenic behaviours were analyzed for cluster formation (physical activity, sitting time, and diet). Sociodemographic variables were sex, age, and food insecurity. The Two-step cluster, the Rao-Scott chi-square test, and a meta-analysis were performed for data analysis.

Results

Three to four cluster solutions were identified in each country, and most clusters are unhealthy. The All-day sitters-very poor diet cluster was observed in Paraguay, Peru, Suriname, Chile, Guyana, Argentina, Brazil, Colombia, and Ecuador, with a pooled prevalence of 17.8% (95% CI:15.0; 20.7) amongst South American countries, with the highest prevalence observed in Argentina [26.8% (95% CI: 26.7; 26.9)]. Girls were more likely to belong to the unhealthiest clusters.

Conclusions

The lifestyle behaviours of South American adolescents coexist negatively, and there is a severe obesogenic risk for this population. The synergy between physical inactivity and poor/very poor diet was clustered together in all countries, and our analysis did not reveal any natural healthy clusters. Furthermore, girls are at a disadvantage, given that they are the majority in clusters with unhealthy profiles in South America.
Auxin treatment reduces inflorescences number and delays bud development in the alternate bearing Citrus cultivar Murcott mandarin
Authors: Haim Dor , Pochamreddy Madhuri , Doron-Faigenboim Adi , Kamara Itzahk , Ben-Ari Giora , Sadka Avi
Published: January 2025

Specific cultivars of many commercial fruit tree undergo cycles of heavy fruit load (ON-crop) one year, followed by low fruit load (OFF-crop) the next (termed alternate bearing). Fruit load may affect flowering at various developmental stages, and its presence is suggested to generate a flowering-inhibitory signal. In a previous report, we showed that the presence of fruit induces polar auxin transport from the fruit into the stem, interfering with indole acetic acid (IAA) release from the bud, and thus elevating its levels in the bud meristem. To better understand the relationship between auxin homeostasis in the bud and flowering, IAA or 2,4-Dichlorophenoxyacetic acid (2,4-D) were applied with the polar auxin transport blocker 2,3,5-triiodobenzoic acid (TIBA) to OFF-crop ‘Murcott’ mandarin trees during the flowering-induction period. The treatment reduced inflorescences number and delayed bud development. Transcriptome analysis following the treatment revealed a reduction in the expression of a few flowering-control genes, including LEAFY and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE. In addition, genes related to carbohydrate metabolism were reduced. We suggest that the elevation of auxin levels in the bud by heavy fruit load directly affects the expression of flowering-control, flower-development, and developmental genes.
Screening of Stevia rebaudiana (Bertoni) susceptibility to Septoria steviae through leaf disk inoculation
Authors: Le Bihan Zoe , Gaudin Jonathan , Rasouli Diako , Boutet Solene , Laurencon Marianne , Cosson Patrick , Hastoy Cecile , Rolin Dominique , Schurdi-Levraud Valerie
Published: January 2025

Stevia rebaudiana Bertoni is a perennial cultivated plant that produces steviol glycosides, natural acaloric sweet compounds in its leaves. Many pathogens are capable of infecting this species. Among these pathogens, Septoria steviae, the causal agent of Septoria Leaf Spot, is the most widely described on S. rebaudiana. The objective of this study is to validate a leaf disk screening method for S. rebaudiana response to Septoria steviae infection on 10 S. rebaudiana genotypes with contrasting responses to the fungus. Three independent experiments were carried out in which forty leaf discs per genotype were infected with an inoculum at a concentration of 105 conidia / mL or with water. The response of the 10 genotypes was scored through image analysis. Image analysis was conducted at 9, 12, 15, 18 and 21 days after inoculation (DAI), allowing the proportion of symptomatic foliar area (PLSA) and AUDPC to be quantified. The evaluation of symptom speed development was realized through a linear regression between PLSA and time, for each tested genotype. Genotypes exhibited the lowest susceptibility at 21 DAI, with Cult102_SPA and Cult76_GER displaying 3% of the surface symptomatic. Genotypes with the highest susceptibility were Cult33_FRA and Cult75_GER, with 24% severity. These results correlate with visual scoring performed at 21 DAI and with previous inoculation protocols on S. rebaudiana cuttings, by maintaining the ranking of the different genotypes whatever the test. The development of a leaf-disk inoculation method offers new avenues for breeding strategies to develop tolerant or resistant S. rebaudiana cultivars.
Evaluating ASC-4 Transfer Rates in Cataract Surgery: Insights into Timing and Causes of Hospital Transfers
Authors: Stange Nicholas R. , Rauen Matthew P.
Published: January 2025

Purpose:

To describe the causes, timing, and contributing factors of direct hospital transfer cases from an ophthalmology-specific ambulatory surgery center and to identify potential strategies for decreasing future transfers.

Setting:

A large ophthalmology surgery center in Des Moines, Iowa.

Design:

Retrospective review.

Methods:

A retrospective chart review was performed on patients requiring hospital transfer from a Midwest ophthalmology-specific surgery center from March 2022 through July 2024. Variables reviewed included patient demographics, comorbidities, prior surgeries/surgical complications, results of pre-operative physical exams, type of surgery and anesthesia performed, the type and timing of each complication, and the reasons for transfer. Each transfer was assessed for its necessity, preventability, and outcome.

Results:

A total of 22 patients required hospital transfer out of 24,960 admissions for a rate of 0.88 per 1,000 admissions (95% CI: 0.58-1.33). Only 5 (23%) transfer cases were temporally related to anesthesia or surgery. The other 17 (77%) had concerns first noted prior to the induction of anesthesia. Nine (41%) of the surgeries were completed, 1 (5%) partially completed, and the remaining 12 (55%) surgeries were cancelled. The reasons for transfer were largely cardiac and/or blood pressure related (18/22, 82%). Nearly a third of the transfers (7/22, 32%) were considered preventable.

Conclusion:

Hospital transfers from ASCs are rare and all-cause hospital transfer rates may overestimate the true risk of ocular surgery. Most patients requiring hospital transfer were identified in the pre-operative area. Greater attention to preoperative physical exam reports could potentially prevent some hospital transfers.
A Preliminary Application of Bird Surveys Using Environmental DNA Technology: in Futian Mangrove Nature Reserve
Authors: Zhang Song , Ye Xiao , Chen Jiang , Liu Xiao Jun , Jin Tao
Published: January 2025

Futian Mangrove Nature Reserve is a vital habitat for birds in Shenzhen city of China, and the diversity of bird species is of considerable concern. Traditional surveys depend on direct observation and expert assessment, necessitating significant manpower for tracking. This study utilized environmental DNA metabarcoding technology to gather 128 environmental samples of water, soil, and air, along with samples of bird feces and feathers collected during the summer and winter of 2023. A total of 72 bird operational taxonomic units (OTUs) were identified. The results revealed variations in bird detection across different environmental samples, with air samples yielding 52 bird OTUs, water samples 29, and soil samples 23. Detected bird OTUs were notably higher in winter samples compared to summer. Additionally, the average number of bird OTUs detected in air samples during summer and winter was 14.9 and 10.1, respectively, significantly exceeding those found in the corresponding water and soil samples. The identification of bird feces and feather samples confirmed the presence of the identified bird species in the environmental samples. This study concludes that environmental DNA technology can serve as a valuable complementary method for monitoring bird diversity, with different environmental samples showing distinct preferences in bird detection.
Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning
Authors: Yan Chengwei , Zhang Yu , Feng Jiuxin , Hua Heyang , Ruan Zhihan , Li Zhen , Li Siyu , Yan Chaoyang , Li Pingjing , Liu Jian , Chen Shengquan
Published: January 2025

Cell Painting (CP), as a high-throughput imaging technology, generates extensive cell-stained imaging data, providing unique morphological insights for biological research. However, CP data contains three types of technical effects, referred to as triple effects, including batch effects, gradient-influenced row and column effects (well position effects). The interaction of various technical effects can obscure true biological signals and complicate the characterization of CP data, making correction essential for reliable analysis. Here, we propose cpDistiller, a triple-effect correction method specially designed for CP data, which leverages a pre-trained segmentation model coupled with a semi-supervised Gaussian mixture variational autoencoder utilizing contrastive and domain-adversarial learning. Through extensive qualitative and quantitative experiments across various CP profiles, we demonstrate that cpDistiller effectively corrects triple effects, especially well position effects, a challenge that no current methods address, while preserving cellular heterogeneity. Moreover, cpDistiller effectively captures system-level phenotypic responses to genetic perturbations and reliably infers gene functions and interactions both when combined with scRNA-seq data and independently. cpDistiller also excels at identifying gene and compound targets, which is a critical step in drug discovery and broader biological research.
An improved FLARE system for recording and manipulating neuronal activity
Authors: Zhou Guanwei , Li Ruonan , Bartolik Ola , Ma Yuqian , Wan Wei Wei , Meng Jennifer , Hu Yujia , Ye Bing , Wang Wenjing
Published: January 2025

Recording and manipulating neuronal ensembles that underlie cognition and behaviorin vivois challenging. FLARE is a light– and calcium-gated transcriptional reporting system for labeling activated neurons on the order of minutes. However, FLARE is limited by its sensitivity to prolonged neuronal activities. Here, we present an improved version of FLARE, termed cytoFLARE. cytoFLARE incorporates cytosolic expression of the transcription factor and a more sensitive pair of calcium sensing domains. We showed that cytoFLARE provides more calcium– and light-dependent signals in HEK293T cells and higher signal-to-background ratios in neuronal cultures. We further established cytoFLARE transgenicDrosophilamodels and applied cytoFLARE to label activated neurons upon sensory or optogenetic stimulation within a defined time window. Notably, through cytoFLARE-driven expression of an optogenetic actuator, we successfully reactivated neurons involved in the larval nociceptive system. Our findings demonstrate the first characterization and application of time-gated calcium integrators inDrosophila.
Intrinsic Opening of BK Channels Derives from Inherent Leakage in Hydrophobic Gating
Authors: Jia Zhiguang , Zhang Guohui , Shi Jingyi , Cui Jianmin , Chen Jianhan
Published: January 2025

The big potassium (BK) channels remain open with a small limiting probability ofPo∼ 10-7at minimal Ca2+and negative voltages < −100 mV. The molecular origin and functional significance of such “intrinsic opening” are not understood. Here we combine atomistic simulations and electrophysiological experiments to show that the intrinsic opening of BK channels is an inherent property of the vapor barrier, generated by hydrophobic dewetting of the BK inner pore in the deactivated state. The vapor barrier only gives rise to a finite free energy barrier, of ∼ 8 kcal/mol, and cannot completely shut down K+flow even when the voltage sensor domains are fully deactivated. This results in the leaking currents that can be measured at negative voltages as the indication of intrinsic opening. The shallow limiting slope ofPoat negative voltages results primarily from the electric field effects on the permeating ion through the vapor barrier. We further demonstrate that the vapor barrier can be perturbed by inner pore mutations and truncation of the cytosolic domains, leading to predicable changes in limiting slope measurements. Therefore, the intrinsic opening in BK channels, and possibly in other ion channels, opens up an opportunity to experimentally study hydrophobic gating. Our results further suggest that intrinsic opening in BK channels is the fundamental basis for the allosteric mechanism of activation by both voltage and Ca2+.
Morpho-functional timeline of progressive cystic fibrosis pancreatic exocrine and endocrine pathology derived from semi-quantitative scoring and AI-driven quantitative image analysis
Authors: Al-Selwi Yara , Tiniakos Dina , Richardson Sarah J , Flaxman Christine S , Russell Lydia , Palmer Matthew , Coulthard Rowan , Maheshwari Rashmi , Dyson Nicola , Honkanen-Scott Minna , Klöppel Günter , Shaw James AM , Kattner Nicole
Published: January 2025

Cystic fibrosis (CF) is associated with pancreatic exocrine insufficiency (PEI) early in life and diabetes in up to 50% of adults. The underlying CF-related sequential changes within the pancreas associated with exocrine and endocrine insufficiency remain incompletely understood due to scarcity of available human tissue, protracted disease course and absence of established robust and reproducible analytical approaches. This study aimed to develop and apply a systematic analysis cross-sectionally to CF pancreatic tissue samples from donors over a wide age range to construct a timeline related to the main exocrine and endocrine changes underlying progressive disease. Based on a histopathological semi-quantitative scoring system and AI-driven quantitative image analysis pancreatic changes were individually evaluated and classified according to three patterns: fibrotic; fibrotic and lipotic; and lipoatrophic. This systematic evaluation was applied to 29 CF and 58 control donors without pancreatic disease. Rapid loss of acinar tissue with virtually complete absence by the age of 7 years was confirmed, mirrored by fatty tissue replacement – changes underlying PEI and likely preceding progression towards diabetes. Ductal blockage by thickened secretions was associated with increasing ductal dilatation accompanied by peri-ductal fibrosis, followed by ductal loss with involution of associated fibrosis in parallel with increasing adipocyte proportional area (PA). Remaining ducts were relatively small surrounded by residual fibrosis. Islets became increasingly clustered initially surrounded by activated pancreatic stellate cells (PSCs) and fibrosis and then disorganised by interposing fibrotic tissue between endocrine cell regions and surrounded by residual collagen stranding in a ‘lipoatrophic’ pancreas. Overall islet mass was not significantly reduced but β-cell PA was significantly reduced from birth without further loss over time. We concluded that the natural history of pancreatic CF progresses inexorably from peri-ductal fibrosis to global fat replacement with relatively well-maintained islet mass but PSC-associated fibrotic islet remodelling circumstantially implicated in β-cell failure.
Lymphoid-tissue-on-chip recapitulates human antibody responses in vitro
Authors: Teufel Claudia , Schlemmer Anna-Sophie , Eiken Andrea W. , Wagoner Zachary W. , Vöhringer Dennis , Christ Lena , Dulovic Alex , Marsall Patrick , Fandrich Madeleine , Brás Eduardo J.S. , Marzi Julia , Bärhold Friederike , Philipp Julia , Becker Sven , Wagar Lisa E , Loskill Peter
Published: January 2025

In the past decades, vaccine development has made great strides. Nevertheless, more often than not, vaccine candidates fail in advanced stages of development and clinical trials. A key reason is the poor predictive value of non-clinical in vivo and in vitro models, due to either species-specific differences in the immune response or insufficient reflection of physiological vaccine mechanisms. Reliable modeling of human adaptive immune responses is a prerequisite to understand processes leading to vaccine-induced protective immunization and to drive informed decisions in vaccine development pipelines. Here, we present a centrifugal microfluidics based organ-on-chip approach to generate an organotypic high density lymphoid tissue on-chip. The model enables long-term culture of lymphoid tissue and raised antigen-specific antibody responses against influenza vaccines even after four weeks on-chip. Antibody response of different magnitude and quality could be induced both by direct antigen exposure as well as by recruitment of antigen-presenting cells from the periphery. The model represents an attractive approach to evaluate the impact of the mode of antigen delivery on adaptive immune responses. Beyond applications in vaccine development, the lymphoid-tissue-on-chip provides a platform to study cellular interactions during homeostasis, immune responses and long-term impact of immunomodulators over several weeks.
Distinct causes of three phenotypic hallmarks of hematopoietic aging
Authors: Chia Jennifer J , Singh Apeksha , Lin Yusheng , Popko Noa , Mastro David , Liu Yi , Tran Tiffany , King Jennifer K , Rao Dinesh S. , Hoffmann Alexander
Published: January 2025

Hematopoietic aging is characterized by chronic inflammation associated with myeloid bias, HSC accumulation, and functional HSC impairment. Yet it remains unclear how inflammation promotes these aging phenotypes. NFkappaB both responds to and directs inflammation, and we present an experimental model of elevated NFkappaB activity (IkappaBminus) to dissect its role in hematopoietic aging phenotypes. We found that while elevated NFkappaB activity is not sufficient for HSC accumulation, HSC-autonomous NFkappaB activity impairs their functionality, leading to reduced bone marrow reconstitution. In contrast, myeloid bias is driven by the IkappaBminus proinflammatory bone marrow milieu as observed functionally, epigenomically, and transcriptomically. A new scRNA-seq HSPC labeling framework enabled comparisons with aged murine and human HSC datasets, documenting an association between HSC-intrinsic NFkappaB activity and quiescence, but not myeloid bias. These findings delineate separate regulatory mechanisms that underlie the three hallmarks of hematopoietic aging, suggesting that they are specifically and independently therapeutically targetable.
Investigation of the HLA locus in autopsy-confirmed progressive supranuclear palsy
Authors: Wang Jinguo , Forrest Shelley L. , Dasari Sathish , Tanaka Hidetomo , Rogaeva Ekaterina , Tartaglia M. Carmela , Fox Susan , Lang Anthony E. , Kalyaanamoorthy Subha , Kovacs Gabor G.
Published: January 2025

Objectives

Progressive supranuclear palsy (PSP) is a neurodegenerative disease showing pathological tau accumulation in subcortical neurons and glial cells. The human leukocyte antigen (HLA) locus on chromosome 6 is a polymorphic region with complex linkage patterns that has been implicated in several autoimmune and neurological disorders. TheHLAlocus has not been systematically examined in PSP. It is unclear whether tau and HLA can interact to induce an autoimmune disease mechanism.

Methods

We evaluated an autopsy confirmed PSP cohort (n=44) and compared allele/haplotype frequencies to those of the reference group of a local deceased Canadian donor pool. We performed HLA/Tau peptide binding prediction and modelling of HLA Class II and Tau Peptide interactions.

Findings

Odds ratio was 2.94 (95% CI 1.01 to 8.55; p=0.047) forDQB1*06:01 allele, and 2.59 (95% CI 1.39 to 4.83; p=0.0025) for the narcolepsy associated haplotype (DRB1*15:01DQB1*06:02). One patient with 4 repeat tau PSP type pathology was a carrier of the IgLON5-associated haplotype (DRB1*10:01DQB1*05:01). HLA/Tau peptide binding prediction and modelling of HLA Class II/Tau Peptide interactions revealed strong binding tau peptides but not the PSP protofilament fold for alleles DQA1*01:02DQB1*06:02 and DQA1*01:03DQB1*06:01.

Conclusion

Our study suggests that epitopes within the tau peptide may bind to HLA alleles that are found in a subset of PSP patients supporting the notion of an autoimmune pathophysiological component. These findings have implications for subtyping and stratifying patients for therapies, including those targeting immune modulation.
Testing the extreme plastic mycelium hypothesis: Does grazing induce developmental plasticity in saprotrophic fungi?
Authors: Aguilar-Trigueros C.A. , Boddy L. , Fricker M.D.
Published: January 2025

Phenotypic plasticity—the ability of a genotype to alter its phenotype in response to environmental changes—can play a crucial role in maximizing fitness in fluctuating environments. However, plasticity comes at a cost, as the energy required to transform a phenotype imposes limits on its extent. While limits to plasticity are well-documented in many organisms, they are not well understood in modular organisms like filamentous fungi. Fungi have highly flexible morphologies, allowing individual organisms to adjust their phenotype in response to local environmental conditions. This flexibility has led to speculation that fungi exhibit "extreme phenotypic plasticity," making them an interesting system for studying plasticity mechanisms. To test this idea, we analyzed the grazer-induced morphological plasticity of four cord-forming fungal species exposed to different soil microfauna with varying feeding behaviors, using a phenotypic trajectory analysis framework. We hypothesized that grazing would drive convergence towards a common "grazing-resistant phenotype" across species, due to the extreme flexibility of fungal mycelia. Alternatively, we proposed that species would follow unique developmental trajectories in response to grazers, reflecting species-specific plasticity limits. Our results showed that fungal species accounted for most of the morphological variation, with grazers having only a small but significant effect. Moreover, we did not observe convergence towards a common grazing-resistant phenotype; instead, each species followed distinct developmental pathways within species-specific limits, which varied widely. Some species altered up to 30% of their phenotype in response to grazers, while others showed as little as 1% variation. These findings suggest a more nuanced view of fungal plasticity, where morphological plasticity might not be the most effective response to grazing pressure. We speculate that the observed differences in plasticity limits may correlate with the complexity of cord formation in different species. These constraints on fungal morphological plasticity offer new insights into how fungi adapt to dynamic ecological conditions and underscore the need to explore alternative phenotypic responses to environmental pressures. Our study highlights the need to refine plasticity theories, particularly for organisms with complex, modular structures like fungi.
Enabling Atomistic Modeling and Simulation of Complex Curved Cellular Membranes with xMAS Builder
Authors: Trebesch Noah , Tajkhorshid Emad
Published: January 2025

As more powerful high performance computing resources are becoming available, there is a new opportunity to bring the unique capabilities of molecular dynamics (MD) simulations to cell-scale systems. Membranes are ubiquitous within cells and are responsible for a diverse set of essential biological functions, but building atomistic models of cell-scale membranes for MD simulations is immensely challenging because of their vast sizes, complex geometries, and complex compositions. To meet this challenge, we have developed xMAS Builder (Experimentally-DerivedMembranes ofArbitraryShape Builder), which is designed to take experimental lipidomics and structural (e.g., electron microscopy and tomography) data as input and use them to build MD-ready models of cellular membrane systems. To test xMAS Builder's capabilities, we have used it to build two models (one ~12.0 million atoms and the other ~11.6 million atoms) of a test system with a representative complex lipid composition and geometry. The two models, which differed only in their lipid packing densities, both maintained their membrane integrity during an extended MD simulation (250 ns and 386 ns), but their highly divergent relaxation dynamics indicate that the proper packing density of curved membranes is determined by leaflet volume rather than surface area. These results suggest that xMAS Builder's algorithms produce high quality models and that simulation of these models will provide profound biophysical insights into the behavior of cellular membranes.
The role of induced polarization in drug discovery applications
Authors: Mohamed Ashraf , Brooks Bernard R. , Amin Muhamed
Published: January 2025

Induced polarization plays a pivotal role in ligand-protein binding by enhancing both the specificity and strength of molecular interactions. As a ligand approaches a protein, their respective electronic clouds redistribute in response to each other’s electrostatic fields—a phenomenon governed by induced polarization. The response of a molecule’s electron density to an external field is quantitatively described by its polarizability tensor. In this study, we calculated polarizability tensors for thousands of drug-like molecules from the CHEMBL database, focusing on compounds targeting the Thrombin, Estrogen Receptor alpha, and Phosphodiesterase 5A proteins using Density Functional Theory (DFT). We show that a machine learning model based on atomic hybridization accurately predict the polarizabilities eigenvalues, calculated with DFT. Then, we build a neural network and random forest models to predict the IC50’s based on the same features. The success of these models, despite utilizing a limited number of features, underscores the critical role of induced polarizabilities in determining binding energies.
Genome assemblies of Indiandesicattle reveals hotspots of rearrangements and immune-related genetic diversity
Authors: Azam Sarwar , Sahu Abhisek , Kadivella Mohammad , Khan Aamir Waseem , Neupane Mahesh , Tassell Curtis P Van , Rosen Benjamin D , Gandham Ravi Kumar , Rath Subha Narayan , Majumdar Subeer S
Published: January 2025

India, home to the world’s largest cattle population, hosts native dairy breeds essential to its agricultural economy because of their adaptability and resilience. This study characterizes the genomes of five prominent breeds Gir, Kankrej, Red Sindhi, Sahiwal and Tharparkar, highlighting their unique genomic characteristics. Thede novoassemblies ranged from 2.70-2.78 Gb in size, with 90% of the genomes assembled in just 56 to 1,663 scaffolds. The use of reference-guided scaffolding further enhanced these genomes, resulting in 93.3-96.7% pseudomolecule coverage with strong BUSCO scores (94.1-95.5%). Comparative analyses revealed 87–95% synteny with the Brahman genome and identified 19.84–153.16 Mb of structural rearrangements per genome, including inversions, translocations, and duplications. Synteny diversity analysis uncovered 10,643 perfectly collinear regions spanning 87.3 Mb and 6,622 hotspots of rearrangement (HOT regions) covering 55.18 Mb. These HOT regions, characterized by high synteny diversity, were significantly enriched with immune-related genes. Moreover, immune-related gene clusters, including MHC, NKC, and LRC, were identified within HOT regions in thedesireference genome. Our findings provide valuable insights into the genetic diversity ofdesicattle breeds. The high-quality genome assemblies generated in this study will serve as valuable resources for future research in genetic improvement, disease resistance, and environmental adaptation.
Rising temperatures favour parasite virulence and parallel molecular evolution following a host jump
Authors: Hector Tobias E , Kreiner Julia M , Forward James C , Hoang Kim L , Stevens Emily J , Johnson Serena , Li Jingdi , King Kayla C
Published: January 2025

Climate change is facilitating the poleward emergence of parasites, increasing the risk of jumping into new animal species, including humans. Whether more virulent or transmissible variants will spread during these climate-driven outbreaks is unclear. We experimentally evolved a wild parasitic bacterium, across the thermal range (20-30°C) and extremes (35°C) of Cape Verde - the site of field collection - in a novel, temperate animal host. At the parasite's typical warm environmental temperature, we found that virulence escalated across evolutionary time. Parasites evolved at hot temperatures, towards the limit of host-parasite survival, displayed a 'cryptic' virulence boost, deadlier once infecting animals at cooler temperatures. Patterns of molecular evolution were constrained to parallel changes in fewer loci at extreme temperatures. Our findings suggest that rising temperatures will leave predictable phenotypic and genomic signatures on evolving parasites as they emerge with climate change.
Digital Phage Biology in Droplets
Authors: Givelet Louis , von Schönberg Sophie , Katzmeier Florian , Simmel Friedrich C.
Published: January 2025

Since their discovery, bacteriophages – viruses that infect bacteria – have been an invaluable source of insight for molecular biology and have provided a plethora of molecular components for biotechnology. Driven by the imminent global antibiotic crisis, interest in using bacteriophages as antimicrobial agents has strongly increased in the past few years. While standard quantification of phage counts and infectivity by double-layer plaque assays (DLA) have provided foundational insights, they are limited by their inability to monitor infection dynamics over time and the inflexibility in experimental setups. Here, we introduce a novel high-throughput method using droplet microfluidics to quantify individual phage infection events, enhancing the understanding of phage-host dynamics at the single-event level. By co-encapsulating individual phages and bacteria in microfluidic droplets, we can control key experimental parameters such as exposure time and the ratio of phages to bacteria. Our system allows for precise quantification of lysis events and the direct observation of lysis kinetics unaffected by the continuous release of progeny phages that is typical in bulk cultures. Moreover, our method is potentially applicable to any phage-host pair. Our findings suggest that droplet microfluidics can provide a more accurate and dynamic understanding of phage biology. This approach could be particularly valuable in the development of phage-based antimicrobial strategies in the face of rising antibiotic resistance.
Synthetic and plant-derived multivalent galactans as modulators of cancer-associated galectins-3 and -9
Authors: Pfeifer Lukas , Mueller Kim-Kristine , Müller Maximilian Thal , Philipp Lisa-Marie , Sebens Susanne , Classen Birgit
Published: January 2025

Galectins are β-galactoside-binding proteins with numerous functions. Some of them are involved in proliferation and metastasis of cancer, making them promising therapeutic targets. As different plant glycans have been shown to bind to galectins, plant saccharides might be potential galectin inhibitors. To produce plant galactans rich in galactose and smaller in size, we degraded arabinogalactan-proteins fromEchinacea purpureaandZostera marinaas well as arabinogalactan from larch. As galectin (Gal)-3 and -9 both have been described to be involved in cancer development, we quantified the binding capacities of the different galactans to both galectins by biolayer-interferometry. Our results revealed that all plant-derived galactans and Yariv reagents with terminal galactose and lactose residues bind to Gal-3 in micromolar ranges. Surprisingly, only the higher charged galactans fromZostera marinashowed affinity to Gal-9. Investigations of two different pancreatic cancer cell lines (Panc1 and Panc89) and different cell variants thereof revealed that Gal-3 was expressed by both cell lines with a significantly higher Gal-3 level in Panc1 cells compared to Panc89 cells. Conversely, Gal-9 was only detected in Panc89 cells. The findings revealed that galactans are promising sources to develop galectin antagonists and plant galactans from different species express specificities for distinct galectins.
An animal model of coronary microvascular dysfunction (CMD) in the female spontaneously hypertensive rat: the role of diet
Authors: Najjar Rami S. , Mehta Puja K. , Gewirtz Andrew T.
Published: January 2025

Coronary microvascular dysfunction (CMD) drives angina in patients with ischemia non-obstructive coronary artery disease, a condition that is more prevalent in females. Effective treatment strategies and a detailed mechanistic understanding of CMD remain limited, in part, due to scarcity of physiologically relevant animal models. Indeed, while CMD has been studied in animals with diabetes and/or fed high-fat diets, in fact, hypertension is the predominant risk factor for CMD in humans but is not captured by these models. Thus, we characterized the CMD that arose in female spontaneously hypertensive rats (SHRs). We measured coronary flow reserve, alongside basic cardiovascular function in SHRs and normotensive Wistar Kyoto rats (WKYs) fed a purified diet, as well as SHRs consuming a grain-based chow (GBC) diet. SHRs on a purified diet, but not WKYs or SHRs consuming GBC, exhibited impaired coronary flow reserve as assessed by echocardiography. Thus, SHRs develop a diet-dependent CMD, which can serve as a model to study hypertension-related CMD.

Graphical Abstract
A High-Throughput Bone Marrow 3D Co-Culture System to Develop Resistance to B Cell Receptor Signaling Targeted Agents in B Cell Non-Hodgkin Lymphoma
Authors: Zadro Alex , Arribas Alberto , Colombo Maria Vittoria , Cannas Eleonora , Spriano Filippo , Cascione Luciano , Mensah Afua Adjeiwaa , Simonetta Federico , Petta Dalila , Arrigoni Chiara , Candrian Christian , Moretti Matteo , Bertoni Francesco
Published: January 2025

B cell receptor (BCR) signaling plays a central role in the pathogenesis of B cell lymphomas, making it a crucial therapeutic target. The advent of BCR-targeted inhibitors, particularly those directed at PI3K and BTK, has revolutionized treatment for B cell non-Hodgkin lymphoma (B-NHL). However, therapeutic resistance remains a significant clinical challenge. Increasing evidence suggests that the tumor microenvironment (TME), particularly the bone marrow (BM) microenvironment, is crucial in driving cancer progression and therapeutic resistance. The BM microenvironment provides a specialized niche where lymphoma cells can evade therapy through interactions with stromal cells and extracellular matrix (ECM) components. Bone marrow stromal cells (BMSCs) contribute significantly to this resistance.

In this study, we developed anin vitro3D model to better understand B cell lymphoma biology and drug resistance mechanisms. We co-cultured lymphoma cell lines with primary BMSCs in a 3D fibrin gel matrix using a high-throughput and automated system. Our results revealed that BMSCs modulate lymphoma cell growth and reduce their sensitivity to the PI3K inhibitor copanlisib and the BTK inhibitor ibrutinib. Furthermore, this model allowed us to identify IGFBP-3, Serpin E1, and PTX-3 as potential mediators of therapeutic resistance. These findings underscore the value of using 3D co-culture models in preclinical settings to more accurately study drug resistance, as they more closely simulate the BM microenvironment’s complexity than traditional 2D models, thus improving the predictive value of drug testing in B cell lymphomas.Visual Abstract