bluuebunny/crossref_metadata_2025 huggingface dataset:
Make or break: The influence of expected challenges and rewards on the motivation and experience associated with cognitive effort exertion
Authors: Zhang Yue , Leng Xiamin , Shenhav Amitai
Published: December 2023

Challenging goals can induce harder work but also greater stress, in turn potentially undermining goal achievement. We sought to examine how mental effort and subjective experiences thereof interact as a function of challenge level and the size of the incentives at stake. Participants performed a task that rewarded individual units of effort investment (correctly performed Stroop trials) but only if they met a threshold number of correct trials within a fixed time interval (challenge level). We varied this challenge level (Study 1, N = 40), and the rewards at stake (Study 2, N = 79), and measured variability in task performance and self-reported affect across task intervals. Greater challenge and higher rewards facilitated greater effort investment but also induced greater stress, while higher rewards (and lower challenge) simultaneously induced greater positive affect. Within intervals, we observed an initial speed up then slowdown in performance, which could reflect dynamic reconfiguration of control. Collectively, these findings further our understanding of the influence of task demands and incentives on mental effort exertion and wellbeing.
Low-intensity pulsed ultrasound stimulation (LIPUS) modulates microglial activation following intracortical microelectrode implantation
Authors: Li Fan , Gallego Jazlyn , Tirko Natasha N , Greaser Jenna , Bashe Derek , Patel Rudra , Shaker Eric , Van Valkenburg Grace E , Alsubhi Alanoud S , Wellman Steven , Singh Vanshika , Padill Camila Garcia , Gheres Kyle W. , Bagwell Roger , Mulvihill Maureen , Kozai Takashi D.Y.
Published: December 2023

Microglia are important players in surveillance and repair of the brain. Their activation mediates neuroinflammation caused by intracortical microelectrode implantation, which impedes the application of intracortical brain-computer interfaces (BCIs). While low-intensity pulsed ultrasound stimulation (LIPUS) can attenuate microglial activation, its potential to modulate the microglia-mediated neuroinflammation and enhance the bio-integration of microelectrodes remains insufficiently explored. We found that LIPUS increased microglia migration speed from 0.59±0.04 to 1.35±0.07 µm/hr on day 1 and enhanced microglia expansion area from 44.50±6.86 to 93.15±8.77 µm2/min on day 7, indicating improved tissue healing and surveillance. Furthermore, LIPUS reduced microglial activation by 17% on day 6, vessel-associated microglia ratio from 70.67±6.15 to 40.43±3.87% on day 7, and vessel diameter by 20% on day 28. Additionally, microglial coverage of the microelectrode was reduced by 50% in week 1, indicating better tissue-microelectrode integration. These data reveal that LIPUS helps resolve neuroinflammation around chronic intracortical microelectrodes.
Predicting the Purity of Multispecific Antibodies From Sequence Using Machine Learning: Methods and Applications
Authors: Mazurek Aviva , Davis Athena , Comeau Stephen R. , Tsang Kenny , Rivera Javier , Huang Zhong-Fu , Holt John , Kumar Sandeep , Kasturirangan Srinath
Published: December 2023

Multispecific antibodies are prominent therapeutic agents, but many molecular formats and drug candidates that show promise during molecular discovery stages cannot be scaled up and developed into drugs due to inadequate developability. During the discovery stages, the selection of molecule format(s), molecule design, purity, and initial physiochemical stability testing criteria largely rely on scientists’ experience. Machine learning, however, can identify hidden trends in large datasets, aiding in the selection of drug candidates with improved developability. In this study, we present a machine learning approach to predict antibody purity, measured by the percentage of monomer after protein A purification. Using the amino acid sequences of variable regions, molecular formats, germlines and germline pairings, and calculated physiochemical properties as inputs, machine learning models were trained to predict the percentage of monomer for a given multispecific antibody (Figure 1). The dataset employed in this study consists of ∼500 multi-specific antibodies generated during BI’s internal drug discovery programs. Our results indicate that machine learning, when applied to sequence, germline, and format data, can effectively predict antibody percentage of monomer. Incorporating this approach into high-throughput multispecific antibody screening processes can save time and resources by reducing the need to test a large subset of potentially unstable antibodies. While this study focused on percentage of monomer as a test case, similar approaches can be employed to predict other antibody properties, such as melting temperature (Tm), hydrophobicity (aHIC), and solution stability properties (AC-SINS).
blik: an extensible napari plugin for cryo-ET data visualisation, annotation and analysis
Authors: Gaifas Lorenzo , Timmins Joanna , Gutsche Irina
Published: December 2023

Powerful, workflow-agnostic and interactive visualisation is essential for the ad-hoc, human-in-the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and annotation of cryo-ET data, they are often integrated as part of monolithic processing pipelines, or focused on a specific task and offering limited reusability and extensibility. With each software suite presenting its own pros and cons and often tools tailored to address specific challenges, seamless integration between available pipelines is often a difficult task. As part of the effort to enable such flexibility and move the software ecosystem towards a more collaborative and modular approach, we developedblik, an open-sourcenapariplugin for visualisation and annotation of cryo-ET data (source code:https://github.com/brisvag/blik).blikoffers fast, interactive, and user-friendly 3D visualisation thanks tonapari, and is built with extensibility and modularity at the core. Data is handled and exposed through well-established scientific Python libraries such asnumpyarrays andpandasdataframes. Reusable components (such as data structures, file read/write, and annotation tools) are developed as independent Python libraries to encourage reuse and community contribution. By easily integrating with established image analysis tools – even outside of the cryo-ET world –blikprovides a versatile platform for interacting with cryo-ET data. On top of core visualisation features – interactive and simultaneous visualisation of tomograms, particle picks and segmentations –blikprovides an interface for interactive tools such as manual particle picking, surface-based and filament-based particle picking and image segmentation, as well as simple filtering tools. Additional self-containednapariplugins developed as part of this work also implement interactive plotting and selection based on particle features, and label interpolation for easier segmentation. Finally, we highlight the differences with existing software and showcaseblik’s applicability in biological research.
The Effects of Physical and Mental Fatigue on Time Perception
Authors: Goudini Reza , Zahiri Ali , Alizaheh Shahab , Drury Benjamin , Anvar Saman Hadjizadeh , Daneshjoo Abdolhamid , Behm David G
Published: December 2023

The subjective perception of time holds a foundational significance within the realm of human psychology and our conceptualizations of reality and how we elucidate the chronological progression of events within our lives. While there have been some studies examining the effects of exercise on time perception during the exercise period, there are no studies investigating the effects of fatiguing exercise on time perception after the exercise intervention. This study aimed to investigate the effects of physical and mental fatigue on time estimates over 30-seconds (5-, 10-, 20-, and 30-seconds) immediately after exercise and 6-minutes after the post-test. Seventeen healthy and recreationally active volunteers (14 males, 3 females) were subjected to three conditions: physical fatigue, mental fatigue, and control. All participants completed a familiarization and three 30-minute experimental conditions (control, physical fatigue (cycling at 65% peak power output), and mental fatigue (Stroop task for 1100 trials) on separate days. Heart rate and body temperature were recorded at the pre-test, start, 5-, 10-, 20-, 30-seconds of the interventions, post-test, and 6-min follow-up. Rating of perceived exertion (RPE) was recorded four times during the intervention. Time perception was measured prospectively (at 5-, 10-, 20-, and 30-seconds) at the pre-test, post-test, and 6-minute follow-up. Physical fatigue significantly (p=0.001) underestimated time compared to mental fatigue and control conditions at the post-test and follow-up, with no significant differences between mental fatigue and control conditions. Heart rate, body temperature, and RPE were significantly (all p=0.001) higher with physical fatigue compared to mental fatigue and control conditions during the intervention and at the post-test. This study demonstrated that cycling-induced fatigue led to time underestimation compared to mental fatigue and control conditions. It is crucial to consider that physical fatigue has the potential to lengthen an individual’s perception of time estimates in sports or work environments.
A Meta-model for ADMET Property Prediction Analysis
Authors: Padi Sarala , Cardone Antonio , Sriram Ram D.
Published: December 2023

In drug discovery analysis chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties play a critical role. These properties allow the quantitative evaluation of a designed drug’s efficacy. Several machine learning models have been designed for the prediction of ADMET properties. However, no single method seems to enable the accurate prediction of these properties. In this paper, we build a meta-model that learns the best possible way to combine the scores from multiple heterogeneous machine learning models to effectively predict the ADMET properties. We evaluate the performance of our proposed model against the Therapeutics Data Commons (TDC) ADMET benchmark dataset. The proposed meta-model outperforms state-of-the-art methods such as XGBoost in the TDC leaderboard, and it ranks first in five and in the top three positions for fifteen out of twenty-two prediction tasks.
Crucial role for Sodium Hydrogen Exchangers in SGLT2 inhibitor-induced arterial relaxations
Authors: Forrester Elizabeth A , Benítez-Angeles Miguel , Redford Kaitlyn E. , Rosenbaum Tamara , Abbott Geoffrey W , Barrese Vincenzo , Dora Kim , Albert Anthony P , Dannesboe Johs , Salles-Crawley Isabelle , Jepps Thomas A , Greenwood Iain A
Published: December 2023

1

Introduction

Sodium dependent glucose transporter 2 (SGLT2 or SLC5A2) inhibitors effectively lower blood glucose and are also approved treatments for heart failure independent of raised glucose. One component of the cardioprotective effect is reduced cardiac afterload but the mechanisms underlying peripheral relaxation are ill defined and variable. We speculated that SGLT2 inhibitors promoted arterial relaxation via the release of the potent vasodilator calcitonin gene-related peptide (CGRP) from sensory nerves independent of glucose transport.

Experimental approach

The functional effects of SGLT2 inhibitors (dapagliflozin, empagliflozin, ertugliflozin) and the sodium/hydrogen exchanger 1 (NHE1) blocker cariporide were determined on pre-contracted mesenteric and renal arteries from male Wistar rats using Wire-Myography. SGLT2, NHE1, CGRP and TRPV1 expression in both arteries was determined by Western blot and immunohistochemistry. Kv7.4/5/KCNE4 and TRPV1 currents were measured in the presence and absence of dapagliflozin and empagliflozin.

Results

All SGLT2 inhibitors produced a concentration dependent relaxation (1µM-100µM) of mesenteric arteries that was considerably greater than in renal arteries. Cariporide relaxed mesenteric arteries but not renal arteries. Immunohistochemistry with TRPV1 and CGRP antibodies revealed a dense innervation of sensory nerves in mesenteric arteries that was absent in renal arteries. Consistent with a greater sensory nerve component, the TRPV1 agonist capsaicin produced significantly greater relaxations in mesenteric arteries compared to renal arteries. Relaxations to dapagliflozin, empagliflozin and cariporide were attenuated by incubation with the CGRP receptor antagonist BIBN-4096, the Kv7 blocker linopirdine and the TRPV1 antagonist AMG-517 as well as by depletion of neuronal CGRP. Neither dapagliflozin nor empagliflozin directly activated heterologously expressed TRPV1 channels or Kv7 channels. Strikingly, only NHE1 colocalised with TRPV1 in sensory nerves, and cariporide pre-application prevented the relaxant response to SGLT2 inhibitors.

Conclusions

SGLT2 inhibitors relax mesenteric arteries by a novel mechanism involving the release of CGRP from sensory nerves following inhibition of the Na+/H+exchanger.
Exploring the neuronal and systemic physiological contributions to spontaneous cerebral fluctuations – Insights from functional MRI in The Maastricht Study
Authors: Vergoossen L.W.M. , Jansen J.F.A. , Schram M.T. , Jong J.J.A. de , Boxtel M.P.J. van , Reulen J.P.H. , Houben A.J.H.M. , Greevenbroek M.M.J. , Huybrechs D. , Backes W.H.
Published: December 2023

Objective

Functional MRI (fMRI) is sensitive to changes in the blood oxygen level-dependent (BOLD) signal, which originates from neurovascular coupling, the mechanism that links neuronal activity to changes in cerebral blood flow. Isolating the native spontaneous neuronal fluctuations from the BOLD signal of the resting-state is challenging, as the signal induced by neuronal activity represents only a small part of this signal. Furthermore, many other non-neuronal (systemic) oscillations contribute, such as from the cardiovascular and respiratory system with frequencies partly overlapping those of the spontaneous fluctuations. The objective of this study is to investigate to what extent various systemic physiological signals are associated with the measured BOLD signal, in particular the frequency interval pertaining to the spontaneous cerebral fluctuations (10-100 mHz). Additionally, we investigate whether these associations were independent of cardiometabolic risk factors.

Methods

Within the population-based Maastricht Study, 3T resting-state functional MRI and physiological measures, covering cardiac, respiratory, myogenic, neurogenic, and endothelial activity, were acquired (n=1,651, 48% woman, aged 59±8 years). As both neuronal and non-neuronal physiological signals contain frequencies that vary over time, a wavelet transformation (WT) was used. Time-series were decomposed into seven wavelet subbands, and for each subband, the energy of the BOLD signal was calculated. Multivariable linear regression analysis was used to investigate the association of the physiological measures, in particular cognitive function, with the wavelet energy per subband, independent of cardiometabolic risk factors.

Results

We found that physiological measures were associated with the energy of certain frequency subbands of the spectrum of the measured fMRI signal. Both cognitive performance and blood pressure variations, as measures of neurogenic and myogenic activity respectively, were associated with the energy of the frequency subband 3 (31.2-62.5 mHz). Furthermore, cardiac and respiratory activity were associated with the energy of the high frequency subband 1 (>125 mHz), and endothelial activity with the energy of low frequency subbands 6 and 7 (<10 mHz). Part of these associations were dependent on cardiometabolic risk factors.

Conclusion

We found an association between myogenic and neurogenic activity and the frequency specific BOLD signal. Our findings highlight the strong intertwining of neuronal, vascular, and cardiometabolic activity and emphasize the importance of a proper selection of the resting-state frequency range in fMRI studies on cognitive function.
RCT-Twin-GAN Generates Digital Twins of Randomized Control Trials Adapted to Real-world Patients to Enhance their Inference and Application
Authors: Thangaraj Phyllis M. , Shankar Sumukh Vasisht , Oikonomou Evangelos K. , Khera Rohan
Published: December 2023

Background

Randomized clinical trials (RCTs) are designed to produce evidence in selected populations. Assessing their effects in the real-world is essential to change medical practice, however, key populations are historically underrepresented in the RCTs. We define an approach to simulate RCT-based effects in real-world settings using RCT digital twins reflecting the covariate patterns in an electronic health record (EHR).

Methods

We developed a Generative Adversarial Network (GAN) model,RCT-Twin-GAN, which generates a digital twin of an RCT (RCT-Twin) conditioned on covariate distributions from an EHR cohort. We improved upon a traditional tabular conditional GAN,CTGAN, with a loss function adapted for data distributions and by conditioning on multiple discrete and continuous covariates simultaneously. We assessed the similarity between a Heart Failure with preserved Ejection Fraction (HFpEF) RCT (TOPCAT), a Yale HFpEF EHR cohort, and RCT-Twin. We also evaluated cardiovascular event-free survival stratified by Spironolactone (treatment) use.

Results

By applyingRCT-Twin-GANto 3445 TOPCAT participants and conditioning on 3445 Yale EHR HFpEF patients, we generated RCT-Twin datasets between 1141-3445 patients in size, depending on covariate conditioning and model parameters. RCT-Twin randomly allocated spironolactone (S)/placebo (P) arms like an RCT, was similar to RCT by a multi-dimensional distance metric, and balanced covariates (median absolute standardized mean difference (MASMD) 0.017, IQR 0.0034-0.030). The 5 EHR-conditioned covariates in RCT-Twin were closer to the EHR compared with the RCT (MASMD 0.008 vs 0.63, IQR 0.005-0.018 vs 0.59-1.11). RCT-Twin reproduced the overall effect size seen in TOPCAT (5-year cardiovascular composite outcome odds ratio (95% confidence interval) of 0.89 (0.75-1.06) in RCT vs 0.85 (0.69-1.04) in RCT-Twin).

Conclusions

RCT-Twin-GANsimulates RCT-derived effects in real-world patients by translating these effects to the covariate distributions of EHR patients. This key methodological advance may enable the direct translation of RCT-derived effects into real-world patient populations and may enable causal inference in real-world settings.
Modelling the cost-effectiveness of TasP and PrEP in female sex workers in Cotonou, Benin
Authors: Cianci F , Geidelberg L , Mitchell KM , Kessou L , Mboup A , Diabate S , Behanzin L , Guedou FA , Zannou DM , Geraldo N , Goma-Matsétsé E , Giguère K , Aza-Gnandji M , Diallo M , Kêkê R , Bachabi M , Dramane K , Lafrance C , Affolabi D , Gagnon MP , Gangbo F , Silhol R , Terris-Prestholt F , Boily MC , Alary M , Vickerman P
Published: December 2023

Introduction

Treatment as prevention (TasP) and pre-exposure prophylaxis (PrEP) could impact the HIV epidemic among Female Sex Workers (FSW) but their cost-effectiveness is uncertain in this group. This study aims to model the cost-effectiveness of TasP and PrEP among FSW in Cotonou, Benin.

Methods

A demonstration study assessed TasP and PrEP use among FSW in Cotonou. A dynamic HIV transmission model was developed to estimate the impact of this intervention and published elsewhere. Incremental economic costs of the study were collected prospectively capturing both provider and FSW costs. The incremental cost-effectiveness ratio per HIV infection and disability-adjusted life years (DALY) averted were estimated over a 20 year time horizon with costs converted to USD 2020 and both costs and DALYs discounted at 4.5% per year. Different cost scenarios were modelled to investigate the cost-effectiveness of the intervention as delivered by the government reflecting current day implementation and resource costs.

Results

The mean provider annual economic cost per FSW on TasP was $646, with an initiation cost of $347 and mean annual user costs were $16. The mean initiation costs for PrEP were $268, mean annual provider costs were $359-$499 and annual user cost $15-$21 depending on adherence level. TasP was found to be cost saving for all cost scenarios examined compared to routine HIV care for FSW. PrEP was not cost-effective for any cost scenario, population coverage or adherence level examined.

Conclusion

Our results support TasP but not PrEP for FSW in our setting. A streamlined, outreach delivery model with reduced costs should be investigated to assess its cost-effectiveness in this setting.
Analysis of Engagement withCuidaTEXT, a Text Message Intervention for Dementia Caregiver Support among Latinos
Authors: Medina Valerie , Watts Amber , Fracachán-Cabrera Monica , Hazlewood Cameo , Ramirez-Mantilla Mariana , Vidoni Eric D. , Perales-Puchalt Jaime
Published: December 2023

Objectives

To assess the impact of a text message intervention,CuidaTEXT, on participant engagement and its subsequent associations with socio-demographic factors, acceptability measures, and clinical outcomes among Latino dementia caregivers.

Methods

CuidaTEXTis a six-month, bilingual, and bidirectional intervention. We enrolled 24 Latino caregivers in a one-arm feasibility trial. Participants received approximately one automatic daily text message and could engage with the intervention by texting specific keywords (e.g., STRESS to receive messages about stress-coping), and by chat-texting with a live coach. We used metrics and psychometric scales to quantify variables.

Results

Participants sent a total of 1,847 messages toCuidaTEXT. Higher engagement was associated with higher intervention satisfaction (r=0.6, p=0.007), as were several other acceptability outcomes. We found no associations between engagement withCuidaTEXTand sociodemographic or clinical outcomes (p>0.05).

Conclusion

Encouraging interaction withCuidaTEXTmight lead to higher levels of satisfaction with the intervention. However, it might be that those who are highly satisfied, engage more withCuidaTEXT. Future research should determine the directionality of these associations.

Clinical Implications

Increasing opportunities to engage in text messaging may increase Latino caregivers’ satisfaction with caregiver support interventions.
Early-stage idiopathic pulmonary fibrosis is characterized by bronchoalveolar accumulation of SPP1+macrophages
Authors: Yu Jiangyan , Thomas Jake , Haub Jessica , Pizarro Carmen , Zhang Miaomiao , Biener Leonie , Becker Matthias , Zhang Lili , Kapellos Theodore S. , Schulte Wolfgang , Schultze Joachim L. , Hasenauer Jan , Skowasch Dirk , Schlitzer Andreas
Published: December 2023

Patients affected by idiopathic pulmonary fibrosis (IPF), a progressive chronic and eventually fatal lung disease with unknown cause, suffer from delayed diagnosis and limited personalized treatment options due to the lack of predictive and staging relevant disease markers. Prior studies focused on the cellular and transcriptomic changes found in lung tissue during terminal IPF-associated lung fibrosis. In clinical routine, bronchoscopy is applied for diagnosis and staging of suspected IPF affected individuals, thus providing us with a clinically applicable window, to study the cellular and transcriptional changes within affected individuals at the time of diagnosis. Here we study a cohort consisting of 11 IPF affected individuals and 11 healthy controls. We investigate their single cell transcriptomic profile alongside the surface phenotype of alveolar-resident immune cells. Single cell transcriptional analysis reveals accumulation of SPP1+macrophages (SPP1+Mφ) within the alveolar space during early stage diagnosed IPF, in the absence of a decline in lung function. SPP1+Mφ were characterized by high expression of lipid storage and handling genes, accumulation of intracellular cholesterol and expression of proinflammatory cytokine expression.In silicodevelopmental trajectory analysis revealed that SPP1+Mφ are likely derived from classical monocytes. Finally, to confirm the clinical diagnostic value of SPP1+Mφ, we developed a flow cytometry panel to rapidly identify and test for the presence of SPP1+Mφ in bronchoalveolar lavage samples. The new panel has confirmed the increased frequency of SPP1+Mφ in early-IPF in an independent validation cohort. Taken together, we show that SPP1+Mφ are associated with early IPF pathogenesis in the absence of a decline in lung function, thus providing a clinically valuable markers for diagnosis of early IPF in clinical practice.

Highlights

IPF patients can be stratified into early and advanced disease groups based on clinical features.

Single cell transcriptomic and high dimensional flow cytometry enabled mapping of the myeloid compartment across the continuum of idiopathic pulmonary fibrosis associated disease states.

SPP1+Mφ accumulated during early clinical stage of IPF.

Development of a clinically applicable SPP1⁺Mφ identification panel.
AKAP150-anchored PKA regulation of synaptic transmission and plasticity, neuronal excitability and CRF neuromodulation in the lateral habenula
Authors: Simmons S.C. , Flerlage W.J. , Langlois L.D. , Shepard R.D. , Bouslog C. , Thomas E.H. , Gouty K.M. , Sanderson J.L. , Gouty S. , Cox B.M. , Dell’Acqua M.L. , Nugent F.S.
Published: December 2023

Numerous studies of hippocampal synaptic function in learning and memory have established the functional significance of the scaffolding A-kinase anchoring protein 150 (AKAP150) in kinase and phosphatase regulation of synaptic receptor and ion channel trafficking/function and hence synaptic transmission/plasticity, and neuronal excitability. Emerging evidence also suggests that AKAP150 signaling may play a critical role in brain’s processing of rewarding/aversive experiences. Here we focused on an unexplored role of AKAP150 in the lateral habenula (LHb), a diencephalic brain region that integrates and relays negative reward signals from forebrain striatal and limbic structures to midbrain monoaminergic centers. LHb aberrant activity (specifically hyperactivity) is also linked to depression. Using whole cell patch clamp recordings in LHb of male wildtype (WT) and ΔPKA knockin mice (with deficiency in AKAP-anchoring of PKA), we found that the genetic disruption of PKA anchoring to AKAP150 significantly reduced AMPA receptor (AMPAR)-mediated glutamatergic transmission and prevented the induction of presynaptic endocannabinoid (eCB)-mediated long-term depression (LTD) in LHb neurons. Moreover, ΔPKA mutation potentiated GABAAreceptor (GABAAR)-mediated inhibitory transmission postsynaptically while increasing LHb intrinsic neuronal excitability through suppression of medium afterhyperpolarizations (mAHPs). Given that LHb is a highly stress-responsive brain region, we further tested the effects of corticotropin releasing factor (CRF) stress neuromodulator on synaptic transmission and intrinsic excitability of LHb neurons in WT and ΔPKA mice. As in our earlier study in rat LHb, CRF significantly suppressed GABAergic transmission onto LHb neurons and increased intrinsic excitability by diminishing small-conductance potassium (SK) channel-mediated mAHPs. ΔPKA mutation-induced suppression of mAHPs also blunted the synaptic and neuroexcitatory actions of CRF in mouse LHb. Altogether, our data suggest that AKAP150 complex signaling plays a critical role in regulation of AMPAR and GABAAR synaptic strength, glutamatergic plasticity and CRF neuromodulation possibly through AMPAR and potassium channel trafficking and eCB signaling within the LHb.
Comprehensive chromatome profiling identifies metabolic enzymes on chromatin in healthy and cancer cells
Authors: Kourtis S , Guirola M , Pardo-Lorente N , Ghose R , Garcia-Cao M , Gañez-Zapater A , Haynes S , Fontaine F , Muller A , Sdelci S
Published: December 2023

Metabolic and epigenetic rewiring are widely considered hallmarks of cancer, with emerging evidence of crosstalk between them. Anecdotal evidence of metabolic enzymes moonlighting in the chromatin environment has suggested how this crosstalk might be facilitated, but the extent of nuclear relocalization of metabolic enzymes remains elusive. Here, we provide a comprehensive chromatin proteomics resource across cancer lineages as well as healthy samples and demonstrate that metabolic enzyme moonlighting on chromatin is widespread across tissues and pathways. We show that the abundance of metabolic enzymes on chromatin is tissue-specific, with oxidative phosphorylation proteins depleted in lung cancer samples, perhaps suggesting an interplay between cell identity and nuclear metabolism. Finally, we explore metabolic functions in the chromatin environment and show that one-carbon folate enzymes are associated with DNA damage and repair processes, providing an approach to explore non-canonical functions of metabolic enzymes.
4D bioprinted self-folding scaffolds enhance cartilage formation in the engineering of trachea
Authors: Chiesa Irene , Esposito Alessio , Vozzi Giovanni , Gottardi Riccardo , De Maria Carmelo
Published: December 2023

Trachea defects that required surgical interventions are increasing in number in the recent years, especially for pediatric patients. However, current gold standards, such as biological grafts and synthetic prothesis, do not represent an effective solution, due to the lack of mimicry and regeneration capability. Bioprinting is a cutting-edge approach for the fabrication of biomimetic scaffold to empower tissue engineering toward trachea replacement. In this study, we developed a self-folding gelatin-based bilayer scaffold for trachea engineering, exploiting the 4D bioprinting approach, namely the fabrication of dynamic scaffolds, able to shape morph in a predefined way after the application of an environmental stimulus. Indeed, starting form a 2D flat position, upon hydration, this scaffold forms a closed tubular structure. An analytical model, based on Timoshenko’s beam thermostats, was developed, and validated to predict the radius of curvature of the scaffold according to the material properties and the scaffold geometry. The 4D bioprinted structure was tested with airway fibroblast, lung endothelial cells and ear chondral progenitor cells (eCPCs) toward the development of a tissue engineered trachea. Cells were seeded on the scaffold in its initial flat position, maintained their position after the scaffold actuation and proliferated over or inside it. The ability of eCPCs to differentiate towards mature cartialge was evaluated. Interestingly, real-time PCR revealed that differentiating eCPCs on the 4D bioprinted scaffold promote healthy cartilage formation, if compared with eCPCs cultured on 2D static scaffold. Thus, eCPCs can perceive scaffold folding and its final curvature and to react to it, towards the formation of mature cartilage for the airway.
A novel method of testing the antimicrobial potentials ofExiguobacterium aurantiacum, Lysinibacillus boronitoleransandBacillus megaterium
Authors: Jain Radhika , Belwalkar Mugdha , Shukla Varsha , Lokur Anushree , Rege Mayuri
Published: December 2023

Microorganisms can be an effective source for antimicrobial compounds including peptides that provide an evolutionary advantage to them in specific niches. Prior studies have noted the antimicrobial properties ofExiguobacterium aurantiacum, Lysinibacillus boronitoleransandBacillus megateriumbut they used time- and resource-intensive procedures to prepare the extracts (2, 10). We wanted to explore a more cost-effective, time-effective and simpler method of testing the antimicrobial potential of bacterial extracts. Our extraction protocol is a one-step incubation of the organism in the solvent overnight, followed by a standard well diffusion based assay to test its antimicrobial effect. We tested this method with three cultures isolated from the premises of Mumbai railway stations:E. aurantiacum, L. boronitoleransandBacillus megaterium. These extracts were tested against human pathogensStaphylococcus aureusandEnterococcus faecalis. E. aurantiacum, L. boronitoleransandB. megateriuminhibitedS. aureusby 9.17 ± 0.42, 9.25 ± 0.48 and 10.50 ± 1.5 mm, respectively, andE. faecalisby 15.79 ± 2.25, 14.21 ± 0.88 and 17.5 ± 2.89 mm, respectively. This approach is therefore suggested to be effective for screening the antimicrobial activity of these bacteria.
Pan-cancer analysis of pyrimidine metabolism reveals signaling pathways connections with chemoresistance role
Authors: Ramesh Vignesh , Demirdizen Mert , Pinna Luisa , Doktor Thomas Koed , Siddiqui Mohammad Aarif , Ceppi Paolo
Published: December 2023

Deregulated nucleotide metabolism, and in particular increased pyrimidine metabolism (PyMet), has been shown to contribute to various pathological features of cancer including chemoresistance and epithelial-to-mesenchymal transition. However, cancer often encompasses complex signaling and metabolic pathway cascades for its progression, and understanding of these molecular regulatory processes in pyrimidine metabolism is quite limited. Therefore, a comprehensive pan-cancer analysis in around 10,000 gene expression profiles of 32 cancer types was employed using a pathway-based approach utilizing gene-sets representing various signaling and metabolic pathways. The analysis identified several top connections with PyMet including TERT, MTOR, DAX1, HOXA1, TP53 and TNC implying an inter-dependency of regulations which in turn was linked to the chemoresistance mechanisms. PyMet-signaling interactions were validated within vitroderived gene-sets from endogenous thymidylate synthase (TYMS)-promoter activity reporter, fromTYMSknockdown and from brequinar treatment, and further at single cell transcriptome level. Strikingly, brequinar treatment profile showed a strong inverse association pattern with doxorubicin chemoresistance in multiple cancer types. The study highlights the PyMet-pathway interactions and its role in chemoresistance, thereby providing an effective tool for improving PyMet targeting strategy in cancer. The analysis as an accessible resource is available at:www.pype.compbio.sdu.dk

Highlights

Pan-cancer analysis showed pyrimidine metabolism connections with signaling pathways Top pathway interactors of pyrimidine metabolism were TERT, HOXA1, TP53 and TNC In vitro derived pyrimidine gene-sets recapitulate cancer patients’ pathway analysis Pyrimidine associated pathways confer chemoresistance in multiple cancer types Pyrimidine metabolic inhibitor brequinar reversed doxorubicin chemoresistance feature
Adaptable Fabrication of Vascularized Milliscale Tissues in Membrane-Free Organ Chips Manufactured with 3D Printed Molds
Authors: Byrne C. Ethan , Conrad K. Michael , Martier Ashley T. , Fortes Gabrielle , Kpeli G. Wills , Olsen Elisabet , Bralower William , Culp Caroline C. , Wendell Max , Boone Keefer A. , Mondrinos Mark J.
Published: December 2023

Inexpensive stereolithography (SLA) 3D printing enables rapid prototyping of resin molds for polydimethylsiloxane (PDMS) soft lithography and organ chip fabrication, but geometric distortion and surface roughness of SLA resins can impede the development of adaptable manufacturing workflows. This study reports post-processing procedures for manufacturing SLA-printed molds built with a Formlabs F3 printer that produce fully cured, flat, patently bonded, and optically clear PDMS organ chips. User injection loading tests with iterated guide structure designs were conducted to achieve engineering reduction to practice of milliscale membrane-free organ chips (MFOC), defined as reproducible loading of aqueous solutions without failure of surface tension-based liquid patterning. The optimized manufacturing workflow was applied to further engineer milliscale MFOC for specific applications in modeling vascular physiology and pathobiology. The open lateral interfaces of bulk tissues seeded in MFOC facilitate the formation of anastomoses with internal vasculature to create milliscale perfusable vascular beds. After optimizing bulk tissue vasculogenesis in MFOC, we developed a method for seeding the bulk tissue interfaces with a confluent endothelium to stimulate self-assembly of perfusable anastomoses with the internal vasculature. Rocker- and pump-based flow-conditioning protocols were tested to engineer enhanced barrier function of the perfusable internal vasculature. Modularity of the MFOC design enabled creation of a multi-organ device that was used to model decaying gradients of cancer-associated vascular inflammation in organ compartments positioned at increasing distances from a tumor compartment. These easily adaptable methods for designing and fabricating vascularized microphysiological systems can accelerate their adoption in a diverse range of preclinical laboratory settings.
Segmentation of supragranular and infragranular layers in ultra-high resolution 7Tex vivoMRI of the human cerebral cortex
Authors: Zeng Xiangrui , Puonti Oula , Sayeed Areej , Herisse Rogeny , Mora Jocelyn , Evancic Kathryn , Varadarajan Divya , Balbastre Yael , Costantini Irene , Scardigli Marina , Ramazzotti Josephine , DiMeo Danila , Mazzamuto Giacomo , Pesce Luca , Brady Niamh , Cheli Franco , Pavone Francesco Saverio , Hof Patrick R. , Frost Robert , Augustinack Jean , van der Kouwe Andŕe , Iglesias Juan Eugenio , Fischl Bruce
Published: December 2023

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Lever-aging recent advancements in ultra-high resolutionex vivoMRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers inex vivoMRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphereex vivoscans at 120µm, we propose a multi-resolution U-Nets framework (MUS) that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation, while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.
Imaging the dynamics of uterine contractions in early pregnancy
Authors: Dawson Madeline , Flores Diana , Zou Lisa , Anandasenthil Shivani , Mahesh Rohit , Zavala Olmo , Arora Ripla
Published: December 2023

The myometrium or smooth muscle of the uterus contracts throughout the life of the organ. Uterine muscle contractility is essential for reproductive processes including sperm and embryo transport, and during the uterine cycle to remove menstrual effluent or estrus debris. Even still, uterine contractions have primarily only been studied in the context of preterm labor. This is partly due to a lack of methods for studying the contractile characteristics of the uterine muscle in the intact organ. Here, we describe an imaging-based method to evaluate the contractility of both the longitudinal and circular muscles of the uterus in the cycling stages and in early pregnancy. By transforming the image-based data into 3D spatiotemporal contractility maps, we calculate waveform characteristics of muscle contractions, including amplitude, frequency, wavelength, and velocity. We report that the native organ is highly contractile during the progesterone-dominant diestrus stage of the cycle when compared to the estrogen-dominant proestrus and estrus stages. We also observed correlations between contractility during pre-implantation stages of pregnancy and observed embryo movement patterns. During the first phase of embryo movement when clustered embryos move towards the middle of the uterine horn, uterine contractions are dynamic and non-uniform between different segments of the uterine horn. In the second phase of embryo movement, contractions are more uniform and rhythmic throughout the uterine horn. Finally, when our method is applied toLpar3mutant uteri that display faster embryo movement, we observe global and regional increases in contractility. Our method provides a means to understand the wave characteristics of uterine smooth muscle in response to modulators and in genetic mutants. Better understanding uterine contractility in the early pregnancy stages is critical for the advancement of artificial reproductive technologies and a possibility of modulating embryo movement during clinical embryo transfers.
Population size interacts with reproductive longevity to shape the germline mutation rate
Authors: Zhu Luke , Beichman Annabel , Harris Kelley
Published: December 2023

Mutation rates vary across the tree of life by many orders of magnitude, with lower mutation rates in species that reproduce quickly and maintain large effective population sizes. A compelling explanation for this trend is that large effective population sizes facilitate selection against weakly deleterious “mutator alleles” such as variants that interfere with the molecular efficacy of DNA repair. However, in multicellular organisms, the relationship of the mutation rate to DNA repair efficacy is complicated by variation in reproductive age. Long generation times leave more time for mutations to accrue each generation, and late reproduction likely amplifies the fitness consequences of any DNA repair defect that creates extra mutations in the sperm or eggs. Here, we present theoretical and empirical evidence that a long generation time amplifies the strength of selection for low mutation rates in the spermatocytes and oocytes. This leads to the counterintuitive prediction that the species with the highest germline mutation rates per generation are also the species with most effective mechanisms for DNA proofreading and repair in their germ cells. In contrast, species with different generation times accumulate similar mutation loads during embryonic development. Our results parallel recent findings that the longest-lived species have the lowest mutation rates in adult somatic tissues, potentially due to selection to keep the lifetime mutation load below a harmful threshold.

Significance Statement

All cells accumulate mutations due to DNA damage and replication errors. When mutations occur in germ tissues including sperm, eggs, and the early embryo, they create changes in the gene pool that can be passed down to future generations. Here, we examine how rates of germline mutations vary within and between mammalian species, and we find that species which reproduce at older ages tend to accumulate fewer mutations per year in their sperm and eggs. This finding suggests that the evolution of humans’ long reproductive lifespan created evolutionary pressure to improve the fidelity of DNA maintenance in germ tissues, paralleling the pressure to avoid accumulating too many mutations in the body over a long lifespan.
Glial swip-10expression controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis
Authors: Rodriguez Peter , Kalia Vrinda , Gibson Chelsea L. , Gichi Zayna , Rajoo Andre , Matier Carson D. , Pezacki Aidan T. , Xiao Tong , Carvelli Lucia , Chang Christopher J. , Miller Gary W. , Khamoui Andy V. , Boerner Jana , Blakely Randy D.
Published: December 2023

Cuprous copper (Cu(I)) is an essential cofactor for enzymes supporting many cellular functions including mitochondrial respiration and suppression of oxidative stress. Neurons are particularly dependent on these pathways, with multiple neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease, associated with their dysfunction. Key features of Cu(I) contributions to neuronal healthin vivoremain to be defined, owing largely to the complex processes involved in Cu(I) production, intracellular transport, and systemic redistribution. Here, we provide genetic and pharmacological evidence thatswip-10is a critical determinant of systemic Cu(I) levels inC. elegans, with deletion leading to systemic deficits in mitochondrial respiration, production of oxidative stress, and neurodegeneration. These phenotypes can be reproduced in wild-type worms by Cu(I)-specific chelation and offset inswip-10mutants by growth on the Cu(I) enhancing molecule elesclomol, as well as by glial expression of wildtypeswip-10.MBLAC1, the most closely related mammalian ortholog toswip-10, encodes for a pre-mRNA processing enzyme for H3 histone, a protein whose actions surprisingly include an enzymatic capacity to produce Cu(I) via the reduction of Cu(II). Moreover, genome-wide association studies and post-mortem molecular studies implicate reductions ofMBLAC1expression in risk for AD with cardiovascular disease comorbidity. Consistent with these studies, we demonstrate that the deposition of β-amyloid plaques, an AD pathological hallmark, in worms engineered to express human Aβ1-42,is greatly exaggerated by mutation ofswip-10. Together, these studies identify a novel glial-expressed, and pathway for Cu(I) production that may be targeted for the treatment of AD and other neurodegenerative diseases.

Significance Statement

Devastating neurodegenerative diseases such as Alzheimer’s disease, and Parkinson’s disease are associated with disruptions in copper (Cu) homeostasis. Alterations in Cu(I) give rise to increased oxidative stress burden, mitochondrial and metabolic dysfunction, and can accelerate production and/or potentiate toxicity of disease-associated protein aggregates. Here, using the model systemCaenorhabditis elegans, we establish a role for the geneswip-10in systemic Cu(I) homeostasis. Perturbation of this pathway in worms recapitulates biochemical, histological, and pathological features seen in human neurodegenerative disease. We reveal that these changes can be suppressed pharmacologically and arise whenswip-10expression is eliminated from glial cells. Our work implicatesswip-10and orthologs as key players in Cu(I) homeostasis that may be exploitable to treat multiple neurodegenerative diseases.
Reversibly-bonded Microfluidic Devices for Stable Cell Culture and Rapid, Gentle Cell Extraction
Authors: Feng Xiaohan , Wai Cheng Lily Kwan , Lin Xuyan , Wu Angela Ruohao
Published: December 2023

Microfluidics chips have emerged as significant tools in cell culture due to their capacity for supporting cells to adopt more physiologically relevant morphology in 3D compared with traditional cell culture in 2D. Currently, irreversible bonding methods commonly used in chip fabrication mean that chips cannot be detached from their substrate without destroying the chip structure, which makes it challenging to do further analysis on cells that have been cultured on-chip. Some reversible bonding techniques exist but are restricted to certain materials, or require complex processing procedures. Here, we demonstrate a simple and reversible polydimethylsiloxane (PDMS)-polystyrene (PS) bonding technique that allows devices to withstand extended operation while pressurized, and supports long-term stable cell cultures. Importantly, it allows rapid and gentle live cell extraction for further downstream manipulation and characterization after long-term on-chip culturing, or even further subculturing. Our new approach could greatly facilitate microfluidic chip-based tissue and cell cultures, overcoming current analytical limitations and opening up new avenues for downstream uses of on-chip cultures, including 3D-engineered tissue structures for biomedical applications.