bluuebunny/crossref_metadata_2025 huggingface dataset:
Recurrence patterns in a large contemporary cohort of patients with non-muscle invasive bladder cancer
Authors: Hof Jasper P. , Kiemeney Lambertus A. , Aben Katja K.H. , van der Heijden Antoine G. , Vrieling Alina , Vermeulen Sita H.
Published: December 2024

Background and Objective

Patients with non-muscle invasive bladder cancer (NMIBC) frequently experience recurrences, yet, the timing and characteristics of subsequent recurrences are understudied. We aim to describe subsequent recurrences in a large, contemporary, population-based cohort.

Methods

We included 1,915 patients from the UroLife study and the Nijmegen Bladder Cancer Study, diagnosed with primary NMIBC between 2011 and 2021. The conditional 1-, 3- and 5-year risks of first to fourth recurrence were calculated using Kaplan-Meier risks, stratified by clinicopathological factors. Patterns of subsequent tumours were described and visualised.

Key Findings and Limitations

We observed 671 first recurrences and 400 subsequent recurrences. The 3-year conditional recurrence risks for first, second and third recurrence were 31%, 45% and 54%, respectively, and were similar for NMIBC risk groups. Recurrence after a low-, intermediate- or high-risk tumour (either primary or recurrent) was again of low-, intermediate- or high-risk in 74%, 62% and 44% of cases, respectively. Ten patients with low/intermediate-risk NMIBC and 89 patients with high-risk NMIBC progressed to muscle-invasive or metastatic bladder cancer. Seven out of these ten (70%) and 13 out of these 89 (15%) patients had a high-risk recurrence before progression. This study was limited to a patient cohort from The Netherlands.

Conclusions and Clinical Implications

Our study provides novel and reliable estimates of recurrence rates and patterns in NMIBC from a large, contemporary, population-based cohort. Recurring NMIBC tumours often exhibit similar clinicopathological characteristics, and patients with primary low- or intermediate-risk NMIBC who progress to MIBC/mBC often have a high-risk recurrence before progression. These results can inform research into NMIBC recurrences and surveillance schedules.
Quantifying absolute treatment effect heterogeneity for time-to-event outcomes across different risk strata: divergence of conclusions with risk difference and restricted mean survival difference
Authors: Maas Carolien C.H.M. , Kent David M. , Dinmohamed Avinash G. , van Klaveren David
Published: December 2024

Background

Risk-based analyses are increasingly popular for understanding heterogeneous treatment effects (HTE) in clinical trials. For time-to-event analyses, the assumption that high-risk patients benefit most on the clinically important absolute scale when hazard ratios (HRs) are constant across risk strata might not hold. Absolute treatment effects can be measured as either the risk difference (RD) at a given time point or the difference in restricted mean survival time (ΔRMST) which aligns more closely with utilitarian medical decision-making frameworks. We examined risk-based HTE analyses strata in time-to-event analyses to identify the patterns of absolute HTE across risk strata, and whether ΔRMST may lead to more meaningful treatment decisions than RD.

Methods

Using artificial and empirical time-to-event data, we compared RD—the difference between Kaplan-Meier estimates at a certain time point—and ΔRMST—the area between the Kaplan-Meier curves—across risk strata and show how these metrics can prioritize different subgroups for treatment. We explored scenarios involving constant HRs while varying both the overall event rates and the discrimination of the risk models.

Results

When event rates and discrimination were low, RD and ΔRMST increased monotonically, with high-risk patients benefitting more than low-risk patients. As the event rate increased and/or discrimination increased: 1) a “sweet spot” pattern emerged: intermediate-risk patients benefit more than low-risk and high-risk patients; and 2) RD understates the benefit in high-risk patients.

Conclusions

The pattern of HTE characterized by RD may diverge substantially from ΔRMST, potentially leading to treatment mistargeting. Therefore, we recommend ΔRMST for assessing absolute HTE in time-to-event data.

Key messages

To quantify absolute heterogeneous treatment effect (HTE) in time-to-event data, the difference in restricted mean survival time (ΔRMST) is more intuitive and comprehensive, less dependent on the time horizon, and better captures HTE when the hazard ratio (HR) of treatment varies over time, compared to the risk difference (RD).

We examined risk-based HTE analyses in time-to-event analyses to identify the patterns of absolute HTE across different risk strata, and whether ΔRMST may lead to more meaningful treatment decisions than RD.

Even with a constant HR, intermediate-risk patients may benefit more than low-risk and high-risk patients as event rates increase, a phenomenon known as a “sweet spot” pattern.

The RD does not accurately reflect the benefit for high-risk patients when event rates and/or discrimination of the risk model are high, unlike to the ΔRMST.

We recommend the ΔRMST for assessing absolute HTE, as the RD may potentially lead to treatment mistargeting.
Bayesian Feature Selection for Multi-valued Treatment Comparisons: An Electronic Health Records Study of Vasopressor Effectiveness
Authors: Qian Yunzhe , Ma Bowen
Published: December 2024

Analyzing treatment effectiveness from electronic health records (EHR) presents unique challenges in causal inference, particularly when comparing multiple treatment options with high-dimensional covariates. We propose a novel framework combining instrumental variable (IV) analysis with advanced Bayesian feature selection methods and neural networks to estimate causal effects in multi-valued treatment settings. Our approach addresses three key methodological challenges: handling multiple treatment comparisons simultaneously, comparing Bayesian feature selection methods, and selecting relevant features while capturing complex nonlinear relationships in outcome models.

Through extensive simulation studies, we demonstrate that spike-and-slab priors achieve superior performance in treatment effect estimation with the lowest mean absolute bias (0.071) compared to ALL (0.074), LASSO (0.080), and Bayesian LASSO (0.083) methods. The consistency of bias control across treatment pairs demonstrates the robustness of our Bayesian feature selection approach, particularly in identifying clinically relevant predictors.

We apply this framework to compare three commonly used vasopressors (norepinephrine, vasopressin, and phenylephrine) using MIMIC-IV data[1]. Using physician prescribing preferences as instruments[2, 3, 4], our analysis reveals a clear hierarchical pattern in treatment effectiveness. Vasopressin demonstrated superior effectiveness compared to both norepinephrine (ATE = 0.134, 95% CI [0.115, 0.152]) and phenylephrine (ATE = 0.173, 95% CI [0.156, 0.191]), while phenylephrine showed inferior outcomes compared to norepinephrine (ATE = -0.040, 95% CI [-0.048, -0.031]).

Our methodological framework provides a robust approach for analyzing multi-valued treatments in high-dimensional observational data, with broad applications beyond vessopressors in critical care. The integration of instrumental variable analysis, Bayesian feature selection, and advanced modeling techniques offers a promising direction for using EHR data to inform treatment decisions while addressing key challenges in causal inference.
Self-generated chemotaxis of mixed cell populations
Authors: Uçar Mehmet Can , Alsberga Zane , Alanko Jonna , Sixt Michael , Hannezo Edouard
Published: December 2024

Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally guided by self-generated signaling gradients rather than long-range, pre-patterned cues. However, how heterogeneous mixtures of cells interact non-reciprocally and navigate through self-generated gradients remains largely unexplored. Here we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that relative chemotactic sensitivity of cell populations controls their long-time coupling and co-migration dynamics, with boundary conditions such as external cell- and attractant reservoirs substantially influencing the migration patterns. We further predict an optimal parameter regime that leads to robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the co-migration of different immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell co-migration appears close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a phase diagram that illustrates non-trivial interplays between chemotactic and mechanical non-reciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for emergent multicellular navigation.
«The LAMP-CRISPR-Cas13a technique for detecting CBASS-mechanism of phage resistance in bacteria»
Authors: Ortiz-Cartagena Concha , Fernández-Grela Patricia , Armán Lucia , Ibarguren Clara , Blasco Lucía , Pablo-Marcos Daniel , Bleriot Inés , Fernández-García Laura , Fernández Cuenca Felipe , Barrio-Pujante Antonio , Aracil Belén , Tomás María
Published: December 2024

Antimicrobial resistance (AMR) is an important threat to public health that has led to the development of innovative alternative treatments for bacterial infections, such as phage therapy. However, one of the greatest disadvantages of phage therapy is the generation of phage-resistant bacterial mutants via bacterial defence mechanisms, which are mainly contained in genomic islands (GIs) and controlled by the quorum sensing (QS) network. In this study, 309 pathogenic islands (PAIs) harbouring a total of 22.1 % of proteins related to anti-phage defence (APD) were detected in the genome of 48 K. pneumoniae strains. Several type I and type II CBASS systems were also detected in the genome of the 48 K. pneumoniae strains, but only 2 type II CBASS systems were located in PAIs. We constructed a knockout K. pneumoniae strain, not expressing the cyclase gene from the type II CBASS system present in PAIs, to study the regulatory role of QS in expressing the gene. As the anti-phage CBASS system is an abortive infection (Abi) system, the role of the type II CBASS system in regulating cell viability was assessed. The knockout strain was confirmed by targeting the LAMP-CRISPR-Cas13a technique specifically to the cyclase gene, and the same protocol was also used to detect the gene of the main cyclase in these type I CBASS systems, i.e. APECO1. The study findings demonstrate the regulatory role of the QS network in anti-phage defence systems.

Finally, this is the first work which development an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 hours) in optimizing phage therapy by detecting bacterial resistance mechanisms, by predicting the potential inefficacy of a therapeutic phage and thus improving patient prognosis.
Development of Learning Objectives for Non-Major Introductory Biology Using a Delphi Method
Authors: Brickman Peggy , Gormally Cara
Published: December 2024

Biology faculty have consensus-based guidelines based on Vision and Change principles about what to teach introductory biology majors. In contrast, faculty have not reached a consensus concerning the learning goals for introductory non-majors courses. Yet, more than 8 out of 10 undergraduates are not science majors. The goal of this study was to develop and evaluate learning objectives for non-majors introductory biology courses. We performed a modified-Delphi study of learning objectives (LOs) for non-majors biology. We engaged a total of 38 biology faculty experts from institutions across the US in three iterative rounds to identify, rate, discuss, and re-rate >300 LOs for non-majors biology courses. Faculty provided feedback to determine whether the LOs are critical for students to learn and if the LOs encompass what students need to learn about this issue, as well as if anything is missing. As a result of expert evaluation, 60.7% of LOs (164) were deemed critical. Experts also suggested 22 additional new LOs.
Scoring information integration with statistical quality control enhanced cross-run analysis of data-independent acquisition proteomics data
Authors: Gao Mingxuan , Gupta Shubham , Yang Wenxian , Yu Rongshan , Röst Hannes L.
Published: December 2024

The peptide-centric strategy is widely applied in data-independent acquisition (DIA) proteomics to analyze multiplexed MS2 spectra. However, current software tools often rely on single-run data for peptide peak identification, leading to inconsistent quantification across heterogeneous datasets. Match-between-runs (MBR) algorithms address this by aligning peaks or elution profiles across runs post-analysis but they are oftenad-hocand lack statistical frameworks for controlling peak quality, resulting in false positives and reduced quantitative reproducibility. Here we present DreamDIAlignR, a cross-run peptide-centric tool that integrates peptide elution behavior across runs with a deep learning peak identifier and signal alignment algorithm for consistent peak picking and FDR-controlled scoring. DreamDIAlignR outperformed state-of-the-art MBR methods, identifying up to 25.6% more quantitatively changing proteins on a benchmark dataset and 38.5% more on a cancer dataset. Additionally, DreamDIAlignR establishes an improved methodology for performing MBR compatible with existing DIA analysis tools, thereby enhancing the overall quality of DIA analysis.
Sex differences in frailty and the impact of frailty on blood pressure control in older adults with hypertension: a multi-center observational study in Vietnam
Authors: Nguyen Tan Van , Nguyen Vien Thi , Wong Wei Jin , Amsalu Erkihun , Ngo Trinh Kim Thi , Woodward Mark , Nguyen Tu Ngoc
Published: December 2024

Background

Frailty is common in older adults with hypertension and can affect blood pressure (BP) control. Sex differences related to frailty and cardiovascular physiology may contribute to the effective treatment of hypertension.

Aim

to examine the prevalence of frailty in older adults with hypertension and its association with uncontrolled BP, with a particular focus on differences by sex.

Methods

This study was conducted at the outpatient clinics of two major hospitals in Vietnam from June 2023 to June 2024. Frailty was defined by a Clinical Frailty Scale of ≥4. Uncontrolled BP was defined as systolic BP ≥140 mmHg or diastolic BP ≥90 mmHg, averaged over recordings in the last 6 months. Multivariable logistic regression was applied to identify the association between frailty and uncontrolled BP. The odds ratios (ORs) for uncontrolled BP of each risk factor were estimated by sex, with interaction terms fitted between each risk factor and sex to obtain the women-to-men ratio of ORs (ROR).

Results

There were 1038 participants (326 women, 712 men). They had a mean age of 73.3 (SD7.4). The prevalence of frailty was 28.6% in all participants, higher in women (35.3%) than men (25.6%), p=0.001. The overall rate of uncontrolled BP was 26.7%. In women, the frail had a significantly higher rate of uncontrolled BP (33.9%) compared to the non-frail (20.9%), but no significant differences among men (26.4% in the frail vs. 27.5% in the non-frail). The adjusted ORs of frailty on uncontrolled BP were 1.70 (1.00–2.90) in women, 0.84 (0.57–1.25) in men; women-to-men ROR 2.02 (1.04–3.92).

Conclusion

In older adults with hypertension, frailty was more common in women and was associated with an increased risk of having uncontrolled BP in women only. These findings highlight the need for sex-specific approaches in managing hypertension in older populations.
Evaluation of Large Language Models in Thailand’s National Medical Licensing Examination
Authors: Saowaprut Prut , Rodis Wabina Romen Samuel , Yang Junwei , Siriwat Lertboon
Published: December 2024

Advanced general-purpose Large Language Models (LLMs), including OpenAI’s Chat Generative Pre-trained Transformer (ChatGPT), Google’s Gemini and Anthropic’s Claude, have demonstrated capabilities in answering clinical questions, including those with image inputs. The Thai National Medical Licensing Examination (ThaiNLE) lacks publicly accessible specialist-confirmed study materials. This study aims to evaluate whether LLMs can accurately answer Step 1 of the ThaiNLE, a test similar to Step 1 of the United States Medical Licensing Examination (USMLE). We utilized a mock examination dataset comprising 300 multiple-choice questions, 10.2% of which included images. LLMs capable of processing both image and text data were used, namely GPT-4, Claude 3 Opus and Gemini 1.0 Pro. Five runs of each model were conducted through their application programming interface (API), with the performance assessed based on mean accuracy. Our findings indicate that all tested models surpassed the passing score, with the top performers achieving scores more than two standard deviations above the national average. Notably, the highest-scoring model achieved an accuracy of 88.9%. The models demonstrated robust performance across all topics, with consistent accuracy in both text-only and image-enhanced questions. However, while the LLMs showed strong proficiency in handling visual information, their performance on text-only questions was slightly superior. This study underscores the potential of LLMs in medical education, particularly in accurately interpreting and responding to a diverse array of exam questions.
Anthelmintic resistance against benzimidazoles and macrocyclic lactones in strongyle populations on cattle farms in northern Germany
Authors: Ehnert Paula , Krücken Jürgen , Fiedler Stefan , Horn Fabian , Helm Christina S. , Neubert Ann , Weiher Wiebke , Terhalle Werner , Steuber Stephan , Daher Ricarda , von Samson-Himmelstjerna Georg
Published: December 2024

Anthelmintic resistance (AR) in cattle gastrointestinal nematodes (GIN) is an increasing global concern, with low to moderate levels recently documented in Central Europe. This study reports on resistance against both macrocyclic lactones (MLs) and benzimidazoles (BZs), highlighting that AR is spreading. The Fecal Egg Count Reduction Test (FECRT) remains the primary tool for AR assessment, yet differing methodologies and recent guideline updates complicate resistance interpretation across studies. Statistical methods, such as Bayesian approaches used by eggCounts and bayescount, yield varying confidence intervals, further influencing results. Notably, the nemabiome analysis identifiedOstertagia ostertagiandCooperia oncophoraas predominant species in the region, though unexpected diversity among farms with additional GIN species occurring sometimes even at high frequency, suggests morphological analysis of coprocultures may underestimate species prevalence. Detecting AR against both drug classes on some farms underscores the urgency of implementing sustainable strategies, such as targeted selective treatment and combinations of anthelmintics with different mode of action, to prevent scenarios of multi-drug resistance observed elsewhere. Effective resistance management requires immediate discussions with veterinarians and stakeholders to steer toward informed, preventive measures in cattle farming.
QUANTIFYING ACYL CHAIN INTERDIGITATION IN SIMULATED BILAYERS VIA DIRECT TRANSBILAYER INTERACTIONS
Authors: Chaisson Emily H. , Heberle Frederick A. , Doktorova Milka
Published: December 2024

In a lipid bilayer, the interactions between lipid hydrocarbon chains from opposing leaflets can influence membrane properties. These interactions include the phenomenon of interdigitation, in which an acyl chain of one leaflet extends past the bilayer midplane and into the opposing leaflet. While static interdigitation is well understood in gel phase bilayers from X-ray diffraction measurements, much less is known about dynamic interdigitation in fluid phases. In this regard, atomistic molecular dynamics simulations can provide mechanistic information on interleaflet interactions that can be used to generate experimentally testable hypotheses. To address limitations of existing computational methodologies which provide results that are either indirect or averaged over time and space, here we introduce three novel ways of quantifying the extent of chain interdigitation. Our protocols include the analysis of instantaneous interactions at the level of individual carbon atoms, thus providing temporal and spatial resolution for a more nuanced picture of dynamic interdigitation. We compare the methods on bilayers composed of lipids with equal total number of carbon atoms but different mismatches between the sn-1 and sn-2 chain lengths. We find that these metrics, which use freely available software packages and are easy to implement, provide complementary details that help characterize various features of lipid-lipid contacts at the bilayer midplane. The new frameworks thus allow for a deeper look at fundamental molecular mechanisms underlying bilayer structure and dynamics, and present a valuable expansion of the membrane biophysics toolkit.
Test-retest reliability of TMS-evoked potentials over fMRI-based definitions of non-motor cortical targets
Authors: Sayalı Ceyda , Gogulski Juha , Granö Ida , Lioumis Pantelis , Barrett Frederick S.
Published: December 2024

Objective

This study assessed the test-retest reliability of TMS-evoked potentials (TEPs) across two cortical regions—dorsolateral prefrontal cortex (DLPFC), and angular gyrus— in comparison to motor cortex (M1), using individualized and literature-based targeting approaches. The study compared the reliability of single-pulse TMS, short-interval intracortical inhibition (SICI), and long-interval intracortical inhibition (LICI) protocols to evaluate TEP consistency in these regions.

Methods

Seventeen healthy participants underwent two TMS-EEG sessions spaced by at least one week, with targets for DLPFC and angular gyrus identified using resting-state functional connectivity (RS) and Neurosynth-based functional overlays. Motor cortex was targeted using resting motor threshold (RMT). Early TEPs were quantified as peak-to-peak amplitude, in dBμV. Test-retest reliability of early TEPs was calculated using the concordance correlation coefficient (CCC) for each region and protocol.

Results

M1 demonstrated the highest TEP reliability (CCCmean = 0.59), while DLPFC (CCCmean = 0.40) and angular gyrus (CCCmean = 0.45) showed lower reliability, particularly for anterior DLPFC targets. Neurosynth-based DLPFC targets exhibited slightly higher CCC values (mean CCC = 0.57) compared to RS-based targets (mean CCC = 0.30), but the difference was not statistically significant. No significant differences in reliability were found across single pulse and paired pulse protocols. Lateral targets, DLPFC and angular gyrus, showed lower reliability in comparison to motor cortex which might have been caused by muscle artifacts.

Conclusion

While individualized functional targeting methods provide advantages in engaging specific brain networks, their reliability for TEP measurements remains lower than the RMT-based approach for motor cortex. Future studies should integrate neuroimaging-based targeting with real-time TEP monitoring to enhance reliability in non-motor regions. This approach could enhance the precision of TMS-EEG protocols, especially for clinical applications targeting cortical regions like the DLPFC and angular gyrus.
Implicit modeling of the conformational landscape and sequence allows scoring and generation of stable proteins
Authors: Cho Yehlin , Dauparas Justas , Tsuboyama Kotaro , Rocklin Gabriel , Ovchinnikov Sergey
Published: December 2024

Generative protein modeling provides advanced tools for designing diverse protein sequences and structures. However, accurately modeling the conformational landscape and designing sequences—ensuring that the designed sequence folds into the target structure as its most stable structure—remains a critical challenge. In this study, we present a systematic analysis of jointly optimizingP(structure|sequence) andP(sequence|structure), which enables us to find optimal solutions for modeling the conformational landscape. We support this approach with experimental evidence that joint optimization is superior for (1) designing stable proteins using a joint model (TrROS (TrRosetta) and TrMRF) (2) achieving high accuracy in stability prediction when jointly modeling (half-masked ESMFold pLDDT+ ESM2 Pseudo-likelihood). We further investigate features of sequences generated from the joint model and find that they exhibit higher frequencies of hydrophilic interactions, which may help maintain both secondary structure registry and pairing.
Asymmetries in foveal vision
Authors: Jenks Samantha K. , Carrasco Marisa , Poletti Martina
Published: December 2024

Visual perception is characterized by known asymmetries in the visual field; human’s visual sensitivity is higher along the horizontal than the vertical meridian, and along the lower than the upper vertical meridian. These asymmetries decrease with decreasing eccentricity from the periphery to the center of gaze, suggesting that they may be absent in the 1-deg foveola, the retinal region used to explore scenes at high-resolution. Using high-precision eyetracking and gaze-contingent display, allowing for accurate control over the stimulated foveolar location despite the continuous eye motion at fixation, we investigated fine visual discrimination at different isoeccentric locations across the foveola and parafovea. Although the tested foveolar locations were only 0.3 deg away from the center of gaze, we show that, similar to more eccentric locations, humans are more sensitive to stimuli presented along the horizontal than the vertical meridian. Whereas the magnitude of this asymmetry is reduced in the foveola, the magnitude of the vertical meridian asymmetry is comparable but, interestingly, reversed: objects presented slightly above the center of gaze are more easily discerned than when presented at the same eccentricity below the center of gaze. Therefore, far from being uniform, as often assumed, foveolar vision is characterized by perceptual asymmetries. Further, these asymmetries differ not only in magnitude but also in direction compared to those present just ∼4deg away from the center of gaze, resulting in overall different foveal and extrafoveal perceptual fields.
Distinct Classes of Lamin-Associated Domains are Defined by Differential Patterns of Repressive Histone Methylation
Authors: Martin Caden J. , Nagarajan Prabakaran , Oser Elizabeth A. , Popova Liudmila V. , Parthun Mark R.
Published: December 2024

A large fraction of the genome interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in genome organization and gene regulation across development. Despite much work, LAD structure and regulation are not fully understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here we profile Lamin B1, HP1β, H3K9me3, H3K9me2, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into 3 groups, each enriched in a unique set of histone modifications and genomic features. Each group is defined by a different heterochromatin modification (H3K9me3, H3K9me2, or H3K27me3), suggesting that all three of these marks play important roles in regulation of LAD chromatin and potentially of lamina association. We also discover unique features of LAD borders, including a LAD border-specific enrichment of H3K14ac. These results reveal important distinctions between LADs and highlight the rich diversity and complexity in LAD structure and regulatory mechanisms.
An Agent-Based Model of Metabolic Signaling Oscillations inBacillus subtilisBiofilms
Authors: Mulder Obadiah J. , Kostman Maya Peters , Almodaimegh Abdulrahmen , Edge Michael D. , Larkin Joseph W.
Published: December 2024

Microbes of nearly every species can form biofilms, communities of cells bound together by a self-produced matrix. It is not understood how variation at the cellular level impacts putatively beneficial, colony-level behaviors, such as cell-to-cell signaling. Here we investigate this problem with an agent-based computational model of metabolically driven electrochemical signaling inBacillus subtilisbiofilms. In this process, glutamate-starved interior cells release potassium, triggering a depolarizing wave that spreads to exterior cells and limits their glutamate uptake. More nutrients diffuse to the interior, temporarily reducing glutamate stress and leading to oscillations. In our model, each cell has a membrane potential coupled to metabolism. As a simulated biofilm grows, collective membrane potential oscillations arise spontaneously as cells deplete nutrients and trigger potassium release, reproducing experimental observations. We further validate our model by comparing spatial signaling patterns and cellular signaling rates with those observed experimentally. By oscillating external glutamate and potassium, we find that biofilms synchronize to external potassium more strongly than to glutamate, providing a potential mechanism for previously observed biofilm synchronization. By tracking cellular glutamate concentrations, we find that oscillations evenly distribute nutrients in space: non-oscillating biofilms have an external layer of well-fed cells surrounding a starved core, whereas oscillating biofilms exhibit a relatively uniform distribution of glutamate. Our work shows the potential of agent-based models to connect cellular properties to collective phenomena and facilitates studies of how inheritance of cellular traits can affect the evolution of group behaviors.
SMAD4 Mutation Drives Gut Microbiome Shifts Toward Tumor Progression in Colorectal Cancer
Authors: Gates Travis J , Wangmo Dechen , Boorsma Bergerud Kyra M , Keel Bridget , Staley Christopher , Subramanian Subbaya
Published: December 2024

Colorectal cancer (CRC) progression is driven by a series of sequential mutations in key driver genes, yet the factors underpinning tumor advancement and metastasis remain incompletely understood. Mutations in TP53 and SMAD4, in particular, are associated with poor treatment response and enhanced CRC pathogenesis. Although gut microbiome dysbiosis is implicated in CRC initiation and inflammation, the interactions between the microbiome and specific CRC driver mutations, especially those promoting metastasis, are poorly defined. In this study, we used triple mutant (Apc, Kras, Tp53; AKP) and quadruple mutant (Apc, Kras, Tp53, Smad4; AKPS) organoid-based orthotopic mouse models of CRC to examine the impact of SMAD4 mutation on tumor progression, metastasis, and microbiome composition. AKP and AKPS organoids were endoscopically implanted into the colons of individually housed C57BL/6 mice, and fecal samples were collected weekly over an 8-week period. Our results reveal significant differences in metastatic potential and microbial community dynamics between the two tumor models. AKPS tumors exhibited metastasis to the lymph nodes, liver, and lungs, whereas AKP tumors remained confined to the colon. Longitudinal microbiome analysis showed shifts in microbial composition within each tumor model. Both AKP and AKPS models demonstrated enrichment ofFaecalibaculumand a decrease inDubosiellaover time; however, additional shifts were observed with distinct taxa associated with late-stage tumors in each group. Notably, the AKPS model exhibited higher relative abundances of pro-inflammatory taxa, includingTuricibacter, Romboutsia, and Akkermansia, suggesting that SMAD4 mutation promotes a more immunosuppressive and pro-metastatic microbiome profile. These findings underscore the role of SMAD4 in modulating the microbiome in a manner that favors CRC metastasis and suggests potential microbial targets for therapeutic intervention to slow CRC progression. This work provides new insights into the microbiome’s role in CRC mutagenesis and metastasis, highlighting the interplay between host genetics and gut microbiota in driving cancer aggressiveness.
A Vulnerable Subtype of Dopaminergic Neurons Drives Early Motor Deficits in Parkinson’s Disease
Authors: Fushiki Akira , Ng David , Lewis Zachary R. , Yadav Archana , Saraiva Tatiana , Hammond Luke A. , Wirblich Christoph , Tasic Bosiljka , Menon Vilas , da Silva Joaquim Alves , Costa Rui M.
Published: December 2024

In Parkinson’s disease, dopaminergic neurons (DANs) in the midbrain gradually degenerate, with ventral substantia nigra pars compacta (SNc) DANs exhibiting greater vulnerability.

However, it remains unclear whether specific molecular subtypes of ventral SNc DANs are more susceptible to degeneration in PD, and if they contribute to the early motor symptoms associated with the disease. We identified a subtype ofSox6+DANs,Anxa1+, which are selectively lost earlier than other DANs, and with a time course that aligns with the development of motor symptoms in MitoPark mice. We generated a knock-in Cre mouse line forAnxa1+DANs and showed differential anatomical inputs and outputs of this population. Further, we found that the inhibition of transmitter release inAnxa1+neurons led to bradykinesia and tremor. This study uncovers the existence of a selectively vulnerable subtype of DANs that is sufficient to drive early motor symptoms in Parkinson’s disease.
Dynamic Grouping of Ongoing Activity in V1 Hypercolumns
Authors: Zhang Rui , Wang Jiayu , Cai Xingya , Tang Rendong , Lu Haidong D.
Published: December 2024

Neurons’ spontaneous activity provides rich information about the brain. A single neuron’s activity has close relationships with the local network. In order to understand such relationships, we studied the spontaneous activity of thousands of neurons in macaque V1 and V2 with two-photon calcium imaging. In V1, the ongoing activity was dominated by global fluctuations in which the activity of majority of neurons were correlated. Neurons’ activity also relied on their relative locations within the local functional architectures, including ocular dominance, orientation, and color maps. Neurons with similar preferences dynamically grouped into co-activating ensembles and exhibited spatial patterns resembling the local functional maps. Different ensembles had different strengths and frequencies. This observation was consistent across all hypercolumn-sized V1 locations we examined. In V2, different imaging sites had different orientation and color features. However, the spontaneous activity in the sampled regions also correlated with the underlying functional architectures. These results indicate that functional architectures play an essential role in influencing neurons’ spontaneous activity, and can be explained by a network model that integrates diverse horizontal connections among similar functional domains.
EnsembleFlex: Protein Structure Ensemble Analysis Made Easy
Authors: Schneider Melanie , Marquez José Antonio , Leach Andrew R
Published: December 2024

EnsembleFlex is a novel tool designed to perform dual-scale flexibility analysis of protein structure ensembles, encompassing both backbone and side-chain dynamics. It integrates dedicated superposition methodologies, two dimension reduction techniques, customizable clustering, an automated ligand binding site analysis and analysis of conserved water molecules, enhancing the accuracy of ensemble flexibility analysis and visualisation. With a user-friendly, no-coding graphical interface as well as a code-based option, EnsembleFlex is accessible to a broad range of researchers. The tool complements experimental ensemble data analysis with predictive methods based on elastic network models, bridging the gap between experimental and computational approaches in protein flexibility analysis, and does so from a global backbone-based perspective, as well as from a focused side-chain and binding site-centred point of view. The need for reliable, streamlined, fast, and user-friendly tools for structural ensemble analysis is critical in today’s research environment, and EnsembleFlex addresses these needs efficiently, offering an accessible solution that integrates powerful analysis methods in a single package. Its wide applicability across various domains of molecular design underscores the importance of streamlined flexibility analysis in scientific research.
Testing various combinations of cryoprotective agents for human skin cryopreservation by vitrification method
Authors: Riabinin Andrei , Pankratova Maria , Rogovaya Olga , Vorotelyak Ekaterina , Vasiliev Andrey
Published: December 2024

Modern translational medicine, pharmacology and other fields require effective skin cryopreservation technology. Vitrification is promising technology for this aim. This rapid freezing technique minimizes hexagonal ice crystals formation, time of stress condition for cells in samples and dehydration both in the cytoplasm of cells and in the extracellular space. This study is aimed at finding the optimal combination of extracellular (sucrose, mannitol, polyethylene glycol and FBS) and intracellular (DMSO, glycerol, ethylene glycol) cryoprotective agents to achieve the highest viability and tissue structure preservation of skin samples after vitrification.
Xolography for Biomedical Applications: Dual-color Light-sheet Printing of Hydrogels with Local Control over Shape and Stiffness
Authors: Stoecker Lena , Cedillo-Servin Gerardo , König Niklas F. , Graaf Freek V. de , Jiménez Marcela García , Hofmann Sandra , Ito Keita , Wentzel Annelieke S. , Castilho Miguel
Published: December 2024

Abstract

Current challenges in tissue engineering include creation of extracellular environments that support and interact with cells using biochemical, mechanical, and structural cues. Spatial control over these cues is currently limited due to a lack of suitable fabrication techniques. This study introduces Xolography, an emerging dual-color light-sheet volumetric printing technology, to achieve control over structural and mechanical features for hydrogel-based photoresins at micro-to macroscale while printing within minutes. We propose a water-soluble photoswitch photoinitiator system and are the first to demonstrate Xolography with a library of naturally-derived, synthetic, and thermoresponsive hydrogels. Centimeter-scale, three-dimensional constructs with positive features of 20 µm and negative features of ∼ 100 µm are fabricated with control over mechanical properties (compressive moduli 0.2 kPa – 6.5 MPa). Notably, switching from binary to grayscaled light projection enables spatial control over stiffness (0.2 – 16 kPa). As a proof of concept, grayscaled Xolography is leveraged with thermoresponsive hydrogels to introduce reversible anisotropic shape changes beyond isometric shrinkage. We finally demonstrate Xolography of viable cell aggregates, laying the foundation for cell-laden printing of dynamic, cell-instructive environments with tunable structural and mechanical cues in a fast one-step process. Overall, these innovations unlock unique possibilities of Xolography across multiple biomedical applications.
Collapse of directed functional hierarchy under classical serotonergic psychedelics
Authors: Vohryzek Jakub , Kringelbach Morten L , Lopez-Sola Edmundo , Garcia Guzman Elvira , Timmermann Christopher , Roseman Leor , Tagliazucchi Enzo , Ruffini Giulio , Carhart-Harris Robin , Deco Gustavo , Sanz Perl Yonatan
Published: December 2024

It has been proposed that psychedelics induce profound functional changes to the hierarchical organisation of the human brain. Yet the term hierarchy is currently not well defined in neuroscience. Here, we use a precise definition of hierarchy, grounded in the theory of thermodynamics, which allows the quantification of temporal asymmetry in the directionality of information flow. We quantified the changes to the directed functional hierarchy of the brain under three classical serotonergic psychedelics - psilocybin, LSD and DMT. We found that all three psychedelics induce a reduction of the directed functional hierarchy, such that they display lower levels of global and network temporal asymmetry and a contraction of the two main patterns of variation of temporal asymmetry. Crucially, our results imply that the brain's directed functional hierarchy is collapsed under psychedelics, interpreted as yielding a more flexible brain. This enhanced flexibility in brain organisation under psychedelics may underpin the altered cognition and behaviour observed during these states, and, possibly afterwards, be suggestive of therapeutic potential.
A critical role of FAK signaling in Rac1-driven melanoma cell resistance to MAPK pathway inhibition
Authors: Riordan Jesse D. , Nathanson Teagan A. , Varzavand Afshin , Hawkins Adeline A. , Peplinski Rebekah M. , Hannan Elizabeth C. , Bibeau Faith A. , Freesmeier Nathaniel J. , Jilek Madison C. , Coma Silvia , Pachter Jonathan A. , Dupuy Adam J. , Stipp Christopher S.
Published: December 2024

The Rac1 P29S hotspot mutation in cutaneous melanoma is associated with resistance to MAPK pathway inhibitors (MAPKi) and worse clinical outcomes. Moreover, activation of Rac1 guanine exchange factors (GEFs) also promotes MAPKi-resistance, particularly in undifferentiated melanoma cells. Here we delineate mechanisms of Rac1-driven MAPKi-resistance and identify strategies to inhibit the growth of this class of cutaneous melanomas. We find that Rac1-driven melanomas manifest pleiotropic resistance mechanisms including (i) reduced dependence on BRAF/MEK, (ii) activation of alternative MAPK pathways utilizing Jun kinase and p38 MAP kinase, and (iii) a partial reliance on YAP/TAZ signaling. Importantly, although Rac1-driven melanoma cells display reduced dependence on BRAF/MEK, they are not completely ERK-independent. Additionally, the presence of activated Rac1 appears to create a dependency on focal adhesion kinase (FAK) signaling in undifferentiated melanoma cells. Therefore, despite the pleiotropic mechanisms of Rac1-driven MAPKi resistance, we find that combined inhibition of RAF and MEK with the RAF/MEK clamp auvotometinib and FAK with the FAK inhibitor defactinib is a promising approach for suppressing the growth of Rac1-driven melanoma cells. Thus, the avutometinib plus defactinib combination, which is currently being investigated for brain metastatic cutaneous melanoma may also have utility against Rac1-driven MAPKi-resistance in heavily pre-treated, advanced disease.
Temperature-based MHC class-I multimer peptide exchange for human HLA-A, B and C
Authors: Pothast Cilia R. , Derksen Ian , van der Plas – van Duijn Anneloes , el Hebieshy Angela , Huisman Wesley , Franken Kees L.M.C. , Neefjes Jacques , Luimstra Jolien J. , Griffioen Marieke , Kester Michel , Vermeer Maarten H. , Heemskerk Mirjam H.M. , Scheeren Ferenc A.
Published: December 2024

T cell recognition of specific antigens presented by major histocompatibility complexes class-I (MHC-I) can play an important role during immune responses against pathogens and cancer cells. Detection of T cell immunity is based on assessing the presence of antigen-specific cytotoxic CD8+ T cells using MHC class-I (MHC-I) multimer technology. Previously we have designed conditional peptides for HLA-A*02:01, H-2Kband HLA-E that form stable peptide-MHC-I-complexes at low temperatures and dissociate when exposed to a defined elevated temperature. The resulting conditional MHC-I complex can easily and without additional handling be exchanged with a peptide of interest, allowing to exchange peptides in a ready-to-use multimer and a high-throughput manner. Here we present data that this peptide-exchange technology is a general applicable, ready-to-use and fast approach to load many different peptides in MHC-I multimers for alleles of the HLA-A, HLA-B and HLA-C loci. We describe the development of conditional peptides for HLA-A*03:01, HLA-A*11:01, HLA-B*07:02 and HLA-C*07:02 that only form stable peptide-MHC-I complexes at low temperatures, allowing peptide exchange at higher defined temperature. We document the ease and flexibility of this technology by monitoring CD8+ T cell responses to virus-specific peptide-MHC complexes in patients.

Graphical abstract

Highlights

T cell immunity relies on antigen-specific CD8+ T cells recognizing peptide MHC-I complexes.

Establishing temperature-based peptide exchange across multiple HLA alleles, resulting in a robust, easy, and fast system to generate peptide MHC-I complexes.

Temperature-based MHC class-I multimer demonstrate applicability across major MHC-I gene families for monitoring CD8+ T cell responses.

Easy high-throughput peptide exchange potential, enhancing clinical utility of MHC multimer technology.
Adaptive Optics Rolling Slit Ophthalmoscope: Combining cellular-resolution, high-speed and large field-of-view in a multimodal retinal imager
Authors: Krafft Léa , Senee Pierre , Brad Ana Alexandra , Atlan Michael , Paques Michel , Thouvenin Olivier , Mecê Pedro , Meimon Serge
Published: December 2024

Label-free optical imaging systems capable of monitoring dynamic biological processes over a large field-of-view (FOV) are essential for advancing our understanding of retinal and neurovascular health. However, existing imaging modalities often involve trade-offs between spatial resolution, contrast, FOV, and frame rate. In this study, we present the Adaptive Optics Rolling Slit Ophthalmoscope (AO-RSO), a novel imaging system that integrates the high-speed, wide-FOV capabilities of camera-based systems with the enhanced contrast and multimodal functionality of point-scanning techniques—without compromising resolution or speed. The AO-RSO utilizes line illumination synchronized with the rolling shutter of a high-speed sCMOS camera, enabling precise and dynamic spatial selection of detected photons: back-scattered photons for near-confocal bright-field imaging and forward-scattered photons for phase-contrast imaging of translucent retinal features. This system successfully visualizes diverse retinal structures, including cone and rod photoreceptors, nerve fiber bundles, red blood cells, vessel walls, and ganglion cells, across a wide retinal area (4.5°× 2.5°). With a large FOV and frame rates up to 200 Hz, the AO-RSO enables the quantification of blood flow, tracking of red blood cells within hundreds of capillaries, and evaluation of thousands of photoreceptors in the living human retina. This capability opens new opportunities for functional neuronal imaging, neurovascular coupling studies, and the early detection of retinal and neurodegenerative diseases.