bluuebunny/crossref_metadata_2025 huggingface dataset:
CDNF rescues human iPSCs-derived dopamine neurons through direct binding to unfolded protein response sensors PERK and IRE1α
Authors: Kovaleva Vera , Shpironok Olesya , Yu Li-Ying , Ivanova Larisa , Fudo Satoshi , Happonen Lotta J. , Toots Urve , Ustav Mart , Kajander Tommi , Karelson Mati , Saarma Mart
Published: January 2025

Cerebral dopamine neurotrophic factor (CDNF) is an unconventional trophic factor that protects dopamine neurons in cellular and animal models of Parkinson’s disease (PD). CDNF was safe and well tolerated in phase 1 clinical trials for PD treatment, and currently, its peptide analogue is under investigation in phase 1 clinical trials for PD. Despite prominent neuroprotective and neurorestorative activity, the receptors and exact mechanism of CDNF functioning have been obscure. Intracellularly acting CDNF exerts cytoprotection by attenuating endoplasmic reticulum (ER) stress and unfolded protein response (UPR). We demonstrated that this activity occurs through the direct binding of CDNF to ER transmembrane UPR sensors PERK and IRE1α for purified proteins and in cells. We identified CDNF mutants deficient for binding to UPR sensors. CDNF binding to PERK and IRE1α appeared to be crucial for the survival of mouse dopamine neurons in culture. Importantly for clinical translation, CDNF rescues human induced pluripotent stem cell-derived dopamine neurons and promotes their regeneration. CDNF binding to UPR sensors alleviated terminal UPR and promoted neurite outgrowth of human dopamine neurons through direct binding to PERK and IRE1α. CDNF binding to BiP was dispensable for the neuroprotective and neurorestorative activity of CDNF. Therefore, CDNF, or small molecules mimicking its binding to UPR sensors and acting selectively on dopamine neurons with activated UPR, are promising drug candidates for PD treatment.
Optimization-based dietary recommendations for healthy eating
Authors: Wang Xu-Wen , Weiss Scott T. , Hu Frank B. , Liu Yang-Yu
Published: January 2025

Various diet scores have been developed to assess compliance with dietary guidelines. Yet, enhancing those diet scores is very challenging. Here, we tackle this issue by formalizing an optimization problem and solving it with simulated annealing. Our optimization-based dietary recommendation (ODR) approach, evaluated using Diet-Microbiome Association study data, provides efficient and reasonable recommendations for different diet scores. ODR has the potential to enhance nutritional counseling and promote dietary adherence for healthy eating.
Evidence for systematic - yet task- and motor-contingent - rhythmicity of auditory perceptual judgements
Authors: Fabio Cécile , Kayser Christoph
Published: January 2025

Numerous studies advocate for a rhythmic mode of perception; however, the evidence in the context of auditory perception remains inconsistent. We propose that the divergent conclusions drawn from previous work stem from conceptual and methodological issues. These include ambiguous assumptions regarding the origin of perceptual rhythmicity, variations in listening tasks and attentional demands, differing analytical approaches, and the reliance on fixed participant samples for statistical testing. To systematically address these points, we conducted a series of experiments in which human participants performed auditory tasks involving monaural target sounds presented against binaural white noise backgrounds, while also recording eye movements. These experiments varied in whether stimuli were presented randomly or required motor initialization by the participant, the necessity of memory across trials and the manipulation of attentional demands across modalities. Our findings challenge the notion of universal rhythmicity in hearing, but support the existence of paradigm- and ear-specific fluctuations in perceptual sensitivity and response bias that emerge at multiple frequencies. Notably, the rhythmicity for sounds in the left and right ears appears to be largely independent among participants, and the strength of rhythmicity in behavioural data is linked to oculomotor activity and attentional requirements of the task. Overall, these results resolve conflicting conclusions drawn in previous work and provide specific avenues for further studies into the rhythmicity of auditory perception.
GlioME: A Novel Organoid Model Retaining the Glioma Mi-croenvironment for Personalized Drug Screening and Thera-peutic Evaluation
Authors: Zheng Chengjun , Chen Qiaodong , Wang Peng , Zhang Delong , Fang Zheng , Feng Yutong , Chen Jie , Chen Jiahong , Fu Yiwen , Yang Bao , Zhao Qian , Sun Fei , Zhang Ying , Jiang Tao , Zheng Lemin , Bao Zhaoshi
Published: January 2025

Glioma is an aggressive brain tumor with a poor prognosis. Establishing an in vitro culture model that closely replicates the cellular composition and microenvironment of the original tumor has been challenging, limiting its clinical applications. Here, we present a novel approach to generate glioma organoids with a microenvironment (GlioME) from patient-derived glioma tissue. These organoids maintain the genetic and epigenetic characteristics of the pri-mary tumor and preserve cell-to-cell interactions within the tumor microenvironment, including resident immune cells. Bulk RNA sequencing, whole exome sequencing, and DNA methylation analysis were used to confirm the molecular similarities between the organoids and primary glioma tissues. Immunofluorescence and flow cytometry were used to assess immune cell viability, comparing GlioME with floating glioma organoids. GlioME exhibited high responsiveness to chemotherapy and targeted therapy, demonstrating its potential for therapeutic screening applications. Notably, GlioME accurately predicted patient response to the recently approved MET inhibitor, vebreltinib. Thus, this organoid model provides a reliable in vitro platform for glioma microenvironment-related research and clinical drug screening.
In vitrodisintegration of lozenge in oral cavity
Authors: Pham Quoc Dat , Edman Martin , Lindell Katarina , Wahlgren Marie
Published: January 2025

The aim of this study is to develop a newin vitrodisintegration method for lozenges in the oral cavity (OC) by mimicking physiologically relevant conditions in the OC including saliva flow rate and suction. Disintegration of solid-state dosage forms in the OC can be employed for local absorption in the OC or for delivering to the succeeding parts of the gastrointestinal tract. Understanding the disintegration is important before gaining insight into dissolution and absorption. Here abrasion force and rate exerted on the lozenge during the disintegration are controlled by a texture analyser. We showed that a higher flow rate and more frequent abrasion can lead to a faster disintegration, while variation of the compression force within a range in this study does not affect the disintegration statistically. The results are relevant to different types of consumers with variation in saliva production, for example, people with salivary dysfunction including elderly people. It is also important to consider these effects when formulating flavor and taste of lozenge that can affect consumer perception and consequently suction force and rate or saliva production. We could also observe disintegrated but not dissolved parts of the lozenge by using this apparatus, demonstrating the importance of the correlation between disintegration and dissolution when considering drug absorption in the OC to overcome the challenges of drug clearance from the OC by swallowing.
Instantaneous Frequency: A New Functional Biomarker for Dynamic Brain Causal Networks
Authors: Tang Haoteng , Dai Siyuan , Guo Lei , Gu Pengfei , Liu Guodong , Leow Alex D. , Thompson Paul M. , Huang Heng , Zhan Liang ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2025

This study introduces instantaneous frequency (IF) analysis as a novel method for characterizing dynamic brain causal networks from fMRI blood-oxygen-level-dependent (BOLD) signals. Effective connectivity, estimated using dynamic causal modeling (DCM), is analyzed to derive IF sequences, with the average IF across brain regions serving as a potential biomarker for global network oscillatory behavior. Analysis of data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), Open Access Series of Imaging Studies (OASIS), and Human Connectome Project (HCP) demonstrates the method’s efficacy in distinguishing between clinical and demographic groups, such as cognitive decline stages, sex differences, and sleep quality levels. Statistical analyses reveal significant group differences in IF metrics, highlighting its potential as a sensitive indicator for early diagnosis and monitoring of neurodegenerative and cognitive conditions.

Graphical Abstract

Highlights

The study introduces instantaneous frequency (IF) as a novel biomarker derived from dynamic brain effective connectivity, capturing temporal fluctuations in brain networks.

The proposed IF biomarker effectively differentiates between various clinical stages, such as Mild Cognitive Impairment (MCI) and Alzheimer’s Disease (AD), and demographic factors, including sex and sleep quality.

The robustness and clinical relevance of the IF biomarker are validated using three independent datasets: ADNI, OASIS, and HCP, demonstrating its potential in cognitive and neurological research.
Accurate calling of low-frequency somatic mutations by sample-specific modeling of error rates
Authors: Lin Yixin , Oroperv Carmen , Porsgård Peter Sørud , Frydendahl Boll Johansen Amanda , Rasmussen Mads Heilskov , Bataillon Thomas , Schierup Mikkel Heide , Andersen Claus Lindbjerg , Almstrup Kristian , Besenbacher Søren
Published: January 2025

Calling rare somatic variants from NGS data is more challenging than calling inherited variants, especially if the somatic variant is only present in a small fraction of the cells in the sequenced biopsy. In this case, having a good estimate of the error rate of a specific base in a particular read becomes essential. In paired-end sequencing, where some DNA fragments are shorter than twice the read length, the overlapping regions of the read pairs are an ideal resource for training models to discern context-dependent base error rates, as any discordant bases in the overlaps must be caused by a sequencing error or an alignment error. We have created a new tool named BBQ (an acronym for Better Base Quality) that uses overlapping reads to estimate the error rate conditional on the mutation type, sequence context, and base quality. We also estimate how much the error rate of concordant bases in overlapping reads is decreased compared to bases in non-overlapping reads. Results show that overlapping reads can remove sequencing errors induced by DNA damage and that the increased quality of overlapping reads differs between samples and mutation types, reflecting different damage patterns between samples. We use the error models to call rare somatic variants. Sequencing data from a testis biopsy and a cell-free DNA sample serve as a proof-of-concept for rare germ cell mutation calling and for detecting rare cancer mutations. We find that using the sample-specific error models of BBQ allows us to call rare somatic variants with fewer false positives than existing tools such as Mutect2 and Strelka2.
CSF1R-CAR T cells induce CSF1R signalling and promote cancer cell growth
Authors: Callahan Aurora , Zhang Xinyan , Wang Amber , Mojumdar Aisharja , Zeng Longhui , Su Xiaolei , Salomon Arthur R.
Published: January 2025

Chimeric antigen receptor (CAR) T cells have transformed the landscape of cancer therapy and demonstrate unprecedented success in treating relapsed/refractory blood cancers. The mechanism underlaying the interactions and responses of CAR T cells and their targets remain incompletely understood. Previous studies focus on the activation of CAR T cells and attempt to optimise CAR design to increase efficacy, meanwhile ignoring tumours and their responses to CAR ligation. Here, we evaluate the signalling capacity of a second generation CSF1-tageted CSF1R CAR compared with a scFv-targeted CD19-CAR using a SILAC co- culture approach coupled with phosphotyrosine (pY) enrichment and LC-MS/MS. We show that ligation of CSF1R-expressing THP1 cells with CSF1R-CAR T cells induces CSF1R-like signalling in THP1 cells, whereas no target cell signalling response is observed after CD19- CAR/Raji B cell ligation. Using small molecule inhibitors of Lck, actin polymerisation, and CSF1R, we find that CAR-induced CSF1R signalling in THP1 cells depends exclusively on CSF1R kinase activity with no participation from T cell activation. Consistently, CSF1R- CAR T cells promote THP1 growth at low effector-to-target (E:T) ratios but prevent THP1 growth at high E:T ratios. Our data provide evidence for an unintended consequence of CARs; CAR-induced signalling in cancer cells. These data may have broad implications for the choice of CAR antigen for optimal clinical efficacy.

One Sentence Summary:CSF1R-CAR activates intracellular signalling cascades in THP1 cells, which promote THP1 cell growth.
Cardiovascular autonomic dysfunction precedes cardiovascular disease and all-cause mortality: 11-year follow-up of the ADDITION-PRO study
Authors: Schaarup Jonas R. , Bjerg Lasse , Hansen Christian S. , Grove Erik L. , Andersen Signe T. , Vistisen Dorte , Brage Søren , Sandbæk Annelli , Witte Daniel R.
Published: January 2025

Background

Cardiovascular autonomic dysfunction remains a silent complication in people at high risk of diabetes. We aim to determine the impact of week-long heart rate variability (HRV) on the risk of cardiovascular events and mortality in this population.

Methods

Week-long HRV and mean heart rate (mHR) were measured in 1,627 participants from the ADDITION-PRO study between 2009-2011. As measurement for HRV, we calculated a proxy for standard deviation of normal heartbeat (SDNN) both weekly, daily and hourly. Data on cardiovascular events (CVD) and all-cause mortality were obtained from Danish patient registers until 2021. We fitted poisson regression to determine incidence rate ratios (IRR) for major adverse cardiovascular events (MACE) (myocardial infarction, stroke, cardiovascular death), heart failure, and all-cause mortality.

Results

Mean (SD) age was 66 years (7), and 47 % were women. The population had a mean (SD) week-long SDNN of 139.0 (32.3) ms. Week-long HRV index SDNN showed an IRR of 0.82 (CI: 0.69; 0.97), 0.76 (CI: 0.58; 0.99), and 0.79 (CI: 0.66; 0.94) per SD for MACE, heart failure, and all-cause mortality, respectively. The risk for MACE, heart failure, and all-cause mortality was higher at SDNN values below 120ms. SDNN measurements taken from 6:00-7:00 AM showed the strongest association with the risk of MACE. Lower SDNN was consistently associated with higher all-cause mortality risk across all hours of the day. Adjustment for concurrent physical acceleration and heart rate did not materially change the magnitude of these associations. Night-time heart rate was associated with a higher risk of MACE, heart failure and all-cause mortality.

Conclusion

Cardiovascular autonomic dysfunction, measured by week-long HRV, is associated with higher risk of CVD, heart failure and all-cause mortality. Certain time frames of the day for HRV and heart rate under free-living conditions showed higher risk of CVD. Hence, long-term HRV and the diurnal response are linked with CVD risk among people with high risk of diabetes. Studies exploring the benefit of HRV modifications in CVD prevention are warranted.
Associations between the mid-adolescent external exposome and proteomic biomarkers of mental health
Authors: Wang Zhiyang , Drouard Gabin , Afonin Aleksei , Botella Núria , Peuters Carmen , Piironen Aino-Kaisa , Whipp Alyce. M. , Cheval Boris , Šulc Libor , Heinonen-Guzejev Marja , Foraster Maria , Gulliver John , Selander Jenny , Dadvand Payam , Júlvez Jordi , van Kamp Irene , Kanninen Katja M. , Kaprio Jaakko ,   Equal-Life Scientific Team
Published: January 2025

The exposome, encompassing all external and internal environmental factors, provides a comprehensive understanding of the complex etiology of mental health. This study investigated the relationship between the external exposome during mid-adolescence and plasma proteomic biomarkers of mental health in 935 participants from the FinnTwin12 (Finland) and WALNUTs (Spain) cohorts. The mid-adolescent external exposome included 60 exposures. Biomarkers included 26 plasma proteins (mean age 22) for FinnTwin12 and 31 (mean age 13) for WALNUTs. The exposome-wide proteome-wide analysis revealed seven exposures (related to lifestyle, indoor environmental quality, natural environment, and family environment) linked to six proteins. Greenspace-related exposures were associated with proteins in both cohorts. However, these exposures showed no direct association with concurrent measures: the psychopathology factor or depressive symptoms. Twin analyses indicated genetic influences in some covariations between exposures and proteins. These findings provide evidence for mid-adolescents about the association between external environments and proteomic biomarkers of mental health.
Prevalence and factors associated with undernutrition among under-five children with sickle cell disease at Mulago National Referral Hospital, Uganda: A facility-based cross-sectional study
Authors: Namubamba Annet , Wamani Henry , Namaganda Agnes , Namagala Umusalima , Cheputyo Priscilla , Muramuzi Dan , Kamukama Saul
Published: January 2025

Background

Sickle cell disease (SCD) significantly contributes to under-five morbidity and mortality in sub-Saharan Africa and increases vulnerability to undernutrition. However, limited studies exist on the prevalence of undernutrition and its associated factors among children under five years with SCD in Uganda. We assessed the prevalence of undernutrition and its associated factors among children with SCD aged 6-59 months attending the sickle cell clinic at Mulago National Referral Hospital in Kampala, Uganda.

Methods

A facility-based cross-sectional study was conducted among 329 children aged 6-59 months. Data was collected in August 2022 using a structured questionnaire and analyzed using STATA version 14.0. Modified Poisson regression was used to identify the factors associated with undernutrition.

Results

The prevalence of undernutrition among children with SCD aged 6-59 months was 31.3% (n=103) 95% CI 26.5, 36.5; 27.4% (n=90) 95% CI 22.8, 32.5 were stunted, and 14.3% (n=47) 95% CI 10.8, 18.5 were underweight. Undernutrition among children with SCD was statistically significantly associated with children below 24 months but not breastfeeding (aPR=1.27; 95% CI: 1.09-1.48; P-0.002), not immunized against measles (aPR=1.31; 95% CI: 1.02-1.68; P-0.03), and child not taking hydroxyurea drug (aPR=1.5; 95% CI: 1.07-2.08; P-0.017).

Conclusion

Early weaning of children, not being immunized against measles, and the child not taking hydroxyurea drug were great contributors to undernutrition. There is a need for sensitization of the caretakers about these predictors, and integrating hydroxyurea treatment in the standard care package of management of SCD in Uganda.
Correlation study of serum 25 hydroxyvitamin D with peripheral neuropathy in type 2 diabetes
Authors: Chen Senzhen , Chen Jinfeng , Huang Mengting , Yan Yiling , Zheng Shujing , Chen Nuoqi
Published: January 2025

Objective

To investigate the correlation between serum 25 hydroxyvitamin D (25 (OH) D) and peripheral neuropathy of type 2 diabetes (Diabetic Peripheral N europathy, DPN) and its predictive value for DPN.

Methods

The subjects were divided into deficient group, insufficient group and normal group, and the relationship between 25(OH)D and DPN and the correlation of 25(OH)D and DPN with various indicators were analyzed.

Results

Comparing the DPN group with the NDPN group, 25(OH)D3(22.10±0.77ng/ml vs 24.45±0.66ng/ml), 25(OH)D total (23.12±0.74ng/ml vs 25.68±0.67ng/ml), BMI, RHR, TG, FT3, BUN between the two groups (P <0.05), 25(OH)D3,25(OH)D total, FT3, BMI, and RHR are risk factors for DPN. The ROC curve showed that the optimal cutoff for 25(OH)D3 predicting DPN in T2DM was 18.85ng/ml (AUC 0.76,95% CI 0.697-8.823) and the optimal cutoff for 25(OH)D predicting T2DM was 19.94ng/ml (AUC 0.765,95% CI 0.703-0.828).

Conclusion

25(OH)D can be used as a simple and effective screening method to predict the occurrence of DPN for total 25(OH)D<19.94ng/ml or 25(OH)D3<18.85ng/ml.
Brain age is longitudinally associated with sensorimotor impairment and mild cognitive impairment in subacute stroke
Authors: Marin-Pardo Octavio , Khan Mahir H. , Chakraborty Stuti , Borich Michael R. , Castillo Mayerly , Cole James H. , Cramer Steven C. , Donnelly Miranda R. , Fokas Emily E. , Fullmer Niko H. , Gumarang Jeanette R. , Hayes Leticia , Kim Hosung , Kumar Amisha , Marks Emily. A. , Rosario Emily R. , Schambra Heidi M. , Schweighofer Nicolas , Song Grace C. , Taga Myriam , Tavenner Bethany P. , Winstein Carolee , Liew Sook-Lei
Published: January 2025

BACKGROUND

Brain age, a proxy of overall brain health estimated from structural neuroimaging, has been associated with sensorimotor performance in chronic stroke. Similarly, post-stroke cognitive outcomes have been associated with accelerated brain aging. However, the relationships between brain age, sensorimotor, and cognitive outcomes in early subacute stroke (<3 months after onset) are less understood.

METHODS

In this work, we investigated associations between stroke survivors’ brain-predicted age difference (brain-PAD, quantified as a person’s brain age minus their chronological age) and longitudinal measurements of motor impairment (Fugl-Meyer Upper Extremity Assessment [FMUE]) and cognitive impairment (Montreal Cognitive Assessment [MoCA]) in subacute stroke. We used high-resolution T1-weighted MRIs from 44 participants at baseline and three months after stroke onset to investigate associations between brain-PAD, MoCA, and FMUE scores with robust linear mixed-effects regression models and mediation analyses.

RESULTS

We found negative associations between baseline brain-PAD and FMUE at baseline (β=-0.87, p=0.029) and three months (β=-0.87, p=0.011). Baseline brain-PAD was also negatively correlated with MoCA at three months (β=-0.13, p=0.015) but not at baseline (β=-0.11, p=0.141). Baseline brain-PAD was not associated with changes in FMUE (β=-0.01, p=0.930) or MoCA (β=-0.03, p=0.579). Finally, MoCA was not associated with FMUE at either time point, nor did it mediate the relationship between brain-PAD and FMUE.

CONCLUSION

Overall, we show that baseline brain age predicts both motor and cognitive outcomes at three months. However, motor and cognitive outcomes are not directly associated with one other. This suggests that brain age is representative of changes in multiple, distinct neurological pathways post-stroke. Further research with longer time intervals is needed to examine whether brain age also predicts chronic stroke outcomes.
Healthcare Unplugged: Disparities in Broadband Internet and Health Facility Access Among US Counties
Authors: Kohli Khushi , Wang Stephanie , Chou Cody , Jain Bhav , Shah Kavya M. , Kohli Mahi , Dee Edward Christopher , Palakodeti Sandeep
Published: January 2025

Despite telehealth expansion, access may remain lacking in high-burden communities with limited brick-and-mortar health facilities. We aimed to i) examine the relationship between broadband internet access and health facility availability and ii) explore disparities in broadband access. Using data from the 2017 National Neighborhood Data Archive, we obtained data on population density of outpatient care centers, diagnostic labs, and nursing/residential care facilities for 3133 US counties. Broadband access and sociodemographic data were obtained from the 2020 Mapping Broadband Health in America Platform and 2022 American Community Survey. Two-sample t-tests and multivariable linear regressions quantified the association between broadband internet access and health facility density, adjusting for sociodemographic covariates.

Counties with low broadband access had 12% fewer outpatient care centers and 48% fewer diagnostic labs than counties with high broadband access (all P < 0.001). A 1% increase in county population without broadband corresponds with a decrease of 0.0451 outpatient care centers, 0.0237 diagnostic labs, and 0.0886 nursing/residential care facilities per 100,000 people (all P < 0.001). Counties with limited in-person health facilities face reduced access to broadband internet, particularly in rural, low-income communities. Expanding broadband infrastructure and health services in these regions is essential.
Flavoproteins as native and genetically encoded spin probes forin cellESR spectroscopy
Authors: Chauviré Timothée , Chandrasekaran Siddarth , Dunleavy Robert , Freed Jack H. , Crane Brian R.
Published: January 2025

Flavin cofactors are attractive Electron Spin Resonance (ESR) probes for proteins because cellular reductants and light can generate their semiquinone states. We have used ESR spectroscopy to study the bacterial transmembrane aerotaxis receptor (Aer) in its nativeEscherichia colimembrane environment. Optimization of the spectroscopic (electronic relaxation times) and cell growth (isotopic labeling) conditions allowed for measurements of Aer with its partners - the histidine kinase (CheA) and the coupling protein (CheW) - in native signaling arrays. Continuous-wave ESR measurements at room temperature showed a rigid Aer flavin immobilized in the cofactor pocket and Q-band electron nuclear double resonance (ENDOR) measurements identified a predominant anionic semiquinone radical statein cell. Q-band four-pulse double electron-electron resonance (4P-DEER) measurements indicated a 4.1 nm distance between the two flavins of an Aer homodimer, consistent with previousin vitromeasurements, but also revealed additional separationsin cellindicative of chemoreceptor arrays, not previously observed for Aer. For general application, we further developed a genetically encoded Light-Oxygen and Voltage (LOV) domain for incorporation into target proteins as an ESR probe of structural propertiesin cell. This approach provides a framework to elucidate protein oligomeric states and conformations that are difficult to reproducein vitro.
Effects of recombination on multi-drug resistance evolution inPlasmodium falciparummalaria
Authors: Tran Kien Trung , Nguyen Tran Dang , Weissman Daniel B , Li Eric Zhewen , Mok Sachel , Small-Saunders Jennifer L , Bousema Teun , Zupko Robert J , Tran Thu Nguyen-Anh , Boni Maciej F
Published: January 2025

When multiple beneficial alleles are present in a population but not linked together in any one individual, there is no general evolutionary result that determines whether recombination will speed up or slow down the emergence and evolution of genotypes carrying multiple beneficial alleles. Translated to infectious disease control, this evolutionary uncertainty means that when multiple types of drug resistance are present we do not know whether recombination will act more strongly to (1) bring together single-resistant genotypes into multi-drug resistant (MDR) genotypes, or (2) break apart MDR genotypes into single-resistant genotypes. In this paper, we introduce a new version of an established and validated individual-based malaria transmission model where we have added individual mosquito bites, interrupted feeding by mosquitoes, 25 drug-resistance related loci, and individual recombination events of differentPlasmodium falciparumgenotypes inside the mosquito. Recombination amongP. falciparumgenotypes in this model occurs from two sources of variation, multi-clonal infections and interrupted feeding by mosquitoes, and we show that 80% to 97% of MDR recombinant falciparum genotypes are projected to occur from single uninterrupted bites on hosts with multi-clonal infections (for malaria prevalence > 5%). Increases in the model’s interrupted feeding rate slowly increase the number of recombination events occurring from interrupted feeds. A comparison of drug-resistance management strategies with this new model shows that, over a 15-year timeframe, triple artemisinin-combination therapies (ACT) strategies show the largest reductions in treatment failures and the longest delays until artemisinin resistance reaches a critical 1% threshold. Multiple first-line therapies (MFT) are second best under these criteria, and ACT cycling approaches are third best. MFT strategies generate a greater diversity of recombinant genotypes but fewer recombination events generating MDR and slower emergence of these recombinant MDR genotypes.
Chromatin accessibility classification of TAD boundaries discloses new architectural proteins
Authors: Jacome-Lopez Karina , Ledesma-Dominguez Leonardo , Esquivel-Lopez Ayerim , Perez-Molina Rosario , Penagos-Puig Andres , Aguilar-Lomas Amaury , Furlan-Magaril Mayra
Published: January 2025

3D genome organization is crucial to modulate gene expression. Topologically Associated Domains (TADs) isolate genes and their regulatory elements within the same topological neighborhood, avoiding crosstalk between regulatory elements. Perturbation of domain boundaries causes aberrant genomic contacts and gene expression misregulation. Architectural proteins such as CTCF and the cohesin complex are critical to form boundaries. However, we still lack a complete understanding of what makes a boundary more effective at insulating genomic contacts than others. To understand how domains are structured, we experimentally classified boundaries according to their chromatin accessibility as a proxy of protein occupancy in K562 human cells. We found that highly accessible boundaries are occupied by more proteins, are more robust contact insulators, have a more conserved CTCF DNA-binding motif and are more conserved across cell types in contrast to less accessible ones. By exploring the proteins enriched at boundaries with different accessibility, we found that CTCF and cohesin, together with REST, form a module, and ZFN316, together with EMSY, form another module, and both modules occupy boundaries very frequently. Finally, by using CRISPR-Cas9 mediated genetic edition of ZNF316 DNA-binding motif at a robust domain boundary, we demonstrate that ZNF316 can block chromatin contacts in the absence of CTCF. Our results emphasize the importance of protein combination and abundance to support boundary strength and propose ZNF316 as a novel architectural protein.
A direct interaction between the RNA-binding proteins Staufen and Tm1-I/C regulatesoskarmRNP composition and transport
Authors: Gaber Thomas , Grabowski Julia , Simon Bernd , Monecke Thomas , Williams Tobias , Roman Vera , Chao Jeffrey , Hennig Janosch , Ephrussi Anne , Niessing Dierk , Heber Simone
Published: January 2025

In theDrosophilafemale germline,oskarmessenger RNA is transported on microtubules from the nurse cells to the posterior pole of the oocyte, where it is translated. Transport ofoskartranscripts from the nurse cells into the oocyte requires dynein, while localization of the mRNAs within the oocyte to the posterior pole is dependent upon kinesin-1. Staufen, a dsRNA-binding protein, has been shown to bind theoskarmRNA transport complex in the oocyte and inactivate dynein; however, it remains unclear how kinesin is activated. Here, using surface plasmon resonance, nuclear magnetic resonance spectroscopy and RNA imaging within egg chambers, we demonstrate that Staufen directly interacts with Tm1, a non-canonical kinesin adaptor. This work provides a molecular explanation for the previously unclear role of Staufen inoskarmRNA localization.
Source to sensor coupling (SoSeC) as an effective tool to localize interacting sources from EEG and MEG data
Authors: Goeschl Florian , Kaziki Dionysia , Leicht Gregor , Engel Andreas K , Nolte Guido
Published: January 2025

A standard approach to estimate interacting sources from EEG or MEG data is to first calculate a coupling between all pairs of voxels on a predefined grid within the brain and then average or maximize this coupling matrix along each column or row. Depending on the chosen coupling measure and grid size this approach can be computationally very costly, in particular when a bias is supposed to be removed. We here suggest to replace this approach by a maximization of coupling between each source and the signal in sensor space. The idea is that any neuronal activity which can be estimated from recorded data must be present in sensor space in the first place. Using the imaginary part of coherency as coupling measure makes sure that we do not confuse this source to sensor coupling with a coupling of a source to itself. We found that this approach is hundreds of times faster than the conventional approach. Results for EEG resting state data indicate that the new approach has more statistical power than the conventional approach. The presentation of this specific method is augmented with a discussion of conceptual issues for various forms of vector beamformers and eLoreta.
LAG3 marks activated but hyporesponsive NK cells
Authors: Vasilyeva Valeria , Makinson Olivia , Chan Cynthia , Park Maria , O’Dwyer Colin , Ali Ayad , Ul Haq Khan Abrar , Tanese de Souza Christiano , Hasim Mohamed S. , Asif Sara , Kurdieh Reem , Abou-Hamad John , Yakubovich Edward , Hodgins Jonathan , Haddad Paul Al , Pietropaolo Giuseppe , Mazej Julija , Seo Hobin , Huang Quitong , Nersesian Sarah , Chay Damien , Jacquelot Nicolas , Cook David , Lee Seung-Hwan , Sciumè Giuseppe , Waggoner Stephen , Ardolino Michele , Marotel Marie
Published: January 2025

Natural Killer (NK) cells are critical for immunosurveillance yet become dysfunctional in contexts such as chronic stimulation by viral infections or cancer. This phenomenon is similar to T cell exhaustion but less well characterized, which limits therapeutic interventions. As shown for T cells, NK cells often display an increased expression of immune checkpoint proteins (ICP) following chronic stimulation, and ICP blockade therapies are currently being explored for several cancer types, which have remarkable patient benefits. Nevertheless, the nature of ICP expression in NK cells is still poorly documented. In this study, we aimed to identify the conditions that lead to and the phenotype of immune checkpoint LAG3 (Lymphocyte-activation gene 3) expressing NK cells. Using various experimental models, we found that LAG3 is expressed by murine NK cells upon activation in different contexts, including in response to cancer and acute viral infections. LAG3 marks a subset of immature, proliferating and activated cells, which, despite activation, have a reduced capacity to respond to a broad range of stimuli. Further characterization also revealed that LAG3+ NK cells exhibit a transcriptional signature similar to that of exhausted CD8+ T cells. Taken together, our results support the use of LAG3 as a marker of dysfunctional NK cells across diverse chronic and acute inflammatory conditions.
Host and rabies virus gene expression is shaped by human brain cell type and reveals a preexisting pro-viral transcriptional state in astrocytes
Authors: Feige Lena , Young Karl , Cerapio Juan Pablo , Kozaki Tatsuya , Kergoat Lauriane , Libri Valentina , Ginhoux Florent , Hasan Milena , Ameur Lamya Ben , Chin Gregory , Goode Zach , Bourhy Hervé , Saunders Arpiar
Published: January 2025

Rabies virus (RABV) proteins play dual roles during the infection of complex neural tissue, the generation and spread of new virions and the active inhibition of cellular innate immune pathways, both contributing to rabies’ lethality. While spatially-distinct RABV protein residues specializing in virus-centric and immune-inhibitory functions have been identified, how these dual functions interact to shape infection outcomes across diverse types of host brain cells is unknown. To “unmask” and study how innate immune inhibition affects the transcriptional regulation of the human and viral genome with cellular resolution, we performed single-cell RNA sequencing of co-cultured human brain cell types, comparing infection dynamics of a wild-type RABV isolate virus to a mutant virus in which six critical point mutations in the phosphoprotein (P) and matrix (M) RABV proteins selectively neuter antagonism of interferon- and NF-κB- dependent cellular responses. Our analysis reveals that RABV gene expression is shaped by host cell type and that wild-type RABV infection induces small-scale, cell-type conserved transcriptional programs that may support infection by hijacking transcriptional feedback systems that control pro-viral host cell factors while minimizing anti-viral responses. In contrast to accepted models, disinhibited innate immune signaling increases RABV transcriptional output across infected cell types. Most strikingly, we discovered a subpopulation of astrocytes that supports an average of 6-fold higher viral mRNA expression through a massive host cell transcriptional change involving ∼38% of astrocyte expressed genes. Our analysis suggests that these astrocytes we term “pro-viral” are a rare subtype present in the human brain and are primed to play a protective role during viral infection in concert with interferon-sensitive microglia recalcitrant to infection.
An in-cell approach to evaluate E3 ligases for use in targeted protein degradation
Authors: Zheng Yunan , Singh Anamika , Niu Zeqi , Marin Violeta , Young Jonathon , Richardson Paul , Hemshorn Marcus L. , Cooley Richard B. , Karplus P. Andrew , Warder Scott , Vasudevan Anil , Reitsma Justin M. , Mehl Ryan A.
Published: January 2025

One of the major challenges in evaluating the suitability of potential ∼700 E3 ligases for target protein degradation (TPD) is the lack of binders specific to each E3 ligase. Here we apply genetic code expansion (GCE) to encode a tetrazine-containing non-canonical amino acid (Tet-ncAA) site-specifically into the E3 ligase, which can be conjugated with strained trans-cyclooctene (sTCO) tethered to a neo-substrate protein binder by click chemistry within living cells. The resulting E3 ligase minimally modified and functionalized in an E3-ligand free (ELF) manner, can be evaluated for TPD of the neo-substrate. We demonstrate that CRBN encoded with clickable Tet-ncAA, either in the known immunomodulatory drug (IMiD)-binding pocket or across surface, can be covalently tethered to sTCO-linker-JQ1 and recruit BRD2/4 for CRBN mediated degradation, indicating the high plasticity of CRBN for TPD. The degradation efficiency is dependent on location of the Tet-ncAA encoding on CRBN as well as the length of the linker, showing the capability of this approach to map the surface of E3 ligase for identifying optimal TPD pockets. This ELF-degrader approach has the advantages of not only maintaining the native state of E3 ligase, but also allowing the interrogation of E3 ligases and target protein partners under intracellular conditions and can be applied to any known E3 ligase.
Warm temperature modifies cell fates to reduce stomata production in Arabidopsis
Authors: Saiz-Pérez Josué , Baekelandt Alexandra , Illescas-Miranda Jonatan , Sterck Lieven , Vuylsteke Marnik , Kim Eun-Ji , Guo Boyu , Desvoyes Bénédicte , Gutierrez Crisanto , Russinova Eugenia , Fenoll Carmen , Mena Montaña
Published: January 2025

Stomatal abundance decrease in Arabidopsis triggered by warm-temperature is attributed to PIF4-mediated repression ofSPEECHLESS(SPCH)expression. We identified the unknown developmental and transcriptional basis of this adaptive response.

We traced stomatal lineages in vivo using cell-identity marker lines and mutants, quantified epidermal traits and conducted RNA sequencing under oscillating temperatures.

Prolonged warm-temperature or PIF4-overexpression altered cell-fates, inducing diverted stomatal precursors (DPs) that lacked stomatal fate, accounting for stomata reduction. DPs originated from meristemoids that lostSPCHexpression, lackedMUTEexpression and exited the cell cycle. Short warm-temperature pulses allowed later recovery ofSPCHexpression, and did not induce DPs or stomata reduction. Comparison of transcriptomes obtained during warm-temperature pulses with stomatal lineage cell-specific profiles identified gene expression changes and contrasted their reversibility. Though warm-temperature silenced key stomatal drivers, most lineages formed stomata through partly modified transcriptional landscapes that promoted uncommitted cell identities and included alternative pathways.

Expression changes in stomatal regulators and cell-fate changes explain lineage progression under fluctuating temperatures. Since short-term temperature oscillations prevail in natural conditions, the requirement of long warm-temperature exposure to trigger DPs would prevent stomata reduction by occasional temperature rises. Promoting uncommitted lineage stages provides flexibility to stomatal development under environmental changes.
Binding items to contexts through conjunctive neural representations with the Method of Loci
Authors: Huang Jiawen , Manglik Akshay , Dutra Nick , Tarder-Stoll Hannah , Chamberlain Taylor , Ajemian Robert , Zhang Qiong , Norman Kenneth A. , Baldassano Christopher
Published: January 2025

Schematic prior knowledge can provide a powerful scaffold for episodic memories, yet the neural mechanisms underlying this scaffolding process are still poorly understood. A crucial step of the scaffolding process is the way in which details of a new episode are connected to an existing schema, forming a robust memory representation that can be easily accessed in the future. A unique testbed for studying this binding process is a mnemonic technique called the Method of Loci (MoL), in which people meaningfully connect items to be remembered with a well-learned list of imagined loci. We collected fMRI data from participants in 3 longitudinal sessions while they were enrolled in a month-long MoL training course, all of whom showed dramatic improvements in their ability to remember lists of 20 or 40 words. We obtained neural patterns when the loci and objects are presented by themselves, when they are combined into an integrated representation at encoding, and when the integrated representation was subsequently retrieved, as well as verbal descriptions from the participants about the way they associated each item to each locus. We found that in default mode network regions, including medial prefrontal cortex (mPFC), the combined representations of loci and items are highly conjunctive: the unified locus-item representation was substantially different from a linear combination of the isolated locus and item representation, reflecting the addition of new integrative details specific to each combined pair. The conjunctive component of the representation reflected the particular creative details generated by individual participants and increased over time as participants gained expertise in MoL. Our findings reveal a critical role for the default mode network in creating meaningful connections between new information and well-learned schematic contexts.
Urban effects on timing and variability of diel activity differ across passerine species and seasons
Authors: Capilla-Lasheras Pablo , Branston Claire J. , Baker Paul , Cochrane Cara , Helm Barbara , Dominoni Davide M.
Published: January 2025

1. Life on Earth is adapted to rhythmic cycles in environmental conditions throughout the day and year via diel patterns of behavioural activity.

2. Urban conditions can disrupt such behavioural rhythms of activity. However, most studies so far have investigated urban effects on patterns of activity of single species in a single season. Additionally, we know little about the level of between and within-individual variation in urban and non-urban populations, and whether they differ.

3. Here, we use automated radio telemetry to record patterns of daily activity in six passerine species (blackbird, robin, great tit, blue tit, dunnock and chaffinch) across two urban and two forest populations during the pre-breeding and post-breeding season. We investigate urban effects on five activity-related traits: time of activity onset, time of activity end, duration of diurnal activity, level of diurnal activity and level of nocturnal activity. We employ statistical tools that allow us to estimate urban effects on mean phenotypic values, but also quantify urbanversusforest differences in between-individual and within-individual phenotypic variation.

4. We found the strongest urban effects on time of activity onset in blackbirds and robins during the pre-breeding season: urban populations of blackbird and robin started their daily activity earlier than their forest counterparts. We did not find this effect in the other species. Urban populations of all species showed higher levels of nocturnal activity than forest populations, but this effect was not offset by lower diurnal activity, suggesting that urban birds may incur higher daily energetic demands.

5. Lastly, our analysis revealed large and consistent differences in variation in the investigated timing traits. Urban birds were more variable between individuals, implying lower population synchronization, and more variable within individuals, implying less consistent behaviour than their forest counterparts. Conversely, activity levels were more variable in forest birds.

6. We conclude that, for birds, urban life is associated with less rest, less consistency, and lower synchronicity, but that effect sizes depend on species and time of the year. Our results warn against generalising the effects of urbanisation on daily rhythms of birds, and call for future studies to understand the mechanisms behind species and seasonal differences.
TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues
Authors: Yu Yang , Wang Shuang , Li Jinpu , Yu Meichen , McCrocklin Kyle , Kang Jing-Qiong , Ma Anjun , Ma Qin , Xu Dong , Wang Juexin
Published: January 2025

The spatial organization of cells plays a pivotal role in shaping tissue functions and phenotypes in various biological systems and diseased microenvironments. However, the topological principles governing interactions among cell types within spatial patterns remain poorly understood. Here, we present theTriangulation Cellular CommunityMotifNeuralNetwork (TrimNN), a graph-based deep learning framework designed to identify conserved spatial cell organization patterns, termed Cellular Community (CC) motifs, from spatial transcriptomics and proteomics data. TrimNN employs a semi-divide-and-conquer approach to efficiently detect over-represented topological motifs of varying sizes in a triangulated space. By uncovering CC motifs, TrimNN reveals key associations between spatially distributed cell-type patterns and diverse phenotypes. These insights provide a foundation for understanding biological and disease mechanisms and offer potential biomarkers for diagnosis and therapeutic interventions.
Gene regulatory networks and essential transcription factors for de novo originated genes
Authors: Peng Junhui , Wang Bing-Jun , Svetec Nicolas , Zhao Li
Published: January 2025

The regulation of gene expression is crucial for the functional integration of evolutionarily young genes, particularly those that emerge de novo. However, the regulatory programs governing the expression of de novo genes remain unknown. To address this, we applied computational methods to single-cell RNA sequencing data, identifying key transcription factors likely instrumental in regulating de novo genes. We found that transcription factors do not have the same propensity for regulating de novo genes; some transcription factors contain more de novo genes than others in their regulon. Leveraging genetic and genomic tools inDrosophila, we further examined the role of two key transcription factors and the regulatory architecture of novel genes. Our findings identify key transcription factors associated with the expression of de novo genes and provide new insights into how modifications in existing transcription factors enable the emergence, maintenance, and regulation of de novo genes.