bluuebunny/crossref_metadata_2025 huggingface dataset:
Coverage of Congenital Anomalies: Ensuring Lasting Smiles Act in Legislation
Authors: Lentskevich Marina A. , Yau Alice , Chwa Emily , Reddy Narainsai K. , Gosain Arun K.
Published: March 2024

The Ensuring Lasting Smiles Act (ELSA) is a federal bill that would require all health federally regulated insurance products to cover the full treatment of a congenital anomaly or congenital disability until complete restoration of normal function or appearance. ELSA has been a key federal priority for the Legislative Advocacy Committee of the American Society of Plastic Surgeons since the 115th Congress in 2018. Although it has gained momentum, particularly in the 117th Congress, the bill remains stalled. Congressional Budget Office review, conducted in March of 2022, appears to have overestimated this bill’s cost for the private sector, secondary to an alleged lack of data on the prevalence of the conditions, extent of treatments and their costs, and the current extent of private sector coverage. The present review highlights the progress of the ELSA bill and serves to illustrate the hurdles involved in passing significant health care bills. This review emphasizes the need for health care professionals to provide their congressional representatives with accurate information on realistic cost of currently covered treatments of congenital defects, the necessary treatments not currently covered by insurance, and additional out-of-pocket costs covered by patients. A concerted effort by plastic surgeons should provide tools for ELSA legislative champions to reintroduce and pass the bill during the 118th Congress. This process highlights the essential role of organized medicine in advocating for the successful passage of health care legislation.
Bidirectional Associations Between Loneliness, Emotional Support, and Sleep in Daily Life
Authors: Dickman Kristina D. , Thomas Mark C. , Chin Brian N. , Kamarck Thomas W.
Published: March 2024

Objective

Evidence suggests a link between positive social relationship perceptions and improved sleep (e.g., quality, efficiency) across the life span. Less work has probed the directionality of these relationships. Here, we report findings from the first study to examine bidirectional between- and within-person associations between loneliness and emotional support with daily life measures of sleep.

Methods

Participants were 389 healthy adults aged 40 to 64 years (61% female) who completed hourly surveys assessing loneliness and perceptions of emotional support over the course of 4 days. Measures of actigraphy-assessed sleep and nightly sleep quality were also assessed for 7 to 10 days.

Results

Individuals with lower average daily loneliness showed higher sleep quality and efficiency than individuals with higher loneliness (r= −0.19,p< .001;r= −0.14,p= .008, respectively), and greater average emotional support was likewise linked with better sleep quality (r= 0.18,p< .001). Controlling for neuroticism attenuated the effects of average loneliness on sleep. Within-person analyses showed unexpected bidirectional effects. Specifically, days in which people felt relatively lonelier were followed by nights with greater sleep efficiency (γ= 1.08,p= .015), and nights when people reported relatively poorer sleep quality were followed by days with greater emotional support (γ= −0.04,p= .013). These unexpected findings are probed in exploratory analyses.

Conclusions

Individuals with higher loneliness and lower emotional support report poorer sleep quality and efficiency, on average. Day-to-day fluctuations in perceptions of social relationships may affect the following night’s sleep, and vice versa.
Long-Term Home EEG Recording: Wearable and Implantable Devices
Authors: Rehman Mahnoor , Higdon Lindsay M. , Sperling Michael R.
Published: March 2024

Electroencephalography (EEG) monitoring has served as a cornerstone in the diagnostic and therapeutic evaluation of epilepsy since its development. This has been accomplished with short-term inpatient video-EEG hospitalization enabling observation of both the semiological and the electrographic features of seizures or with short-term home ambulatory EEG or video-EEG. The advantages of inpatient video-EEG monitoring are limited by high cost, inconvenience, and inability to monitor patients for long periods (weeks or months) as might be done in the outpatient setting. This limitation has impelled the development of wearable EEG devices, which aim to capture high-quality long-term EEG data in a user-friendly and unobtrusive manner. This review article aims to summarize three broad categories of wearable EEG devices, including scalp, subcutaneous, and intracranial EEG. In this review, we will discuss the features of each type of device and the implications for the management of epilepsy. This review does not aim to describe every wearable EEG device on the market but instead seeks to provide a broad overview of the various categories of device that are available, giving examples of each and those in development (with no intention to recommend or advocate for any particular product).
Self-Supervised Learning Reveals Clinically Relevant Histomorphological Patterns for Therapeutic Strategies in Colon Cancer
Authors: Liu Bojing , Polack Meaghan , Coudray Nicolas , Quiros Adalberto Claudio , Sakellaropoulos Theodore , Crobach Augustinus S.L.P. , van Krieken J. Han J.M. , Yuan Ke , Tollenaar Rob A.E.M. , Mesker Wilma E. , Tsirigos Aristotelis
Published: March 2024

Self-supervised learning (SSL) automates the extraction and interpretation of histopathology features on unannotated hematoxylin-and-eosin-stained whole-slide images (WSIs). We trained an SSL Barlow Twins-encoder on 435 TCGA colon adenocarcinoma WSIs to extract features from small image patches. Leiden community detection then grouped tiles into histomorphological phenotype clusters (HPCs). HPC reproducibility and predictive ability for overall survival was confirmed in an independent clinical trial cohort (N=1213 WSIs). This unbiased atlas resulted in 47 HPCs displaying unique and sharing clinically significant histomorphological traits, highlighting tissue type, quantity, and architecture, especially in the context of tumor stroma. Through in-depth analysis of these HPCs, including immune landscape and gene set enrichment analysis, and association to clinical outcomes, we shed light on the factors influencing survival and responses to treatments like standard adjuvant chemotherapy and experimental therapies. Further exploration of HPCs may unveil new insights and aid decision-making and personalized treatments for colon cancer patients.
Comparison of Alternative pre-mRNA Splicing and Gene Expression Patterns in Midbrain Lineage Cells Carrying Familial Parkinson’s Disease Mutations
Authors: Lee Yeon J. , Syed Khaja , Busquets Oriol , Li Hanqin , Dunnack Jesse , Sahagun Atehsa , Bateup Helen S. , Soldner Frank , Hockemeyer Dirk , Rio Donald C.
Published: March 2024

Parkinson’s disease (PD) is a devastating neurodegenerative disorder, with both genetic and environmental causes. Human genetic studies have identified ∼20 inherited familial genes that cause monogenic forms of PD. We have investigated the effects of individual familial PD mutations by developing a medium-throughput platform using genome-editing to install individual PD mutations in human pluripotent stem cells (hPSCs) that we subsequently differentiated into midbrain lineage cells including dopaminergic (DA) neurons in cell culture. Both global gene expression and pre-mRNA splicing patterns in midbrain cultures carrying inherited, pathogenic PD mutations in the PRKN and SNCA genes were analyzed. This analysis revealed that PD mutations lead to many more pre-mRNA splicing changes than changes in overall gene RNA expression levels. Importantly, we have also shown that these splicing changes overlap with changes found in PD patient postmortem brain sample RNA-seq datasets. These pre-mRNA splicing changes are in genes related to cytoskeletal and neuronal process formation, as well as splicing factors and spliceosome components. We predict that these mutation-specific pre-mRNA isoforms can be used as biomarkers for PD that are linked to the familial PD mutant genotypes.
Strategies for Inducing and Validating Zinc Deficiency and Zinc Repletion
Authors: Wenegieme Tara-Yesomi , Elased Dalia , McMichael Kelia E. , Rockwood Jananie , Hasrat Khanzada , Ume Adaku C. , Marshall Andrea G. , Neikirk Kit , Kirabo Annet , Elased Khalid M. , Hinton Antentor , Williams Clintoria R.
Published: March 2024

Given the growing interest in the role of zinc in the onset and progression of diseases, there is a crucial demand for reliable methods to modulate zinc homeostasis. Using a dietary approach, we provide validated strategies to alter whole-body zinc in mice, applicable across species. For confirmation of zinc status, animal growth rates as well as plasma and urine zinc levels were evaluated. The accessible and cost-effective methodology outlined will increase scientific rigor, ensuring reproducibility in studies exploring the impact of zinc deficiency and repletion on the onset and progression of diseases.

New and Noteworthy

This methods paper details 1) dietary approaches to alter zinc homeostasis in rodents, and 2) qualitative and quantitative methods to ensure the zinc status of experimental animals. The outlined accessible and cost-effective protocol will elevate scientific rigor, ensuring reproducibility in studies exploring the impact of zinc deficiency and repletion on the onset and progression of a multitude of health conditions and diseases.

Graphical Abstract
LRRK2G2019S mutation suppresses differentiation of Th9 and Treg cells via JAK/STAT3
Authors: Zheng Ningbo , Jaffery Roshni , Guerrero Ashley , Hou Jiakai , Pan Yuchen , Zhou Fang , Chen Si , Xu Chunyu , Egan Nicholas A. , Bohat Ritu , Chen Ken , Schwarzschild Michael A. , Chen Xiqun , Peng Weiyi
Published: March 2024

The Leucine-rich repeat kinase-2 (LRRK2) G2019S mutation, resulting in aberrantly enhanced kinase activity, is one of the well-recognized genetic risk factors in Parkinson’s Disease (PD). Increased LRRK2 activity was also observed in immune cells from PD patients. Emerging results have also unveiled an upsurge in α-synuclein (α-syn)-specific CD4+T cell responses in PD patients. Given thatLRRK2mutations in PD are germline mutations, there are unmet meets to explore whetherLRRK2G2019S mutation contributes to the pathogenesis of PD via altering CD4+T-cell functions. To fill this knowledge gap, we generated a new T cell receptor (TCR) transgenic mouse strain bearingLRRK2G2019S knock-in mutation, OT-II/LRRK2 (Refer to Mut). As CD4+T cells from OT-II mice specifically recognize ovalbumin, this new strain enables us to explore the impact ofLRRK2G2019S mutation on T-cell functions in an antigen-specific manner. We found that the abundance and proliferation of major immune subsets in spleen tissue from Mut mice are comparable to wild-type (OT-II, Refer to WT) control. However, when we characterized T cell differentiation in these two strains, T cells derived from Mut mice displayed increased Th2 differentiation (IL-4) and decreased Th9 (IL-9) and Treg (Foxp3+%) differentiation.LRRK2G2019S mutation significantly altered the expression levels of master transcription factors (TFs) for T cell differentiation. Specifically, Mut T cells displayed an increase in mRNA expression ofGata3(TF for Th2), a decrease in expression ofIrf4andFoxp3(TFs for Th9 and Treg, respectively). Mechanistically,LRRK2mutation decreased IL-9 production and Treg cell population through the JAK/STAT3 signaling. In conclusion, LRRK2 plays a critical role in regulating T cell differentiation, warranting further studies to evaluate the impacts of altered T cell differentiation led byLRRK2mutation in dopaminergic neuron damages.
Corneal keratocytes, fibroblasts, and myofibroblasts exhibit distinct transcriptional profilesin vitro
Authors: Poole Kara , Iyer Krithika S. , Schmidtke David W. , Petroll W. Matthew , Varner Victor D.
Published: March 2024

Purpose

After stromal injury to the cornea, the release of growth factors and pro-inflammatory cytokines promotes the activation of quiescent keratocytes into a migratory fibroblast and/or fibrotic myofibroblast phenotype. Persistence of the myofibroblast phenotype can lead to corneal fibrosis and scarring, which are leading causes of blindness worldwide. This study aims to establish comprehensive transcriptional profiles for cultured corneal keratocytes, fibroblasts, and myofibroblasts to gain insights into the mechanisms through which these phenotypic changes occur.

Methods

Primary rabbit corneal keratocytes were cultured in either defined serum-free media (SF), fetal bovine serum (FBS) containing media, or in the presence of TGF-β1 to induce keratocyte, fibroblast, or myofibroblast phenotypes, respectively. Bulk RNA sequencing followed by bioinformatic analyses was performed to identify significant differentially expressed genes (DEGs) and enriched biological pathways for each phenotype.

Results

Genes commonly associated with keratocytes, fibroblasts, or myofibroblasts showed high relative expression in SF, FBS, or TGF-β1 culture conditions, respectively. Differential expression and functional analyses revealed novel DEGs for each cell type, as well as enriched pathways indicative of differences in proliferation, apoptosis, extracellular matrix (ECM) synthesis, cell-ECM interactions, cytokine signaling, and cell mechanics.

Conclusions

Overall, these data demonstrate distinct transcriptional differences among cultured corneal keratocytes, fibroblasts, and myofibroblasts. We have identified genes and signaling pathways that may play important roles in keratocyte differentiation, including many related to mechanotransduction and ECM biology. Our findings have revealed novel molecular markers for each cell type, as well as possible targets for modulating cell behavior and promoting physiological corneal wound healing.
Beyond guilty by association at scale: searching for causal variants on the basis of genome-wide summary statistics
Authors: He Zihuai , Chu Benjamin , Yang James , Gu Jiaqi , Chen Zhaomeng , Liu Linxi , Morrison Tim , Belloy Michael E. , Qi Xinran , Hejazi Nima , Mathur Maya , Le Guen Yann , Tang Hua , Hastie Trevor , Ionita-laza Iuliana , Candes Emmanuel , Sabatti Chiara
Published: March 2024

Understanding the causal genetic architecture of complex phenotypes is essential for future research into disease mechanisms and potential therapies. Here, we present a novel framework for genome-wide detection of sets of variants that carry non-redundant information on the phenotypes and are therefore more likely to be causal in a biological sense. Crucially, our framework requires only summary statistics obtained from standard genome-wide marginal association testing. The described approach, implemented in open-source software, is also computationally efficient, requiring less than 15 minutes on a single CPU to perform genome-wide analysis. Through extensive genome-wide simulation studies, we show that the method can substantially outperform usual two-stage marginal association testing and fine-mapping procedures in precision and recall. In applications to a meta-analysis of ten large-scale genetic studies of Alzheimer s disease (AD), we identified 82 loci associated with AD, including 37 additional loci missed by conventional GWAS pipeline. The identified putative causal variants achieve state-of-the-art agreement with massively parallel reporter assays and CRISPR-Cas9 experiments. Additionally, we applied the method to a retrospective analysis of 67 large-scale GWAS summary statistics since 2013 for a variety of phenotypes. Results reveal the method's capacity to robustly discover additional loci for polygenic traits and pinpoint potential causal variants underpinning each locus beyond conventional GWAS pipeline, contributing to a deeper understanding of complex genetic architectures in post-GWAS analyses.
Widespread evolution of poricidal flowers: A striking example of morphological convergence across flowering plants
Authors: Russell Avery Leigh , Zenil-Ferguson Rosana , Buchmann Stephen L. , Jolles Diana D. , Kriebel Ricardo , Vallejo-Marín Mario
Published: March 2024

The evolution of tube-like floral morphologies that control pollen release via small openings (functionally poricidal flowers) represents a taxonomically and geographically widespread instance of repeated and independent evolution of a functionally similar morphology. Poricidal flowers are often closely associated with buzz pollination by bees, but we lack an updated angiosperm-wide survey of their phylogenetic distribution.

We identify all presently known angiosperm genera containing poricidal flowers via a literature survey. We determined the phylogenetic distribution of poricidal flowers and minimum number of independent gains and losses via a genus-level and species level angiosperm-wide phylogeny. We estimated if evolution of poricidal flowers is associated with changes in speciation/extinction via diversification rate analyses.

Poricidal flowers occur across at least 87 angiosperm families and 635 genera containing > 28,000 species. At the genus level, more than 200 independent gains and 145 independent losses of poricidal flowers occurred. Across angiosperms, genus-level analyses suggest poricidal flower evolution is associated with lower net diversification rates (origination-extinction). Species-level analyses argue no diversification linked to poricidal morphology but within the two focal families we found family-specific diversification effects.

We present different hypotheses for the functional significance of poricidal flowers, including its association with buzz pollination, and suggest future directions for studies elucidating the extent to which morphological and functional convergence of poricidal flowers are correlated.
Evaluation Of Suitability Analysis of Gangetic Water from Upper, Middle, And Lower Ganga Rivers
Authors: Balkrishna Acharya , Ghosh Sourav , Nagose Ashwani , Joshi Divya , Singh Shelly , Kumud  , Saxena Aditi , Taneja Sanyam , Arya Vedpriya
Published: March 2024

This study assesses the suitability of water from distinct segments of the Ganga River in India for drinking, irrigation, and industrial purposes, utilizing various indices. Conducted in MAR-MAY 2023, water samples were collected from multiple sites along the river, and categorized into upper, middle, and lower stretches. The findings revealed differing levels of suitability for various purposes among the sampled sites within each stretch. Parameters for drinking water quality generally adhered to specified limits across all stretches, except for E. coli, emphasizing the importance of disinfection measures. Moreover, the study evaluated irrigation suitability, with most sites falling within the good to excellent range, albeit some exhibiting elevated sodium levels, particularly in the lower stretch. Analysis of major ion abundance revealed an alkaline nature dominated by sodium and potassium ions over calcium and magnesium ions across all stretches. Heavy metal concentrations were either within specified limits or absent, indicating minimal industrial pollution. However, caution is warranted regarding industrial applications due to water aggressiveness, as suggested by indices such as the Langelier saturation index and Ryznar stability index, which hint at potential corrosion issues. Water quality in the Ganga River in India exhibited variability across the upper, middle, and lower stretches, with each segment presenting unique characteristics and suitability levels. Continuous monitoring and control measures, especially concerning the most probable number (MPN) of contaminants, are imperative to ensure the sustainability of water quality and meet the diverse usage needs along the river. The evaluation of Gangetic water from the Upper, Middle, and Lower Ganga Rivers is crucial for understanding water quality in one of India’s vital river basins. This study assesses physical, chemical, and biological parameters to determine suitability for drinking, irrigation, and aquatic life. Factors like pH, dissolved oxygen, turbidity, nutrients, heavy metals, and microbial load are analyzed to reveal water quality and potential risks. Temporal and spatial variations, influenced by natural processes and human activities, are explored. The findings aid in sustainable water management and conservation in the Gangetic basin, addressing the urgent need to safeguard this critical resource.
Suppressing APOE4-induced mortality and cellular damage by targeting VHL
Authors: Jiang Wei I. , Cao Yiming , Xue Yue , Ji Yichun , Winer Benjamin Y. , Zhang Mengqi , Singhal Neel S. , Pierce Jonathan T. , Chen Song , Ma Dengke K.
Published: March 2024

Mortality rate increases with age and can accelerate upon extrinsic or intrinsic damage to individuals. Identifying factors and mechanisms that curb population mortality rate has wide-ranging implications. Here, we show that targeting the VHL-1 (Von Hippel– Lindau) protein suppressesC. elegansmortality caused by distinct factors, including elevated reactive oxygen species, temperature, andAPOE4, the genetic variant that confers high risks of neurodegeneration in Alzheimer’s diseases and all-cause mortality in humans. These mortality factors are of different physical-chemical nature, yet result in similar cellular dysfunction and damage that are suppressed by deleting VHL-1. Stabilized HIF-1 (hypoxia inducible factor), a transcription factor normally targeted for degradation by VHL-1, recapitulates the protective effects of deleting VHL-1. HIF-1 orchestrates a genetic program that defends against mitochondrial abnormalities, excess oxidative stress, cellular proteostasis dysregulation, and endo-lysosomal rupture, key events that lead to mortality. GeneticVhlinhibition also alleviates cerebral vascular injury and synaptic lesions inAPOE4mice, supporting an evolutionarily conserved mechanism. Collectively, we identify the VHL-HIF axis as a potent modifier of APOE4 and mortality and propose that targeting VHL-HIF in non-proliferative animal tissues may suppress tissue injuries and mortality by broadly curbing cellular damage.
Zero Shot Health Trajectory Prediction Using Transformer
Authors: Renc Pawel , Jia Yugang , Samir Anthony E. , Was Jaroslaw , Li Quanzheng , Bates David W. , Sitek Arkadiusz
Published: March 2024

Integrating modern machine learning and clinical decision-making has great promise for mitigating healthcare’s increasing cost and complexity. We introduce the Enhanced Transformer for Health Outcome Simulation (ETHOS), a novel application of the transformer deep-learning architecture for analyzing high-dimensional, heterogeneous, and episodic health data. ETHOS is trained using Patient Health Timelines (PHTs)—detailed, tokenized records of health events—to predict future health trajectories, leveraging a zero-shot learning approach. ETHOS represents a significant advancement in foundation model development for healthcare analytics, eliminating the need for labeled data and model fine-tuning. Its ability to simulate various treatment pathways and consider patient-specific factors positions ETHOS as a tool for care optimization and addressing biases in healthcare delivery. Future developments will expand ETHOS’ capabilities to incorporate a wider range of data types and data sources. Our work demonstrates a pathway toward accelerated AI development and deployment in healthcare.
Resolving atomic-level dynamics and interactions of high molecular weight hyaluronic acid by multidimensional solid-state NMR
Authors: Rampratap Pushpa , Lasorsa Alessia , Arunachalam Abinaya , Kamperman Marleen , Walvoort Marthe T.C. , van der Wel Patrick C.A.
Published: March 2024

High molecular weight (HMW) hyaluronic acid (HA) is a highly abundant natural polysaccharide and a fundamental component of the extracellular matrix (ECM). Its size and concentration regulate tissues’ macro- and microenvironments, and its upregulation is a hallmark feature of certain tumors. Yet, the conformational dynamics of HMW-HA and how it engages with components of the ECM microenvironment remain poorly understood on the molecular level. Probing the molecular structure and dynamics of HMW polysaccharides in a hydrated, physiological-like environment is crucial but also technically challenging. Here, we deploy advanced magic-angle-spinning (MAS) solid-state NMR (ssNMR) spectroscopy in combination with isotopic enrichment to enable an in-depth study of HMW-HA to address this challenge. This approach resolves multiple coexisting HA conformations and dynamics as a function of environmental conditions. By combining13C-labeled HA with unlabeled ECM components, we detect by MAS NMR HA-specific changes in global and local conformational dynamics as a consequence of hydration and ECM interactions. These measurements reveal atom-specific variations in dynamics and structure of the N-acetylglucosamine (GlcNAc) moiety of HA. We discuss possible implications for interactions that stabilize the structure of HMW-HA and facilitate its recognition by HA-binding proteins. The described methods apply similarly to studies of the molecular structure and dynamics of HA in tumor contexts and in other biological tissues, as well as HMW-HA hydrogels and nanoparticles used for biomedical and/or pharmaceutical applications.
Quadriceps-hamstrings muscle co-activation during the swing phase of walking is modulated by task constraints in healthy adults
Authors: Van Can Ellis A.M. , Houdijk Han , Buurke Tom J.W.
Published: March 2024

Background: Muscle co-activation, the simultaneous activation of muscles or muscle groups, is a common strategy to enhance the stability of the musculoskeletal system. However, co-activation can also be the consequence of underlying neurological impairments. To better understand and discern functional co-activation during walking, this study explored the difference in quadriceps-hamstrings co-activation during the swing phase of walking and an isolated leg-swinging movement in healthy adults. Methods: Twelve healthy young adults performed walking and isolated leg-swinging at slow (0.6 m/s) and comfortable speed. Isolated leg-swinging was frequency and amplitude matched to the walk conditions. Electromyography signals from m. vastus lateralis, m. rectus femoris, m. biceps femoris, and m. semitendinosus were recorded. Pearson correlation coefficient (Pearson-CI) was calculated as a measure of rate of co-activation. Area under the curve (AUC-CI) was calculated as a measure of co-activation magnitude. Co-activation indices were calculated for both metric across the four muscle pairs and averaged into a single quadriceps-hamstrings CI for each metric. Results: The results showed a higher Pearson-CI, but not AUC-CI, during walking compared to isolated leg-swinging, specifically during mid- and terminal-swing at both speeds. AUC-CI, but not Pearson-CI, was significantly higher during slow speed, compared to comfortable speed. Conclusion: Quadriceps-hamstrings co-activation towards the end of the swing phase during walking reflects preparation for heel-strike, which is not present in isolated leg-swinging. Therefore, an isolated leg-swinging task could serve as a feasible method to distinguish pathological from functional muscle co-activation during walking.
PI3K-dependant reprogramming of hexokinase isoforms controls glucose metabolism and functional responses of B lymphocytes
Authors: Paradoski Brandon T , Hou Sen , Mejia Edgard M , Olayinka-Adefemi Folayemi , Fowke Danielle , Hatch Grant M , Saleem Ayesha , Banerji Versha , Hay Nissim , Zeng Hu , Marshall Aaron J
Published: March 2024

B lymphocyte metabolic reprogramming is essential for B cell differentiation and mounting a healthy immune response. The PI3K signaling pathway regulates B cell metabolism, but the mechanisms involved are not well understood. Here we report that signaling via PI3K8 can impact B cell glucose metabolism and immune functions via selective upregulation of hexokinase 2 (HK2). Three HK enzymes can catalyze the critical first step for glucose utilization and may selectively direct glucose into specific catabolic and anabolic pathways. While HK1 is constitutively expressed in B cells, HK2 is strikingly upregulated during B cell activation in a PI3K8-dependent manner. HK2 shows a unique distribution between mitochondrial and cytoplasmic pools that is also regulated by PI3K. Genetic deletion of HK2 significantly impairs extracellular acidification rate and glycolytic ATP production despite strong expression of HK1. B cell-specific deletion of HK2 in mice caused mild perturbations in B cell development but did not prevent generation of mature B cell subsets. HK2-deficient B cells show altered functional responsesin vitroand evidence of metabolic adaptation to become less dependent on glucose and more dependent on glutamine. HK2-deficient B cells exhibit impaired glycolysis, altered metabolite profiles and altered flux of labeled glucose carbons into the pentose phosphate pathway. Upon immunization, HK2-deficient mice exhibit impaired generation of germinal centre B cells, plasmablasts and antibody responses. We further found that HK2 expression in primary human chronic lymphocytic leukemia (CLL) cells was associated with recent proliferation and could be reduced by PI3K inhibition. Our study identifies hexokinase 2 upregulation as a functionally important component of B cell metabolic reprogramming dependent on the PI3K pathway.
Secondary microglia formation center in the human fetal brain
Authors: Song Chenyun , Chen Xinyu , Ji Rong , Liu Yang , Zhang Ling , Gao Lu , He Qizhi , Ma Lixiang , Saiyin Hexige
Published: March 2024

Yolk sac-derived microglia migrate and populate the brain during development, constituting 10−15% of the total brain cells. The human brain is the largest and most complex brain with the highest cognitive capacity among all species. Therefore, the limitations of rodent brain studies in interpreting the human brain are evident. By co-immunostaining microglia in 50 µm fetal brain sections from 7.5 to 16 gestational weeks (gw) and combining high-resolution scanning, we identified a highly proliferative microglia aggregate (0.108−2.129 mm2) that expanded in Down’s Syndrome fetal brain (4.168 mm2) and was located near the ganglion eminence, in which Ki67+microglia accounted for 23.4% of total microglia compared to 6.3% in other brain regions. The microglia in the aggregates lack phagocytic bulbs, membrane ruffles, and long/branching processes compared to microglia in other brain regions. Introducing human microglia into cortical organoids, but not macrophages, replicated proliferative microglial aggregates on the brain organoid surface and sufficiently penetrated deeper regions of the cortical organoids. Penetrating microglia display phagocytic capacity, enhance immunity, and accelerate the maturation of brain organoids. The large proliferative microglial aggregate may be a unique secondary microglial formation center in the human fetal brain to compensate for the enormous microglial demands during brain expansion.
Indirect Haptic Disturbances Enhance Motor Variability, with Divergent Effects on Skill Transfer
Authors: Arink Wouter , Poggensee Katherine L. , Beckers Niek , Abbink David A. , Marchal-Crespo Laura
Published: March 2024

Research on motor learning has found evidence that learning rate is positively correlated with the learner’s motor variability. However, it is still unclear how to robotically promote that variability without compromising the learner’s sense of agency and motivation, which are crucial for motor learning. We propose a novel method to enhance motor variability during learning of a dynamic task by applying pseudorandom perturbing forces to the internal degree of freedom of the dynamic system rather than directly applying the forces to the learner’s limb. Twenty healthy participants practiced swinging a virtual pendulum to hit oncoming targets, either with the novel method or without disturbances, to evaluate the effect of the method on motor learning, skill transfer, motivation, and agency. We evaluated skill transfer using two tasks, changing either the target locations or the task dynamics by shortening the pendulum rod. The indirect haptic disturbance method successfully increased participants’ motor variability during training compared to training without disturbance. Although we did not observe group-level differences in learning, we observed divergent effects on skill generalization. The indirect haptic disturbances seemed to promote skill transfer to the altered task dynamics but limited transfer in the task with altered target positions. Motivation was not affected by the haptic disturbances, but future work is needed to determine if indirect haptic noise negatively impacts sense of agency. Increasing motor variability by indirect haptic disturbance is promising for enhancing skill transfer in tasks that incorporate complex dynamics. However, more research is needed to make indirect haptic disturbance a valuable tool for real-life motor learning situations.
Pharmacological Characterization of SDX-7320/Evexomostat: a Novel Methionine Aminopeptidase Type 2 Inhibitor with Anti-Tumor and Anti-Metastatic Activity
Authors: Cornelius Peter , Mayes Benjamin A. , Petersen John S. , Turnquist David J. , Dufour Pierre J. , Shanahan James M. , Carver Bradley J.
Published: March 2024

Methionine aminopeptidase type 2 (MetAP2) is a ubiquitous, evolutionarily conserved metalloprotease fundamental to protein biosynthesis which catalyzes removal of the N-terminal methionine residue from nascent polypeptides. MetAP2 is an attractive target for cancer therapeutics based upon its over-expression in multiple human cancers, the importance of MetAP2-specific substrates whose biological activity may be altered following MetAP2 inhibition, and additionally, that MetAP2 was identified as the target for the anti-angiogenic natural product, fumagillin. Irreversible inhibition of MetAP2 using fumagillin analogs has established the anti-angiogenic and anti-tumor characteristics of these derivatives, however, their full clinical potential has not been realized due to a combination of poor drug-like properties and dose-limiting CNS toxicity. This report describes the physicochemical and pharmacological characterization of SDX-7320 (evexomostat), a polymer-drug conjugate of the novel MetAP2 inhibitor (MetAP2i) SDX-7539.In vitrobinding, enzyme and cell-based assays demonstrated that SDX-7539 is a potent and selective MetAP2 inhibitor. In utilizing a high molecular weight, water-soluble polymer to conjugate the novel fumagillol-derived, cathepsin-released, MetAP2i SDX-7539, limitations observed with prior generation, small-molecule fumagillol derivatives were ameliorated including reduced CNS exposure of the MetAP2i, and prolonged half-life enabling convenient administration. Multiple xenograft and syngeneic cancer models were utilized to demonstrate the anti-tumor and anti-metastatic profile of SDX-7320. Unlike polymer-drug conjugates in general, reductions in small molecule-equivalent efficacious doses following polymer conjugation were observed. SDX-7320 has completed a Phase 1 clinical safety study in late-stage cancer patients and is currently being evaluated in multiple Phase 1b/2 clinical studies in patients with advanced solid tumors.
The influence of scaffold deformation and fluid mechanical stimuli on bone tissue differentiation
Authors: Moliner Laia , Wills Carlos Ruiz , Camara Oscar , Olivares Andy L.
Published: March 2024

Bone tissue engineering enables the self-healing of bone fractures avoiding the graft surgery risks. Scaffolds are designed to transfer global mechanical load to cells, and the structure-blood flow interaction is crucial for cell differentiation, proliferation, and migration. Numerical models often consider the effect of solid on the fluid or vice-versa, nevertheless, fluid-structure interactions (FSI) are not usually explored. The present study aims to develop in-silico FSI models to evaluate tissue differentiation capability of different scaffold designs. This is accomplished by analyzing the relation between scaffold strain deformation and fluid mechanical stimuli developed at the cell microscopic level. Cubic regular structures with cylinder and sphere pore based of 60%, 70% and 80% porosity were modelled in finite element analysis. Static or dynamic compression and inlet steady state or transient state fluid profile were considered. Fluid-structure interactions have been performed, and cell differentiation studies considering the octahedral shear strain and fluid shear stress have been compared. Results indicate that high porous scaffold with low compression and fluid perfusion rates promote bone tissue proliferation. Moreover, mechanical stimulation seems to help bone formation and to inhibit cartilage phenotype. Results showed that neglecting the interaction between the scaffold and fluid flow could lead to substantial overestimation of bone differentiation. This study enhances our understanding of the role of dynamic mechanical simulations in tissue formation; allowing the improvement of scaffold design to face complex bone fractures.
The molecular landscape of cellular metal ion biology
Authors: Aulakh Simran Kaur , Lemke Oliver , Szyrwiel Lukasz , Kamrad Stephan , Chen Yu , Hartl Johannes , Muelleder Michael , Nielsen Jens , Ralser Markus
Published: March 2024

Metal ions play crucial roles in cells, yet the broader impact of metal availability on biological networks remains underexplored. We generated genome-wide resources, systematically quantifying yeast cell growth, metallomic, proteomic, and genetic responses upon varying each of its essential metal ions (Ca, Cu, Fe, K, Mg, Mn, Mo, Na, Zn), over several orders of magnitude. We find that metal ions deeply impact cellular networks, with 57.6% of the proteome, including most signalling pathways, responding. While the biological response to each metal is distinct, our data reveals common properties of metal responsiveness, such as concentration interdependencies and metal homeostasis. We describe a compendium of metal-dependent cellular processes and reveal that several understudied genes can be functionally annotated based on their metal responses. Furthermore, we report that metalloenzymes occupy central nodes in the metabolic network and are more likely to be encoded by isozymes, resulting in system-wide responsiveness to metal availability.
Gene expression and eQTL analysis reflect the heterogeneity in the inflammatory status of the duodenal epithelial lining in coeliac disease
Authors: Ramírez-Sánchez Aarón D. , Zühlke Stephanie , Aguirre-Gamboa Raúl , Vochteloo Martijn , Franke Lude , Lundin Knut E.A. , Withoff Sebo , Jonkers Iris H.
Published: March 2024

In coeliac disease (CeD), the epithelial lining (EL) of the small intestine is severely damaged through a complex auto-inflammatory response that results in intraepithelial lymphocytes (IELs) attacking epithelial cells (ECs). To better understand the changes occurring in the EL in CeD, including after initiation of a gluten-free diet, and the regulatory mechanisms that affect mucosal homeostasis, we investigated ECs and IELs in the CeD duodenal EL using RNA-seq and eQTL analysis on predicted cell types. The study included 82 duodenal biopsies from volunteers, grouped into controls (CTRL), gluten-free diet treated CeD (TCD) and untreated CeD (UCD). We identified 2,868 differential expressed genes, which clustered into four sets with specific functions related to CeD. Two sets, one upregulated for cell cycle function and one downregulated for digestion, transmembrane transport, and laminin pathways, defined three groups of samples based on inflammation status: non-inflamed, mild inflammation or severe inflammation. These inflammation states correlated with but were not specific to disease state. The remaining two sets of genes were enriched for immune, extracellular matrix, and barrier functions. These latter two sets allowed the classification of samples into their disease conditions: CTRL, TCD, and UCD. Finally, deconvoluting eQTL effects from ECs and immune cells in the EL identified 7 and 9 cell-type-mediated eQTL genes, respectively. In sum, we identified genes expressed in the duodenal EL whose expression might be used as biomarkers to assess CeD condition and its mucosal and immune status.

Highlights

Gene expression in epithelial lining in CeD patients reflects inflammation status

The transcriptome can classify epithelium as no, mild, or severe inflammation

Cell cycle, absorption, and basal lamina genes are indicators of mucosal damage

Immune and extracellular matrix genes distinguish untreated from treated cases

Predicted-cell-type eQTLs pinpoint effects in immune and epithelial cells
Remembrance with gazes passed: Eye movements precede continuous recall of episodic details of real-life events
Authors: Barker Ryan M. , Armson Michael J. , Diamond Nicholas B. , Liu Zhong-Xu , Wang Yushu , Ryan Jennifer D. , Levine Brian
Published: March 2024

Autobiographical memory entails reconstructing the visual features of past events. Eye movements are associated with vivid autobiographical recollection, but this research has yet to capitalize on the high temporal resolution of eye-tracking data. We aligned eye movement data with participants’ simultaneous free recall of a verified real-life event, allowing us to assess the temporal correspondence of saccades to production of episodic and non-episodic narrative content at the millisecond level. Eye movements reliably predicted subsequent episodic – but not non-episodic – details by 250-1100 ms, suggesting that they facilitate episodic recollection by reinstating spatiotemporal context during vivid recollection. Assessing the relationship of oculomotor responses to naturalistic memory informs theory as well as diagnosis and treatment of conditions involving pathological recollection, such as Alzheimer’s disease and post-traumatic stress disorder (PTSD).
Finding divergent sequences of homomorphic sex chromosomes via diploidized nanopore-based assembly from a single male
Authors: Filipović Igor , Marshall John Macky , Rašić Gordana
Published: March 2024

Although homomorphic sex chromosomes can have non-recombining regions with elevated sequence divergence between its complements, such divergence signals can be difficult to detect bioinformatically. If found in genomes of e.g. insect pests, these sequences could be targeted by the engineered genetic sexing and control systems. Here, we report an approach that can leverage long-read nanopore sequencing of a single XY male to identify divergent regions of homomorphic sex chromosomes. Long-read data are used for de novo genome assembly that is diploidized in a way that maximizes sex-specific differences between its haploid complements. We show that the correct assembly phasing is supported by the mapping of nanopore reads from the male's haploid Y-bearing sperm cells. The approach revealed a highly divergent region (HDR) near the centromere of the homomorphic sex chromosome of Aedes aegypti, the most important arboviral vector, for which there is a great interest in creating new genetic control tools. HDR is located ~5Mb downstream of the known male-determining locus on chromosome 1 and is significantly enriched for ovary-biased genes. While recombination in HDR ceased relatively recently (~1.4 MYA), HDR gametologs have divergent exons and introns of protein coding genes, and most lncRNA genes became X-specific. Megabases of previously invisible sex-linked sequences provide new putative targets for engineering the genetic systems to control this deadly mosquito. Broadly, our approach expands the toolbox for studying cryptic structure of sex chromosomes.
The potential of undersown species identity vs. diversity to manage disease in crops
Authors: Cappelli Seraina Lisa , Domeignoz Horta Luiz Alberto , Gerin Stephanie , Heinonsalo Jussi , Lohila Annalea , Raveala Krista , Schmid Bernhard , Shrestha Rashmi , Tiusanen Mikko Johannes , Thitz Paula , Laine Anna-Liisa
Published: March 2024

In the absence of chemical control with its negative side effects, fungal pathogens can cause large yield losses, requiring us to develop agroecosystems that are inherently disease resistant. Grassland biodiversity experiments often find plant species diversity to reduce pathogen pressure, but whether incorporating high biodiversity levels in agricultural fields have similar effects remains largely unknown.

We tested if undersown plant species diversity could reduce barley disease, and whether the effect was mediated through above- or belowground mechanisms, by combining an agricultural field trial with a soil transplant experiment.

As predicted, barley disease decreased in the presence of undersown plants. Undersown species richness had no effect, but their abundance led to early season disease reduction. Aboveground mechanisms underpinned this disease reduction. Barley yield slightly decreased with increasing undersown species richness, and undersown species varied in their impact on yield.

We identified two undersown species with similar functional traits that contributed most to disease reduction and had the potential to increase barley yield. Furthermore, our results indicate that aboveground mechanisms caused this. We show that agroecosystem functioning can be improved without trade-offs on yield by targeted selection of undersown species.
Direct retino-iridal projections and intrinsic iris contraction mediate the pupillary light reflex in early vertebrates
Authors: Jiménez-López Cecilia , Rivas-Ramírez Paula , Barandela Marta , Núñez-González Carmen , Megías Manuel , Pérez-Fernández Juan
Published: March 2024

The pupillary light reflex (PLR) adapts the amount of light reaching the retina, protecting it and improving image formation. Two PLR mechanisms have been described in vertebrates. First, the pretectum receives retinal inputs and projects to the Edinger-Westphal nucleus (EWN), which targets the ciliary ganglion through the oculomotor nerve (nIII). Postganglionic fibers enter the eye-globe, travelling to the iris sphincter muscle. Additionally, some vertebrates exhibit an iris-intrinsic PLR mechanism mediated by sphincter muscle cells that express melanopsin inducing muscle contraction. Given the high degree of conservation of the lamprey visual system, we investigated the mechanisms underlying the PLR to shed light onto their evolutionary origins. Recently, a PLR mediated by melanopsin was demonstrated in lampreys, suggested to be brain mediated. Remarkably, we found that PLR is instead mediated by direct retino-iridal cholinergic projections, a mechanism not demonstrated before, although suggested to be present in mice. This retina-mediated PLR acts synergistically with the iris-intrinsic mechanism mediated by melanopsin, which has contribution of gap junctions, as in other vertebrates. In contrast, we show that lampreys lack the brain-mediated PLR. Our results suggest that two eye-intrinsic PLR mechanisms were present in early vertebrate evolution, whereas the brain-mediated PLR has a more recent origin.