bluuebunny/crossref_metadata_2025 huggingface dataset:
Pilot educational intervention for the care of adolescents with autism spectrum disorder during puberty
Authors: McMahon Marcie , Cooney-Miner Dianne , Bourne Melissa , Brown Holly
Published: June 2024

Puberty is a particularly vulnerable time for individuals with autism spectrum disorder (ASD) during which baseline challenges are exacerbated, functioning often deteriorates, and additional barriers emerge. Specific concerns include increased vulnerability, decreased safety, and increased mood and behavioral disturbances. Youth with ASD need guidance and explicit instruction/skill development on topics such as hygiene/self-care, appropriate sexual activity, and menstruation management. Lack of provider preparation, knowledge, and confidence, along with stigma about the needs and capabilities of individuals with ASD, are major barriers to care. Initiatives to expand the preparation of health care personnel, including nurse practitioners, to provide quality care to individuals with ASD are essential. This article describes the results of a pilot project using a brief, self-guided educational intervention for developing and practicing family nurse practitioners. Before and after viewing the educational module, participants completed author-created surveys assessing their self-perceived knowledge, attitudes, and intent to change practice. Expert analysis of survey items provided face validity. Comparison of mean presurvey and postsurvey responses showed significant increases in self-perceived knowledge, attitudes, and intent to implement practice changes. Lack of confidence was endorsed as the most common remaining barrier to change. Findings indicate that the brief module improved participants' self-reported knowledge, attitudes, and intent to implement practice recommendations. Such interventions can be easily incorporated into nursing education and professional development and are appropriate for dissemination to nurse practitioners working within and outside primary care settings, as well as to related service providers.
The GalaFLEX “Empanada” for Direct-to-Implant Prepectoral Breast Reconstruction
Authors: Karp Nolan , Sorenson Thomas J. , Boyd Carter J. , Hemal Kshipra , Lin Alexandra , Robinson Isabel S. , Choi Mihye
Published: June 2024

Prepectoral breast reconstruction poses unique challenges, including a lower tolerance for mastectomy flap skin necrosis and seroma formation. With appropriate patient selection, prepectoral breast reconstruction is a valuable reconstructive option with numerous benefits. Although mastectomy skin necrosis is largely out of the control of the reconstructive surgeon, mitigation of seroma formation is critical. Strategies to reduce its incidence have been thoroughly discussed. Whereas there are many contributing factors, one tenet of prepectoral breast reconstruction is adequate pocket control. Reducing dead space and microshifting of the implant in the breast pocket is an important factor for averting seroma formation and implant displacement. Textured devices allowed the breast implant to sit more securely in the soft-tissue pocket. Given widespread concern for their involvement with breast implant–associated anaplastic large-cell lymphoma, macrotextured devices are no longer used in the United States. The authors describe their method of using poly-4-hydroxybutyrate synthetic absorbable mesh to effectively create a textured breast implant for use in prepectoral implant-based breast reconstruction.
Risk factors for progression from prediabetes to diabetes among older people with HIV
Authors: Masters Mary Clare , Tassiopoulos Katherine , Bao Yajing , Wu Kunling , Koletar Susan L. , Rubin Leah H. , Yang Jingyan , Overton Edgar T. , Letendre Scott , Brown Todd T. , Erlandson Kristine M. , Palella Frank J. ,   for the ACTG A5322 Study Team
Published: June 2024

Objective:

Risk factors for progression from prediabetes mellitus (pre-DM) to diabetes mellitus (DM) among people with HIV (PWH) receiving modern antiretroviral therapy (ART) require better characterization.

Design:

AIDS Clinical Trials Group (ACTG) A5322 (HAILO) was an observational cohort study of PWH ≥40 years old. Participants initiated ART through ACTG randomized clinical trials.

Methods:

We used Cox proportional hazards regression models to identify risk factors for development of DM among HAILO participants with pre-DM.

Results:

Among 1035 HAILO participants, 74 (7%) had pre-DM at entry and another 679 (66%) developed pre-DM during follow-up. Of 753 PWH with pre-DM, 167 (22%) developed DM. In multivariable models, the risk of developing DM was greater with higher BMI, lower CD4 count (≤200 cells/mm3), hypertriglyceridemia, or higher waist circumference at pre-DM diagnosis (P < 0.01).

Conclusion:

Rates of pre-DM and progression to DM remain high among virally suppressed PWH receiving modern ART regimens. Traditional risks for DM, such as higher BMI or waist circumference, are associated with increased risk of incident DM among PWH with pre-DM. The association between lower CD4+ and progression to DM suggests a role for advanced immunodeficiency and inflammation. Further investigation of interventions aimed at preventing DM among PWH with pre-DM is needed. Optimizing prevention and treatment for DM may be an intervenable opportunity to improve long-term outcomes for PWH.
EXPLORING THE PROGNOSTIC NECROPTOSIS-RELATED GENES AND UNDERLYING MECHANISM IN SEPSIS USING BIOINFORMATICS
Authors: Liu Jie , Li Lin , He Shuyang , Zheng Xin , Zhu Dan , Kong Guangyao , Li Ping
Published: June 2024

Sepsis is a life-threatening disease due to a dysregulated host response to infection, with an unknown regulatory mechanism for prognostic necroptosis-related genes (NRGs). Using GEO datasets GSE65682 and GSE134347, we identified six NRG biomarkers (ATRX, TSC1, CD40, BACH2, BCL2, and LEF1) with survival and diagnostic significance through Kaplan-Meier (KM) and receiver operating characteristic (ROC) analyses. Afterward, the ingenuity pathway analysis (IPA) highlighted enrichment in hepatic fibrosis pathways and BEX2 protein. Moreover, we examined their regulatory targets and functional links with necroptotic signaling molecules via miRDB, TargetScan, Network analyst, and GeneMANIA. The molecular regulatory network displayed that hsa-miR-5195-3p and hsa-miR-145-5p regulated ATRX, BACH2, and CD40, while YY1 showed strong connectivity, concurrently controlling LEF1, ATRX, BCL2, BACH2, and CD40. CD40 exhibited similar expression patterns to RIPK3 and MLKL, and LEF1 was functionally associated with MLKL. Additionally, DrugBank analysis identified paclitaxel, docetaxel, and rasagiline as potential BCL2-targeting sepsis treatments. Finally, real-time quantitative PCR confirmed ATRX, TSC1, and LEF1 downregulation in sepsis samples, contrasting CD40’s increased expression in CTL samples. In conclusion, ATRX, TSC1, CD40, BACH2, BCL2, and LEF1 may be critical regulatory targets of necroptosis in sepsis, providing a basis for further necroptosis-related studies in sepsis.
Analyzing the Evolution of Needle and Ultrasound Probe Manipulation Skills of Interventional Radiology Trainees With Time and Experience
Authors: Weinstein Jeffrey L. , Ali Hamza , Mitchell John D. , Sarwar Ammar , Palmer Matthew R. , MacLellan Christopher , Matyal Robina , Ahmed Muneeb
Published: June 2024

Purpose

To test the hypothesis that hand motion analysis can measure the progression of needle and ultrasound probe manipulation skills of interventional radiology trainees in central venous line placement.

Materials and Methods

An expert cohort of 6 interventional radiologists and 4 anesthesiologists and a trainee cohort of 6 novice trainees (<50 central lines) and 5 experienced trainees (>50 central lines) performed simulated central venous access. Four novices and 1 experienced trainee repeated the task 1 year later. An electromagnetic motion tracking system tracked the needle hand and ultrasound probe. Path length, translational, and rotational movements were calculated separately for the needle hand and probe sensor. These metrics were used to calculate motion metrics based scores on a scale of 0 to 3 for each sensor. Nonparametric statistics were used, and the data are reported as median ± interquartile range.

Results

Comparing novice and experienced trainees, there was a significant difference in probe scores (experienced vs. novice: 1 ± 2 vs. 0 ± 0, P = 0.04) but not in needle-hand scores (1 ± 1.5 vs. 0 ± 1, P = 0.26). Trainees showed a significant increase in probe scores at the 1-year follow-up (baseline vs. follow-up: 0 ± 1 vs. 2.5 ± 1.8, P = 0.003), but no significant difference was observed in the needle manipulation metrics. Experts differed significantly from experienced trainees for all metrics for both sensors (P < 0.05), with the exception of the path length of the probe.

Conclusions

Acquisition of improved dexterity of the probe may occur before improvement in the dexterity with the needle hand for interventional radiology trainees.
Corpus Callosum–Mediated Interhemispheric Interactions in Cervical Spondylotic Myelopathy
Authors: Lo Yew Long , Hwang Ruby , Teng Peggy Pei Chee , Tan Yam Eng
Published: June 2024

Purpose:

The corpus callosum is crucial for interhemispheric interactions in the motor control of limb functions. Human and animal studies suggested spinal cord pathologies may induce cortical reorganization in sensorimotor areas. We investigate participation of the corpus callosum in executions of a simple motor task in patients with cervical spondylotic myelopathy (CSM) using transcranial magnetic stimulation.

Methods:

Twenty patients with CSM with various MRI grades of severity of cord compression were compared with 19 normal controls. Ipsilateral silent period, contralateral silent period, central motor conduction time, and transcallosal conduction time (TCT) were determined.

Results:

In both upper and lower limbs, TCTs were significantly increased for patients with CSM than normal controls (p < 0.001 for all), without side-to-side differences. Ipsilateral silent period and contralateral silent period durations were significantly increased bilaterally for upper limbs in comparison to controls (p < 0.01 for all), without side-to-side differences. There were no significant correlations of TCT with central motor conduction time nor severity of CSM for both upper and lower limbs (p > 0.05 for all) bilaterally.

Conclusions:

Previous transcranial magnetic stimulation studies show increased motor cortex excitability in CSM; hence, increased TCTs observed bilaterally may be a compensatory mechanism for effective unidirectional and uniplanar execution of muscle activation in the distal limb muscles. Lack of correlation of TCTs with severity of CSM or central motor conduction time may be in keeping with a preexistent role of the corpus callosum as a predominantly inhibitory pathway for counteracting redundant movements resulting from increased motor cortex excitability occurring after spinal cord lesions.
Understanding and Assisting the Recovery of Non-English-Speaking Trauma Survivors: Assessment of the NESTS Pathway
Authors: Antunez Alexis G , Herrera-Escobar Juan P , Ilkhani Saba , Hoffman Ana , Foley Katie M , Zier Carolyn , Campbell Lorna , Pinkes Nathaniel , Valverde Madeline D , Ortega Gezzer , Reidy Emma , Reich Amanda J , Salim Ali , Levy-Carrick Nomi , Anderson Geoffrey A
Published: June 2024

BACKGROUND:

Spanish-speaking trauma and burn patients have unique needs in their postdischarge care navigation. The confluence of limited English proficiency, injury recovery, mental health, socioeconomic disadvantages, and acute stressors after hospital admission converge to enhance patients’ vulnerability, but their specific needs and means of meeting these needs have not been well described.

STUDY DESIGN:

This prospective, cross-sectional survey study describes the results of a multi-institutional initiative devised to help Spanish-speaking trauma and burn patients in their care navigation after hospitalization. The pathway consisted of informational resources, intake and follow-up surveys, and multiple points of contact with a community health worker who aids in accessing community resources and navigating the healthcare system.

RESULTS:

From January 2022 to November 2023, there were 114 patients identified as eligible for the Non-English-Speaking Trauma Survivors pathway. Of these, 80 (70.2%) were reachable and consented to participate, and 68 were approached in person during their initial hospitalization. After initial screening, 60 (75.0%) eligible patients had a mental health, social services, or other need identified via our survey instrument. During the initial consultation with the community health worker, 48 of 60 patients with any identified need were connected to a resource (80%). Food support was the most prevalent need (46, 57.5%). More patients were connected to mental health resources (16) than reported need in this domain (7).

CONCLUSIONS:

The Non-English-Speaking Trauma Survivors pathway identified the specific needs of Spanish-speaking trauma and burn patients in their recovery, notably food, transportation, and utilities. The pathway also addressed disparities in postdischarge care by connecting patients with community resources, with particular improvement in access to mental healthcare.
Electroconvulsive Therapy Changes Immunological Markers in Patients With Major Depressive Disorder
Authors: Young Jonathan R. , Evans Mariah K. , Hwang Julie , Kritzer Michael D. , Kellner Charles H. , Weiner Richard D.
Published: June 2024

Major depressive disorder (MDD) is a highly prevalent and disabling condition. As such, understanding the causes of and treatment options for MDD is critical. Electroconvulsive therapy (ECT) remains the gold standard depression treatment, but the molecular mechanisms that underlie its effects are still largely unknown. One such explanation hinges on the immuno-inflammatory correlates of ECT treatment, given mounting evidence supporting the inflammatory hypothesis of depression. This review aims to provide an overview of the suggested immunomodulatory effects of ECT and the predictive value of immune biomarkers in relation to treatment outcomes and side effects. We conducted a preregistered, systematic literature search utilizing MEDLINE (PubMed), Embase (Elsevier), and PsycINFO (EBSCO) databases. We employed keywords related to MDD, ECT, gut microbiome, and the immune system. We only included human subjects research published between 1985 and January 13, 2021. Twenty-six unique studies were included in our analyses. Findings indicate a proinflammatory profile associated with MDD, with immune biomarkers exhibiting acute and chronic changes following ECT. Consistently, lower baseline interleukin 6 levels and higher C-reactive protein levels are correlated with a greater reduction in depressive symptoms following ECT. Furthermore, included studies emphasize the predictive value of peripheral immune changes, specifically interleukin 6 and tumor necrosis factor α, on cognitive outcomes following ECT. Given these results, further exploration of the potential roles of immunomodulatory effects on ECT treatment outcomes, as well as adverse cognitive side effects, is indicated.
Correlation Between ECT Quality Measures and Likelihood to Transition From Acute to Continuation and Maintenance ECT
Authors: Schuster Haley , Walters Ryan W. , Mathy Jacob , Ramaswamy Sriram , Alsakaf Imad
Published: June 2024

Objectives

To evaluate the association between 3 ECT quality measures (seizure duration, Postictal Suppression Index [PSI], and heart rate response) and therapeutic compliance as indicated by transitioning from acute to continuation to maintenance phases of ECT.

Methods

This was a retrospective chart review of patients who received ECT between July 2016 and July 2019. ECT quality measures were lagged by 1 ECT session to examine the effect of the prior session's quality measure on progressing to a higher ECT phase at the subsequent ECT session. Associations with therapeutic compliance were analyzed using mixed-effects ordinal regression and mixed-effects partial proportional odds models.

Results

Seizure duration was associated with 8% higher adjusted odds of progressing to out of the acute phase (95% confidence interval [CI]: 2% to 15%, P = 0.007) and 18% higher adjusted odds of progressing to the maintenance phase (95% CI: 10% to 28%, P < 0.001); PSI was associated with 9% higher adjusted odds of progressing out of the acute phase (95% CI: 3% to 16%, P = 0.005), whereas heart rate response was not statistically associated with therapeutic compliance. Greater therapeutic compliance was also associated with bilateral electrode placement and older age.

Conclusions

Longer seizure duration was associated with greater therapeutic compliance across all ECT phases, PSI was associated with progressing out of the acute phase, and heart rate response was not associated with therapeutic compliance. Our findings assist ECT psychiatrists in optimizing ECT quality measures to promote better compliance with ECT.
Structure transfer and consolidation in visual implicit learning
Authors: Garber Dominik , Fiser József
Published: June 2024

Transfer learning, the re-application of previously learned higher-level regularities to novel input, is a key challenge in cognition. While previous empirical studies investigated human transfer learning in supervised or reinforcement learning for explicit knowledge, it is unknown whether such transfer occurs during naturally more common implicit and unsupervised learning and, if so, how it is related to memory consolidation. We compared the transfer of newly acquired explicit and implicit abstract knowledge during unsupervised learning by extending a visual statistical learning paradigm to a transfer learning context. We found transfer during unsupervised learning but with important differences depending on the explicitness/implicitness of the acquired knowledge. Observers acquiring explicit knowledge during initial learning could transfer the learned structures immediately. In contrast, observers with the same amount but implicit knowledge showed the opposite effect, a structural interference during transfer. However, with sleep between the learning phases, implicit observers, while still remaining implicit, switched their behaviour and showed the same pattern of transfer as explicit observers did. This effect was specific to sleep and not found after non-sleep consolidation. Our results highlight similarities and differences between explicit and implicit learning while acquiring generalizable higher-level knowledge and relying on consolidation for restructuring internal representations.
Baseline dependent differences in the perception of changes in visuomotor delay
Authors: Vigh Gesche , Limanowski Jakub
Published: June 2024

The detection of, and adaptation to delayed visual movement feedback has been extensively studied. One important open question is whether the Weber-Fechner Laws hold in the domain of visuomotor delay; i.e., whether the perception of changes in visuomotor delay depends on the amount of delay already present during movement. To address this, we developed a virtual reality based, continuous hand movement task, during which participants had to detect changes in visuomotor mapping (delay): Participants (N=40) performed continuous, auditory-paced grasping movements, which were measured with a data glove and transmitted to a virtual hand model. The movements of the virtual hand were delayed between 0-700ms with the delay changing repeatedly in a roving oddball design. Participants had to indicate any perceived delay changes by key press. This design allowed us to investigate detection accuracy and speed related to the magnitude of the delay change, and to the “baseline” delay present during movement, respectively. As expected, larger delay changes were detected more accurately than smaller ones. Surprisingly, delay changes were detected more accurately and faster when participants moved under large > small delays. These results suggest that visual movement feedback delay indeed affects the detection of changes in visuomotor delay, but not as predicted by the Weber-Fechner Laws. Instead, bodily action under small delays may have entailed a larger tolerance for delay changes due to embodiment-related intersensory conflict attenuation; whereas better change detection at large delays may have resulted from their (visual) saliency due to a strong violation of visuomotor predictions.
Interferon-γ and IL-27 positively regulate type 1 regulatory T-cell development during adaptive tolerance
Authors: Lecky David A.J. , Sheriff Lozan , Rouvray Sophie T. , George Lorna S. , Drummond Rebecca A. , Wraith David C. , Bending David
Published: June 2024

Strong T-cell receptor (TCR) and IL-27 signalling influence type-1 regulatory (Tr1) T-cell development but whether other signals determine their differentiation is unclear. Utilising Tg4 TCR transgenic mice we established a model for rapid Tr1 cell induction. A single high dose of [4Y]-MBP peptide drove the differentiation ofIl10+T-cells withbona fideTr1 cell protein and mRNA signatures. Kinetic transcriptional analysis revealed that the Tr1 cell module was transient and preceded by a burst ofIfngtranscription in CD4+ T-cells. Neutralisation of IFNγ reduced Tr1 cell frequency and strong TCR signalling markers, which was correlated with reduced macrophage activation. Antibody depletion experiments inferred that T-cells – but not NK cells – provided the relevant source of IFNγ. Additionally, we show that blocking IL-27 in combination with IFNγ neutralisation additively reduced Tr1 cell frequencyin vivo. These findings reveal that during strong tolerogenic TCR signalling IFN-γ has a non-redundant regulatory role in augmenting the differentiation of Tr1 cellsin vivo.
SuperSpot: Coarse Graining Spatial Transcriptomic Data into Metaspots
Authors: Teleman Matei , Gabriel Aurélie AG , Hérault Léonard , Gfeller David
Published: June 2024

Spatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. As of today, thousands of genes can be detected across hundreds of thousands of spots. Akin to standard single-cell RNA-Seq data, spatial transcriptomic data are very sparse due to the limited amount of RNA within each spot. Building upon the metacell concept, we present a workflow, called SuperSpot, to combine adjacent and transcriptionally similar spots into “metaspots”. The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution. We demonstrate that metaspots can be used to reduce the size of spatial transcriptomic data and remove some of the dropout noise.

Availability and implementation

SuperSpot is an R package available athttps://github.com/GfellerLab/SuperSpot.
AFC kinases function as thermosensors that regulate warm temperature-responsive growth inArabidopsis
Authors: Dimos-Röhl Benjamin , Ostwaldt Felix , Bäsmann Jannik , Hausmann Paula , Kreisz Philipp , Krischke Markus , Lutsch Christoffer , Müller Philipp C. , Strauch Miriam , Weiste Christoph , Zhu Tingting , De Smet Ive , Heyd Florian , Maag Daniel
Published: June 2024

Plants respond to elevated temperatures with enhanced elongation growth and an upward movement of their leaves. These adaptive growth responses depend on a rapid transcriptional, post-transcriptional and post-translational reprogramming. It is unclear, however, how temperature information is sensed and integrated with the cellular splicing machinery to establish warm-temperature dependent splicing patterns. In animals, CDC2-LIKE KINASES (CLKs) function as body temperature sensors that control temperature-dependent alternative splicing through the phosphorylation of serine/arginine-rich (SR) proteins. Here, we demonstrate that the CLK-homologous ARABIDOPSIS FUS3-COMPLEMENTING (AFC) kinases function as temperature sensors that regulate post-transcriptional RNA processing to control warm temperature-dependent growth responses in Arabidopsis. We show that the contrasting temperature-activity profiles of the three Arabidopsis AFCs depend on specific structural elements including a conserved activation segment within the kinase domain. By combining protein structure prediction with site-directed mutagenesis, we provide insights into structural features that determine different temperature-activity profiles of the three AFC paralogs. Subsequent analyses ofafcmutant plants demonstrate their requirement for hypocotyl elongation growth and thermonastic leaf movement at elevated temperature. Impaired hypocotyl elongation ofafctriple mutant seedlings was accompanied by defects in temperature-dependent splicing especially affecting the post-transcriptional regulation of transcripts encoding splicing factors. Finally, based on transcriptomics, immunodetection and mutant analyses our data indicate SR34 and SR34a as phosphorylation targets that mediate temperature-dependent post-transcriptional RNA processing downstream of AFCs. In conclusion, the characterisation of Arabidopsis AFC kinases as thermosensors provides compelling evidence that temperature-controlled AFC activity is evolutionarily conserved between plants and animals.
Abiotic stress-induced chloroplast and cytosolic Ca2+ dynamics in the green alga Chlamydomonas reinhardtii
Authors: Pivato Matteo , Costa Alex , Wheeler Glen L , Ballottari Matteo
Published: June 2024

Calcium (Ca2+)-dependent signalling plays a well-characterized role in the perception and response mechanisms to environmental stimuli in plant cells. In the context of a constantly changing environment, it is fundamental to understand how crop yield and microalgal biomass productivity are affected by external factors. Ca2+ signalling is known to be important in different physiological processes in microalgae but many of these signal transduction pathways still need to be characterized. Here, the role of compartment-specific Ca2+ signalling was investigated in Chlamydomonas reinhardtii in response to environmental stressors such as nutrient availability, osmotic stress, temperature fluctuations and carbon sensing. An in vivo single-cell imaging approach was adopted to directly visualize signalling processes at the level of specific subcellular compartments, using Chlamydomonas reinhardtii lines expressing a genetically encoded ratiometric Ca2+ indicator. Hyper-osmotic shock caused cytosolic and chloroplast Ca2+ elevations, whereas high temperature and inorganic carbon availability primarily induced Ca2+ transients in the chloroplast. In contrast, hypo-osmotic stress only induced Ca2+ elevations in the cytosol. The results herein reported show that compartment-specific signalling pathways are likely to play an important role in the response of Chlamydomonas to these stimuli providing new understanding of the mechanisms exploited by microalgae to respond to specific natural conditions.
Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during cell growth arrest
Authors: Neri Francesco , Zheng Shuyuan , Watson Mark , Desprez Pierre-Yves , Gerencser Akos A. , Campisi Judith , Wirtz Denis , Wu Pei-Hsun , Schilling Birgit
Published: June 2024

Cellular senescence has been strongly linked to aging and age-related diseases. It is well established that the phenotype of senescent cells is highly heterogeneous and influenced by their cell type and senescence-inducing stimulus. Recent single-cell RNA-sequencing studies identified heterogeneity within senescent cell populations. However, proof of functional differences between such subpopulations is lacking. To identify functionally distinct senescent cell subpopulations, we employed high-content image analysis to measure senescence marker expression in primary human endothelial cells and fibroblasts. We found that G2-arrested senescent cells feature higher senescence marker expression than G1-arrested senescent cells. To investigate functional differences, we compared IL-6 secretion and response to ABT263 senolytic treatment in G1 and G2 senescent cells. We determined that G2-arrested senescent cells secrete more IL-6 and are more sensitive to ABT263 than G1-arrested cells. We hypothesize that cell cycle dependent DNA content is a key contributor to the heterogeneity within senescent cell populations. This study demonstrates the existence of functionally distinct senescent subpopulations even in culture. This data provides the first evidence of selective cell response to senolytic treatment among senescent cell subpopulations. Overall, this study emphasizes the importance of considering the senescent cell heterogeneity in the development of future senolytic therapies.
A combinatorially complete epistatic fitness landscape in an enzyme active site
Authors: Johnston Kadina E. , Almhjell Patrick J. , Watkins-Dulaney Ella J. , Liu Grace , Porter Nicholas J. , Yang Jason , Arnold Frances H.
Published: June 2024

Protein engineering often targets binding pockets or active sites which are enriched in epistasis— non-additive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a non-native environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a new, large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

Significance statement

Predictive models for protein engineering seek to capture the relationship between protein sequence and function. While many methods and datasets exist for predicting the effects of single substitutions across a range of protein functions, fewer capture interactions among substitutions, which are much more difficult to predict. Even fewer do this comprehensively for a catalytic function. To provide a testbed for evaluating predictive models for enzyme engineering, we constructed and analyzed a 160,000-member enzyme sequence-fitness dataset at four interacting residues near the active site of tryptophan synthase, capturing significant non-additive effects of substitutions on catalytic function. It is necessary to predict and understand such interactions in order to efficiently traverse evolutionary landscapes and build machine learning models that accelerate protein engineering.
Nuclear transport at full amino-acid resolution
Authors: Dekker Maurice , de Vries Hendrik W. , Wortelboer Koen A. , Beekhuis Harm Jan , Van der Giessen Erik , Onck Patrick R.
Published: June 2024

Recent studies of nuclear pore complexes (NPCs) have provided detailed descriptions of the core scaffold structures, yet fall short in resolving the dynamic FG-meshwork with similar pre-cision. Here, we present a novel modeling framework that enables the simulation of nuclear transport at full amino-acid resolution. We describe the distributions of the different FG-Nups in the central transporter and highlight the dynamic nature of the FG-meshwork, with FG–FG interaction lifetimes on the order of nanoseconds. Our findings reveal that Nsp1, the most abundant FG-Nup in the NPC, creates a central meshwork due to its unique bimodal structure, that is essential for controlling both passive and active transport. By introducing nuclear transport receptors (NTRs)—in the form of Kap95—to the pore, we demonstrate that NTRs play a key role in increasing the energy barrier for translocation of inert particles. We observe a dynamic interplay between high affinity binding to FG-motifs and the temporal fluctuations of the FG-meshwork, leading to local low-density pockets, so-called voids, through which Kaps move. Furthermore, we show that the introduction of Kaps to the FG-meshwork results in a clear “dirty velcro” mechanism with slower Kaps decorating the sticky surface of the high-density GLFG-assembly, thus enabling fast translocation of Kaps through the center of the pore.
Evidence of lesions from Epstein-Barr virus infection in human breast cancer genomes
Authors: Friedenson Bernard
Published: June 2024

Epstein-Barr virus (EBV) infects essentially all humans and provides no benefit. EBV can cause nasopharyngeal cancer (NPC), Burkitt’s lymphoma (BL), and perhaps breast cancer. Breast tissues from patients with breast cancer are more likely to be EBV-positive than tissues from healthy controls. However, EBV is not a proven cause of breast cancer because the tissues are not consistently EBV-positive. If EBV causes breast cancer, it would have to do it without an active infection. Other cancers with known viral origins do not require continuing presence of the virus. However, the "hit and run" theory is difficult to test for breast cancer without a proven EBV connection.

Here, I test this theory with multiple independent bioinformatic analyses. First, hundreds of breast cancer genomes contained characteristic methylation scars that indicate a cleared EBV infection. The genomes had further differential hypermethylation near positions where EBV reprograms normal cells into malignancy. Second, genomes from EBV cancers and breast cancers inactivated the same tumor-suppressive mechanisms. Third, deletions were identified on chromosome 3p in EBV cancers that shift cells to oxidative glycolysis, a prominent breast cancer phenotype known as the Warburg effect. Similar 3p deletions were found in breast cancer genomes. Fourth, somatic hypermutation clusters in EBV-cancers marked genome positions in breast cancers near translocations and focal oncogene amplification. EBV deregulation of deaminase and estrogen-induced topoisomerase explain these translocation breakpoints. Fifth, several alternate explanations for these results were ruled out. Finally, only limited segments of EBV DNA matched the human genome, making it possible that a childhood vaccine would end breast cancer.
Predicting the Risk of Asthma Development in Youth Using Machine Learning Models
Authors: Xie Matthew , Xu Chenliang
Published: June 2024

Asthma is a chronic respiratory disease characterized by wheezing and difficulty breathing, which disproportionally affects 4.7 million children in the U.S. Currently, there is a lack of asthma predictive models for youth with good performance. This study aims to build machine learning models to better predict asthma development in youth using easily accessible national survey data. We analyzed cross-sectional combined 2021 and 2022 National Health Interview Survey (NHIS) data from 9,716 youth subjects with their corresponding parent information. We built several machine learning models with various sampling techniques (under- or over-sampling) for asthma prediction in youth, including XGBoost, Neural Networks, Random Forest, Support Vector Machine (SVM), and Logistic Regression. We examined the associations of potential risk factors identified from both Random Forest and Least Absolute Shrinkage and Selection Operator (LASSO) with asthma in youth. Between the different sampling techniques, undersampling the major class (subjects without asthma) yielded the best results in terms of the area under the curve (AUC) and F1 scores for the different predictive models. The Logistic Regression performed the best with the under-sampled data, yielding an AUC score of 0.7654 and an F1 score of 0.3452. In addition, we have identified additional important factors associated with asthma development in youth, such as low family poverty ratio and parents ever had asthma. This study successfully built machine learning models to predict asthma development in youth with good model performance. This will be important for early screening and detection of asthma in youth.
Modular Fluorescent Cholesterol Naphthalimide Probes And Their Application For Cholesterol Trafficking Studies In Cells
Authors: Rubio Vicente , McInchak Nicholas , Fernandez Genesis , Benavides Dana , Herrera Diana , Jimenez Catherine , Mesa Haylee , Meade Jonathan , Zhang Qi , Stawikowski Maciej J.
Published: June 2024

Development of fluorescent cholesterol analogs to better understand subcellular cholesterol trafficking is of great interest for cell biology and medicine. Our approach utilizes a bifunctional 1,8-naphthalimide scaffold with a push-pull character, modified on one side with a head group and a linker on the other side connecting it to cholesterolviaan ester bond. Through structure-function studies, we’ve explored how different substituents—linkers and head groups—affect the ability of these fluorescent cholesterol naphthalimide analogs (CNDs) to mimic natural cholesterol behavior at both molecular and cellular levels.

We categorized the resulting analogs into three groups: neutral, charged, and those featuring a hydroxyl group. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Extensive all-atom molecular dynamics simulations helped us examine how these analogs perform in model membranes compared to cholesterol. Additionally, we investigated the partitioning of these fluorescent probes in phase-separated giant unilamellar vesicles. We evaluated the uptake and distribution of these probes within mouse fibroblast cells and astrocytes, for their subcellular distributions in lysosomes and compared that to BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of the fluorescent probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesterol probes bearing distinct spectral, biophysical, and cellular targeting features, which makes it a valuable toolkit for the investigation of subcellular distribution and trafficking of cholesterol and its derivatives.
Mechanoreceptor Piezo1-Mediated Interleukin Expression in Conjunctival Epithelial Cells: Linking Mechanical Stress to Ocular Inflammation
Authors: Fukuoka Seiya , Adachi Naoki , Ouchi Erika , Ikemoto Hideshi , Okumo Takayuki , Onda Hidetoshi , Sunagawa Masataka
Published: June 2024

Purpose

Mechanical stress on the ocular surface, such as from eye-rubbing, has been reported to lead to inflammation and various ocular conditions. We hypothesized that the mechanosensitive Piezo1 channel in the conjunctival epithelium contributes to the inflammatory response at the ocular surface after receiving mechanical stimuli.

Methods

Human conjunctival epithelial cells (HConjECs) were treated with Yoda1, a Piezo1-specific agonist, and various allergens to measure cytokine expression levels using qRT-PCR and Western blot. Piezo1 activation-induced intracellular signaling pathways were also investigated. Mechanical stretching experiments were conducted to simulate Piezo1 activation in HConjECs. Inin vivostudies, using immunohistochemistry, rats were administered Yoda1 eye drops to examine the inflammatory response in the conjunctiva and Piezo1-induced signaling activation.

Results

HConjECs expressed functional Piezo1 channel, and its activation significantly increased IL-6 and IL-8 expression through the p38 MAPK-CREB pathway. Piezo1-induced [Ca2+]ielevation was crucial for the production of IL-6. Mechanical stretching mimicked these effects.In vivo, Yoda1 administration led to enhanced immunoreactivity of phospho-p38 MAPK and phospho-CREB and increased IL-6 in the rat conjunctival epithelium. Significant neutrophil infiltration was also observed after Piezo1 channel activation without affecting eosinophil numbers.

Conclusion

Mechanical stress-induced Piezo1 channel activation in conjunctival epithelial cells can cause ocular inflammation by upregulating pro-inflammatory cytokines via the p38 MAPK-CREB pathway and promoting neutrophil infiltration. These findings suggest that mechanical stimuli on ocular surface tissues are significant risk factors for ocular inflammation.

Highlights

Piezo1 channel activation increased IL-6 via p38 MAPK-CREB pathway in Human conjunctival epithelial cells (HConjECs).

Piezo1 activation mimicked fungal extract but not pollen or dust mite.

Mechanical stretching mimicked Piezo1 effects, boosting IL-6 production in HConjECs.

Piezo1 activation elevated p-p38 MAPK, p-CREB, and IL-6 in the rat conjunctiva.

Piezo1 activation leads to neutrophil infiltration in the rat conjunctival epithelium.

Graphical abstract

Mechanosensitive Piezo1 channel activation induces IL-6 expression in the conjunctival epithelial cells via elevation of [Ca2+]iand activation of p38 MAPK and transcription factor CREB.

Mechanical stress stimulates Piezo1 channel and Ca2+influx through it, which induces activation of p38 MAPK. A transcription factor CREB is phosphorylated after p38 MAPK activation, then promotesIL-6transcription.
Aromatase in adipose tissue exerts an osteoprotective function in male mice via phosphate regulation
Authors: Ikedo Aoi , Yamashita Michiko , Hoshino Maiko , Okuno Yosuke , Koike Megumi , Uga Minori , Tanifuji Kazuya , Segawa Hiroko , Fukumoto Seiji , Imai Yuuki
Published: June 2024

Aromatase contributes to maintenance of bone mass because male patients with loss-of-function mutations ofCYP19A1exhibit bone loss. Treatment with aromatase inhibitor also causes bone loss in men and post-menopausal women, suggesting that part of the anabolic effect of testosterone in men is dependent on estradiol (E2) biosynthesized by aromatase in non-gonadal tissues. It remains unclear how locally biosynthesized E2 contributes to maintenance of bone mass. We examined the function of aromatase in local tissues rather than gonads using cell-type specific aromatase knockout (KO) mice. Because osteoblast-specific aromatase KO mice exhibited no bone phenotype, we focused on adipose tissue, known as a reservoir of steroid hormones and analyzed the bone phenotypes of adipose tissue-specific aromatase KO (AroΔaP2) mice. Sixteen-week-old maleAroΔaP2mice exhibited significantly lower bone mineral density in tibia and femur, especially in trabecular bone, than controls. Bone histomorphometry showed thatAroΔaP2mice exhibited an insufficient calcification bone phenotype with increased osteoid volume and width, and decreased osteoclast area and numbers. Moreover, serum phosphate, renal phosphate reabsorption and FGF23 were significantly lower inAroΔaP2, suggesting that the insufficient calcification phenotype inAroΔaP2was not caused by excessive FGF23 activities. Finally, we analyzed NaPi2a and NaPi2c, phosphate transporters localized in the kidney, and found that protein levels in renal brush border membrane vesicles were lower inAroΔaP2. These results indicate that estrogens locally biosynthesized by aromatase in adipocytes can play a significant role in bone mass maintenance via regulation of phosphate reabsorption in the kidney by NaPi2.

Impact Statement

Male adipocyte-specific aromatase KO mice (AroΔaP2) exhibited bone loss and increased osteoid due to decreased serum phosphate and urinary phosphate reabsorption as a result of reduced NaPi2 proteins expression in the kidney.
Astrocytic glutamate regulation is implicated in the development of stress-related psychiatric disorders
Authors: Kaul Dominic , Curry Amber R , Gerstner Nathalie , Fröhlich Anna S , Smith Caine C , Sutherland Greg T , Dottori Mirella , Ziller Michael J , Binder Elisabeth B , Knauer-Arloth Janine , Mechawar Naguib , Schwab Sibylle G , Ooi Lezanne , Matosin Natalie
Published: June 2024

Severe psychological stress is one of the most potent risk factors for developing a mood or psychotic disorder, yet the underlying molecular mechanisms are poorly understood. Astrocytes are a key brain cell type associated with stress and psychiatric phenotypes in animals, but how this translates to humans is largely unknown. Here, we show that cortical astrocytes are persistently changed both physically and molecularly in humans with psychiatric disorders exposed to profound stress before diagnosis. By profiling the diversity of human astrocytes with single nucleus and spatial transcriptomics, we identified distinct alterations to glutamate-related synaptic functions, supported by histological quantification of >20,000 astrocytes. Alterations were pronounced in females compared to males and in cases exposed to profound stress during childhood. The use of human pluripotent stem cell-derived astrocytes confirmed that glutamate signalling is directly impacted by glucocorticoid activation. Our findings suggest that astrocytes are strategic pharmacological targets for future intervention strategies.
Control of epiblast cell fate by mechanical cues
Authors: Guillot Charlène , Djeffal Yannis , Serra Mattia , Pourquié Olivier
Published: June 2024

In amniotes, embryonic tissues originate from multipotent epiblast cells, arranged in a mosaic of presumptive territories. How these domains fated to specific lineages become segregated during body formation remains poorly understood. Using single cell RNA sequencing analysis and lineage tracing in the chicken embryo, we identify epiblast cells contributing descendants to the neural tube, somites and lateral plate after completion of gastrulation. We show that intercalation after cell division generates important movements of epiblast cells which lead to their relocation to different presumptive territories, explaining this broad spectrum of fates. This tissue remodeling phase is transient, being soon followed by the establishment of boundaries restricting cell movements therefore defining the presumptive territories of the epiblast. Finally, we find that the epiblast faces distinct mechanical constraints along the antero-posterior axis, leading to cell fate alterations when challenged. Together, we demonstrate the critical role of mechanical cues in epiblast fate determination.
Integrating episodic and spatial context signals in the hippocampus
Authors: Nitsch Alexander , de Haas Naomi , Garvert Mona M. , Doeller Christian F.
Published: June 2024

Episodic and spatial memory are the two key components of the mnemonic system in humans. Episodic memory enables us to remember events from the past whereas spatial memory enables us to form a map-like representation of the environment. Interestingly, these seemingly different functions rely on the same brain structure: the hippocampus. Yet, how the hippocampus supports both at the same time remains unclear. Here, we tested the hypotheses that the hippocampus supports these two systems either via a common coding mechanism or via a parallel processing mechanism. To this end, we combined functional magnetic resonance imaging (fMRI) with an episodic life-simulation task and a spatial virtual reality task to manipulate episodic and spatial context associations of objects. We then investigated fMRI adaptation effects between these objects as a result of shared contexts. We found that the fMRI signal in the anterior hippocampus scaled with the combined prediction of shared episodic and spatial contexts, in line with the idea of a common coding mechanism. We found no evidence for a parallel processing mechanism, as there were no differences between episodic and spatial effects. The common coding effect for episodic and spatial memory dovetails with the broader notion of domain-general hippocampal cognitive maps.