bluuebunny/crossref_metadata_2025 huggingface dataset:
Esophageal achalasia presenting as recurrent pneumonia in children: A case series
Authors: Asseri Ali Alsuheel , Shati Ayed A. , Al-Benhassan Ibrahim , Jabali Shahad H. , Alolah Taghreed A. , Albarqi Nada H. , Alqahtani Mansour S.
Published: November 2024

Esophageal achalasia (EA) is a rare primary esophageal motility disorder that is considered a rare etiology of dysphagia among infants and children. The proposed primary pathophysiology is related to the loss of ganglion cells in the distal esophageal sphincters, particularly in the Auerbachian muscle layer, which then leads to the dysmotility and failure of lower esophageal sphincter relaxation. Dysphagia, vomiting, poor weight gain, cough, and recurrent aspiration pneumonia are the most common presenting complaints. Herein, we report 3 cases of EA who presented with chronic cough and recurrent aspiration pneumonia. This study reviewed 3 pediatric patients with typical symptoms of EA. All the patients were admitted and referred to the pediatric pulmonology service for evaluation of recurrent pneumonia and suspected aspiration syndrome. All patients underwent a barium esophagogram as a part of the aerodigestive workup of recurrent vomiting, dysphagia, and aspiration pneumonia. Additionally, all the patients underwent workup for other associated congenital anomalies, which included echocardiography, brain magnetic resonance imaging, and an abdominal ultrasound. All patients had EA and presented with recurrent pneumonia. All patients had isolated EA, and none had any evidence of Allgrove syndrome. Pneumatic balloon dilatation was performed for all patients at the same time as the upper gastrointestinal endoscopy. Later, all the patients underwent a laparoscopic Heller myotomy and had no postoperative complications, and their symptoms resolved. EA is a rare condition in children, yet it can be a serious and life-threatening condition if left untreated. Our cases emphasize the significance of considering achalasia in children who experience esophageal dysphagia and recurrent pneumonia. Several pediatric cases have been reported in which respiratory involvement was the primary manifestation of achalasia. These cases highlight the importance of considering gastrointestinal disorders, particularly EA, in the differential diagnosis of children who experience recurrent pneumonia. Early diagnosis and treatment with laparoscopic Heller myotomy can lead to good outcomes for children with achalasia.
Early Telephone-Based Frailty Screening With the Vulnerable Elders Survey in Adults Aged 75 Years and Older With Lung and Gynecological Cancer
Authors: Cabrera-Jaime Sandra , Hernández-Marfil Anais , Adamuz-Tomas Jordi , Sánchez-Martín Silvia
Published: November 2024

Background

The International Society of Geriatric Oncology recommends that all older people with cancer have a geriatric evaluation before beginning treatment.

Objective

To determine the prevalence of frailty in people 75 years and older diagnosed with lung or gynecological cancer and evaluate the adaptation of standard therapeutic strategies based on frailty, following the implementation of telephone-based frailty screening with the Vulnerable Elders Survey (VES-13).

Interventions/Methods

We performed a retrospective observational study in 362 people screened by an advanced practice nurse before their first oncology appointment. We collected secondary data from electronic medical records. The main variables were degree of frailty (according to VES-13 and comprehensive geriatric assessment), type of cancer treatment (standard and prescribed), treatment completion, sociodemographic characteristics, and comorbidities.

Results

The VES-13 detected 186 people (51.4%) at risk of health deterioration, and the comprehensive geriatric assessment confirmed some degree of frailty in 157 people (43.4%), with aκcoefficient of 0.84. People with more comorbidities, greater frailty, and more geriatric syndromes were more likely to need treatment readjustment (P< .001).

Conclusions

Telephone-based frailty screening by an advanced practice nurse showed high applicability, with very good agreement between the proportion of people classified as frail before the initial visit and in the subsequent geriatric assessment.

Implications for Practice

A protocol for establishing frailty risk through telephone screening by an advanced practice nurse facilitates the care process and helps clinicians adapt therapeutic decision-making to the needs of each patient and their family.
GHOSTS: Generation of synthetic hospital time series for clinical machine learning research
Authors: Zhumagambetov Rustam , Giesa Niklas , Boie Sebastian D. , Haufe Stefan
Published: November 2024

Machine learning (ML) holds great promise to support, improve, and automatize clinical decision-making in hospitals. Data protection regulations, however, hinder abundantly available routine data from being shared across sites for model training. Generative models can overcome this limitation by learning to synthesize hospital data from a target population while ensuring data privacy. Clinical time series acquired during intensive care are, however, difficult to model using established techniques, especially due to uneven sampling intervals. Here we introduce GHOSTS (Generator of Hospital Time Series), a novel generator of synthetic patient trajectories that is capable of generating heterogeneous hospital data including realistic time series with uneven sampling intervals. We further design a suite of novel benchmarks, GHOSTS-Bench. We train GHOSTS on a large cohort of patient data from the MIMIC-IV critical care dataset and measure the quality of the generated data in terms of how faithfully the distributions of individual features in the real data are approximated, how well spatio-temporal dynamics in the multivariate time series are preserved, and how well ML models trained on the generated data can solve a clinical prediction task on the real data. We observe that GHOSTS outperforms a state-of-the-art approach, DoppelGANger, with respect to these criteria.
The Accumulation of Progerin Underlies the Loss of Aortic Smooth Muscle Cells in Hutchinson-Gilford Progeria Syndrome
Authors: Kim Paul H. , Kim Joonyoung R. , Heizer Patrick J. , Jung Hyesoo , Tu Yiping , Presnell Ashley , Scheithauer Julia , Yu Rachel G. , Young Stephen G. , Fong Loren G.
Published: November 2024

Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disorder characterized by multiple aging-like phenotypes, including disease in large arteries. HGPS is caused by an internally truncated prelamin A (progerin) that cannot undergo the ZMPSTE24-mediated processing step that converts farnesyl-prelamin A to mature lamin A; consequently, progerin retains a carboxyl-terminal farnesyl lipid anchor. In cultured cells, progerin and full-length farnesyl-prelamin A (produced inZmpste24−/–cells) form an abnormal nuclear lamin meshwork accompanied by nuclear membrane ruptures and cell death; however, these proteins differ in their capacity to cause arterial disease. In a mouse model of HGPS (LmnaG609G), progerin causes loss of aortic smooth muscle cells (SMCs) by ∼12 weeks of age. In contrast, farnesyl-prelamin A inZmpste24−/–mice does not cause SMC loss—even at 21 weeks of age. In young mice, aortic levels of farnesyl-prelamin A inZmpste24−/–mice and aortic levels of progerin inLmnaG609G/+mice are the same. However, the levels of progerin and other A-type lamins increase with age inLmnaG609G/+mice, whereas farnesyl-prelamin A and lamin C levels inZmpste24−/–mice remain stable.Lmnatranscript levels are similar, implying that progerin influences nuclear lamin turnover. We identified a likely mechanism. In cultured SMCs, the phosphorylation of Ser-404 by AKT (which triggers prelamin A degradation) is reduced in progerin. In mice, AKT activity is significantly lower inLmnaG609G/+aortas than in wild-type orZmpste24−/–aortas. Our studies identify that the accumulation of progerin inLmnaG609Gaortas underlies the hallmark arterial pathology in HGPS.

One Sentence Summary

The age-related accumulation of progerin in smooth muscle cells (SMCs) explains the loss of arterial SMCs in Hutchinson-Gilford progeria syndrome.
Counterfactual Diffusion Models for Mechanistic Explainability of Artificial Intelligence Models in Pathology
Authors: Žigutytė Laura , Lenz Tim , Han Tianyu , Hewitt Katherine J. , Reitsam Nic G. , Foersch Sebastian , Carrero Zunamys I. , Unger Michaela , Pearson Alexander T. , Truhn Daniel , Kather Jakob Nikolas
Published: November 2024

Background

Deep learning can extract predictive and prognostic biomarkers from histopathology whole slide images, but its interpretability remains elusive.

Methods

We develop and validate MoPaDi (Morphing histoPathology Diffusion), which generates counterfactual mechanistic explanations. MoPaDi uses diffusion autoencoders to manipulate pathology image patches and flip their biomarker status by changing the morphology. Importantly, MoPaDi includes multiple instance learning for weakly supervised problems. We validate our method on four datasets classifying tissue types, cancer types within different organs, center of slide origin, and a biomarker – microsatellite instability. Counterfactual transitions were evaluated through pathologists’ user studies and quantitative cell analysis.

Results

MoPaDi achieves excellent image reconstruction quality (multiscale structural similarity index measure 0.966–0.992) and good classification performance (AUCs 0.76–0.98). In a blinded user study for tissue-type counterfactuals, counterfactual images were realistic (63.3–73.3% of original images identified correctly). For other tasks, pathologists identified meaningful morphological features from counterfactual images.

Conclusion

MoPaDi generates realistic counterfactual explanations that reveal key morphological features driving deep learning model predictions in histopathology, improving interpretability.
KOnezumi-AID: A Software to Automate the Design of Multiplex Knockouts Using Target-AID
Authors: Taki Taito , Morimoto Kento , Mizuno Seiya , Kuno Akihiro
Published: November 2024

With the groundbreaking advancements in genome editing technologies, particularly CRISPR-Cas9, creating knockout mutants has become highly efficient. However, the CRISPR-Cas9 system introduces DNA double-strand breaks, which can increase the risk of chromosomal rear-rangements, presenting a major obstacle when attempting to knockout multiple genes simultaneously. Base editing systems like Target-AID provide a safer alternative by enabling precise base modifications without requiring DNA double-strand breaks, making them a promising solution for addressing this challenge. Nevertheless, the absence of adequate tools to support Target-AID-based gene knockouts highlights the need for a comprehensive system to design guide RNA (gRNA) for the simultaneous knockout of multiple genes. Here, we present KOnezumi-AID, a command-line tool designed to facilitate gRNA design for Target-AID-mediated genome editing. KOnezumi-AID supports gene knockout strategies by inducing premature termination codons or promoting exon skipping. It generates experiment-ready gRNA designs for both mouse and human genomes. Additionally, KOnezumi-AID offers batch processing capabilities, enabling rapid and precise gRNA design for large-scale genome editing projects such as CRISPR screening. In summary, KOnezumi-AID provides an efficient and user-friendly tool for gRNA design, streamlining genome editing workflows and advancing gene knockout research.
AutoPM3: Enhancing Variant Interpretation via LLM-driven PM3 Evidence Extraction from Scientific Literature
Authors: Li Shumin , Wang Yiding , Liu Chi-Man , Huang Yuanhua , Lam Tak-Wah , Luo Ruibang
Published: November 2024

Rare diseases, affecting 300 million people globally, often result from genetic variants. Wholegenome sequencing has made variant detection more cost-effective, but interpreting these variants remains challenging. Current clinical practice combines quantitative evidence and literature, which is complex and time-consuming. We introduce AutoPM3, a method for automating the extraction of ACMG/AMP PM3 evidence from scientific literature using open-source LLMs. It combines an optimized RAG system for text comprehension and a TableLLM equipped with Text2SQL for data extraction. We evaluated AutoPM3 using our collected PM3-Bench, a dataset from ClinGen with 1,027 variant-publication pairs. AutoPM3 significantly outperformed other methods in variant hit andin transvariant identification, thanks to the four key modules. Additionally, we wrapped AutoPM3 with a user-friendly interface to enhance its accessibility. This study presents a powerful tool to improve rare disease diagnosis workflows by facilitating PM3-relevant evidence extraction from scientific literature.
Imaging Infants and Children with Investigational Handheld Optical Coherence Tomography with Widefield Lens: A Pilot Study
Authors: Li Angela S. , Imperio Ryan , Tran-Viet Du , Mangalesh Shwetha , Prakalapakorn S. Grace , Vajzovic Lejla , Maldonado Ramiro , Freedman Sharon F. , Chen Xi
Published: November 2024

Handheld optical coherence tomography (OCT) systems have shown promises to provide detailed evaluation of the pediatric retina. It is less stressful for preterm infants compared to binocular indirect ophthalmoscopy and shows promises for screening for retinopathy of prematurity. There are currently only one commercially available non-contact handheld OCT systems, and no commercially available widefield handheld OCT systems. Here we report and evaluate the first use of the Theia Imaging Investigational handheld OCT system with widefield lens (T1-W, Theia Imaging, Durham, NC) in pediatric subjects. We compare the OCT en face view to handheld widefield or tabletop ultra-widefield fundus photographs and evaluate the ability to visualize the vitreoretinal interface, intraretinal, subretinal and choroidal features on cross-sectional OCT scans.
High-accuracy prediction of 5-year progression-free melanoma survival using spatial proteomics and few-shot learning on primary tissue
Authors: Möller Anna , Ostalecki Christian , Hartebrodt Anne , Breininger Katharina , Erdmann Michael , Uderhardt Stefan , Baur Andreas , Blumenthal David B.
Published: November 2024

Emerging techniques in imaging-based spatial proteomics (ISP) enable in-depth insights into the architecture and protein abundance of tissue(s). Explainable machine learning (xML) models promise to yield substantial advances in ISP data-based diagnosis and prognosis. However, a clinical application of these new possibilities predicting the course of a tumor has not been suggested yet. Here, we use a few-shot learning workflow on histological multi-antigen images to predict 5-year progression-free survival (PFS) in melanoma. We address the problem of a relatively small cohort (n= 22), by utilizing a pre-trained convolutional neural network (CNN) model, which we further pre-train on a proxy task for which more samples were available (n= 39) before fine-tuning for PFS prediction. Our approach yielded a model achieving an accuracy of more than 90%, outperforming baseline models trained on clinical data by around 10%. Using an xML technique, we identified immune infiltration and proteins associated with tumor progression as crucial predictors. This indicated that our models’ PFS predictions are not only highly accurate but also grounded in a relevant biological background.
Comparative antioxidant activity ofOcimum gratissimumandJatropha tanjorensis2024
Authors: Ike Emmanuel Chukwuebuka , Wokota Paschal N. , Nnenna Gabez Lynda
Published: November 2024

Introduction

The leaves ofOcimum gratissimumandJatropha tanjorensisare widely used together as vegetables in food and in several preparations for medicinal purposes. For this reason, their combined antioxidant potentials were evaluated to ascertain if such preparations should be encouraged or otherwise in relation to their individual antioxidant effects.

Materials and Methods

the combined extract ofO.gratissimumandJ. tanjorensis(CEOJ) were serially diluted into different concentrations; concentrations of 1.9µg/ml, 3.91µg/ml, 7.81µg/ml, 15.63µg/ml, 31.25µg/ml, 62.5µg/ml, 125µg/ml and 250µg/ml were made and used for the assays. the single extracts were also diluted into similar concentrations. DPPH in methanol was used as blank for the DPPH-free radical scavenging assay. The absorbance of the concentrations and that of the controls were read at 517nm and 562nm for the DPPH assay using a spectrophotometer.

Results

The result of the DPPH-free radical scavenging assay showed a synergistic antioxidant effects in CEOJ with an inhibition percentage of 71.39% higher thanJ. tanjorensisalone (66.80%)O. gratissimumalone (53.56%) and ascorbic acid (56%).

Conclusion

This results therefore inferred that the CEOJ produced better antioxidant activity than when used as a separate extract.
Intelligence and Cognitive Flexibility Selectively Modulate Working Memory Functioning
Authors: Zhang Heming , Meng Chun , Xu Xinyu , Hu Xin , Zhang Ziqian , Klugah-Brown Benjamin , Biswal Bharat B.
Published: November 2024

Working memory is a key component of intelligence, which can be underpinned by task connectome, while cognitive flexibility plays a role in adaptive and executive function that supports working memory processes. However, it remains unknown how intelligence and cognitive flexibility modulate working memory functioning, in terms of behavioural performance and task-related brain hierarchy. Current study investigated the working memory task-related behaviour and brain connectomic gradient in healthy adults together with their intelligence and cognitive flexibility measures. Results showed cognitive flexibility and intelligence were not significantly correlated with each other but with working memory function. Principal component and partial least square analysis revealed that nearly half of variance was explained by their overlap component, which linked with task gradient values of frontoparietal and ventral attention network representing executive, control and cognitive functioning. Individuals with higher intelligence and cognitive flexibility showed less distance between frontoparietal/ventral attention network and unimodal regions in gradient axis during working memory performance. Further analyses demonstrated that task gradient of frontoparietal and ventral attention network was significantly associated with working memory function, and selectively mediated by cognitive flexibility and intelligence, which may suggest partly convergent neural mechanisms for higher order functions that are involved in working memory functioning. In conclusion, current study provides new insight into the relationship among task connectomic gradient, working memory, intelligence, and cognitive flexibility, which helps understand the multi-component model of working memory and underlying task gradient principle.
MethylGPT: a foundation model for the DNA methylome
Authors: Ying Kejun , Song Jinyeop , Cui Haotian , Zhang Yikun , Li Siyuan , Chen Xingyu , Liu Hanna , Eames Alec , McCartney Daniel L , Marioni Riccardo E. , Poganik Jesse R. , Moqri Mahdi , Wang Bo , Gladyshev Vadim N.
Published: November 2024

DNA methylation serves as a powerful biomarker for disease diagnosis and biological age assessment. However, current analytical approaches often rely on linear models that cannot capture the complex, context-dependent nature of methylation regulation. Here we present MethylGPT, a transformer-based foundation model trained on 226,555 (154,063 after QC and deduplication) human methylation profiles spanning diverse tissue types from 5,281 datasets, curated 49,156 CpG sites, and 7.6 billion training tokens. MethylGPT learns biologically meaningful representations of CpG sites, capturing both local genomic context and higher-order chromosomal features without external supervision. The model demonstrates robust methylation value prediction (Pearson R=0.929) and maintains stable performance in downstream tasks with up to 70% missing data. Applied to age prediction across multiple tissue types, MethylGPT achieves superior accuracy compared to existing methods. Analysis of the model’s attention patterns reveals distinct methylation signatures between young and old samples, with differential enrichment of developmental and aging-associated pathways. When finetuned to mortality and disease prediction across 60 major conditions using 18,859 samples from Generation Scotland, MethylGPT achieves robust predictive performance and enables systematic evaluation of intervention effects on disease risks, demonstrating potential for clinical applications. Our results demonstrate that transformer architectures can effectively model DNA methylation patterns while preserving biological interpretability, suggesting broad utility for epigenetic analysis and clinical applications.
Critical assay parameters facilitating confident detection of expression changes, fusions and short variants in RNA isolated from tissue
Authors: Kubik Slawomir , Matyszczak Izabela , Toda Nicholas , Magrinelli Elia , Helleboid Pierre-Yves , Smith Ewan , Bezrukov Fedor , Ryder Chloe , Lopez Jonathan , Harlé Alexandre , Xu Zhenyu
Published: November 2024

Molecular assays based on next-generation sequencing of RNA can provide clinically relevant information by measuring gene expression levels, identifying gene fusions, aberrant transcript isoforms and detecting small variants. Nevertheless, achieving good performance and reliable result interpretation present a significant challenge.

In this work, we dissect the impact of various technical factors on the concurrent detection of several biomarker types using a hybridization enrichment-based targeted RNA sequencing applied to a cohort of more than one hundred samples derived from diverse solid tumors.

We demonstrate that several critical parameters inferred from the sequencing data should be controlled to interpret the results accurately. These include molecular coverage of reference genes as a proxy of RNA conversion, DNA content measure, and the extent of target molecular coverage. We summarize our findings with recommendations allowing maximum reliable information recovery from targeted RNA sequencing data.
Signatures of selective sweeps in urban and rural white clover populations
Authors: Santangelo James S. , Johnson Marc T. J. , Ness Rob W.
Published: November 2024

Urbanization is increasingly recognized as a powerful force of evolutionary change. However, anthropogenic sources of selection can often be similarly strong and multifarious in rural habitats, but these are often ignored in studies of urban evolutionary ecology. Despite numerous examples of phenotypic differentiation between urban and rural populations, we still lack an understanding of the genes enabling adaptation to these contrasting habitats and the genetic architecture underlying urban and rural adaptation. In this study, we conducted whole genome sequencing of 120 urban, suburban, and rural white clover plants from Toronto, Canada. We used these data to identify signatures of selective sweeps across the genome using both SFS and haplotype-based approaches, and characterize the architecture of selective sweeps. We found evidence for selection in genomic regions involved in abiotic stress tolerance and growth/development in both urban and rural populations. Urban and rural populations did not differ in the proportion of hard vs. soft sweeps, though urban populations were characterized by wider sweeps, which may indicate differences in the strength or timescale of selection. In addition, patterns of allele frequency and haplotype differentiation suggest that most sweeps are incomplete. These results highlight how both urban and rural habitats are driving ongoing selection in white clover populations, and motivate future work disentangling the genetic architecture of ecologically important phenotypes, and estimating the strength and timescale of selection underlying adaptation to contemporary anthropogenic habitats.
Synergy of LPS and Shiga-toxin exposure on the RNA expression program of cultured human umbilical vein endothelial cells
Authors: Svilar David , van der Ent Martijn A. , Siemieniak David , Ginsburg David , Cleuren Audrey C.
Published: November 2024

Background

Hemolytic uremic syndrome (HUS) is a primary thrombotic microangiopathy that can cause acute renal failure, particularly in children, and is commonly triggered by Shiga toxin-producingEscherichia coli(STEC) infection. Although previousin vitrostudies have shown that Shiga toxin (STX) can directly affect the endothelium, gram-negative bacteria such asE. colialso contain lipopolysaccharide (LPS) which is known to independently activate endothelial cells. Furthermore, studies in mice and baboons have shown a synergistic effect of LPS and STX in inducing HUS when administered simultaneously.

Objective

Determine how LPS, STX, or combined LPS/STX treatment affect the gene expression program of endothelial cells.

Methods

Human umbilical vein endothelial cells (HUVECs) were treated with STX, LPS or a combination of STX and LPS for either 4 or 24 hours, after which unbiased RNA sequencing analysis was performed.

Results

Four-hour treatment with LPS resulted in a greater number of differentially expressed genes as compared to treatment with STX. In contrast, 24-hour treatment with LPS or STX induced similar numbers of differentially expressed genes. Dual treatment with both toxins resulted in a synergistic effect, showing significant up-or downregulation of multiple transcripts that were not observed in either single treatment group, particularly at the 24-hour timepoint.

Conclusion

Our data provide a resource for assessing the role of endothelial cell gene expression in the pathogenesis of STEC infection and suggest that the responses of these cells to LPS, STX, or combined LPS/STX treatment are unique and temporally regulated.
Evidence of causality between Closure and Open-Ended Evolution in the Kauffman model
Authors: Faggian M.
Published: November 2024

Evolution is a highly intricate process marked by the generation of novelty, which necessitates the historical and collective organization of individuals. In this paper, we investigate the relationship between biological organization and Open-Ended Evolution (OEE), with a particular focus on the causal connection between the two. To provide quantitative evidence for this causal link within a chemical system, we apply assembly theory to assess how the emergence of auto-catalytic sets impacts the complexity dynamics within Kauffman’s model. In the second part of the paper, we strengthen this conjecture by analyzing the effects of the simplest auto-catalytic set on the complexity dynamics in Kauffman’s model, specifically in the absence of parametric correlation. By interpreting auto-catalytic sets as organizational structures in chemical systems, our findings provide the first numerical support for investigating the causal relationship between biological organization and OEE. This work represents a promising area for the initial study of the dynamical relationship between OEE and biological organization, and may advance the understanding of their connection in theoretical biology.
Reengineering mRNA lipid nanoparticles for systemic delivery to pancreas
Authors: Isaac Ivan , Patel Luv , Tran Nguyen , Singam Amarnath , Guha Prasun , Park Seungman , Bhattacharya Chandrabali
Published: November 2024

Lipid nanoparticles (LNPs) hold transformative potential for nucleic acid delivery, with applications ranging from clinical use, particularly in COVID-19 vaccines, to gene therapy and cancer immunotherapy. Traditional LNPs are composed of four components: ionizable lipids, cholesterol, helper lipids, and PEGylated lipids. However, a significant hurdle remains the need for more efficient and selective systemic delivery vehicles, as most targets are challenging to reach and primarily accumulate in the liver following intravenous administration, largely due to Apolipoprotein E (ApoE) mediated uptake in the blood. Recent studies have shown that introducing cationic or anionic lipids as a fifth component in the LNPs has resulted in lung- and spleen-specific mRNA expression. In this study, we report that incorporating endogenous ligands, such as vitamins, as a fifth component can enhance the extrahepatic localization of LNPs. Vitamins are highly biocompatible, possess excellent targeting potential, influence immune response, improve cellular uptake, and increase the stability of mRNA LNPs. We developed a library of 100 LNPs containing luciferase mRNA by partially replacing ionizable lipids with this fifth component and evaluated their efficacy both in vitro and in vivo. From comprehensive batch analysis screening, we identified two formulations with cholecalciferol (vitamin D3) as a fifth component that demonstrated selective systemic delivery to the pancreas (> 99%) with high efficacy. Among these, C-CholF3 emerged as the top formulation, exhibiting robust and sustained protein expression in the pancreas for up to 3 days in a dose-dependent manner with minimal toxicity that makes it suitable for repeated administration. Furthermore, C-CholF3 also demonstrated pancreas-specific gene editing in the Ai14 transgenic mouse model, showing high expression of TdTomato. This underscores its translational potential for protein replacement and CRISPR/Cas9-mediated gene editing in currently incurable pancreatic diseases.
Microtubule plus-end dynamics are tightly coupled to the turnover of the MOR1 polymerase
Authors: Eng Ryan C , Halat Laryssa S , Kuo Chak-Chung , Rakei Aida , Costain Cecily D , Diehl Kamryn A , Blutrich Ron , Lechner Bettina , Zhang Yi , Walia Ankit , Alonso Jose M , Coombs Daniel , Wasteneys Geoffrey O
Published: November 2024

MOR1/XMAP215/Dis1/Stu2 family proteins function as polymerases that promote microtubule assembly through tubulin-interacting N-terminal tumor-overexpressed gene (TOG) domains. It remains unclear how the polymerase activity of these proteins is coordinated with their movement along the growing microtubule lattice. Previously, it was found that a L174F mutation in the N-terminal TOG domain of the 217 kDaArabidopsis thalianaMICROTUBULE ORGANIZATION 1 (MOR1) protein impaired microtubule growth and shrinkage rates in a temperature-dependent manner. In this study, we used a homologous recombination strategy to generate stable transgenic lines expressing full-length MOR1 and mutant mor1-1L174Fproteins tagged with the yellow fluorescent protein YPet. When expressed inmor1mutant backgrounds, MOR1-3xYPet showed strong association with both the growing and shrinking microtubule plus ends, consistent with its involvement in both polymerization and depolymerization. By contrast, when expressed in a wild-type background, MOR1-3xYPet was redistributed along the microtubule lattice, microtubule growth rates were reduced, and plant growth was stunted. By quantifying fluorescence recovery after photobleaching, we confirmed that MOR1 has greater affinity for the plus end than the lattice. Exploiting the FRAP technique further, we identified a positive and linear correlation between microtubule polymerization rates and MOR1 turnover at the microtubule plus end. When microtubule growth rates were reduced in the mor1-1-YPet line by shifting the temperature from 21 to 30°C and for MOR1-3xYPet under taxol treatments, MOR1’s turnover was delayed. In contrast, microtubule growth rates and MOR1 turnover were hastened at 30°C or after CRISPR/Cas9-mediated knock out of the CLASP protein. These findings support a new model whereby MOR1 has finite processivity on the microtubule, catalyzing a limited fixed number of tubulin additions before dissociation.

HIGHLIGHTS

MOR1 has high affinity for both growing and shrinking microtubule plus ends, consistent with a function in both polymerization and depolymerization events.

MOR1 has greater affinity for microtubule plus ends than the lattice, and lattice binding associated with overexpression is detrimental to plant growth.

MOR1 transiently associates with the microtubule plus end, the duration of which is tightly coupled with its polymerase activity.
Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases
Authors: Lee Donghoon , Koutrouli Mikaela , Masse Nicolas Y. , Hoffman Gabriel E. , Kinrot Seon , Wang Xinyi , N.M. Prashant , Pjanic Milos , Clarence Tereza , Tsetsos Fotios , Mathur Deepika , Burstein David , Therrien Karen , Hong Aram , Casey Clara , Shao Zhiping , Alvia Marcela , Argyriou Stathis , Monteiro Fortes Jennifer , Katsel Pavel , Auluck Pavan K. , Barnes Lisa L. , Marenco Stefano , Bennett David A. ,   PsychAD Consortium, Jensen Lars Juhl , Girdhar Kiran , Voloudakis Georgios , Haroutunian Vahram , Bendl Jaroslav , Fullard John F. , Roussos Panos
Published: November 2024

Neurodegenerative and neuropsychiatric diseases impose a significant societal and public health burden. However, our understanding of the molecular mechanisms underlying these highly complex conditions remains limited. To gain deeper insights into the etiology of different brain diseases, we used specimens from 1,494 unique donors to generate a population-scale single-cell transcriptomic atlas of the human dorsolateral prefrontal cortex (DLPFC), comprising over 6.3 million individual nuclei. The cohort includes neurotypical controls as well as donors affected by eight common and complex brain disorders: Alzheimer's disease (AD), diffuse Lewy body disease (DLBD), vascular dementia (Vas), Parkinson's disease (PD), tauopathy, frontotemporal dementia, schizophrenia, and bipolar disorder. We show that inter-individual variation accounts for a substantial portion of gene expression variation in the DLPFC. By comparing transcriptomic variation across diseases, we reveal universal signatures enriched in basic cellular functions such as mRNA splicing and protein localization. After discounting these cross-disease signatures, we show strong genetic and transcriptomic concordance among AD, DLBD, Vas, and PD, largely driven by alteration of synaptic signaling functions in neurons. Furthermore, we characterize transcriptomic variation among different AD phenotypes that were distinct from healthy aging. We uncover mitigating effects of interneurons and aggravating effects of immune and vascular cells in AD dementia. Further exploring the effect of the neuropsychiatric symptoms frequently accompanying AD, we identify a link to deep layer excitatory neurons. By constructing transcriptome trajectories that capture AD progression, we show cell-type specific responses implicated in early and late stages of AD. Our atlas provides an unprecedented perspective of the transcriptomic landscape in neurodegenerative and neuropsychiatric diseases, shedding light on shared and distinct processes involving the neuro-immune-vascular systems, and identifying potential targets for therapeutic intervention.
Spatially resolved mapping of cells associated with human complex traits
Authors: Song Liyang , Chen Wenhao , Hou Junren , Guo Minmin , Yang Jian
Published: November 2024

Depicting spatial distributions of disease-relevant cells is crucial for understanding disease pathology. Here, we present a method, gsMap, that integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner. Using embryonic ST datasets covering 25 organs, we benchmarked gsMap through simulation and by corroborating known trait-associated cells or regions in various organs. Applying gsMap to brain ST data, we revealed that the spatial distribution of glutamatergic neurons (glu-neurons) associated with schizophrenia more closely resembles that for cognitive traits than that for mood traits, such as depression. The schizophrenia-associated glu-neurons were distributed near the dorsal hippocampus, with upregulated calcium signaling and regulation genes, while the depression-associated glu-neurons were distributed near the deep medial prefrontal cortex, with upregulated neuroplasticity genes. Our study provides a method for spatially resolved mapping trait-associated cells and demonstrates the gain of biological insights (e.g., spatial distribution of trait-relevant cells and related signature genes) through these maps.
Immunosuppression Drugs Exhibit Differential Effects on Endothelial Cell Function
Authors: Elezaby Aly , Dexheimer Ryan , Wu David , Chan Sze Yu , Chen Ian Y. , Sayed Nazish , Sallam Karim
Published: November 2024

Immunosuppressive medications are widely used to treat patients with neoplasms, autoimmune conditions, and solid organ transplants. Prior studies indicate that immunosuppression drugs can cause adverse vascular remodeling. Given the systemic effects of the drugs, elucidating cell-type specific drug-effects has been challenging. We utilized induced pluripotent stem-cell derived endothelial cells to investigate the role of widely used immunosuppression drugs on endothelial function. We found that among immunosuppression agents, sirolimus reduced basic endothelial cell functions including cell migration, proliferation, acetylated LDL uptake, and angiogenesis properties; while tacrolimus only reduced nitric oxide release. This model allows for investigation of differential effect of immunosuppression drugs on endothelial function that can elucidate mechanisms contributing to adverse vascular profiles observed clinically.
Gene expression and pollen performance indicate altered postmating selection betweenSolanumspecies with different mating systems
Authors: Biewer-Heisler Timothy J , Gibson Matthew JS , Sornay Emily , Moyle Leonie C
Published: November 2024

Postmating prezygotic (PMPZ) traits play an important role in mating success, especially in species where gametes from multiple males compete. Despite this, the effect of mating system transitions, and attendant shifts in the intensity of sexual selection, on specific PMPZ traits and their underlying loci is still poorly understood. Here we assessed differences in pollen PMPZ traits and tissue-specific gene expression (in leaf, pollen, and style) between two closely related plant species with different mating systems—Solanum lycopersicum(selfing) &Solanum pennellii(outcrossing). We focused on species differences in loci with known roles in pollen tube growth rate, including pectin methylesterases (PMEs) and their inhibitors (PMEIs), andin- vitro&in-vivopollen tube growth rates. Among the gene expression differences observed between species, we found that the expression domain of pollen-biased genes was much narrower in the selfing speciesS. lycopersicumcompared to the outcrossing speciesS. pennellii, including for most reproductive PMEs and PMEIs. In addition,S. pennelliihad faster pollen tube growth ratesin-vivo, whileS. lycopersicumhad fasterin-vitropollen tube growth rates. We propose that the lower expression of pollen tube development genes inS. lycopersicumstyle tissue, and reducedin-vivopollen performance, is a result of reduced allocation to stylar mechanisms that modulate pollen tube growth, potentially consistent with relaxed selection on cryptic female choice in the selfing species.

Article Summary

This study investigates the evidence for differential postmating sexual selection in plants, by analyzing reproductive gene expression and pollen performance in twoSolanumspecies with different mating systems. It finds that species differ systematically in pollen tube growth rates, and that pollen (‘male’)-biased genes have higher secondary expression in stylar (‘female’) tissues in the outcrossing species. These observations are consistent with the outcrossing species experiencing stronger selection on female reproductive tract traits that influence male postmating performance. This study evaluates key expectations of sexual selection on postmating traits but does so in the uncommon context of flowering plants.
High G-Forces in Unintentionally Improper Infant Handling: Implications for Shaken Baby Syndrome Diagnosis
Authors: Lee-Confer Jonathan S. , Wayman Lila T. , Havens Kathryn L.
Published: November 2024

Introduction

Abusive head trauma (AHT), commonly referred to as Shaken Baby Syndrome (SBS), is diagnosed in approximately 33 per 100,000 infants annually in the United States. Traditional diagnostic criteria for SBS include subdural, subarachnoid, and retinal hemorrhages. While intentional shaking is a known cause, the potential for similar forces acting on the head resulting from accidental trauma has not been fully explored. This study investigates the biomechanical forces on a model infant’s head during improper handling to determine if such forces could contribute to SBS without malicious intent.

Methods

A realistic silicone infant model was equipped with an inertial measurement unit (IMU) to quantify head accelerations during two conditions: (1) placement of the infant model on a table with the head unsupported, and (2) manual shaking at maximum effort by 2 participants holding the model by the torso. Peak head accelerations were recorded for both conditions, and the results were analyzed for comparative assessment of the forces involved.

Results

The average peak head acceleration when placing the infant model on a table with the head unsupported was +30,952.67 ± 6,540.79 mg, with a range of +19,234.40 to +43,406.30 mg across trials. The average peak head accelerations during maximum effort shaking were significantly lower than placing the infant on the table, averaging 11,430.48 ± 9,539.06,867 vs. 30,952.67 ± 6,540.79 mg, p < 0.0001). There were no significant differences in head accelerations between participants when placing the infant model on the table with the head unsupported (p = 0.93) nor with shaking the baby with maximum effort (p = 0.97).

Discussion

The G-force in this study resulted in higher forces than experienced in an 18-mph car crash and a 5-mph bumper car collision. The study highlights that even accidental non-recommended handling of infants can result in high G-forces to the head, potentially leading to injuries similar to those observed in SBS. These findings highlight the necessity of supporting an infant’s head during handling and warrants caution against prematurely attributing physical abuse in SBS cases without considering unintentional causes.
Smile-to-Bert: A BERT architecture trained for physicochemical properties prediction and SMILES embeddings generation
Authors: Barranco-Altirriba Maria , Würf Vivian , Manzini Enrico , Pauling Josch K. , Perera-Lluna Alexandre
Published: November 2024

Binding affinity and molecular property prediction are crucial for drug discovery. Over the years, deep learning models have been widely used for these tasks; however, large datasets are often needed to achieve strong performances. Pre-training models on vast unlabelled data has emerged as a method to extract contextualised embeddings that boost performance on smaller datasets. SMILES (Simplified Molecular Input Line Entry System) encode molecular structures as strings, making them suitable for natural language processing (NLP). Transformers, known for capturing long-range dependencies, are well-suited for processing SMILES. One such transformer-based architecture is BERT (Bidirectional Encoder Representations from Transformers), which only uses the encoder part of the Transformer and performs classification and regression tasks. Pre-trained transformer-based architectures using SMILES have significantly improved predictions on smaller datasets. Public data repositories such as PubChem, which provide SMILES and physicochemical properties among other data, are essential for pre-training these models. SMILES embeddings that combine chemical structure and physicochemical properties information could further enhance performance on tasks such as binding affinity prediction. For this reason, we introduce Smile-to-Bert, a pre-trained BERT architecture that predicts seven physicochemical properties from SMILES using PubChem data and two different SMILES tokenizers. Moreover, this model generates embeddings that integrate information about molecular structure and physicochemical properties. Regarding the prediction of physicochemical properties, the mean absolute errors obtained are: H-bond acceptors (0.0502), H-bond donors (0.0048), rotatable bonds (0.0949), exact mass (0.5678), TPSA (0.4961), heavy atom count (0.0345), and log-P (0.2219). Additionally, the usefulness of the generated embeddings is evaluated using two binding affinity datasets and their performance is compared to embeddings created by a state-of-the-art Transformer. We show that the SmilesPE tokenizer works better than the atom-level one and that integrating the embeddings generated by Smile-to-Bert to the state-of-the-art Transformer embeddings improves the prediction of binding affinity in one of the datasets. A dashboard for the prediction of physicochemical properties is available athttp://147.83.252.32:8050/, and the code is accessible athttps://github.com/m-baralt/smile-to-bert.
An alternative route for β-hydroxybutyrate metabolism supports fatty acid synthesis in cancer cells
Authors: Kaluba Faith C. , Rogers Thomas J. , Jeong Yu-Jin , Waldhart Althea , Sokol Kelly H. , Lee Cameron J. , Daniels Samuel R. , Longo Joseph , Johnson Amy , Sheldon Ryan D. , Jones Russell G. , Lien Evan C.
Published: November 2024

Cancer cells are exposed to diverse metabolites in the tumor microenvironment that are used to support the synthesis of nucleotides, amino acids, and lipids needed for rapid cell proliferation1–3. Recent work has shown that ketone bodies such as β-hydroxybutyrate (β-OHB), which are elevated in circulation under fasting conditions or low glycemic diets, can serve as an alternative fuel that is metabolized in the mitochondria to provide acetyl-CoA for the tricarboxylic acid (TCA) cycle in some tumors4–7. Here, we discover a non-canonical route for β-OHB metabolism, in which β-OHB can bypass the TCA cycle to generate cytosolic acetyl-CoA forde novofatty acid synthesis in cancer cells. We show that β-OHB-derived acetoacetate in the mitochondria can be shunted into the cytosol, where acetoacetyl-CoA synthetase (AACS) and thiolase convert it into acetyl-CoA for fatty acid synthesis. This alternative metabolic routing of β-OHB allows it to avoid oxidation in the mitochondria and net contribute to anabolic biosynthetic processes. In cancer cells, β-OHB is used for fatty acid synthesis to support cell proliferation under lipid-limited conditionsin vitroand contributes to tumor growth under lipid-limited conditions induced by a calorie-restricted dietin vivo. Together, these data demonstrate that β-OHB is preferentially used for fatty acid synthesis in cancer cells to support tumor growth.
Gaming the cancer-immunity cycle by synchronizing the dose schedules
Authors: Mahmoodifar S. , Newton P.K.
Published: November 2024

We introduce a mathematical model of the cancer-immunity cycle and use it to test several hypotheses regarding the combination, timing, and optimization associated with chemotherapy and immunotherapy dosing schedules in the context of competition and selection pressure. A key conceptual idea is the value of synchronizing the dosing schedules with the fundamental period of the cancer-immunity cycle. The competitors in the population dynamics evolutionary game are the cancer cells, healthy cells, and T-cells, which form a non-transitive rock-paper-scissor chain, mediated by the tumor microenvironment. The chemotherapy and immunotherapy dosing schedules each act as control functions whose timing we synchronize with the fundamental period of the underlying nonlinear dynamical system. With the model, we show among other more detailed results, that chemotherapy and immunotherapy schedules are non-transitive; the best duration of the chemotherapy is around one-quarter of the cancer-immunity cycle, whereas for immunotherapy it is one-half cycle; immunotherapy dosing should preceed chemotherapy dosing. A general conclusion is that optimized timing of the dosing schedules can make up for lower total dose, opening up new possibilities for designing less toxic and more efficacious dosing regimens with drugs currently in use. Obtaining and calibrating more accurate measurements of the cycle-period across patient populations would be an important step in making some of these ideas clinically actionable.