bluuebunny/crossref_metadata_2025 huggingface dataset:
ERGA-BGE Reference Genome ofGluvia dorsalis: An Endemic Sun Spider from Iberian Arid Regions
Authors: Lozano-Fernandez Jesus , Domènech Marc , Ibos Attila , Marcussen Thomas , Struck Torsten H. , Oomen Rebekah , Böhne Astrid , Monteiro Rita , Aguilera Laura , Gut Marta , Câmara Ferreira Francisco , Cruz Fernando , Gómez-Garrido Jèssica , Alioto Tyler S. , De Panis Diego
Published: December 2024

The reference genome ofGluvia dorsalisis the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.
Opposing lineage specifiers induce a pro-tumor hybrid-identity state in lung adenocarcinoma
Authors: Fort Gabriela , Arnold Henry , Camolotto Soledad , Tariq Rushmeen , Waters Anna , O’Toole Kayla , Snyder Eric L.
Published: December 2024

The ability of cancer cells to alter their identity, known as lineage plasticity, is crucial for tumor progression and therapy resistance. In lung adenocarcinoma (LUAD), tumor progression is characterized by a gradual loss of lineage fidelity and the emergence of non-pulmonary identity programs. This can lead to hybrid-identity (hybrid-ID) states in which developmentally incompatible identity programs are co-activated within individual cells. However, the molecular mechanisms underlying these identity shifts remain incompletely understood. Here, we identify the gastrointestinal (GI) transcriptional regulator HNF4α as a critical driver of tumor growth and proliferation in KRAS-driven LUAD. In LUAD cells that express the lung lineage specifier NKX2-1, HNF4α can induce a GI/liver-like state by directly binding and activating its canonical targets. HNF4α also forms an aberrant protein complex with NKX2-1, which disrupts NKX2-1 localization and dampens pulmonary identity within hybrid-ID LUAD. Sustained signaling through the RAS/MEK pathway is critical for maintaining the hybrid-ID state. Moreover, RAS/MEK inhibition augments NKX2-1 chromatin binding at pulmonary-specific genes and induces resistance-associated pulmonary signatures. Finally, we demonstrate that HNF4α depletion enhances sensitivity to pharmacologic KRASG12Dinhibition. Collectively, our data show that co-expression of opposing lineage specifiers leads to a hybrid identity state that can drive tumor progression and dictate response to targeted therapy in LUAD.
HAPLODIPLOIDY ACCELERATES MITOGENOME EVOLUTION IN INSECTS
Authors: Pakrashi Avas , Hebert Paul DN
Published: December 2024

Rates of mitogenome evolution differ among animal lineages, variation which has been linked to life history, ecological traits, and potentially to breeding system. Insects are a good model for examining the latter impacts as, although most are diplodiploids (DD), some lineages reproduce by haplodiploidy (HD) or thelytoky. In this study, we ask if breeding system influences patterns of evolution in the mitogenome using the 658 bp barcode region of the cytochromecoxidase I (COI) gene as a sentinel. Specifically, we ask if the incidence of amino acid substitutions and indels is linked to breeding system. We investigated this matter by examining COI sequences from specimens assigned to 1332 BINs, a species proxy. Belonging to 513 families and 26 orders, these BINs included representatives of roughly half of all insect families. Most are DD, but ten lineages, varying in rank from tribe to order, are HD. Our analysis reveals that HD lineages show higher rates of amino acid substitution than DD. In addition, indels are frequent in HD lineages but are absent in DD taxa with one exception. Among DD, the Strepsiptera is an outlier; its COI shows very rapid amino acid evolution and frequent indels. The accelerated rates of mitogenome evolution in HD lineages suggest that this breeding system facilitates coevolution between the nuclear and mitochondrial genomes.
Prediabetes Phenotype Clusters in the Diabetes Prevention Program Study
Authors: Stroebel Benjamin M. , Gadgil Meghana , Lewis Kimberly , Longoria Kayla , Zhang Li , Flowers Elena
Published: December 2024

Objective

The purpose of this study was to apply clustering methods to identify and characterize prediabetes phenotypes and their relationships with treatment arm and type 2 diabetes (T2D) outcomes in the Diabetes Prevention Program (DPP), and to compare the utility of additional clustering measures in phenotype characterization and T2D risk stratification.

Research Design and Methods

This was a secondary analysis of data from a subset of participants (n=994) from the previously completed Diabetes Prevention Program trial. Unsupervised k-means clustering analysis was applied to derive the optimal number of clusters of participants based on common clinical risk factors alone or common risk factors plus more comprehensive measures of glucose tolerance and body composition.

Results

Five clusters were derived from common clinical characteristics and the addition of comprehensive measures of glucose tolerance and body composition. Within each modeling approach, participants show significantly different levels of risk factors. The clinical only model showed higher accuracy for time to T2D, however the more comprehensive models further differentiated a metabolically health overweight phenotype. For both models, the greatest differentiation in determining time to T2D was in the metformin arm of the trial.

Conclusions

Data driven clustering of patients with prediabetes allows for identification of prediabetes phenotypes at greater risk for disease progression and responses to risk reduction interventions. Further investigation into phenotypic differences in treatment response could enable better personalization of prediabetes and T2D prevention and treatment choices.
Unraveling the Phenotype of Dormant Metastases Controlled by the Immune System
Authors: Chamorro Virginia , Algarra Ignacio , Sanz Verónica , Pulido María , Romero Irene , Chico Estefanía , Millán Marina , Escaño-Maestre María , Linares Isabel , García-Lora Ángel M.
Published: December 2024

During the progression of cancer, metastatic cells frequently enter a dormant phase. The immune system plays a crucial role by restricting the growth of dormant metastases, although it cannot eradicate them. In our laboratory, we developed a preclinical mouse model of metastatic dormancy. Dormant spontaneous metastases are controlled by the immune system of wild-type mice. Depletion of the host immune system causes these metastases to awaken and progress. The elucidation of the phenotype, genes, miRNAs and immune cells involved in the phenomenon of metastatic dormancy may prove in the development of effective strategies for combating metastatic disease. Dormant Metastases are compared with Nude Metastases and Overt Metastases that have never been in dormancy. The findings of the study indicate that the dormant metastases exhibit a unique and differentiated phenotype. This is evidenced by their varied response to nutrient-restrictive conditions, chemotherapeutic agents, and cytokinesin vitro. Additionally, dormant metastases display a unique pattern of gene and miRNA expression. The microenvironment of dormant metastases shows an increase in certain immune cell subpopulations. Immune-controlled dormant metastases exhibit a unique phenotype that can be exploited to discover new biomarkers, as well as to develop therapies to eradicate them or control overt metastases.
Human-immune-system humanized-DRAGA mice are a valuable model to study novel immunotherapies for HIV-1
Authors: Pumtang-on Pongthorn , Goodarzi Negin , Davey Brianna C , Sevcik Emily N , Coleman-Fuller Natalie , Vezys Vaiva , Rao Mangala , Pampusch Mary S , Rendahl Aaron K , Casares Sofia A , Skinner Pamela J
Published: December 2024

Humanized (h)DRAGA mice are a promisingin vivomodel for investigating immunotherapies for treating HIV infections. These mice are not only susceptible to HIV infection, but they also develop functional human immune cells, including T cells and B cells as well as follicular-like structures that mimic lymphoid B cell follicles, where HIV-producing cells concentrate during infection in a manner similar to that found in humans. This study evaluated the safety, tissue targeting, and efficacy of follicular-targeting HIV-specific chimeric antigen receptor (CAR)-T cells (CAR/CXCR5-T cells) in HIV-infected hDRAGA mice. Intravenously-infused CAR/CXCR5-T cells persisted in hDRAGA mice for the duration of the study, peaking six days post-infusion. This study indicated that CAR/CXCR5-T cell treatment is safe, with 100% survival rate of treated mice and no noticeable changes in pathology. Six days after infusion, CAR/CXCR5-T cells had accumulated in the follicle-like structures, with many appearing in direct contact with HIV-producing cells. However, CAR/CXCR5-T cell treatment did not appear to reduce viral loads compared to controls, perhaps because many of the engineered CAR/CXCR5-T cells were themselves infected with HIV, with some CAR/CXCR5-T cells showing evidence of HIV virion release. Future studies will investigate whether CAR/CXCR5-T cells engineered for resistance against HIV infection are effective in reducing viral loads. This study supports the approach of using the HIV-infected hDRAGA mouse model to test cellular immunotherapies for HIV, as the model recapitulates many aspects of HIV infection in human lymphoid follicles.
Evolution of the Jawed Vertebrate (Gnathostomata) Stomach through Gene Repertoire Loss: Findings from Agastric Species
Authors: Dann Jackson , Grützner Frank
Published: December 2024

Independent and convergent gene loss, such as the loss of gastric enzymes (Pga,Pgc) and proton pump subunits (Atp4a,Atp4b) in monotremes and polyphyletic teleost species have been associated with the agastric phenotype – stomachs lacking gross morphology, gastric glands and acid secretion. The loss of the key gastric hormone gastrin (Gast) has been observed in monotremes, but not corroborated in agastric teleosts. Furthermore, it is unclear how this loss affects the evolution and selection of the native receptor (Cckbr), gastrin releasing peptide (Grp) and receptor (Grpr), or if there are further gene losses associated with the agastric phenotype. We investigated the evolution, selection and conservation of the gastrin physiological pathway and novel gastric genes in a broad range of gastric and agastric vertebrates. Our analyses showed no correlation between the losses ofGastandGrprwith the agastric phenotype in vertebrate lineages. We identified genes implicated in gastric mucosal maintenance and development (Gkn1,Gkn2,Tff1,Tff2,Vsig1,Anxa10) that are lost in agastric species except the echidna, which retained some of them (Gkn1,Tff2,Vsig1). Our findings demonstrate a convergent repertoire of gastric genes lost in agastric species, partial retention of gastric functionality in the echidna, and the diversified roles of gastrin pathway constituents in vertebrate lineages.
Voltage Gated Calcium Channel Dysregulation May Contribute to Neurological Symptoms in Calmodulinopathies
Authors: Hussey John W. , DeMarco Emily , DiSilvestre Deborah , Brohus Malene , Busuioc Ana-Octavia , Iversen Emil D. , Jensen Helene H. , Nyegaard Mette , Overgaard Michael T. , Ben-Johny Manu , Dick Ivy E.
Published: December 2024

Calmodulinopathies are caused by mutations in calmodulin (CaM), and result in debilitating cardiac arrythmias such as long-QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). In addition, many patients exhibit neurological comorbidities, including developmental delay and autism spectrum disorder. Until now, most work into these mutations has focused on cardiac effects, identifying impairment of Ca2+/CaM-dependent inactivation (CDI) of CaV1.2 channels as a major pathogenic mechanism. However, the impact of these mutations on neurological function has yet to be fully explored. CaM regulation of voltage-gated calcium channels (VGCCs) is a critical element of neuronal function, implicating multiple VGCC subtypes in the neurological pathogenesis of calmodulinopathies. Here, we explore the potential for pathological CaM variants to impair the Ca2+/CaM-dependent regulation of CaV1.3 and CaV2.1, both essential for neuronal function. We find that mutations in CaM can impair the CDI of CaV1.3 and reduce the Ca2+-dependent facilitation (CDF) of CaV2.1 channels. We find that mutations associated with significant neurological symptoms exhibit marked effects on CaV1.3 CDI, with overlapping but distinct impacts on CaV2.1 CDF. Moreover, while the majority of CaM variants demonstrated the ability to bind the IQ region of each channel, distinct differences were noted between CaV1.3 and CaV2.1, demonstrating distinct CaM interactions across the two channel subtypes. Further, C-domain CaM variants display a reduced ability to sense Ca2+when in complex with the CaVIQ domains, explaining the Ca2+/CaM regulation deficits. Overall, these results support the possibility that disrupted Ca2+/CaM regulation of VGCCs may contribute to neurological pathogenesis of calmodulinopathies.
Retrieval Augmented Protein Language Models for Protein Structure Prediction
Authors: Li Pan , Cheng Xingyi , Song Le , Xing Eric
Published: December 2024

The advent of advanced artificial intelligence technology has significantly accelerated progress in protein structure prediction. AlphaFold2, a pioneering method in this field, has set a new benchmark for prediction accuracy by leveraging the Evoformer module to automatically extract co-evolutionary information from multiple sequence alignments (MSA). However, the efficacy of structure prediction methods like AlphaFold2 is heavily dependent on the depth and quality of the MSA. To address this limitation, we propose two novel models, AIDO.RAGPLM and AIDO.RAGFold, which are pretrained modules forRetrieval-AuGmented protein language model and structure prediction in an AI-driven Digital Organism [1]. AIDO.RAGPLM integrates pre-trained protein language models with retrieved MSA, allowing for the incorporation of co-evolutionary information in structure prediction while compensating for insufficient MSA information through large-scale pretraining. Our method surpasses single-sequence protein language models in perplexity, contact prediction, and fitness prediction. We utilized AIDO.RAGPLM as the feature extractor for protein structure prediction, resulting in the development of AIDO.RAGFold. When sufficient MSA is available, AIDO.RAGFold achieves TM-scores comparable to AlphaFold2 and operates up to eight times faster. In scenarios where MSA is insufficient, our method significantly outperforms AlphaFold2 (ΔTM-score=0.379, 0.116 and 0.059 for 0, 5 and 10 MSA sequences as input). Additionally, we developed an MSA retriever for MSA searching from the UniClust30 database using hierarchical ID generation, which is 45 to 90 times faster than traditional methods, and is used to expand the MSA training set for AIDO.RAGPLM by 32%. Our findings suggest that AIDO.RAGPLM provides an efficient and accurate solution for protein structure prediction.
Peritraumatic C-reactive protein levels predict pain outcomes following traumatic stress exposure in a sex-dependent manner
Authors: McKibben Lauren A. , Layne Miranda N. , Albertorio-Sáez Liz Marie , Zhao Ying , Branham Erica M. , House Stacey L. , Beaudoin Francesca L. , An Xinming , Stevens Jennifer S. , Neylan Thomas C. , Clifford Gari D. , Germine Laura T. , Bollen Kenneth A. , Rauch Scott L. , Haran John P. , Storrow Alan B. , Lewandowski Christopher , Musey Paul I. , Hendry Phyllis L. , Sheikh Sophia , Jones Christopher W. , Punches Brittany E. , Swor Robert A. , Hudak Lauren A. , Pascual Jose L. , Seamon Mark J. , Datner Elizabeth M. , Peak David A. , Merchant Roland C. , Domeier Robert M. , Rathlev Niels K. , O’Neil Brian J. , Sanchez Leon D. , Bruce Steven E. , Sheridan John F. , Harte Steven E. , Kessler Ronald C. , Koenen Karestan C. , Ressler Kerry J. , McLean Samuel A. , Linnstaedt Sarah D.
Published: December 2024

Background

Chronic pain following traumatic stress exposure (TSE) is common. Increasing evidence suggests inflammatory/immune mechanisms are induced by TSE, play a key role in the recovery process versus development of post-TSE chronic pain, and are sex specific. In this study, we tested the hypothesis that the inflammatory marker C-reactive protein (CRP) is associated with chronic pain after TSE in a sex-specific manner.

Methods

We utilized blood-plasma samples and pain questionnaire data from men (n=99) and (n=223) women enrolled inAURORA, a multi-site emergency department (ED)-based longitudinal study of TSE survivors. We measured CRP using Ella/ELISA from plasma samples collected in the ED (‘peritraumatic CRP’, n=322) and six months following TSE (n=322). Repeated measures mixed-effects models were used to assess the relationship between peritraumatic CRP and post-TSE chronic pain.

Results

Peritraumatic CRP levels significantly predicted post-TSE chronic pain, such that higher levels of CRP were associated with lower levels of pain over time following TSE, but only in men (men:β=-0.24,p=0.037; women:β=0.05,p=0.470). By six months, circulating CRP levels had decreased by more than half in men, but maintained similar levels in women (t(290)=1.926,p=0.055). More men with a decrease in CRP levels had decreasing pain over time versus women (men:83% women:65%; Z=2.21,p=0.027).

Conclusions

In men but not women, we found circulating peritraumatic CRP levels predict chronic pain outcomes following TSE and resolution of CRP levels in men over time might be associated with increased pain recovery. Further studies are needed to validate these results.

Peritraumatic circulating CRP levels predicted pain recovery in men following TSE and decreases in CRP levels over time were greater in men compared to women.
Does the habitual dietary intake of adults in Bavaria, Germany, match dietary intake recommendations? – Results of the 3rdBavarian Food Consumption Survey (BVS III)
Authors: Rohm Florian , Wawro Nina , Gimpfl Sebastian , Ohlhaut Nadine , Senger Melanie , Röger Christine , Kussmann Martin , Gedrich Kurt , Linseisen Jakob
Published: December 2024

1

Objective

Monitoring dietary habits is crucial for identifying shortcomings and delineating countermeasures. About 20 years after the last population-based surveys in Bavaria and Germany, dietary habits were assessed to describe the intake distributions and compare these with recommendations at food and nutrient level.

Methods

The 3rdBavarian Food Consumption Survey (BVS III) was designed as a diet survey representative of adults in Bavaria; from 2021 to 2023, repeated 24-hour diet recalls were collected by telephone using the software GloboDiet©. Food (sub-)group and nutrient intake data were modeled with the so-called NCI method, weighted for the deviation from the underlying population. Intake distributions in men and women were described as percentiles. These data were used to estimate the proportion of persons meeting dietary intake recommendations. In addition, food consumption data were compared with the results reported 20 years ago collected by the same methodology (2ndBavarian Food Consumption Survey, BVS II).

Results

Using 24-hour diet recalls of 550 male and 698 female participants, we estimated intake distributions for food (sub-)groups and nutrients. A major proportion of the adult population does not meet the food-based dietary guidelines; this refers to a series of food groups, including fruit and vegetables, legumes, nuts, cereal products, and especially whole grain products, as well as fresh and processed meat. Regarding selected essential nutrients, a considerable proportion of the population was at higher risk of insufficiency from iron (women), zinc (men), and folic acid (both men and women), as already described in previous studies.

Conclusion

A major proportion of the adult Bavarian population does not meet the current food-based dietary guidelines. Compared to BVS II data, favorable changes refer to lower consumption of total meat (especially processed meat) and soft drinks, and an increased intake of vegetables. The conclusions based on the intake of selected essential nutrients hardly changed over time. From a public health perspective, the still low intake of vegetables, fruit, nuts, cereal products, and particularly of whole grain products, and associated higher risks of insufficient supply of several vitamins and minerals call for action for improvement.
Self-Assessment of amyotrophic lateral sclerosis functional rating scale on the patient’s smartphone proves to be non-inferior to clinic data capture
Authors: Steinfurth Laura , Grehl Torsten , Weyen Ute , Kettemann Dagmar , Steinbach Robert , Rödiger Annekathrin , Großkreutz Julian , Petri Susanne , Boentert Matthias , Weydt Patrick , Bernsen Sarah , Walter Bertram , Günther René , Lingor Paul , Koch Jan Christoph , Baum Petra , Weishaupt Jochen H. , Dorst Johannes , Koc Yasemin , Cordts Isabell , Vidovic Maximilian , Norden Jenny , Schumann Peggy , Körtvélyessy Péter , Spittel Susanne , Münch Christoph , Maier André , Meyer Thomas
Published: December 2024

Objective

To investigate self-assessment of the amyotrophic lateral sclerosis functional rating scale–revised (ALSFRS-R) using the patient’s smartphone and to analyze non-inferiority to clinic assessment.

Methods

In an observational study, ALSFRS-R data being remotely collected on a mobile application (App-ALSFRS-R) were compared to ALSFRS-R captured during clinic visits (clinic-ALSFRS-R). ALS progression rate (ALSPR) – as calculated by the monthly decline of ALSFRS-R – and its intrasubject variability (ALSPR-ISV) between ratings were used to compare both cohorts. To investigate non-inferiority of App-ALSFRS-R data, a non-inferiority margin was determined.

Results

691 ALS patients using the ALS-App, and 1895 patients with clinic assessments were included. Clinical characteristics for the App-ALSFRS-R and clinic-ALSFRS-R cohorts were as follows: Mean age 60.45 (SD 10.43) and 63.69 (SD 11.30) years (p<0.001), disease duration 38.7 (SD 37.68) and 56.75 (SD 54.34) months (p<0.001) and ALSPR 0.72 and 0.59 (p<0.001), respectively. A paired sample analysis of ALSPR-ISV was applicable for 398 patients with clinic as well as app assessments and did not show a significant difference (IQR 0.12 [CI 0.11, 0.14] vs 0.12 [CI 0.11, 0.14], p=0.24; Coheńs d =0.06). CI of IQR for App-ALSFRS-R was below the predefined non-inferiority margin of 0.15 IQR, demonstrating non-inferiority.

Conclusions

Patients using a mobile application for remote digital self-assessment of the ALSFRS-R revealed younger age, earlier disease course and faster ALS progression. The finding of non-inferiority of App-ALSFRS-R assessments underscores, that data collection using the ALS-App on the patient’s smartphone can serve as additional source of ALSFRS-R in ALS research and clinical practice.
Application of a general LLM-based classification system to retrieve information about oncological trials
Authors: Dennstädt Fabio , Windisch Paul , Filchenko Irina , Zink Johannes , Putora Paul Martin , Shaheen Ahmed , Gaio Roberto , Cihoric Nikola , Wosny Marie , Aeppli Stefanie , Schmerder Max , Shelan Mohamed , Hastings Janna
Published: December 2024

Purpose

The automated classification of clinical trials and medical literature is increasingly relevant, particularly in oncology, as the volume of publications and trial reports continues to expand. Large Language Models (LLMs) may provide new opportunities for automated diverse classification tasks. In this study, we developed a general-purpose text classification framework using LLMs and evaluated its performance on oncological trial classification tasks.

Methods and Materials

A general text classification framework with adaptable prompt, model and categories for the classification was developed. The framework was tested with four datasets comprising nine binary classification questions related to oncological trials. Evaluation was conducted using a locally hosted version of Mixtral-8x7B-Instruct v0.1 and three cloud-based LLMs: Mixtral-8x7B-Instruct v0.1, Llama3.1-70B-Instruct, and Qwen-2.5-72B.

Results

The system consistently produced valid responses with the local Mixtral-8x7B-Instruct model and the Llama3.1-70B-Instruct model. It achieved a response validity rate of 99.70% and 99.88% for the cloud-based Mixtral and Qwen models, respectively. Across all models, the framework achieved an overall accuracy of >94%, precision of >92%, recall of >90%, and an F1-score of >92%. Question-specific accuracy ranged from 86.33% to 99.83% for the local Mixtral model, 85.49% to 99.83% for the cloud-based Mixtral model, 90.50% to 99.83% for the Llama3.1 model, and 77.13% to 99.83% for the Qwen model.

Conclusions

The LLM-based classification framework exhibits robust accuracy and adaptability across various oncological trial classification tasks. The findings highlight the potential of automated, LLM- driven trial classification systems, which may become increasingly used in oncology.
Integrating Clustering and Semantic Similarity for MAUDE Database Dimensionality Reduction
Authors: Hua Lei
Published: December 2024

Objective

To develop and evaluate an automated methodology for dimensionality reduction of the FDA’s MAUDE database through schema matching and merging.

Methods

We conducted 96 trails integrating clustering algorithms with semantic similarity evaluations using the DeepSeek V2.5 API. This approach identified and merged semantically similar tables. Feature extraction was performed using Term Frequency-Inverse Document Frequency (TF-IDF) vectorization and Sentence Transformer embeddings. The methodology was assessed against manual groupings provided by domain experts using metrics such as Adjusted Rand Index (ARI), Normalized Mutual Information (NMI), precision, recall, and F1 score. Different similarity thresholds (0.7, 0.8, 0.9) were applied to evaluate their impact on table merging performance.

Results

The integration of clustering with semantic similarity evaluations enhanced the F1 score from 0.51 (clustering alone) to 1.00, utilizing fewer than 1,425 API similarity evaluations. Consequently, the number of tables was compressed from 113 to 13–16 table groups, a reduction of 86% to 89%. In addition, the application of clustering algorithms decreased the number of table pair comparisons by 77% to 83%. Sentence Transformer embeddings outperformed TF-IDF vectorization in clustering performance, with F1 scores increasing from a range of approximately 0.51–0.87 to 0.51–0.95 in clustering-only scenarios. DeepSeek V2.5 demonstrated the potential to match and quantify subtle semantic differences across various similarity thresholds, maintaining high merging accuracy with F1 scores reaching up to 1.00.

Conclusion

The proposed automated dimensionality reduction methodology effectively enhances data quality and analysis efficiency within the MAUDE database. By reducing the number of tables to manageable groups, optimizing context lengths, and leveraging DeepSeek V2.5’s semantic matching capabilities, the framework streamlines data processing and ensures compatibility with advanced analytical tools such as Large Language Models (LLMs). This makes the methodology applicable across various industries, facilitating more efficient and accurate data analysis workflows
Conserved interhemispheric morphogenesis in amniotes preceded the evolution of the corpus callosum
Authors: Noji Ryota , Kaneko Mari , Abe Takaya , Kiyonari Hiroshi , Nishikawa Yukihiro , Kumamoto Takuma , Gotoh Hitoshi , Ohtaka-Maruyama Chiaki , Ono Katsuhiko , Yoshizawa Tatsuya , Nomura Tadashi
Published: December 2024

The corpus callosum (CC) is the large axon bundle connecting the telencephalic hemispheres. The CC is formed exclusively in placental mammals, and the lack of comparable structures in other amniotes obscures the evolutionary origin of the CC. We here demonstrate that interhemispheric remodeling, a prior developmental step for CC formation, is highly conserved in non-mammalian amniotes, such as reptiles and birds. In these animal groups, the spatiotemporal dynamics of interhemispheric remodeling are tightly connected with distinct commissural formations. We observed a high degree of similarity between the mammalian CC and reptilian rostral pallial commissure, (RPC) and significant modifications in the avian pallial projection. Furthermore, we determined that Satb2 plays crucial roles in interhemispheric remodeling, which is associated with proper formation of both the CC and RPC in mice and geckoes, via the use of CRISPR-mediated gene-targeting. Our findings suggest that developmental mechanisms for midline remodeling were already present in the common ancestor of amniotes, which contributed to the evolution of eutherian-specific CC formation.
Atomistic Mechanisms of Calcium Permeation Modulated by Q/R Editing and Selectivity Filter Mutations in GluA2 AMPA Receptors
Authors: Heiser Florian , Biedermann Johann , Kuru Ece , Plested Andrew J. R. , Sun Han
Published: December 2024

GluA2 is a key subunit of AMPA receptor ion channels that is abundantly expressed in the vertebrate brain. Post-transcriptional Q/R editing of GluA2 renders AMPARs nearly impermeable to calcium ions, which is crucial for their normal function. Although previous studies have characterized conductivity and selectivity differences between edited and unedited GluA2 variants and heteromeric receptors incorporating GluA2, the atomistic mechanism remains largely unknown. In this study, we investigate ion permeation in the context of multiple Ca2+binding sites along the pore predicted from MD simulations, considering both mutations and co-permeating monovalent ions. Patch clamp electrophysiology recordings confirmed a binding site at the intracellular mouth of the selectivity filter that confers selectivity for calcium over monovalent ions. A patient mutation at the same site has been previously shown to cause neurodevelopmental abnormalities. Furthermore, MD simulations of GluA2 with different arginine copy number at the Q/R site show that Ca2+conduction is blocked in the presence of two arginines, whereas K+is only blocked by four arginines, in explaining the results from decades of electrophysiological work. Finally, MD simulations revealed that Ca2+reduces K+conduction by preferentially occupying the intracellular SF binding site, whereas Na+does not. This result is consistent with electrophysiological results from the D590 mutants, and suggests that divalent binding in the selectivity filter is a major determinant of AMPAR conductance.
Mapping Cryptic Phosphorylation Sites in the Human Proteome
Authors: Gasparotto Dino , Zanon Annarita , Bonaldo Valerio , Marchiori Elisa , Casagranda Massimo , Di Domenico Erika , Copat Laura , Asquini Tommaso Fortunato , Rigoli Marta , Feltrin Sirio Vittorio , Lorenzo Nuria Lopez , Lolli Graziano , Pennuto Maria , Requena Jesùs R. , Stabelli Omar Rota , Minervini Giovanni , Micheletti Cristian , Spagnolli Giovanni , Faccioli Pietro , Biasini Emiliano
Published: December 2024

Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the protein’s inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphosites in health and disease.
Altered spike dynamics drives immune evasion of SARS-CoV-2
Authors: Uğurlu Hasan , Salminen Petja , Yuan Meng , Fagerlund Riku , Mäkelä Anna R , Žusinaite Eva , Kesti Tapio , Rissanen Ilona , Merits Andres , Wilson Ian A , Saksela Kalle
Published: December 2024

Rapid viral escape from protective immunity has been an unwanted hallmark of the COVID-19 pandemic. This escape has been attributed to mutations in critical neutralizing antibody epitopes mainly in the receptor binding domain (RBD) of the viral spike glycoprotein. Here we show that this notion is incomplete. We found that several broadly neutralizing human antibodies isolated over the past years retain an almost undiminished capacity for inhibitory targeting of RBDs of recent highly immunoevasive SARS-CoV-2 strains. Likewise, human sera collected during the pre-Omicron era from persons immunized with original Wuhan-based vaccines were found to contain abundant neutralizing activity targeted against the RBDs of modern Omicron variants. However, this unexpected neutralization sensitivity was observed only when these RBDs were incorporated into a mismatched spike protein backbone, whereas the corresponding native Omicron spike proteins were highly resistant against the same panel of antibodies and human sera. We conclude that changes occurring outside of the RBD and leading to altered conformational dynamics of the spike protein have played a key part in the viral evolution enabling SARS-CoV-2 to escape from neutralizing antibodies that target highly conserved cryptic RBD epitopes.
DNA tensiometer reveals catch-bond detachment kinetics of kinesin-1, -2 and -3
Authors: Noell Crystal R. , Ma Tzu-Chen , Jiang Rui , McKinley Scott A. , Hancock William O.
Published: December 2024

Bidirectional cargo transport by kinesin and dynein is essential for cell viability and defects are linked to neurodegenerative diseases. The competition between motors is described as a tug-of-war, and computational modeling suggests that the load-dependent off-rate is the strongest determinant of which motor ‘wins’. Optical tweezer experiments find that the load-dependent detachment sensitivity of transport kinesins is kinesin-3 > kinesin-2 > kinesin-1. However, when kinesin-dynein pairs were analyzed in vitro, all three kinesin families competed nearly equally well against dynein. One possible explanation is that vertical forces inherent to the large trapping beads enhance motor detachment. Because intracellular cargo range from ∼30 nm to > 1000 nm, vertical forces in vivo are expected to range from near zero to larger than the horizontal forces of transport. To investigate detachment rates against loads oriented parallel to the microtubule, we created a DNA tensiometer comprising a DNA entropic spring that is attached to the microtubule on one end and a kinesin motor on the other. Surprisingly, kinesin dissociation rates at stall were slower than detachment rates during unloaded runs, a property termed a catch-bond. A plausible mechanism, supported by stochastic simulations, is that the strong-to-weak transition in the kinesin cycle is slowed with load. We also find evidence that the long run lengths of kinesin-3 (KIF1A) result from the concatenation of multiple short runs connected by diffusive episodes. The finding that kinesins form catch-bonds under horizontal loads necessitates a reevaluation of the role of cargo geometry in kinesin-dynein bidirectional transport.

Significance Statement

Kinesin and dynein motor proteins transport intracellular cargo bidirectionally along microtubule tracks, with the speed and directionality of transport involving a tug-of-war between the motor teams. We created a ‘DNA tensiometer’ that uses DNA as a spring to measure kinesin performance against loads oriented parallel to the microtubule. We find that dissociation rates paradoxically slow down with imposed loads. Dyneins are also thought to possess this ‘catch-bond’ behavior, meaning that both motors will hang on tightly during a tug-of-war. Previous work showed that combined vertical and horizontal loads cause faster detachment rates under load. Hence, we conclude that the effectiveness of kinesins during bidirectional transport depends strongly on the geometry of their cargo.
Coevolution in Small Heat Shock Protein 1 (HSPB1) is Promoted by Interactions between the Alpha-Crystallin Domain and the Disordered Regions
Authors: Racigh Vanesa , Rodriguez Sawicki Luciana , Bravo Facundo Nicolas Eric , Fornasari Maria Silvina
Published: December 2024

Human HSPB1, a member of the small heat shock protein (sHSP) family, functions as an ATP-independent molecular chaperone crucial for protein quality control and is implicated in several pathologies, including Charcot-Marie-Tooth neuropathy. This study investigates the coevolution of the disordered N-terminal and C-terminal regions (NTR and CTR) with the structured Alpha-Crystallin domain (ACD) of human HSPB1, focusing on interactions that regulate its chaperone activity.

Using a manually curated dataset of HSPB1 orthologs, the composition of critical motifs within the NTR (6VPFSLL11) and CTR (179ITIPV183) that interact with the ACD was analyzed and evolutionary rates per site for the human HSPB1 sequence were estimated. Additionally, structural modeling with AlphaFold 2 was employed to assess the prevalence of these contacts in human HSPB1 models.

The results reveal that while the disordered regions globally evolve faster than the structured ACD, specific residues within the6VPFSLL11and179ITIPV183motifs exhibit reduced evolutionary rates, reflecting evolutionary constraints imposed by the conservation of the protein’s function. Structural modeling further indicates that coevolutionary-like information about the interaction between the6VPFSLL11motif and the ACD is encoded in the multiple sequence alignment used by Alphafold 2.

Altogether, these findings suggest that the disordered regions and the ACD of human HSPB1 likely coevolved, preserving interactions crucial for its chaperone activity self-regulation. This evolutionary mechanism may also be extended to other sHSP featuring interacting motifs in the NTR, CTR, or both, and provides a framework to elucidate why pathogenic variants occurring in regions involved in these contacts contribute to disease.
OST Catalytic Subunit Redundancy Enables Therapeutic Targeting of N-Glycosylation
Authors: Baro Marta , Lee Hojin , Kelley Vanessa , Lou Rongliang , Phoomak Chatchai , Politi Katerina , Zeiss Caroline J. , Van Zandt Michael , Contessa Joseph N.
Published: December 2024

Protein asparagine (N)-glycosylation, which promotes folding and trafficking of cell surface receptors such as the EGFR, has not been considered a viable target in oncology due to the essential and non-redundant enzymatic activities required for glycan synthesis and transfer. In mammals an exception to this rule is the presence of the oligosaccharyltransferase (OST) catalytic subunit paralogs, STT3A and STT3B. Here we delineate the chemical biology of OST inhibitors and develop an approach for limited inhibition of N-glycosylation optimized for downstream effects on EGFR. Small molecules with enhanced pharmacokinetic properties and preferences for STT3A or STT3B were synthesized, characterizedin vitro, and advanced toin vivotesting. The lead from this series, NGI-189, causes tumor regression or growth delay of patient derived and TKI resistant EGFR-mutant lung cancer xenografts without toxicity. Together these results suggest that bioavailable OST inhibitors can be developed as therapeutic agents for oncology.

A mechanistic approach for partial inhibition of N-glycosylation delivers small molecules with anti-tumor activity in EGFR mutant NSCLC.
Evolutionary Constraints on Positional Sequence, Collective Properties and Sequence Style of Tropoelastin Dictated by Fundamental Requirements for Formation and Function of the Extracellular Elastic Matrix
Authors: Keeley Fred W.
Published: December 2024

Elastin is an unusual extracellular matrix protein responsible for the properties of extension and energy-efficient elastic recoil of large blood vessels, heart valves, lung parenchyma and many other vertebrate tissues requiring such resilience. Polymeric elastin is assembled from monomeric tropoelastin by a process involving liquid-liquid phase separation, followed by maturation into an extended elastic matrix, covalently cross-linked through the side chains of lysine residues in the protein and producing a robust biomaterial with the structural integrity to withstand hundreds of millions of cycles of extension and recoil without mechanical failure. Elastin functions as an entropic elastomer, whose properties are the direct result of the inability of the protein to fold into a fixed, stable structure.

Previous investigations of how the unusual properties of polymeric elastin arise from the sequence of tropoelastin have depended primarily on modeling using molecular biological and biophysical methodologies. This study takes a unique alternative approach, using a well-curated database of tropoelastin sequences from more than 80 representative species of Amniotes to identify characteristics that are conserved over more than 300 million years of evolution in order to provide assembly and conformational flexibility requirements of elastins.

Conserved characteristics included preservation not only of regions of linear or positional sequence, but also of collective or compositional characteristics, derived from the sequence but not strictly dependent on positional sequence. A plausible overall consensus sequence for Amniote tropoelastins allowed quantification of residue-by-residue, domain-by-domain and region-by-region levels of sequence conservation, identifying distinct regions of high and low positional sequence conservation. Regions of low positional sequence conservation nevertheless maintained a recognizable, low complexity sequence style characterized by tandem repeats and partial repeats of short, non-polar motifs. Analysis of these motifs indicated hPGhGG, with numerous mutations, insertions and deletions, as the underlying repeating unit in all Amniote tropoelastins.

Together these data identify significant evolutionary constraints dictated by fundamental requirements for formation and functionality of the extracellular elastin matrix. Mutations/polymorphisms in human tropoelastin affecting such well-conserved characteristics might be expected to have phenotypic consequences.
Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients
Authors: Randolph Haley E , Aguirre-Gamboa Raúl , Brunet-Ratnasingham Elsa , Nakanishi Tomoko , Locher Veronica , Ketter Ellen , Brandolino Cary , Larochelle Catherine , Prat Alexandre , Arbour Nathalie , Dumaine Anne , Finzi Andrés , Durand Madeleine , Richards J Brent , Kaufmann Daniel E , Barreiro Luis B
Published: December 2024

Genome-wide association studies performed in patients with coronavirus disease 2019 (COVID-19) have uncovered various loci significantly associated with susceptibility to SARS-CoV-2 infection and COVID-19 disease severity. However, the underlyingcis-regulatory genetic factors that contribute to heterogeneity in the response to SARS-CoV-2 infection and their impact on clinical phenotypes remain enigmatic. Here, we used single-cell RNA-sequencing to quantify genetic contributions tocis-regulatory variation in 361,119 peripheral blood mononuclear cells across 63 COVID-19 patients during acute infection, 39 samples collected in the convalescent phase, and 106 healthy controls. Expression quantitative trait loci (eQTL) mapping across cell types within each disease state group revealed thousands ofcis-associated variants, of which hundreds were detected exclusively in immune cells derived from acute COVID-19 patients. Patient-specific genetic effects dissipated as infection resolved, suggesting that distinct gene regulatory networks are at play in the active infection state. Further, 17.2% of tested loci demonstrated significant cell state interactions with genotype, with pathways related to interferon responses and oxidative phosphorylation showing pronounced cell state-dependent variation, predominantly in CD14+monocytes. Overall, we estimate that 25.6% of tested genes exhibit gene-environment interaction effects, highlighting the importance of environmental modifiers in the transcriptional regulation of the immune response to SARS-CoV-2. Our findings underscore the importance of expanding the study of regulatory variation to relevant cell types and disease contexts and argue for the existence of extensive gene-environment effects among patients responding to an infection.
Contact Lens Wear Alters Transcriptional Responses toPseudomonas aeruginosain Both the Corneal Epithelium and the Bacteria
Authors: Kumar Naren G. , Grosser Melinda R , Wan Stephanie , Schator Daniel , Ahn Eugene , Jedel Eric , Nieto Vincent , Evans David J. , Fleiszig Suzanne M. J.
Published: December 2024

Purpose

Healthy corneas resist colonization by virtually all microbes yet contact lens wear can predispose the cornea to sight-threatening infection withPseudomonas aeruginosa. Here, we explored how lens wear changes corneal epithelium transcriptional responses toP. aeruginosaand its impact on bacterial gene expression.

Methods

Male and female C57BL/6J mice were fitted with a contact lens on one eye for 24 h. After lens removal, corneas were immediately challenged for 4 h withP. aeruginosa. A separate group of naïve mice were similarly challenged with bacteria. Bacteria-challenged eyes were compared to uninoculated naive controls as was lens wear alone. Total RNA-sequencing determined corneal epithelium and bacterial gene expression.

Results

Prior lens wear profoundly altered the corneal response toP. aeruginosa, including: upregulated pattern-recognition receptors (tlr3, nod1), downregulated lectin pathway of complement activation (masp1), amplified upregulation oftcf7,gpr55, ifi205, wfdc2(immune defense) and further suppression ofefemp1(corneal stromal integrity). Without lens wear,P. aeruginosaupregulated mitochondrial and ubiquinone metabolism genes. Lens wear alone upregulatedaxl, grn, tcf7, gpr55(immune defense) and downregulated Ca2+-dependent genesnecab1, snx31 and npr3.P. aeruginosaexposure to prior lens wearing vs. naïve corneas upregulated bacterial genes of virulence (popD), its regulation (rsmY, PA1226) and antimicrobial resistance (arnB,oprR).

Conclusion

Prior lens wear impacts corneal epithelium gene expression altering its responses toP. aeruginosaand howP. aeruginosaresponds to it favoring virulence, survival and adaptation. Impacted genes and associated networks provide avenues for research to better understand infection pathogenesis.