bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear brain connectivity from neurons to networks: quantification, sources and localization
Authors: Raffaelli Giulio Tani , Jiříček Stanislav , Hlinka Jaroslav
Published: November 2024

Since the first studies in functional connectivity, Pearson’s correlation has been the primary tool to determine relatedness between the activity of different brain locations. Over the years, concern over the information neglected by correlation pushed toward using different measures accounting for non-linearity. However, some studies suggest that, at the typical observation scale, a linear description of the brain captures a vast majority of the information. Therefore, we measured the fraction of information that would be lost using a linear description and which regions would be affected the most. We considered fMRI, EEG, iEEG, and single unit spikes to assess how the observation scale impacts the amount of non-linearity. We observe that the information loss is reduced for modalities with large temporal or spatial averaging (fMRI and EEG) and gains relevance on more fine descriptions of the activity (iEEG and single unit spikes). We conclude that for most human applications, Pearson’s correlation coefficient adequately describes pairwise interactions in time series from current recording techniques.

Significance Statement

In neuroimaging, as in other complex systems fields, the increasing interest in network inference by statistical dependencies (i.e. functional connectivity) invites advanced ways to quantify it. Various nonlinear measures, ultimately the Mutual Information, are used as alternatives to conventional linear Pearson’s correlation coefficient. We systematically assess the amount and reliability of detectable non-linearity of brain functional connectivity across imaging modalities and spatial scales. We demonstrate more pronounced nonlinearity in micro-scale recordings, while rather limited and unreliable in more accessible, noninvasive, large-scale modalities: functional magnetic resonance imaging and scalp electro-physiology. This fundamentally supports the use of robust and easily interpretable linear tools in large-scale neuroimaging, and important insights concerning the microscale connectivity nonlinearity, including the link to brain state dynamics.
Single Particle Tracking of Genetically Encoded Nanoparticles: Optimizing Expression for Cytoplasmic Diffusion Studies
Authors: Korunova Elizaveta , Sikirzhystki Vitali , Twiss Jeffery L , Vasquez Paula , Shtutman Michael
Published: November 2024

Single particle tracking (SPT) is a powerful technique for probing the diverse physical properties of the cytoplasm. Genetically encoded nanoparticles provide an especially convenient tool for such investigations, as they can be expressed and tracked in cells via fluorescence. Among these, 40-nm GEMs provide a unique opportunity to explore the cytoplasm. Their size corresponds to that of ribosomes and big protein complexes, allowing us to investigate the effects of the cytoplasm on the diffusivity of these objects while excluding the influence of chemical interactions during stressful events and pathological conditions. However, it has been shown that cytoplasmic viscosity is tightly regulated and plays a crucial role in maintaining homeostasis during protein synthesis and degradation. Despite this, the effects of GEM expression levels on diffusivity remain largely uncharacterized in mammalian cells. To optimize the GEMs tracking and estimate GEMs-expression effects we constructed dox-inducible GEM expression system and compare with a previously reported constitutive expression system. The optimized level of GEMs expression increases the measured diffusivity from 0.29 ± 0.02 μm2/sec in GEMs-overexpressed cells to 0.35 ± 0.02 μm2/sec; improve homogeneity throughout the cell population; and facilitates particle tracking. We also improved the analyses of GEM diffusivity by applying effective diffusion coefficient while considering the type of motion and assessing the heterogeneity in the type of motion by calculating the standard deviations of particle displacements.

Statement of significance

Describing cytoplasmic properties, such as environmental viscosity and protein complex motion, is essential for understanding molecular-level changes in cell function and pathology. A recently developed approach uses self-assembling fluorescent protein probes, expressed in cells, to investigate cytoplasmic properties through single-particle tracking (SPT). One such system employs genetically encoded multimeric (GEM) nanoparticles— scaffold protein structures similar in size to ribosomes. This study addresses a key limitation in SPT of GEMs by examining how varying GEM expression levels affect measured diffusivity and tracking quality in mammalian cells. Our findings demonstrate that controlled GEM expression reduces particle overcrowding, increases measured diffusivity, and enhances track detection. This work contributes valuable insights into optimizing GEM nanoparticle applications for studying cytoplasmic viscosity and motion dynamics.
Impaired complement regulation drives chronic lung allograft dysfunction after lung transplantation
Authors: Kulkarni Hrishikesh S. , Tague Laneshia K. , Calabrese Daniel R. , Liao Fuyi , Liu Zhiyi , Garnica Lorena , Shankar Nishanth , Wu Xiaobo , Kulkarni Devesha H. , Bernardt Cory , Byers Derek , Chen Catherine , Huang Howard J. , Witt Chad A. , Hachem Ramsey R. , Kreisel Daniel , Atkinson John P. , Greenland John R. , Gelman Andrew E.
Published: November 2024

A greater understanding of chronic lung allograft dysfunction (CLAD) pathobiology, the primary cause of mortality after lung transplantation, is needed to improve outcomes. The complement system links innate to adaptive immune responses and is activated early post-lung transplantation to form the C3 convertase, a critical enzyme that cleaves the central complement component C3. We hypothesized that LTx recipients with a genetic predisposition to enhanced complement activation have worse CLAD-free survival mediated through increased adaptive alloimmunity. We interrogated a known functional C3 polymorphism (C3R102G) that increases complement activation through impaired C3 convertase inactivation in two independent LTx recipient cohorts. C3R102G, identified in at least one out of three LTx recipients, was associated with worse CLAD-free survival, particularly in the subset of recipients who developed donor-specific antibodies (DSA). In a mouse orthotopic lung transplantation model, impaired recipient complement regulation resulted in more severe obstructive airway lesions when compared to wildtype controls, despite only moderate differences in graft-infiltrating effector T cells. Impaired complement regulation promoted the intragraft accumulation of memory B cells and antibody-secreting cells, resulting in increased DSA levels. In summary, genetic predisposition to complement activation is associated with B cell activation and worse CLAD-free survival.

BRIEF SUMMARY

Lung transplant recipients genetically predisposed to impaired complement regulation demonstrate worse chronic rejection-free survival. This phenotype is associated with intragraft B cell-activation and donor-specific antibodies.
Mechanism of cooperative strigolactone perception by the MAX2 ubiquitin ligase–receptor–substrate complex
Authors: Vancea Alexandra I. , Huntington Brandon , Steinchen Wieland , Savva Christos , Shahul Hameed Umar F. , Arold Stefan T.
Published: November 2024

Strigolactones (SLs) are a group of plant hormones that regulate various aspects of plant growth and development. Additionally, SLs exuded into the soil promote symbiotic relationships with arbuscular mycorrhizal fungi and stimulate the germination of parasitic plants such asStriga hermonthica. The binding and hydrolysis of SLs by their receptors (D14 in Arabidopsis and HTL inStriga) promote the ubiquitination of transcriptional repressors by Skp1–cullin–F-box (SCF)–type E3 ubiquitin ligases. The mechanistic link between SL perception by D14/HTL and substrate recognition by the E3 remains unclear. We identified an E3–HTL–substrate complex that is sufficiently stable for cryogenic electron microscopy. This complex, composed of SKP1 (ASK1) and substrate (SMAX1) from Arabidopsis, and Striga F-box (MAX2) and SL receptor (HTL7), reveals that the substrate engages in a bidentate association through its N and D2 domains. This interaction, which is both conformationally and compositionally dynamic, directly and allosterically stabilises the MAX2–(SL)HTL7 complex and affects the positioning of ASK1 relative to MAX2. This dynamic positioning influences the proximity between the substrate D2 domain and the ubiquitin-conjugated E2 enzyme. This work advances our understanding of how E3 ligases in plants translate hormone perception into genetic adaptations.
Blackbird: structural variant detection using synthetic and low-coverage long-reads
Authors: Meleshko Dmitrii , Yang Rui , Maharajan Salil , Danko David C , Korobeynikov Anton , Hajirasouliha Iman
Published: November 2024

Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved with short-read sequencing, but long-read SV callers achieve great results on the same datasets. While improvements have been made, high-coverage long-read sequencing is associated with higher costs and input DNA requirements. To decrease the cost one can lower the sequence coverage, but the current long-read SV callers perform poorly with coverage below 10X. Synthetic long-read (SLR) technologies hold great potential for structural variant (SV) detection, although utilizing their long-range information for events smaller than 50 kbp has been challenging. Results: In this work, we propose a hybrid novel integrated alignment- and local-assembly-based algorithm, Blackbird, that uses SLR together with low-coverage long reads to improve SV detection and assembly. Without the need for a computationally expensive whole genome assembly, Blackbird uses a sliding window approach and barcode information encoded in SLR to accurately assemble small segments and use long reads for an improved gap closing and contig assembly. We evaluated Blackbird on simulated and real human genome datasets. Using the HG002 GIAB benchmark set, we demonstrated that in hybrid mode, Blackbird demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5X coverage to achieve F1 scores (0.835 and 0.808 for deletions and insertions) similar to PBSV (0.856 and 0.812) and Sniffles2 (0.839 and 0.804) using 10X Pacbio Hi-Fi long-read coverage.
Simultaneous loss of CAMK2A and CAMK2B reveals endogenous in vivo substrates
Authors: Rigter Pomme M.F. , Bezstarosti Karel , Koc Oguz Can , Perfitt Tyler L. , Demmers Jeroen A.A. , Colbran Roger J. , Stratton Margaret , Elgersma Ype , van Woerden Geeske M.
Published: November 2024

Ca2+/calmodulin-dependent protein kinase 2 (CAMK2) plays a critical role in calcium signaling. Recent gene knockout studies show that CAMK2A and CAMK2B can have distinct roles yet also partially compensate for each other in yet unknown brain functions. In order to provide insight into potential novel CAMK2 functions, we performed parallel phosphoproteomic analyses on non-stimulated cortex tissue from inducibleCamk2aandCamk2bdouble knockout (Camk2af/f;Camk2bf/f;CAG-CreESR) mice and from wild type mice. A total of 5622 phosphorylated peptides derived from 2080 proteins were identified. Phosphorylation at serine/threonine residues in 130 proteins were downregulated in the double knockout mice, including residues in 113 proteins that have not previously been identified as potential CAMK2 substrates. Comparison of amino acid sequences surrounding the downregulated phosphorylation residues provided new insights into the CAMK2-substrate consensus sequencesin vivo. This dataset provides an important resource for future studies examining novel roles for CAMK2 in the brain.
Time-Dependent Material Properties and Composition of the Nonhuman Primate Uterine Layers Through Gestation
Authors: Fodera Daniella M. , Xu Echo Z. , Duarte-Cordon Camilo A. , Wyss Michelle , Fang Shuyang , Chen Xiaowei , Oyen Michelle L. , Rosado-Mendez Ivan , Hall Timothy , Vink Joy Y. , Feltovich Helen , Myers Kristin M.
Published: November 2024

The uterus is central to the establishment, maintenance, and delivery of a healthy pregnancy. Biomechanics is an important contributor to pregnancy success, and alterations to normal uterine biomechanical functions can contribute to an array of obstetric pathologies. Few studies have characterized the passive mechanical properties of the gravid human uterus, and ethical limitations have largely prevented the investigation of mid-gestation periods. To address this key knowledge gap, this study seeks to characterize the structural, compositional, and time-dependent micro-mechanical properties of the nonhuman primate (NHP) uterine layers in nonpregnancy and at three time-points in pregnancy: early 2nd, early 3rd, and late 3rdtrimesters. Distinct material and compositional properties were noted across the different tissue layers, with the endometrium-decidua being the least stiff, most viscous, least diffusible, and most hydrated layer of the NHP uterus. Pregnancy induced notable compositional and structural changes to the endometrium-decidua and myometrium, but no micro-mechanical property changes. Further comparison to published human data revealed notable similarities across species, with minor differences noted for the perimetrium and nonpregnant endometrium. This work provides insights into the material properties of the NHP uterus and demonstrates the validity of NHPs as a model for studying certain aspects of human uterine biomechanics.
Mapping of dI3 neuron sensorimotor circuits across the cervical and lumbar spinal cord
Authors: Nasiri Shahriar , Laliberte Alex M. , Bui Tuan V.
Published: November 2024

From the fine control of hand movements to the dynamic corrective adjustments during locomotion, spinal circuits integrate descending supraspinal and sensory inputs to modulate diverse motor functions. The integration of such a wide range of signals across the spinal cord is primarily mediated by propriospinal interneurons. In this study, we investigate the connectivity of a population of propriospinal interneurons marked by the expression ofIsl1, called dI3 neurons. These dI3s integrate supraspinal and sensory signals to facilitate many important functions, such as hand grasp, locomotion, and motor recovery after spinal cord injury; however, we have a limited understanding of how subpopulations of dI3s modulate network activity across the spinal cord to contribute to these behaviors. Their functional connectivity to motor circuits across the cervical and lumbar spinal cord was assessed through optogenetic activation of dI3s localized in different spinal segments. Our data demonstrates that cervical and lumbar dI3 subpopulations can form local, commissural, intersegmental, and long propriospinal pathways. Furthermore, dI3 subpopulations can be tonically stimulated to elicit locomotor activity. These extensive projection patterns of dI3s across the cervical and lumbar spinal cord suggest that dI3 subpopulations can modulate the activity of multiple motor networks within their respective spinal cord segments or across distant forelimb and hindlimb segments to facilitate a wide variety of motor functions.
Trends in hoaxes of academic communication
Authors: Faulkes Zen
Published: November 2024

Academic journals use peer review to weed out false information, but peer review and other editorial processes are normally confidential. Therefore, individuals sometimes create hoaxes to test whether editorial processes are as robust as they are claimed, or whether they are done at all. This article tracks the occurrence of hoaxes aimed at scholarly publishers and academic conferences since 2000. Since 2009, successful hoaxes usually appeared at a year of one or more a year, usually motivated by academics or journalists exposing so-called “predatory” journals. The apparent rise in the number of hoaxes reflects a lack of transparency in editorial processes at both legitimate and “predatory” journals. Reaction of academic communities to hoaxes varies widely depending on the perceived intent of the target of the hoaxes and whether the hoax demonstrates what the hoaxer claims.
Driving Forces of RNA Condensation Revealed through Coarse-Grained Modeling with Explicit Mg2+
Authors: Li Shanlong , Chen Jianhan
Published: November 2024

RNAs are major drivers of phase separation in the formation of biomolecular condensates, and can undergo protein-free phase separation in the presence of divalent ions or crowding agents. Much remains to be understood regarding how the complex interplay of base stacking, base pairing, electrostatics, ion interactions, and particularly structural propensities governs RNA phase behavior. Here we develop an intermediate resolution model for condensates of RNAs (iConRNA) that can capture key local and long-range structure features of dynamic RNAs and simulate their spontaneous phase transitions with Mg2+. Representing each nucleotide using 6-7 beads, iConRNA accurately captures base stacking and pairing and includes explicit Mg2+. The model does not only reproduce major conformational properties of poly(rA) and poly(rU), but also correctly folds small structured RNAs and predicts their melting temperatures. With an effective model of explicit Mg2+, iConRNA successfully recapitulates experimentally observed lower critical solution temperature phase separation of poly(rA) and triplet repeats, and critically, the nontrivial dependence of phase transitions on RNA sequence, length, concentration, and Mg2+ level. Further mechanistic analysis reveals a key role of RNA folding in modulating phase separation as well as its temperature and ion dependence, besides other driving forces such as Mg2+-phosphate interactions, base stacking, and base pairing. These studies also support iConRNA as a powerful tool for direct simulation of RNA-driven phase transitions, enabling molecular studies of how RNA conformational dynamics and its response to complex condensate environment control the phase behavior and condensate material properties.
The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity
Authors: Chatterjee Emeli , Betti Michael J. , Sheng Quanhu , Lin Phillip , Emont Margo P , Li Guoping , Amancherla Kaushik , Limpitikul Worawan B , Whittaker Olivia Rosina , Luong Kathy , Azzam Christopher , Gee Denise , Hutter Matthew , Flanders Karen , Sahu Parul , Garcia-Contreras Marta , Gokulnath Priyanka , Flynn Charles R. , Brown Jonathan , Yu Danxia , Rosen Evan D. , Jensen Kendall Van-Keuren , Gamazon Eric R. , Shah Ravi , Das Saumya
Published: November 2024

We characterized circulating extracellular vesicles (EVs) in obese and lean humans, identifying transcriptional cargo differentially expressed in obesity. Since circulating EVs may have broad origin, we compared this obesity EV transcriptome to expression from human visceral adipose tissue derived EVs from freshly collected and cultured biopsies from the same obese individuals. Using a comprehensive set of adipose-specific epigenomic and chromatin conformation assays, we found that the differentially expressed transcripts from the EVs were those regulated in adipose by BMI-associated SNPs from a large-scale GWAS. Using a phenome-wide association study of the regulatory SNPs for the EV-derived transcripts, we identified a substantial enrichment for inflammatory phenotypes, including type 2 diabetes. Collectively, these findings represent the convergence of the GWAS (genetics), epigenomics (transcript regulation), and EV (liquid biopsy) fields, enabling powerful future genomic studies of complex diseases.
Multidisciplinary teamwork among healthcare workers in the provision of Prevention of Mother-to-child transmission services in the three tertiary hospitals in Fiji: A qualitative perspective
Authors: Razzaq Amina , Worth Heather , Alam Neeloy Ashraful
Published: November 2024

Introduction

Teamwork is considered as an effective strategy in the provision of quality patient care including the prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV). Multidisciplinary teamwork (collaborative practice) among healthcare workers has widely accepted as a source of optimising healthcare provision and improving patient safety. The World Health Organisation [WHO] endorsed the need to establish effective teamwork within healthcare settings, in a quest to address the challenges of fragmented health systems to improve the utilisation of an efficient and effective workforce and deliver high quality patient care.

Aim

We aim to understand the key contributory factors in establishing effective multidisciplinary teamwork among healthcare workers in providing prevention of mother-to-child transmission services to HIV-positive pregnant women and their infants.

Methods

Data was collected using in-depth interviews. Interviews were conducted in the three tertiary hospitals and associated health clinics in Fiji between April-May 2013 and February-March 2014. Ethical approvals were obtained. A total of 58 healthcare providers were interviewed including doctors (n=12), midwives (n=19), nurses (n= 14), laboratory technicians (n=5) and counsellors (n=8) were interviewed. The data was analysed using thematic analysis.

Results

We found that multidisciplinary teamwork was an overarching theme followed by three sub-themes in discussing what constitutes effective multidisciplinary teamwork among these healthcare providers in delivering PMTCT services to HIV-positive pregnant women and their infants. The three sub themes included: integration of PMTCT services, effective communication and supportive colleagues.

Conclusion

Our findings would be useful in developing strategies to foster teamwork and improve working relationships between healthcare workers in other similar settings.
Gut microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients
Authors: Scalzo Paula L. , Marshall Austin , Soriano Sirena , Curry Kristen , Dulay Mario , Hodics Timea , Quigley Eamonn MM , Treangen Todd J. , Piskorz María M. , Villapol Sonia
Published: November 2024

COVID-19 patients often exhibit altered immune responses and neuropsychiatric symptoms during hospitalization. However, the potential interactions with gut microbiome profiles have not been fully characterized. Here, COVID-19 disease severity was classified as low (27.4%), moderate (29.8%), and critical (42.8%). Fever (66.1%) and cough (55.6%) were common symptoms. Additionally, 27.3% reported somatic symptoms, 27.3% experienced anxiety, 39% had depressive symptoms, and 80.5% reported stress. Gut microbiome profiling was performed using full-length 16S rRNA gene sequencing. Elevated interleukin-6 levels were observed in the most severe cases, indicating systemic inflammation. Reduced gut bacterial diversity was more pronounced in women and obese patients and correlated with higher disease severity. The presence of the genusMitsuokellawas significantly associated with increased physical, stress, anxiety, and depressive symptoms, andGranulicatellawith critically ill patients. These findings suggest a link between mental health status, systemic inflammation, and gut dysbiosis in COVID-19 patients, emphasizing the potential of microbiome-targeted therapies to improve recovery and reduce severe complications.
Cross-ancestral GWAS identifies 29 novel variants across Head and Neck Cancer subsites
Authors: Ebrahimi E , Sangphukieo A , Park HA , Gaborieau V , Ferreiro-Iglesias A , Diergaarde B , Ahrens W , Alemany L , Arantes LMRB , Betka J , Bratman SV , Canova C , Conlon MSC , Conway DI , Cuello M , Curado M , de Carvalho A , de Oliviera J , Gormley M , Hadji M , Hargreaves S , Healy CM , Holcatova I , Hung RJ , Kowalski LP , Lagiou P , Lagiou A , Liu G , Macfarlane GJ , Olshan AF , Perdomo S , Pinto LF , Podesta JV , Polesel J , Pring M , Rashidian H , Gama RR , Richiardi L , Robinson M , Rodriguez-Urrego PA , Santi SA , Saunders DP , Soares-Lima SC , Timpson N , Vilensky M , von Zeidler SV , Waterboer T , Zendehdel K , Znaor A , Brennan P ,   HEADSpAcE Consortium, McKay J , Virani S , Dudding T
Published: November 2024

In this multi-ancestry genome-wide association study (GWAS) and fine mapping study of head and neck squamous cell carcinoma (HNSCC) subsites, we analysed 19,073 cases and 38,857 controls and identified 29 independent novel loci. We provide robust evidence that a 3’ UTR variant inTP53(rs78378222, T>G) confers a 40% reduction in odds of developing overall HNSCC. We further examine the gene-environment relationship ofBRCA2andADH1Bvariants demonstrating their effects act through both smoking and alcohol use. Through analyses focused on the human leukocyte antigen (HLA) region, we highlight that although human papilloma virus (HPV)(+) oropharyngeal cancer (OPC), HPV(-) OPC and oral cavity cancer (OC) all show GWAS signal at 6p21, each subsite has distinct associations at the variant, amino acid, and 4-digit allele level. We also defined the specific amino acid changes underlying the well-known DRB1*13:01-DQA1*01:03-DQB1*06:03 protective haplotype for HPV(+) OPC. We show greater heritability of HPV(+) OPC compared to other subsites, likely to be explained by HLA effects. These findings advance our understanding of the genetic architecture of head and neck squamous cell carcinoma, providing important insights into the role of genetic variation across ancestries, tumor subsites, and gene-environment interactions.
Systematic comparison of phenome-wide admixture mapping and genome-wide association in a diverse biobank
Authors: Cullina Sinead , Shemirani Ruhollah , Asgari Samira , Kenny Eimear E.
Published: November 2024

Biobank-scale association studies that include Hispanic/Latino(a) (HL) and African American (AA) populations remain underrepresented, limiting the discovery of disease associated genetic factors in these groups. We present here a systematic comparison of phenome-wide admixture mapping (AM) and genome-wide association (GWAS) using data from the diverse BioMebiobank in New York City. Our analysis highlights 77 genome-wide significant AM signals, 48 of which were not detected by GWAS, emphasizing the complementary nature of these two approaches. AM-tagged variants show significantly higher minor allele frequency and population differentiation (Fst) while GWAS demonstrated higher odds ratios, underscoring the distinct genetic architecture identified by each method. This study offers a comprehensive phenome-wide AM resource, demonstrating its utility in uncovering novel genetic associations in underrepresented populations, particularly for variants missed by traditional GWAS approaches.
Implementing a consultation service for translating genomic research findings into the clinic: lessons from the SickKids Genome Board
Authors: Pan Amy , Pulsifer Kenzie , Axford Michelle , Dolman Lena , Gallinger Bailey , Liston Eriskay , Stephenson Elizabeth , Szuto Anna , Zahavich Laura , Costain Gregory
Published: November 2024

Objectives

Genome-wide sequencing (GWS) is now used across the breadth of paediatric research. There is a greater potential to identify unexpected, clinically relevant findings with GWS than with the targeted genetic techniques used in prior decades. Individual research teams may not have the expertise to evaluate and manage these findings. The Hospital for Sick Children (SickKids) Genome Board is a no-cost consultation service for researchers with questions arising from genetic aspects of their studies.

Methods

We reviewed all submissions to and recommendations from the Genome Board over the first four years, to identify common questions, themes, and trends.

Results

There were 67 submissions, and a year-over-year increase in volumes. The most common request (60%) was to assess variants identified by GWS for pathogenicity, clinical actionability, and returnability to a study participant. Overall, 23 of 48 reviewed variants were recommended for clinical confirmation and return with genetic counselling. Other categories of submissions included requests to researchers from study participants to release their “raw” genomic data, and for input on protocols related to clinical translation of findings.

Conclusion

The Genome Board provides a generalizable model for centralized triage of clinical questions arising from genomic research at a paediatric centre. Clinicians should be aware that patient participation in genetic research studies can have downstream consequences for their healthcare.
Advancing Question-Answering in Ophthalmology with Retrieval-Augmented Generation (RAG): Benchmarking Open-source and Proprietary Large Language Models
Authors: Nguyen Quang , Nguyen Duy-Anh , Dang Khang , Liu Siyin , Nguyen Khai , Wang Sophia Y. , Woof William , Thomas Peter , Patel Praveen J. , Balaskas Konstantinos , Thygesen Johan H. , Wu Honghan , Pontikos Nikolas
Published: November 2024

Purpose

To evaluate the application of Retrieval-Augmented Generation (RAG), a technique that combines information retrieval with text generation, to benchmark the performance of open-source and proprietary generative large language models (LLMs) in medical question-answering tasks within the ophthalmology domain.

Methods

Our dataset comprised 260 multiple-choice questions sourced from two question-answer banks designed to assess ophthalmic knowledge: the American Academy of Ophthalmology’s Basic and Clinical Science Course (BCSC) Self-Assessment program and OphthoQuestions. Our RAG pipeline involved initial retrieval of documents in the BCSC companion textbook using ChromaDB, followed by reranking with Cohere to refine the context provided to the LLMs. We benchmarked four models, including GPT-4 and three open-source models (Llama-3-70B, Gemma-2-27B, and Mixtral-8×7B, all under 4-bit quantization), under three settings: zero-shot, zero-shot with Chain-of-Thought and RAG. Model performance was evaluated using accuracy on the two datasets. Quantization was applied to improve the efficiency of the open-source models. Effects of quantization level was also measured.

Results

Using RAG, GPT-4-turbo’ s accuracy increased from 80.38% to 91.92% on BCSC and from 77.69% to 88.65 % on OphthoQuestions. Importantly, the RAG pipeline greatly enhanced overall performance of Llama-3 from 57.50% to 81.35% (23.85% increase), Gemma-2 62.12% to 79.23% (17.11% increase), and Mixtral-8×7B 52.89% to 75% (22.11% increase). Zero-shot-CoT had overall no significant improvement on the models’ performance. Quantization using 4 bit was shown to be as effective as using 8 bits while requiring half the resources.

Conclusion

Our work demonstrates that integrating RAG significantly enhances LLM accuracy, especially for privacy-preserving smaller open-source LLMs that can be run in sensitive and resource-constrained environments such within hospitals, offering a viable alternative to cloud-based LLMs like GPT-4-turbo.
Cross-dataset Evaluation of Dementia Longitudinal Progression Prediction Models
Authors: Zhang Chen , An Lijun , Wulan Naren , Nguyen Kim-Ngan , Orban Csaba , Chen Pansheng , Chen Christopher , Zhou Juan Helen , Liu Keli , Yeo B.T. Thomas ,   the Alzheimer’s Disease Neuroimaging Initiative,   the Australian Imaging Biomarkers and Lifestyle Study of Aging
Published: November 2024

Accurate Alzheimer’s Disease (AD) progression prediction is essential for early intervention. The TADPOLE challenge, involving 92 algorithms, used multimodal biomarkers to predict future clinical diagnosis, cognition, and ventricular volume. The winning algorithm, FROG, utilized a Longitudinal-to-Cross-sectional (L2C) transformation to convert variable longitudinal histories into fixed-length feature vectors, which contrasted with most existing approaches that fitted models to entire longitudinal histories, e.g., AD Course Map (AD-Map) and minimal recurrent neural networks (MinimalRNN). The TADPOLE challenge only utilized the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. To evaluate FROG’s generalizability, we trained it on the ADNI dataset and tested it on three external datasets covering 2,312 participants and 13,200 timepoints. We also introduced two FROG variants. One variant, L2C feedforward neural network (L2C-FNN), unified all XGBoost models used by the original FROG with an FNN. Across external datasets, L2C-FNN and AD-Map were the best for predicting cognition and ventricular volume. For clinical diagnosis prediction, L2C-FNN was the best, while AD-Map was the worst. L2C-FNN compared favorably with other approaches regardless of the number of observed timepoints, and when predicting from 0 to 6 years into the future, underscoring its potential for long-term dementia progression prediction. Pretrained ADNI models are publicly available: GITHUB_LINK.
A single center cross-sectional study on the efficacy of low-dose cytarabine and aclramycin combined with granulocyte colony-stimulating factor (CAG regimen) in elder adults with acute myeloid leukemia
Authors: MinXu  , He Chunxiao , Wen Xuemei , Lan Chen , Li Xintong , Hong Yaqun , Li Xiaofan
Published: November 2024

Background

Nowadays, the combination of CAG regimen with targeted therapy and immunotherapy has greatly improved the prognosis of AML patients, but there are controversies about the prognostic factors of CAG regimen alone, especially in AML elders.

Objective

By investigating the survival status of elder patients who received induction CAG regimen in our hospital at the beginning of this century and analyzing the factors affecting survival, we aim to provide scientific evidence for improving the survival of current patients.

Method

The AML elder patients treated with induction CAG regimen including low-dose cytarabine (10 mg/m2per 12 hours, day 1 to 14), aclarubicin(14 mg/m2per day, day 1 to 4), and G-CSF priming (200 ug / m2per day, day 1 to 14) in Fujian Medical University Union Hospital from January 2001 to December 2009 were involved in this research.

Results

Among 92 elderly AML patients, 44 (47.8%) showed clinical efficacy, while 48 (52.2%) experienced treatment failure (including 12 deaths (13.0%)). The main adverse reactions of chemotherapy were bone marrow suppression, with mild non hematological adverse reactions. The median recurrence time was 7 months. The risk factors related efficacy were high blasts, elevated LDH and HBDH.

Conclusion

The CAG regimen is suitable for elderly patients and can be used for the treatment of relapsed refractory AML and secondary AML. The CAG regimen has mild non hematological adverse reactions. After chemotherapy, there is a longer bone marrow suppression period and a higher infection rate; The reason for the improved efficacy of CAG regimen in current patients may be related to the effective reduction of tumor burden during induction combined with target or immunotherapy.
Generating snoRNA-guided Programmable 2’-O-methylation
Authors: Zhao Justin , Cockman Eric , Yin Xinhe , Chao Yvonne , Pecot Chad , Holley Christopher L.
Published: November 2024

Small nucleolar RNAs (snoRNAs) are critical in guiding post-transcriptional modifications like 2’-O-methylation (Nm), which play crucial roles in downstream processes such as splicing and translation. This study tests a novel method for Nm validation, addressing a significant gap in modern Nm research, and offers insight into the intricacies of snoRNA-guided Nm. While mapping of Nm modifications has seen significant improvement within the past decade, no major techniques have been able to validate these potential sites. Additionally, many mapping techniques lack consensus among proposed Nm sites, especially on mRNAs. Without a proper validation technique, Nm research lags compared to its peer post-transcriptional modifications. The RNase H-based Nm-VAQ assay used here quantifies 2’-O-methylation at single nucleotide resolution across various RNA species including rRNA, snRNA, and mRNA. Its optimization for mRNA allows for an unprecedented way to study the effects of Nm modifications in low abundance transcripts. Utilizing this, the study also explores the potential of creating synthetic snoRNAs to guide Nm modifications. Exogenous snoRNAs are shown to rescue Nm in genetic knockout models and can be mutated to guide Nm at any location along the target RNA transcript. Preliminary work indicates that synthetic snoRNAs demonstrate the ability to modify luciferase, impacting translation efficiency. Targeting an exon increases mRNA abundance but decreases protein expression, consistent with previous findings onPxdnmRNA. These findings set the scene for novel understanding of the relationship between snoRNA abundance, 2’-O-methylation efficiency, and Nm’s impact on gene expression.
Accuratede novodesign of high-affinity protein binding macrocycles using deep learning
Authors: Rettie Stephen A. , Juergens David , Adebomi Victor , Bueso Yensi Flores , Zhao Qinqin , Leveille Alexandria N. , Liu Andi , Bera Asim K. , Wilms Joana A. , Üffing Alina , Kang Alex , Brackenbrough Evans , Lamb Mila , Gerben Stacey R. , Murray Analisa , Levine Paul M. , Schneider Maika , Vasireddy Vibha , Ovchinnikov Sergey , Weiergräber Oliver H. , Willbold Dieter , Kritzer Joshua A. , Mougous Joseph D. , Baker David , DiMaio Frank , Bhardwaj Gaurav
Published: November 2024

The development of macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource-intensive and provide little control over binding mode. Despite considerable progress in physics-based methods for peptide design and deep-learning methods for protein design, there are currently no robust approaches forde novodesign of protein-binding macrocycles. Here, we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic peptide binders against protein targets of interest. We test 20 or fewer designed macrocycles against each of four diverse proteins and obtain medium to high-affinity binders against all selected targets. Designs against MCL1 and MDM2 demonstrate KDbetween 1-10 μM, and the best anti-GABARAP macrocycle binds with a KDof 6 nM and a sub-nanomolar IC50in vitro. For one of the targets, RbtA, we obtain a high-affinity binder with KD< 10 nM despite starting from the target sequence alone due to the lack of an experimentally determined target structure. X-ray structures determined for macrocycle-bound MCL1, GABARAP, and RbtA complexes match very closely with the computational design models, with three out of the four structures demonstrating Ca RMSD of less than 1.5 Å to the design models. In contrast to library screening approaches for which determining binding mode can be a major bottleneck, the binding modes of RFpeptides-generated macrocycles are known by design, which should greatly facilitate downstream optimization. RFpeptides thus provides a powerful framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.
ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons
Authors: Irmady Krithi , Scheckel Claudia , Singer Ruth A , Carroll Thomas , Darnell Robert B
Published: November 2024

The neuronal RNA-binding protein (RBP) family nELAVL regulates key neuronal processes by binding directly to target RNA transcripts. In this study, we demonstrate that ELAVL3 is the predominant nELAVL paralog expressed in D1 and D2 medium spiny neurons of the striatum. To investigate its function, we developed ELAVL3 cTag-crosslinking and immunoprecipitation (CLIP) to generate RBP-RNA interaction maps from these neurons. By integrating data from ELAVL3-cTag and Elavl3 knockout mice, we identified distinct regulatory effects of ELAVL3 on alternative splicing of its target transcripts. Notably, ELAVL3 modulates splicing of transcripts encoding proteins critical for glutamate and dopamine receptor signaling. These findings underscore the role of ELAVL3 in RNA-mediated regulation of molecular pathways essential for medium spiny neuron function in the striatum.
Nanopore sequencing of intact aminoacylated tRNAs
Authors: White Laura K. , Radakovic Aleksandar , Sajek Marcin P. , Dobson Kezia , Riemondy Kent A. , del Pozo Samantha , Szostak Jack W. , Hesselberth Jay R.
Published: November 2024

Transfer RNAs (tRNA) are decorated during biogenesis with a variety of modifications that modulate their stability, aminoacylation, and decoding potential during translation. The complex landscape of tRNA modification presents significant analysis challenges and to date no single approach enables the simultaneous measurement of important but disparate chemical properties of individual, mature tRNA molecules. We developed a new, integrated approach to analyze the sequence, modification, and aminoacylation state of tRNA molecules in a high throughput nanopore sequencing experiment, leveraging a chemical ligation that embeds the charged amino acid in an adapted tRNA molecule. During nanopore sequencing, the embedded amino acid generates unique distortions in ionic current and translocation speed, enabling application of machine learning approaches to classify charging status and amino acid identity. Specific applications of the method indicate it will be broadly useful for examining relationships and dependencies between tRNA sequence, modification, and aminoacylation.
Profiling Human iPSC-Derived Sensory Neurons for Analgesic Drug Screening Using a Multi-Electrode Array
Authors: Kuete Christian Fofie , Granja-Vazquez Rafael , Truong Vincent , Walsh Patrick , Price Theodore , Biswas Swati , Dussor Gregory , Pancrazio Joseph , Kolber Benedict
Published: November 2024

Chronic pain is a major global health issue, yet effective treatments are limited by poor translation from preclinical studies to humans. To address this, we developed a high-content screening (HCS) platform for analgesic discovery using hiPSC-derived nociceptors. These cells were cultured on multi-well micro-electrode arrays to monitor activity, achieving nearly 100% active electrodes by week two, maintaining stable activity for at least two weeks. After maturation (28 days), we exposed the nociceptors to various drugs, assessing their effects on neuronal activity, with excellent assay performance (Z’ values >0.5). Pharmacological tests showed responses to analgesic targets, including ion channels (Nav, Cav, Kv, TRPV1), neurotransmitter receptors (AMPAR, GABA-R), and kinase inhibitors (tyrosine, JAK1/2). Transcriptomic analysis confirmed the presence of these drug targets, although expression levels varied compared to primary human dorsal root ganglion cells. This HCS platform facilitates the rapid discovery of novel analgesics, reducing the risk of preclinical-to-human translation failure.

Motivation

Chronic pain affects approximately 1.5 billion people worldwide, yet effective treatments remain elusive. A significant barrier to progress in analgesic drug discovery is the limited translation of preclinical findings to human clinical outcomes. Traditional rodent models, although widely used, often fail to accurately predict human responses, while human primary tissues are limited by scarcity, technical difficulties, and ethical concerns. Recent advancements have identified human induced pluripotent stem cell (hiPSC)-derived nociceptors as promising alternatives; however, current differentiation protocols produce cells with inconsistent and physiologically questionable phenotypes.

To address these challenges, our study introduces a novel high-content screening (HCS) platform using hiPSC-derived nociceptors cultured on multi-well micro-electrode arrays (MEAs). The “Anatomic” protocol, used to generate these nociceptors, ensures cells with transcriptomic profiles closely matching human primary sensory neurons. Our platform achieves nearly 100% active electrode yield within two weeks and demonstrates sustained, stable activity over time. Additionally, robust Z’ factor analysis (exceeding 0.5) confirms the platform’s reliability, while pharmacological validation establishes the functional expression of critical analgesic targets. This innovative approach improves both the efficiency and clinical relevance of analgesic drug screening, potentially bridging the translational gap between preclinical studies and human clinical trials, and offering new hope for effective pain management.
Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA
Authors: Berger Kyle D. , Puthenpeedikakkal Anees M. K. , Mathews David H. , Fu Dragony
Published: November 2024

All tRNAs undergo a series of chemical modifications to fold and function correctly. In mammals, the C32 nucleotide in the anticodon loop of tRNA-Arg-CCU and UCU is methylated to form 3-methylcytosine (m3C). Deficiency of m3C in arginine tRNAs has been linked to human neurodevelopmental disorders, indicating a critical biological role for m3C modification. However, the structural repercussions of m3C modification are not well understood. Here, we examine the structural effects of m3C32 modification on the anticodon stem loop (ASL) of human tRNA-Arg-UCU-4-1, a unique tRNA with enriched expression in the central nervous system. Optical melting experiments demonstrate that m3C modification can locally disrupt nearby base pairing within the ASL while simultaneously stabilizing the ASL electrostatically, resulting in little net change thermodynamically. The isoenergetic nature of the C32 – A38 pair vs the m3C32 – A38 pair may help discriminate against structures not adopting canonical C32 – A38 pairings, as most other m3C pairings are unfavorable. Furthermore, multidimensional NMR reveals that after m3C modification there are changes in hairpin loop structure and dynamics, the structure of A37, and the neighboring A31 – U39 base pair. However, these structural changes after modification are made while maintaining the shape of the C32 – A38 pairing, which is essential for efficient tRNA function in translation. These findings suggests that m3C32 modification could alter interactions of tRNA-Arg isodecoders with one or more binding partners while simultaneously maintaining the tRNA’s ability to function in translation.