bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of search-enabled Pre-trained Large Language Models on retrieval tasks for the PubChem Database
Authors: Sze Ash , Hassoun Soha
Published: August 2024

Databases are indispensable in biological and biomedical research, hosting vast amounts of structured and unstructured data, facilitating the organization, retrieval, and analysis of complex data. Database access, however, remains a manual, tedious, and sometimes overwhelming, task. We investigate in this study the current state of using pre-trained, search-enabled LLMs for data retrieval from biological databases. Equipped with internet search and code generation capabilities, LLMs promise to streamline database access through natural language, expedite search and knowledge retrieval, and provide coherent analytical summaries. As an example database, we focus on evaluating a current search-enabled LLMs (GPT-4o) for retrieval from the PubChem database, a flagship, heavily used database that plays a critical role in biological and biomedical research. As PubChem is an open archival repository, it provides a well-documented programmatic interface that can be exploited through LLM code generation capabilities. We evaluate retrieval tasks for eight common PubChem access protocols that were previously documented. The tasks include identifying interacting genes and proteins, finding drug-like compounds based on structural similarity, retrieving bioactivity data, and locating stereoisomers and isotopomers. We develop a methodology for adopting the protocols into an LLM-prompt, where we supplement the prompt with additional context through iterative prompt refinement as needed. To further evaluate the LLM capabilities, we instruct the LLM to perform the retrieval with and without using programmatic access. We compare the results (referred to as gold and silver answers) when using these retrieval modalities with two traditional retrieval baselines that include running the manual search steps for each reference protocol through the PubChem database web interface, and through the provided PUG (Power-User Gateway) programmatic access. We quantitatively and qualitatively summarize our results, showing that generating programmatic access is more likely to yield the correct answers. We highlight the value and limitations of using current search-based LLMs for database retrieval. We also provide guidance for the future development that can improve the accuracy and reliability of search-based LLMs.
Network-based representation learning enables the identification of risk genes and latent functional pathways in primary open-angle glaucoma
Authors: Cousins Henry C. , Altman Russ B. , Pasquale Louis R.
Published: August 2024

Despite the identification of hundreds of risk genes for primary open-angle glaucoma (POAG), a significant portion of the POAG genetic risk landscape remains unexplored. We hypothesized that unsupervised learning on large protein-protein interaction (PPI) networks could enable comprehensive characterization of the genetic pathways that underlie POAG risk. We used graph representation learning on a proteome-scale PPI network to generate embeddings capturing complex features of each protein’s interactions. Using these embeddings, we trained a model with POAG-associated genes from the DisGeNET database to output an inferred POAG risk score for over 12,000 gene products, which identified known POAG risk genes with an area under the receiver operating characteristic curve of 0.739 (95% CI 0.686-0.792). These included well-known POAG risk genes such asRHOAandMMP3, as well as genes with significant contributions to other ocular diseases. Pathway analysis on the proteome-wide risk scores implicated 20 biological processes in POAG pathogenesis. Furthermore, cluster analysis of embeddings for POAG risk genes revealed 5 distinct functional neighborhoods, including cytokine signaling, coagulation response, collagen biosynthesis, extracellular matrix development, and fatty acid metabolism. Our results suggest that representation learning can recognize important patterns of protein interaction that allowin silicoprioritization of POAG risk genes and pathways.
ClearScope: a fully integrated light sheet theta microscope for sub-cellular resolution imaging without lateral size constraints
Authors: Fay Matthew G. , Lang Peter J. , Denu David S. , O'Connor Nathan J. , Haydock Benjamin W. , Blaisdell Jeffrey O. , Roussel Nicolas , Wilson Alissa L. , Aronson Sage R. , Angstman Paul J. , Gong Cheng , Butola Tanvi , Devinsky Orrin , Basu Jayeeta , Tomer Raju , Glaser Jacob R.
Published: August 2024

Three-dimensional (3D) ex vivo imaging of cleared intact brains of animal models and large human and non-human primate postmortem brain specimens is important for understanding the physiological neural network connectivity patterns and the pathological alterations underlying neuropsychiatric and neurological disorders. Light-sheet microscopy has emerged as a highly effective imaging modality for rapid high-resolution imaging of large cleared samples. However, the orthogonal arrangements of illumination and detection optics in light sheet microscopy limits the size of specimen that can be imaged. Recently developed light sheet theta microscopy (LSTM) technology addressed this by utilizing a unique arrangement of two illumination light paths oblique to the detection light path, while allowing perpendicular arrangement of the detection light path relative to the specimen surface. Here, we report development of a next-generation, fully integrated, and user-friendly LSTM system for rapid sub-cellular resolution imaging uniformly throughout a large specimen without constraining the lateral (XY) size. In addition, we provide a seamlessly integrated workflow for image acquisition, data storage, pre- and post-processing, enhancement, and quantitative analysis. We demonstrate the system performance by high-resolution 3D imaging of intact mouse brains and human brain samples, and complete data analysis including digital neuron tracing, vessel reconstruction and design-based stereological analysis in 3D. This technically enhanced and user-friendly LSTM implementation will enable rapid quantitative mapping of molecular and cellular features of interests in diverse types of very large samples.
Behavioral plasticity and the valence of indirect interactions
Authors: Fahimipour Ashkaan K , Gil Michael A , Hein Andrew M
Published: August 2024

Behavioral plasticity in animals often transforms direct interactions between species, but its effects can spread through ecological networks in unexpected ways, creating indirect interactions that are difficult to predict. We present a theoretical framework to understand how species-level behavioral changes influence these indirect interactions and the overall dynamics of ecological networks. As an illustrative example, we analyze predators that feed on two types of prey, each of which temporarily transitions into a state of reduced activity and growth after evading an attack, to decrease vulnerability. Coarse-grained models show that this hiding behavior can shift the indirect interaction between prey species from apparent competition to mutualism or parasitism. These shifts occur when the predator's capture efficiency falls below a threshold, causing frequent hunting failures. This inefficiency leads to one prey species indirectly protecting the other by drawing predator attention, paradoxically increasing predator biomass due to reduced hunting success. Interestingly, empirical capture probabilities align with the range where such shifts are predicted. We describe these changes in the qualitative nature of species interactions as shifts in "interaction valence," emphasizing how routine animal behaviors can generate indirect effects that defy intuition and reshape community structure through cascading effects across the network.
Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons
Authors: Bendall Emily E. , Zhu Yuwei , Fitzsimmons William J. , Rolfes Melissa , Mellis Alexandra , Halasa Natasha , Martin Emily T. , Grijalva Carlos G. , Talbot H. Keipp , Lauring Adam S.
Published: August 2024

While influenza A virus (IAV) antigenic drift has been documented globally, in experimental animal infections, and in immunocompromised hosts, positive selection has generally not been detected in acute infections. This is likely due to challenges in distinguishing selected rare mutations from sequencing error, a reliance on cross-sectional sampling, and/or the lack of formal tests of selection for individual sites. Here, we sequenced IAV populations from 346 serial, daily nasal swabs from 143 individuals collected over three influenza seasons in a household cohort. Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0.5% frequency threshold. Within-host populations were subject to purifying selection with >75% mutations present at <2% frequency. Children (0-5 years) had marginally higher within-host evolutionary rates than adolescents (6-18 years) and adults (>18 years, 4.4x10-6vs. 9.42x10-7and 3.45x10-6, p <0.001). Forty-five iSNV had evidence of parallel evolution, but were not overrepresented in HA and NA. Several increased from minority to consensus level, with strong linkage among iSNV across segments. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 23/256 loci (9%) in A(H3N2) specimens and 19/176 loci (11%) in A(H1N1)pdm09 specimens, and these were infrequently found in circulation. Overall, we found that within-host IAV populations were subject to purifying selection and genetic drift, with only subtle differences across seasons, subtypes, and age strata. Positive selection was rare and inconsistently detected.
Population Representation of the Confidence in a Decision in the Parietal Cortex
Authors: Zylberberg Ariel , Shadlen Michael N
Published: August 2024

Confidence in a decision is the belief, prior to feedback, that one's choice is correct. In the brain, many decisions are implemented as a race between competing evidence-accumulation processes. We ask whether the neurons that represent evidence accumulation also carry information about whether the choice is correct (i.e., confidence). Monkeys performed a reaction time version of the random dot motion task. Neuropixels probes were used to record from neurons in the lateral intraparietal (LIP) area. LIP neurons with response fields that overlap the choice-target contralateral to the recording site (Tin neurons) represent the accumulation of evidence in favor of contralateral target selection. We demonstrate that shortly before a contralateral choice is reported, the population of Tin neurons contains information about the accuracy of the choice (i.e., whether the choice is correct or incorrect). This finding is unexpected because, on average, Tin neurons exhibit a level of activity before the report that is independent of reaction time and evidence strength—both strong predictors of accuracy. This apparent contradiction is resolved by examining the variability in neuronal responses across the population of Tin neurons. While on average, Tin neurons exhibit a stereotyped level of activity before a contralateral choice, many neurons depart from this average in a consistent manner. From these neurons, the accuracy of the choice can be predicted using a simple logistic decoder. The accuracy of the choice predicted from neural activity reproduces the hallmarks of confidence identified in human behavioral experiments. Therefore, neurons that represent evidence accumulation can also inform the monkey's confidence.
Sapphire-Based Optrode for Low Noise Neural Recording and Optogenetic Manipulation
Authors: Xu Yanyan , Li Ben-Zheng , Huang Xinlong , Liu Yuebo , Liang Zhiwen , Yang Xien , Lin Lizhang , Wang Liyang , Xia Yu , Ridenour Matthew , Huang Yujing , Zhen Yuan , Klug Achim , Pun Sio Hang , Lei Tim C. , Zhang Baijun
Published: August 2024

Electrophysiological recordings of neurons in deep brain regions using optogenetic stimulation are essential to understanding and regulating the role of complex neural activity in biological behavior and cognitive function. Optogenetic techniques have significantly advanced neuroscience research by enabling the optical manipulation of neural activities. Because of the significance of the technique, constant advancements in implantable optrodes that integrate optical stimulation with low-noise, large-scale electrophysiological recording are in demand to improve the spatiotemporal resolution for various experimental designs and future clinical applications. However, robust and easy-to-use neural optrodes that integrate neural recording arrays with high-intensity light emitting diodes (LEDs) are still lacking. Here, we propose a neural optrode based on Gallium Nitride (GaN) on sapphire technology, which integrates a high-intensity blue LED with a 5x2 recording array monolithically for simultaneous neural recording and optogenetic manipulation. To reduce the noise interference between the recording electrodes and the LED, which is in close physical proximity, three metal grounding interlayers were incorporated within the optrode, and their ability to reduce LED-induced artifacts during neural recording was confirmed through both electromagnetic simulations and experimental demonstrations. The capability of the sapphire optrode to record action potentials has been demonstrated by recording the firing of mitral/tuft cells in the olfactory bulbs of mice in vivo. Additionally, the elevation of action potential firing due to optogenetic stimulation observed using the sapphire probe in medial superior olive (MSO) neurons of the gerbil auditory brainstem confirms the capability of this sapphire optrode to precisely access neural activities in deep brain regions under complex experimental designs.
CureSCi Metadata Catalog—finding and harmonizing studies for secondary analysis of hydroxyurea use for sickle cell disease
Authors: Wu Xin , Stratford Jeran , Kesler Karen , Ives Cataia , Hendershot Tabitha , Kroner Barbara , Qin Ying , Pan Huaqin
Published: August 2024

Objectives

Sickle cell disease (SCD) is a rare group of inherited red blood cell disorders that affect hemoglobin, resulting in serious multi-system complications. The limited number of patients available to participate in research studies can inhibit investigating sophisticated relationships. Secondary analysis is a research method that involves using existing data to answer new research questions. Data harmonization enables secondary analysis by combining data across studies, especially helpful for rare disease research where individual studies may be small. The National Heart, Lung, and Blood Institute Cure Sickle Cell Initiative (CureSCi) Metadata Catalog is a web-based tool to identify SCD study datasets for conducting data harmonization and secondary analysis. We present a proof-of-concept secondary analysis to explore factors associated with discontinuation of hydroxyurea, a safe and effective first line SCD therapy, to illustrate the utility of the CureSCi Metadata Catalog to expedite and enable more robust SCD research.

Methods

We performed secondary analysis of SCD studies using a multi-step workflow: develop research questions, identify study datasets, identify variables of interest, harmonize variables, and establish an analysis method. A harmonized dataset consisting of eight predictor variables across five studies was created. Secondary analysis involved a generalized linear model was employed to identify factors that significantly impact hydroxyurea discontinuation.

Results

The CureSCi Metadata Catalog provided a platform to efficiently find relevant studies and design a harmonization strategy to prepare data for secondary analysis. Multivariate analysis of the harmonized identified that patients who are older, are female, had a history of blood transfusion therapy, had episodes of acute chest syndrome, and had the SC sickle cell genotype are more likely to stop hydroxyurea treatment.

Conclusion

This secondary analysis provides a template for how the CureSCi Metadata Catalog expedites dataset discovery of sickle cell studies for identifying relationships between variables or validating existing findings.
Quantifying the Spectrum of Early Motor and Language Milestones in Sex Chromosome Trisomy
Authors: Thompson Talia , Bothwell Samantha , Janusz Jennifer , Wilson Rebecca , Howell Susan , Davis Shanlee , Swenson Karli , Martin Sydney , Kowal Karen , Ikomi Chijioke , Despradel Maria , Ross Judith , Tartaglia Nicole
Published: August 2024

Background and objectives: Sex chromosome trisomy (SCT) is a common chromosomal abnormality associated with increased risks for early developmental delays and neurodevelopmental disorders later in childhood. Our objective was to quantify the spectrum of early developmental milestones in SCT. We hypothesized later milestone achievement in SCT than the general population. Methods: Data were collected as part of the eXtraordinarY Babies Study, a prospective natural history of developmental and health trajectories in a prenatally identified sample of infants with SCT. Parent reported, clinician-validated, early motor and language milestones were collected at 2, 6, 12, 18, 24, and 36-months. Age distributions of milestone achievement were compared with normative data. Results: In all SCT conditions, compared with normative data, there was increased variability and a later median age of skill development across multiple gross motor and expressive language milestones. Results also show a significant amount of overlap with the general pediatric population, suggesting that for many children with prenatally identified SCT, early milestones present within, or close to, the expected timeline. Conclusions: As increasing numbers of infants with prenatal SCT diagnoses present at pediatric practices, we provide an evidence-based schedule of milestone achievement in SCT as a tool for pediatricians and families. Detailed data on SCT milestones can support clinical interpretation of milestone achievement. Increased variability and later median age of milestone acquisition in SCT compared to norms support consideration of all infants with SCT as high risk.
Influence of parenting styles on depression, anxiety, stress and self-esteem of adolescents
Authors: Khadka Rabina , Bhatt Anjali , Thapa Milan , Sharma Anusha , Joshi Manoj , Mishra Durga Khadka
Published: August 2024

Globally, fourteen percent adolescents suffer from mental health issues. Among the many contributing factors to mental health problems, parenting is considered to have a significant effect on both the physical and psychological health of adolescents. This study aimed to assess depression, anxiety, stress, and self-esteem among adolescents and their relationship with parenting style. A community-based cross-sectional study with multistage proportionate sampling was conducted among 583 school-going adolescents from September 2022 to March 2023 in Bheemdatt Municipality, Kanchanpur, Nepal. This study used the previously validated Depression Anxiety and Stress Scale-21 (DASS-21), Rosenberg Self-Esteem Scale, and Parenting Style and Dimension Questionnaire to assess the status and relationships. Variables were analyzed using a multivariate logistic regression model, and a p-value of <0.05 was considered statistically significant. The prevalence of depression, anxiety, and stress among adolescents was found to be 37.39% (95% CI: 33.46 to 41.32), 42.19% (95% CI: 38.18 to 46.19), and 24.69% (95% CI: 21.18 to 28.19), respectively. Likewise, the mean self-esteem score among adolescents was found to be 22.26 ± 3.56. The authoritative parenting style was positively associated with DAS, while the authoritarian and permissive parenting styles were negatively associated with DAS and positively associated with self-esteem. Parent’s age, parent’s education, social support, and bullying, showed strong effects on the research outcomes. These findings highlight the crucial role of parental involvement and support in shaping adolescent mental health, underscoring the need for interventions that encourage positive parenting practices to improve mental health outcomes for adolescents. It is highly recommended that school-based programs focus on raising awareness of mental health issues and offer interventions such as stress management and student counseling. There is a pressing need to effectively monitor and enforce anti-bullying policies within educational settings.
The effect of an incentive billing code on heart failure management in primary care: a population-based study
Authors: Zhou Shijie , Lee Douglas S. , Nguyen Francis , Benipal Harsukh , Perez Richard , Austin Peter C. , Abdel-Qadir Husam , Udell Jacob A. , Demers Catherine
Published: August 2024

Background: To support family physicians (FPs) in managing patients with heart failure (HF), the Ministry of Health in Ontario, Canada, implemented the Q050 billing code in 2008, a pay-for-performance (P4P) incentive for guideline-based HF care. We studied whether the incentive was associated with any change in process-of-care measure, particularly the prescriptions of HF medications. Methods: We identified all patients with HF in Ontario of age>65, who were managed by FPs claiming the Q050 incentive between 2008 and 2021. We counted the number of patients who were prescribed renin-angiotensin system inhibitors (RASi), beta-blockers (BB), mineralocorticoid receptor antagonists (MRA), and diuretics three months before and after the Q050 billing code was claimed for these patients. Where applicable, we classified the agents within each class by whether they are guideline-directed as recommended by the Canadian Cardiovascular Society (CCS). Results: We included 39,425 HF patients in the study. The median age was 80 (IQR 73-85) years; 49% were female. Half were assessed by an internist or cardiologist during the six months before their HF diagnosis. Compared to pre-Q050, there was an increase in RASi prescriptions from 42.5% to 45.8%, BB from 51.9% to 54.4%, MRA from 9.2% to 11.7%, and diuretics from 63.2% to 65.7% after the incentive (p<0.05). There was a decrease in those not on any HF medications from 27.5% to 24.9% (p<0.001). Those with newly diagnosed HF and prompt follow-up with FPs experienced the largest but clinically modest increase in HF medications. Conclusions: To our knowledge, this is the first evaluation of process-of-care measures related to a pay-for-performance program in primary care HF management. The Q050 incentive led to a minimal increase in the prescription of HF medications; there is underutilization of disease-modifying agents. Further research is needed to understand why pay-for-performance programs had no effect on physician prescribing behaviours.
Whole-brain mapping in adult zebrafish and identification of a novel tank test functional connectome
Authors: Rajput Neha , Parikh Kush , Squires Ada , Fields Kailyn K. , Wong Matheu , Kanani Dea , Kenney Justin W.
Published: August 2024

Identifying general principles of brain function requires the study of structure-function relationships in a variety of species. Zebrafish have recently gained prominence as a model organism in neuroscience, yielding important insights into vertebrate brain function. Although methods have been developed for mapping neural activity in larval animals, we lack similar techniques for adult zebrafish that have the advantage of a fully developed neuroanatomy and larger behavioral repertoire. Here, we describe a pipeline built around open-source tools for whole-brain activity mapping in freely swimming adult zebrafish. Our pipeline combines recent advances in histology, microscopy, and machine learning to capturecfosactivity across the entirety of the adult brain. Images captured using light-sheet microscopy are registered to the recently created adult zebrafish brain atlas (AZBA) for automated segmentation using advanced normalization tools (ANTs). We used our pipeline to measure brain activity after zebrafish were subject to the novel tank test. We found thatcfoslevels peaked 15 minutes following behavior and that several regions containing serotoninergic, dopaminergic, noradrenergic, and cholinergic neurons were active during exploration. Finally, we generated a novel tank test functional connectome. Functional network analysis revealed that several regions of the medial ventral telencephalon form a cohesive sub-network during exploration. We also found that the anterior portion of the parvocellular preoptic nucleus (PPa) serves as a key connection between the ventral telencephalon and many other parts of the brain. Taken together, our work enables whole-brain activity mapping in adult zebrafish for the first time while providing insight into neural basis for the novel tank test.
The Fragile X Messenger Ribonucleoprotein 1 regulates the morphology and maturation of human and rat oligodendrocytes
Authors: Ramesh Vidya , Kougianou Ioanna , Tsoukala Eleni , Kozic Zrinko , Burr Karen , Viswanath Biju , Hampton David , Story David , Reddy Bharath Kumar , Pal Rakhi , Dando Owen Robert , Kind Peter C , Chattarji Sumantra , Selvaraj Bhuvaneish Thangaraj , Chandran Siddharthan , Zoupi Lida
Published: August 2024

The Fragile X Messenger Ribonucleoprotein (FMRP) is an RNA binding protein that regulates the translation of multiple mRNAs and is expressed by neurons and glia in the mammalian brain. Loss of FMRP leads to Fragile X Syndrome (FXS), a common inherited form of intellectual disability and autism. While most research has been focusing on the neuronal contribution to FXS pathophysiology, the role of glia, particularly oligodendrocytes, is largely unknown. FXS individuals are characterised by white matter changes which imply impairments in oligodendrocyte differentiation and myelination. We hypothesized that FMRP regulates oligodendrocyte maturation and myelination during postnatal development. Using a combination of human pluripotent stem cell - derived oligodendrocytes and an Fmr1 knockout rat model, we studied the role of FMRP on mammalian oligodendrocyte development. We found that the loss of FMRP leads to shared defects in oligodendrocyte morphology in both rat and human systems in vitro which persist in the presence of FMRP expressing axons in chimeric engraftment models. Our findings point to species-conserved, cell-autonomous defects during oligodendrocyte maturation in FXS.
A simple inland culture system provides insights into ascidian post-embryonic developmental physiology
Authors: Mathiesen Birthe Thuesen , Ohta Mayu , De Magalhaes Boris Pinto , Castelletti Chiara , Perria Vincenzo , Christiaen Lionel , Ohta Naoyuki
Published: August 2024

Maintenance and breeding of experimental organisms are fundamental to life sciences, but both initial and running costs, and hands-on zootechnical demands can be challenging for many laboratories. Here, we aimed to further develop a simple protocol for reliable inland culture of tunicate model species of theCionagenus. We cultured bothCiona robustaandCiona intestinalisin controlled experimental conditions, with a focus on dietary variables, and quantified growth and maturation parameters. From statistical analysis of these standardized datasets, we gained insights into the post-embryonic developmental physiology ofCiona, and inferred an improved diet and culturing conditions for sexual maturation. We showed that body length is a critical determinant of both somatic and sexual maturation, which suggests the existence of systemic control mechanisms of resource allocation toward somatic growth or maturation, and supports applying size selection as a predictor of reproductive fitness in our inland culture, to keep the healthiest animals at low density in the system. In the end, we successfully established a new protocol, including size selection, to promote both sperm and eggs production. Our protocol using small tanks will empower researchers to initiate inlandCionacultures with low costs and reduced space constraints.
High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome
Authors: Nebenfuehr Marcel , Prochotta David , Ben Hamadou Alexander , Janke Axel , Gerheim Charlotte , Betz Christian , Greve Carola , Bolz Hanno Joern
Published: August 2024

Background: The time required for sequencing and de novo assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian de novo genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a model: The Whippet. Findings: We present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%. Conclusions: Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.
A Deep Learning Framework for Predicting Prognostically Relevant Consensus Molecular Subtypes in HPV-Positive Cervical Squamous Cell Carcinoma from Routine Histology Images
Authors: Wang Ruoyu , Gunesli Gozde N. , Skingen Vilde Eide , Valen Kari-Anne Frikstad , Lyng Heidi , Young Lawrence S. , Rajpoot Nasir
Published: August 2024

Despite efforts in human papillomavirus (HPV) prevention and screening, cervical cancer remains the fourth most prevalent cancer among women globally. In this study, we propose an end-to-end deep learning framework to investigate histological correlates of the two consensus molecu-lar subtype (CMS) of HPV-positive cervical squamous cell carcinoma (CSCC) patients. Analysing three international CSCC cohorts (n=545 patients), we demonstrate that the genomically determined CMS can be predicted from routine haematoxylin and eosin (H&E)-stained histology slides, with our Digital-CMS scores achieving significant patient stratifications in terms of disease-specific survival (TCGA p=0.0022, Oslo p=0.0495) and disease-free survival (TCGA p=0.0495, Oslo p=0.0282). In addition, our extensive analyses reveal distinct tumour microenvironment (TME) differences between the two CMS subtypes of the CSCC cohorts. Notably, CMS-C1 CSCC subgroup has markedly increased lymphocyte presence, whereas CMS-C2 subgroup has high nuclear pleomor-phism, an elevated neutrophil-to-lymphocyte ratio, and increased neutrophil density. Analysis of representative histological regions reveals higher degree of malignancy in CMS-C2 patients, as-sociated with poor prognosis. This study introduces a potentially clinically advantageous Digital-CMS score derived from digitised WSIs of routine H&E-stained tissue sections, offers new insights into TME differences impacting patient prognosis and potential therapeutic targets, and identifies histological patterns serving as potential surrogate markers of the two CMS subtypes for clinical application.
A maximum likelihood estimator for quartets under the Cavender-Farris-Neyman model
Authors: Hill Max , Rodriguez Jose Israel
Published: August 2024

We present the Julia package FourLeafMLE.jl, which solves a global optimization problem to perform statistical inference using DNA sequence alignment data for quartets under the Cavender-Farris-Neyman phylogenetic model.
Detection, Isolation and Quantification of Myocardial Infarct with Four Different Histological Staining Techniques
Authors: Wu Xiaobo , Meier Linnea , Liu Tom X , Toldo Stefano , Poelzing Steven , Gourdie Robert G.
Published: August 2024

Precise quantification of myocardial infarction is crucial for evaluating the therapeutic strategies. We developed a robust, color-based semi-automatic algorithm capable of infarct region detection, isolation and quantification with four different histological staining techniques, and the isolation and quantification of diffuse fibrosis in the heart. Our method is developed based on the color difference in the infarct and non-infarct regions after histological staining. Mouse cardiac tissues stained with Masson’s trichrome (MTS), hematoxylin and eosin (H&E), 2,3,5-Triphenyltetrazolium chloride and picrosirius red were included to demonstrate the performance of our method. We demonstrate that our algorithm can effectively identify and produce a clear visualization of infarct tissue for the four staining techniques. Notably, the infarct region on a H&E-stained tissue section can be clearly visualized after processing. The MATLAB-based program we developed holds promise in the infarct quantification. Additionally, our program can isolate and quantify the diffuse fibrotic elements from an MTS-stained cardiac section, which suggested the algorithm’s potential for evaluating pathological cardiac fibrosis in diseased cardiac tissues. In conclusion, we demonstrate that this color-based algorithm is capable of accurately identifying, isolating and quantifying cardiac infarct regions with different staining techniques, as well as the diffuse and patchy fibrosis in MTS-stained cardiac tissues.
Correlating amino acid profiles with improved expression capability of superior CHO based expression platforms
Authors: Sharma Vijeta , Guleria Richa , Mukherjee K. J.
Published: August 2024

A novel modified CHO cell line was constructed by expressing a three gene combination of Bclx(L), Aven and BECN1 which are critical targets of the apoptosis and autophagy pathways. This synergistic combination significantly improved cell viability as well as Rituximab (RTX) expression by 7.5 fold. A comparative amino acid analysis of the modified and control cultures both with and without RTX expression showed interesting changes in amino acid uptake rates. We first compared the utilization of amino acids in the control cells without RTX expression to the control cells with RTX expression where it declined significantly in the later half of the culture with the maximum decrease observed with tyrosine, which instead of uptake got secreted into the medium. The uptake of aspartic and glutamic acid also fell drastically during this period demonstrating the deleterious effect of RTX expression on cellular health. When the modified cells were used for RTX expression, there was conversely a slight increase in amino acid consumption in the later part of the culture with the maximum increase observed with alanine and tyrosine. The differential amino acid consumption rates provided us with an indirect measure of improved cellular health and ability of the modified cells to counter the cellular stress associated with RTX expression. Amino acid analysis could thus become a useful predictive tool to identify the critical features of better host expression platforms.
Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from Theophylline-Binding RNA Aptamer
Authors: Rasouli Ali , Pickard Frank C. , Sur Sreyoshi , Grossfield Alan , Işık Bennett Mehtap
Published: August 2024

Alchemical free energy calculations are widely used to predict the binding affinity of small molecule ligands to protein targets; however, the application of these methods to RNA targets has not been deeply explored. We systematically investigated how modeling decisions affect the performance of absolute binding free energy calculations for a relatively simple RNA model system: theophylline-binding RNA aptamer with theophylline and five analogs. The goal of this investigation was twofold: (1) understanding the performance levels we can expect from absolute free energy calculations for a simple RNA complex and (2) learning about practical modeling considerations that impact the success of RNA binding predictions, which may be different than the best practices established for protein targets. We learned that magnesium ion (Mg2+) placement is a critical decision that impacts affinity predictions. When information regarding Mg2+positions is lacking, implementing RNA backbone restraints is an alternative way of stabilizing RNA structure that recapitulates prediction accuracy. Since mistakes in Mg2+placement can be detrimental, omitting magnesium ions entirely and using RNA backbone restraints is attractive as a risk-mitigating approach. We found that predictions are sensitive to modeling experimental buffer conditions correctly, including salt type and ionic strength. We explored the effects of sampling in the alchemical protocol, choice of the ligand force field (GAFF2/OpenFF Sage), and water model (TIP3P/OPC) on predictions, which allowed us to give practical advice for the application of free energy methods to RNA targets. By capturing experimental buffer conditions and implementing RNA backbone restraints, we were able to compute binding affinities accurately (MAE = 2.2 kcal/mol, Pearson's correlation coefficient = 0.9, Kendall's tau = 0.7). We believe there is much to learn about how to apply free energy calculations for RNA targets and how to enhance their performance in prospective predictions. This study is an important first step for learning best practices and special considerations for RNA-ligand free energy calculations. Future studies will consider increasingly complicated ligands and diverse RNA systems and help the development of general protocols for therapeutically relevant RNA targets.
How Modulation of the Tumor Microenvironment Drives Cancer Immune Escape Dynamics
Authors: Shrestha Pujan , Ghoreyshi Zahra , George Jason T
Published: August 2024

Metastatic disease is the leading cause of cancer-related death, despite recent advances in therapeutic interventions. Prior modeling approaches have accounted for the adaptive immune system's role in combating tumors, which has led to the development of stochastic models that explain cancer immunoediting and tumor-immune co-evolution. However, cancer immune-mediated dormancy, wherein the adaptive immune system maintains a micrometastatic population by keeping its growth in check, remains poorly understood. Immune-mediated dormancy can significantly delay the emergence (and therefore detection) of metastasis. An improved quantitative understanding of this process will thereby improve our ability to identify and treat cancer during the micrometastatic period. Here, we introduce a generalized stochastic model that incorporates the dynamic effects of immunomodulation within the tumor microenvironment on T cell-mediated cancer killing. This broad class of nonlinear birth-death model can account for a variety of cytotoxic T cell immunosuppressive effects, including regulatory T cells, cancer-associated fibroblasts, and myeloid-derived suppressor cells. We develop analytic expressions for the likelihood and mean time of immune escape. We also develop a method for identifying a corresponding diffusion approximation applicable to estimating population dynamics across a wide range of nonlinear birth-death processes. Lastly, we apply our model to estimate the nature and extent of immunomodulation that best explains the timing of disease recurrence in bladder and breast cancer patients. Our findings quantify the effects that stochastic tumor-immune interaction dynamics can play in the timing and likelihood of disease progression. Our analytical approximations provide a method of studying population escape in other ecological contexts involving nonlinear transition rates.
FORCE trained spiking networks do not benefit from faster learning while parameter matched rate networks do
Authors: Newton Thomas Robert , Nicola Wilten Robert
Published: August 2024

There are considerable difficulties in training spiking recurrent neural networks versus the standard recurrent neural networks (RNNs) that are more closely associated with neural firing rates. Here, we investigate where these difficulties arise by training networks of spiking neurons and their parameter matched instantaneous rate RNNs in supervised learning tasks. We FORCE trained leaky integrate-and-fire spiking and their parameter matched instantaneous rate-networks across different dynamical tasks with the FORCE hyperparameters also matched. We found that when the learning rate was slow, spiking and rate networks largely operated identically, with FORCE training discovering highly correlated solutions to the weight matrices, and similar hyperparameter areas of successful convergence. In fact, these weight matrix solutions were broadly interchangeable between networks, with learned spiking network weights able to lead to correct dynamical decoding in the rate network and vice-versa. However, when learning is too fast, the correlations between the learned solutions drop precipitously, and the solutions are no longer swappable between networks, with some supervisors having completely different optimal hyperparameter zones between rate and spiking networks. These networks also qualitatively behave in different ways across network sizes for different learning rates: faster learning leads to better performance in rate networks across network size, while leading to no tangible change across network size in spiking networks aside from network instability. Our results show that some of the difficulties that arise in training spiking neural networks are due to overly fast learning, which rate networks can tolerate, but matched spiking networks cannot.
Perisaccadic perceptual mislocalization strength depends on the visual appearance of saccade targets
Authors: Baumann Matthias P. , Denninger Anna F. , Hafed Ziad M.
Published: August 2024

We normally perceive a stable visual environment despite repetitive eye movements. To achieve such stability, visual processing integrates information across saccades, and laboratory hallmarks of such integration are robustly observed by presenting brief perimovement visual probes. In one classic phenomenon, perceived probe locations are grossly erroneous. This phenomenon is believed to depend, at least in part, on corollary discharge associated with saccade-related neuronal movement commands. However, we recently found that superior colliculus motor bursts, a known source of corollary discharge, can be different for different image appearances of the saccade target. Therefore, here we investigated whether perisaccadic perceptual mislocalization also depends on saccade-target appearance. We asked human participants to generate saccades to either low (0.5 cycles/deg) or high (5 cycles/deg) spatial frequency gratings. We always placed a high contrast target spot at grating center, to ensure matched saccades across image types. We presented brief perisaccadic probes, which were high in contrast to avoid saccadic suppression, and the subjects pointed (via mouse cursor) at their perceived locations. We observed stronger perisaccadic mislocalization for low spatial frequency saccade targets, and for upper visual field probe locations. This was despite matched saccade metrics and kinematics across conditions, and it was also despite matched probe visibility for the different saccade target images (low versus high spatial frequency gratings). To the extent that perisaccadic perceptual mislocalization depends on corollary discharge, our results suggest that such discharge might relay more than just spatial saccade vectors to the visual system; saccade-target visual features can also be transmitted.

Significance

Brief visual probes are grossly mislocalized when presented in the temporal vicinity of saccades. While the mechanisms of such mislocalization are still under investigation, one component of them could derive from corollary discharge signals associated with saccade movement commands. Here, we were motivated by the observation that superior colliculus movement bursts, one source of corollary discharge, vary with saccade-target image appearance. If so, then perisaccadic mislocalization should also do so, which we confirmed.
ASSESSMENT OF PATIENT SAFETY ATTITUDE AMONG DOCTORS AND NURSES AT PUBLIC SPECIALIST HOSPITALS IN MALAYSIA
Authors: SAYED ABDUL HAMID SHARIFAH BALQIS , ISMAIL ANIZA , SULONG SAPERI
Published: August 2024

Patient safety remains a global problem that affects both developed and developing countries. Healthcare organizations should focus on the need of assessing safety culture as that will provide basic understanding on safety related perceptions of their staffs. Objective : This study was aimed to assess baseline level and mean score of every domain of the patient safety attitude among doctors and nurses in public hospitals in Selangor and to identify the determinants associated with patient safety attitude in all domains : teamwork, safety climate, working condition, job satisfaction, stress recognition and perception of management. Method :This was a cross-sectional study utilizing the Safety Attitude Questionnaires (SAQ) involving 142 doctors and 231 nurses in three public hospitals in Selangor. The samples were selected through proportionate stratified random sampling. Data was analysed using descriptive, bivariate and multivariate analysis. Results: The response rate was 83% in which job satisfaction and perception of management received the highest and lowest mean score, respectively. The factors associated with positive patient safety attitude towards 1)teamwork were position (OR 1.99, p=0.03) and history of attending patient safety training (OR 3.228, p = 0.000); 2) safety climate were history of attending patient safety training (OR 7.283, p = 0.000); 3) job satisfaction were education level ( OR 35.709, p=0.000), position (OR 10.598, p=0.000) and history of attending patient safety training (OR 2.883, p = 0.000); 4) perception of management were age (OR 2.084,p=0.021) and work area (OR 2.461,p=0.012); 5) working condition were age (OR2.200,p 0.003) and history of attending patient safety training (OR1.738, p 0.032). Conclusion : Respondents with history of attending patient safety training have more positive attitude towards teamwork, safety climate, job satisfaction and working condition. Improving patient safety culture should be priorotized by the hospital management team to inculcate safety culture in healthcare providers.