bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of RFdiffusion to predict interspecies protein-protein interactions between fungal pathogens and cereal crops
Authors: Haley Olivia C. , Harding Stephen , Sen Taner Z. , Woodhouse Margaret R. , Kim Hye-Seon , Andorf Carson 
Published: September 2024

ABSTRACTPlant pathogenic fungi secrete small proteins known as effectors which help overcome the plant defense response and cause disease. The concept of effector-triggered immunity in plants evolved from the “gene for gene hypothesis” which describes plant resistance or susceptibility to plant pathogens based on interspecies protein-protein interactions (PPIs) between plant-derived resistance (R) genes and pathogen-derived avirulence (Avr) effector genes. Understanding the molecular interactions mediating these host-pathogen interactions in effector-triggered immunity is thus essential to managing fungal disease.In silicomethods of predicting interspecies PPIs have been heavily studied to identify target genes for crop resistance. But conventional sequence-based homology methods (i.e., interlog, domain-based inference) for predicting interspecies PPIs are not as powerful as methods that also incorporate structural homology. The objective of this study was to develop a computational workflow to predict PPIs between pathogenic fungi and their cereal hosts by leveraging recent advances in artificial intelligence and structural biology. This workflow proposes the use of a generative model, RFdiffusion, to predict the structure of truncated segments of proteins likely to bind to query effector proteins. The binder structures were filtered based on the number of contacts at the effectors’ known binding residues. Acceptable structures were then input into FoldSeek to search the host proteome for host proteins containing similar sub-structures. Experimentally-validated PPIs between rice (Oryzae sativacv. ‘Japonica’) and rice blast fungus (Magnaporthe oryzae) were used for workflow validation. The effects of binder length and the binding residues’ mode of action (i.e., residues at active/substrate recognition sites) on the binder quality and presumptive host protein matches were explored. Ultimately, 11 out of 14 experimentally validated PPIs were recovered computationally, indicating a high recall (>78%) for the workflow. The shorter binders recovered most of the PPIs, but may have produced the most false positives, as functional analyses revealed that these host proteins displayed a wide variety of functions. These findings emphasize that subject matter expertise is still required to decipher the prediction results. Yet, this framework for elucidating interactions between fungal pathogens and host proteins could provide valuable insight into mechanisms of susceptibility or resistance at a scale friendly to limited computational resources, and facilitate the development of control strategies that reduce crop diseases.
Variance quantitative trait loci reveal gene-gene interactions which alter blood traits
Authors: Pershad Yash , Poisner Hannah , Corty Robert W , Hellwege Jacklyn N , Bick Alexander G 
Published: September 2024

AbstractGene-gene (GxG) interactions play an important role in human genetics, potentially explaining part of the “missing heritability” of polygenic traits and the variable expressivity of monogenic traits. Many GxG interactions have been identified in model organisms through experimental breeding studies, but they have been difficult to identify in human populations. To address this challenge, we applied two complementary variance QTL (vQTL)-based approaches to identify GxG interactions that contribute to human blood traits and blood-related disease risk. First, we used the previously validated genome-wide scale test for each trait in ∼450,000 people in the UK Biobank and identified 4 vQTLs. Genome-wide GxG interaction testing of these vQTLs enabled discovery of novel interactions between (1)CCL24andCCL26for eosinophil count and plasma CCL24 and CCL26 protein levels and (2)HLA-DQA1andHLA-DQB1for lymphocyte count and risk of celiac disease, both of which replicated in ∼140,000 NIH All of Us and ∼70,000 Vanderbilt BioVU participants. Second, we used a biologically informed approach to search for vQTL in disease-relevant genes. This approach identified (1) a known interaction for hemoglobin between two pathogenic variants inHFEwhich cause hereditary hemochromatosis and alters risk of cirrhosis and (2) a novel interaction between theJAK246/1 haplotype and a variant on chromosome 14 which modifies platelet count,JAK2V617F clonal hematopoiesis, and risk of polycythemia vera. This work identifies novel disease-relevant GxG interactions and demonstrates the utility of vQTL-based approaches in identifying GxG interactions relevant to human health at scale.
Severe Sarcoidosis Demonstrates Heterogenous Immune Dysregulation Across Different Peripheral Immune Cell Types: A Single-Center Single Cell Multi-omic Analysis
Authors: Huang Kai , Vagts Christen , Ascoli Christian , Huang Yue , Sweiss Nadera J. , Finn Patricia W. , Perkins David L. 
Published: September 2024

AbstractSarcoidosis provides unique management challenges due to variable presentation and disease course. In this single-center analysis, we assess transcriptomic and epigenomic differentiators between severe and mild cases of sarcoidosis using peripheral blood. We showcase differences across multiple cell types that highlight decreased immunoregulation and increased inflammation in severe sarcoidosis. We provide an overall framework for the interactions between immune cells in severe sarcoidosis as a basis for future therapeutic research.Visual Abstract
Automatically Identifying Event Reports of Workplace Violence and Communication Failures using Large Language Models
Authors: Becker Mike , Hwang Sy , Schriver Emily , Douma Caryn , Duffy Caoimhe , Atkins Joshua , McShane Caitlyn , Lubken Jason , Hanish Asaf , McGreevey John D. , Regli Susan Harkness , Mowery Danielle L. 
Published: September 2024

AbstractSafety event reporting forms a cornerstone of identifying and mitigating risks to patient and staff safety. However, variabilities in reporting and limited resources to analyze and classify event reports delay healthcare organizations’ ability to rapidly identify safety event trends and to improve workplace safety. We demonstrated how large language models can classify safety event report narratives as workplace violence and communication failures as a first step toward enabling automated labeling of safety event reports and ultimately improving workplace safety.
PANDORA: An AI model for the automatic extraction of clinical unstructured data and clinical risk score implementation
Authors: Castano-Villegas Natalia , Llano Isabella , Jimenez Daniel , Martinez Julian , Ortiz Laura , Velasquez Laura , Zea Jose 
Published: September 2024

ABSTRACTIntroductionMedical records and physician notes often contain valuable information not organized in tabular form and usually require extensive manual processes to extract and structure. Large Language Models (LLMs) have shown remarkable abilities to understand, reason, and retrieve information from unstructured data sources (such as plain text), presenting the opportunity to transform clinical data into accessible information for clinical or research purposes.ObjectiveWe present PANDORA, an AI system comprising two LLMs that can extract data and use it with risk calculators and prediction models for clinical recommendations as the final output.MethodsThis study evaluates the model’s ability to extract clinical features from actual clinical discharge notes from the MIMIC database and synthetically generated outpatient clinical charts. We use the PUMA calculator for Chronic Obstructive Pulmonary Disease (COPD) case finding, which interacts with the model and the retrieved information to produce a score and classify patients who would benefit from further spirometry testing based on the 7 items from the PUMA scale.ResultsThe extraction capabilities of our model are excellent, with an accuracy of 100% when using the MIMIC database and 99% for synthetic cases. The ability to interact with the PUMA scale and assign the appropriate score was optimal, with an accuracy of 94% for both databases. The final output is the recommendation regarding the risk of a patient suffering from COPD, classified as positive according to the threshold validated for the PUMA scale of equal to or higher than 5 points. Sensitivity was 86% for MIMIC and 100% for synthetic cases.ConclusionLLMs have been successfully used to extract information in some cases, and there are descriptions of how they can recommend an outcome based on the researcher’s instructions. However, to the best of our knowledge, this is the first model which successfully extracts information based on clinical scores or questionnaires made and validated by expert humans from plain, non-tabular data and provides a recommendation mixing all these capabilities, using not only knowledge that already exists but making it available to be explored in light of the highest quality evidence in several medical fields.
The Human Cytomegalovirus vGPCR UL33 is Essential for Efficient Lytic Replication in Epithelial Cells
Authors: Freeman MacKenzie R. , Dooley Abigail L. , Beucler Matthew J. , Sanders Wes , Moorman Nathaniel J. , O’Connor Christine M. , Miller William E. 
Published: September 2024

AbstractHuman cytomegalovirus (HCMV) is a β-herpesvirus which is ubiquitous in the human population. HCMV has the largest genome of all known human herpesviruses, and thus encodes a large array of proteins that affect pathogenesis in different cell types. Given the large genome and the ability of HCMV to replicate in a range of cells, investigators have begun to identify viral proteins required for cell type-specific replication. There are four proteins encoded in the HCMV genome that are homologous to human G protein-coupled receptors (GPCRs); these viral-encoded GPCRs (vGPCRs) are UL33, UL78, US27, and US28. In the current study, we find that deletion of all four vGPCR genes from a clinical isolate of HCMV severely attenuates lytic replication in both primary human salivary gland epithelial cells, as well as ARPE-19 retinal epithelial cells as evidenced by significant decreases in immediate early gene expression and virus production. Deletion of UL33 from the HCMV genome also results in a failure to efficiently replicate in epithelial cells, and this defect is manifested by decreased levels of immediate early, early, and late gene expression, as well as reduced viral production. We find that similar to US28, UL33 constitutively activates Gαq-dependent PLC-β signaling to high levels in these epithelial cells. We also find that UL33 transcription is more complicated than originally believed, and there is the potential for the virus to utilize various 5’ UTRs to create novel UL33 proteins that are all capable of constitutive Gαq signaling. Taken together, these studies suggest that UL33 driven signaling is important for lytic HCMV replication in cells of epithelial origin.
Lateralized cerebellar connectivity differentiates auditory pathways in echolocating and non-echolocating whales
Authors: Flem Sophie , Berns Gregory , Inglis Ben , Niederhut Dillon , Montie Eric , Deacon Terrence , Miller Karla L. , Tyack Peter , Cook Peter F. 
Published: September 2024

AbstractWe report the first application of diffusion tractography to a mysticete, which was analyzed alongside three odontocete brains, allowing the first direct comparison of strength and laterality of auditory pathways in echolocating and non-echolocating whales. Brains were imaged post-mortem at high resolution with a specialized steady state free precession diffusion sequence optimized for dead tissue. We conducted probabilistic tractography to compare the qualitative features, tract strength, and lateralization of potential ascending and descending auditory paths in the mysticete versus odontocetes. Tracts were seeded in the inferior colliculi (IC), a nexus for ascending auditory information, and the cerebellum, a center for sensorimotor integration. Direct IC to temporal lobe pathways were found in all animals, replicating previous cetacean tractography and suggesting conservation of the primary auditory projection path in the cetacean clade. Additionally, odontocete IC-cerebellum pathways exhibited higher overall tract strength than in the mysticete, suggesting a role as descending acousticomotor tracts supporting the rapid sensorimotor integration demands of echolocation. Further, in the mysticete, contralateral right IC to left cerebellum pathways were 17x stronger than those between left IC and right cerebellum, while in odontocetes, the laterality was reversed, and left IC to right cerebellum pathways were 2-4x stronger than those between right IC and left cerebellum. The stronger left IC-right cerebellum connectivity observed in odontocetes corroborates the theory that odontocetes preferentially echolocate with their right phonic lips, as the right phonic lips are likely innervated by left-cortical motor efferents that integrate with left-cortical auditory afferents in right cerebellum. This interpretation is further supported by the reversed lateralization of IC-cerebellar tracts observed in the non-echolocating mysticete. We also found differences in the specific subregions of cerebellum targeted by the IC, both between the mysticete and odontocetes, and between left and right sides. This study establishes foundational knowledge on mysticete auditory connectivity and extends knowledge on the neural basis of echolocation in odontocetes.
Human macula formation involves two waves of retinoic acid signaling suppression viaCYP26A1regulating cell cycle exit and cone specification
Authors: Harding Philippa , Wojtynska Maja , Smith Alexander J. , Ali Robin R. , Pearson Rachael A. 
Published: September 2024

AbstractThe human macula is a specialized, M/L cone-rich region of the eye, critical for high acuity vision, but little is known about the pathways regulating its development. Transcriptional regulation by Retinoic Acid (RA) is essential for many aspects of human eye development. Here, we report a striking biphasic expression of the RA-catabolizing enzyme,CYP26A1,in early human macular development between post-conception weeks 6-17. Early inhibition of RA signaling in human retinal organoids (hROs) prompts early cell cycle exit, and an increase in cone photoreceptors, while late inhibition alters cone subtype specification. Conversely,FGF8,which is negatively regulated by RA and vital for High Acuity Area specification in chick, is not expressed in the nascent human macula and had no effect on hRO photoreceptor fate.Graphical abstract
Dopamine release in striatal striosome compartments in response to rewards and aversive outcomes during classical conditioning in mice
Authors: Yoshizawa Tomohiko , Funahashi Makoto 
Published: September 2024

AbstractThe striatum consists of two anatomically and neurochemically distinct compartments, striosomes and the matrix, which receive dopaminergic inputs from the midbrain and exhibit distinct dopamine release dynamics in acute brain slices. Striosomes comprise approximately 15% of the striatum by volume and are distributed mosaically. Therefore, it is difficult to selectively record dopamine dynamics in striosomes using traditional neurochemical measurements in behaving animals, and it is unclear whether distinct dynamics play a role in associative learning. In this study, we used transgenic mice selectively expressing Cre in striosomal neurons, combined with a fiber photometry technique, to selectively record dopamine release in striosomes during classical conditioning. Water-restricted mice could distinguish the conditioned stimulus (CS) associated with saccharin water from the air-puff-associated CS. The air-puff-associated CS evoked phasic dopamine release only in striosomes. Furthermore, air puff presentation induced dopamine release to striosomal neurons but suppressed release to putative matrix neurons. These findings suggest that dopamine is released in a differential manner in striosomes and the matrix in behaving animals and that dopamine release in striosomes is preferentially induced by the air-puff-associated CS and air puff presentation. These findings support the hypothesis that striosomal neurons play a dominant role in aversive stimuli prediction.HighlightsDopamine (DA) release was successfully measured in striosomes of behaving mice.A conditioned stimulus for aversive outcomes induced DA release in striosomes.In striosomes, rewarding and aversive unconditioned stimuli triggered DA release.
Conserved ancillary residues situated proximally to the VIM-2 active site affect its metallo β-lactamase activity
Authors: Jain Diamond , Ajith Tejavath , Verma Jyoti , Chatterjee Debasmita , Ghosh Anindya S. 
Published: September 2024

AbstractVerona-integron-metallo-β-lactamase (VIM-2) is one of the most widespread class B β-lactamase, responsible for β-lactam resistance. Although active-site residues help in metal binding, the residues nearing the active-site possess functional importance. Here, to decipher the role of such residues in the activity and stability of VIM-2, the residues E146, D182, N210, S207, and D213 were selected through in-silico analyses and substituted with alanine using site-directed mutagenesis. The effects of substitution mutations were assessed by comparing the changes in the β-lactam susceptibility pattern of E. coli host cells expressing VIM-2 and its mutated proteins. VIM-2_N210A enhanced the susceptibility of the host by ∼4-8 folds against penicillins and cephalosporins while the expression of VIM-2_D182A radically increased the susceptibility of the host. However, expression of VIM-2_E146A reduced the susceptibility of the host by 2-fold. Further, proteins were purified to homogeneity, and VIM_N210A and VIM_D182A displayed reduced thermal stability than VIM-2. Moreover, in vitro catalytic efficiencies of VIM-2_D182A were drastically reduced against all the β-lactams tested whereas the same were moderately reduced for VIM-2_N210A. Conversely, the catalytic efficiency was marginally altered for VIM_E146A. Overall, we infer that both N210A and D182A substitutions negatively affect the performance of VIM-2 by influencing substrate specificity and stability, respectively.
Intra-hypothalamic circuit orchestrates β-endorphin release following coital ejaculation in male mice
Authors: Zha Xi , Jiao Zhuo-Lei , Li Shuai-Shuai , Liu Xiao-Yao , Li Xing-Yu , Sun Yi-Zhuo , Ding Xiao-Jing , Gao Meng-Tong , Gao Shu-Chen , Chen Ai-Xiao , Lin Jun-Kai , Zhang Wen , Cao Xuan-Zi , Zhang Yan-Li , Yang Rong-Rong , Xu Chun , Xu Xiao-Hong 
Published: September 2024

AbstractSurvey-based evidence suggests that men experience a distinct post-ejaculation affective state1,2, marked by intense pleasure sometimes compared to the euphoric rush from intravenous injection of opioid drugs such as heroin3. However, the intrinsic neural circuit mechanisms underlying the ejaculation-triggered affective state remain unclear. Here, we discovered thatCalbindin1-expressing (Calb1+) neurons in the preoptic area (POA) of the hypothalamus, an evolutionarily conserved regulatory region for male mating behavior4, are specifically activated during ejaculation in male mice. Inhibiting POACalb1+neurons prolongs mating and delays ejaculation. Importantly, POACalb1+neurons transmit the ejaculation signal and activate proopiomelanocortin-expressing (Pomc+) neurons in the arcuate nucleus of the hypothalamus, which show robust and sustained activity lasting for tens of seconds, specifically upon ejaculation. This activity is accompanied by elevated levels of β-endorphins5, opioid peptides secreted byPomc+neurons, post-ejaculation in male mice. Optogenetic activation ofPomc+neurons increases β-endorphins levels and conditioned placed preference, similar to ejaculation. Conversely, intracerebroventricular (i.c.v.) infusion of drugs blockingPomcneuropeptides signaling eliminates ejaculation-conditioned place preference. Collectively, these results elucidate an intra-hypothalamic circuit from POACalb1+neurons to arcuatePomc+neurons that coordinate β-endorphin release with ejaculation, shedding light on the neurobiological basis of the post-ejaculation affective state.
Basal activation of astrocytic Nrf2 in neuronal culture media: challenges and implications for neuron-astrocyte modelling
Authors: Elsharkasi M.M.O , Villani B , Wells G , Kerr F 
Published: September 2024

AbstractAs a gatekeeper of anti-oxidant and anti-inflammatory cell protection, the transcription factor Nrf2 is a promising therapeutic target for several neurodegenerative diseases, leading to the development of Nrf2 activators targeting Keap1-dependent and independent regulatory mechanisms. Astrocytes play a crucial role in regulating neuronal physiology in health and disease, including Nrf2 neuroprotective responses. As neurons require specific conditions for their differentiation and maintenance, most 2D and 3D co-culture systems use medias that are compatible with neuronal differentiation and function, but also ensure astrocyte survival. Few studies, however, assess the molecular adaptations of astrocytes to changes from astrocyte maintenance medias alone, and their subsequent effects on neurons which may represent technical rather than physiological responses.Our findings show that while Nrf2 can be effectively activated by the Keap1-Nrf2 protein-protein interaction disruptor 18e, and classical Nrf2 activators DMF and CDDO-Me, in human primary cortical astrocyte monocultures, their efficacy is lost in LUHMES neuron-astrocyte co-cultures. Further investigation revealed that the Advanced DMEM/F12-based LUHMES differentiation media maximally induced basal Nrf2 activity in astrocytes alone, compared to astrocyte maintenance media, thus preventing pharmacological activation. Although Neurobasal slightly activated basal Nrf2, this was not significant suggesting that this media has less impact on astrocytic Nrf2 activity relative to Advanced DMEM/F12.As Nrf2 is a key regulator of oxidative damage and neuroinflammation, modelling these common features of neurodegenerative diseases may be confounded by environments that maximally activate basal Nrf2. Our findings thus suggest caution in media selection for neuron-astrocyte co-culture in disease modelling and therapeutic Nrf2 activator discovery.
Substrate-specific regulation of mTORC1 activity by G protein-coupled receptors
Authors: Atkinson Samuel J. , Ritchie William Vincent , Thompson Kyle , Thompson Dawn , Hislop James N. , Hatakeyama Riko 
Published: September 2024

AbstractThe mammalian/mechanistic Target of Rapamycin Complex 1 (mTORC1) kinase controls cell growth in response to various external stimuli. mTORC1 has a myriad of substrates, and the activation of distinct downstream pathways has important physiological outcomes. Emerging evidence suggests that mTORC1 can respond to upstream signals in a nuanced manner, differentially regulating individual substrates and downstream biological processes. The nature of signals that determine the signaling selectivity of mTORC1 is not fully understood. Here, we studied mTORC1 regulation by G protein-coupled receptors (GPCRs). We found that muscarinic acetylcholine receptor M5, formyl peptide receptor 2, and beta-2 adrenergic receptor, which are coupled to distinct effector G proteins, all trigger substrate-specific activation of mTORC1. Remarkably, phosphorylation of the TFEB transcription factor, a non-canonical mTORC1 substrate that controls lysosome biogenesis, responded to GPCRs differently, sometimes even oppositely, compared to canonical mTORC1 substrates such as S6K1 and 4EBP1. This study highlights the need to re-evaluate the effects of GPCRs on mTORC1 by parallelly monitoring individual substrates, an important consideration to be made when assessing GPCR ligands as therapeutic tools to manipulate the mTORC1 pathway.