bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-molecule chromatin configurations link transcription factor binding to expression in human cells
Authors: Doughty Benjamin R. , Hinks Michaela M. , Schaepe Julia M. , Marinov Georgi K. , Thurm Abby R. , Rios-Martinez Carolina , Parks Benjamin E. , Tan Yingxuan , Marklund Emil , Dubocanin Danilo , Bintu Lacramioara , Greenleaf William J.
Published: February 2024

The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF’s capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.
Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
Authors: Yao Jianing , Yu Jinglun , Caffo Brian , Page Stephanie C. , Martinowich Keri , Hicks Stephanie C.
Published: February 2024

Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and cell types provide multiple perspectives and a more complete understanding of tissue architecture. Here, we introduce Proust, a scalable tool to predict discrete domains using spatial multi-omics data by combining the low-dimensional representation of biological profiles based on graph-based contrastive self-supervised learning. Our scalable method integrates multiple data modalities, such as RNA, protein, and H&E images, and predicts spatial domains within tissue samples. Through the integration of multiple modalities, Proust consistently demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark datasets and technological platforms.
Optogenetic Locus Coeruleus Stimulation Improves Pupil Size Tracking of Cortical State
Authors: Weiss Evan , (Andy) Liu Yuxiang , Wang Qi
Published: February 2024

Brain state heavily influences our perception, cognition, and behavior. Multiple neuromodulatory systems, including the locus coeruleus – norepinephrine (LC-NE) system, contribute to the regulation of brain state. This research harnesses machine learning and optogenetics technologies to probe the impact of the LC on cortical state and pupillary responses in awake mice. Our integrative approach combines EEG recordings with pupillometry to capture the LC’s optogenetic activation, evoking notable EEG spectral power shifts synchronized with pupil dilation. These changes provide a noninvasive glimpse into the cortical states, modulated by the LC’s activity. Central to our methodology is the application of Support Vector Regression (SVR) modeling, which robustly correlates LC-induced pupillary changes with EEG power fluctuations. These insights help reinforce the LC’s crucial role in modulating prefrontal activity and its regulatory influence over arousal states. Beyond advancing our comprehension of the LC’s function, our work also highlights the potential for developing closed-loop stimulation systems. These systems, integrated with machine-learning techniques and multi-modal data, could offer precise therapeutic interventions for neurological disorders characterized by abnormal arousal states.
ComI inhibits transformation inBacillus subtilisby selectively killing competent cells
Authors: Smith Dominique R. , Kearns Daniel B. , Burton Briana M.
Published: February 2024

Many bacteria build elaborate molecular machines to import DNA via natural competence, yet this activity is often not identified until strains have been handled and domesticated in laboratory settings. For example, one of the best studied Gram-positive model organisms,Bacillus subtilis,has a non-transformable ancestor. Transformation in the ancestral strain is inhibited by a transmembrane peptide, ComI, which is encoded on an extrachromosomal plasmid. Although ComI was shown to be necessary and sufficient to inhibit transformation when produced at high levels under an inducible promoter, the mechanism by which ComI inhibits transformation is unknown. Here, we examine the native regulation and mechanism of transformation inhibition by ComI. We find that under native regulation, ComI expression is restricted in the absence of the plasmid. In the presence of the plasmid, we find that ComI is preferentially expressed in cells that are differentiating into a competent state. The subcellular localization of ComI, however, does not depend on any other competence proteins and permeabilization activity is concentration dependent. Thus over time, the competent cells gradually producing ComI, are permeabilized and killed. Based on these observations we propose a new model for the mechanism of ComI, suggesting a response to competence activation that selectively eliminates the competent subpopulation.

Importance

Natural transformation mechanisms have been studied across several bacterial systems, but few examples of inhibition exist. This work investigates the mechanism of action of a plasmid-encoded transmembrane inhibitor of natural transformation. The data reveal that the peptide can cause cell permeabilization. Permeabilization is synergistic with entry ofBacillus subtilisinto the “competent” state, such that cells with ability to be transformed are preferentially killed. These findings reveal a self-preservation mechanism coupled to the physiological state of the cells that ensures the population can maintain unaltered plasmid and its predicted prophage.
Unraveling the impact of congenital deafness on individual brain organization
Authors: Amaral Lénia , Xiaosha Wang , Yanchao Bi , Ella Striem-Amit
Published: February 2024

Research on brain plasticity, particularly in the context of deafness, consistently emphasizes the reorganization of the auditory cortex. However, a critical question arises: to what extent do all individuals with deafness show the same level of reorganization? To address this question, we examined the individual differences in deafness functional connectivity (FC), specifically from the deprived auditory cortex. Our findings demonstrate a remarkable differentiation between individuals deriving from the absence of shared auditory experiences, resulting in heightened FC variability among deaf individuals, compared to more consistent FC in the hearing group. Notably, connectivity to language regions becomes more diverse across individuals in deafness. This does not stem from delayed language acquisition, as it is found in deaf native signers, who are exposed to rich natural language since birth. However, comparing FC diversity between deaf native signers and deaf delayed signers who were deprived of language in early development, we show that language experience also impacts individual differences, although to a more moderate extent. Overall, our research points out the intricate interplay between brain plasticity and individual differences, shedding light on the diverse ways reorganization manifests among individuals. It further joins findings in blindness, showing that individual differences are affected by sensory experience. Finally, these findings highlight the importance of considering individual differences in personalized rehabilitation for hearing loss.
Caspase-8 activity mediates TNFα production and restrictsCoxiella burnetiireplication during murine macrophage infection
Authors: Osbron Chelsea A. , Lawson Crystal , Hanna Nolan , Koehler Heather S. , Goodman Alan G.
Published: February 2024

Coxiella burnetiiis an obligate intracellular bacteria which causes the global zoonotic disease Q Fever. Treatment options for infection are limited, and development of novel therapeutic strategies requires a greater understanding of howC. burnetiiinteracts with immune signaling. Cell death responses are known to be manipulated byC. burnetii, but the role of caspase-8, a central regulator of multiple cell death pathways, has not been investigated. In this research, we studied bacterial manipulation of caspase-8 signaling and the significance of caspase-8 toC. burnetiiinfection, examining bacterial replication, cell death induction, and cytokine signaling. We measured caspase, RIPK, and MLKL activation inC. burnetii-infected TNFα/CHX-treated THP-1 macrophage-like cells and TNFα/ZVAD-treated L929 cells to assess apoptosis and necroptosis signaling. Additionally, we measuredC. burnetiireplication, cell death, and TNFα induction over 12 days in RIPK1-kinase-dead, RIPK3-kinase-dead, or RIPK3-kinase-dead-caspase-8-/-BMDMs to understand the significance of caspase-8 and RIPK1/3 during infection. We found that caspase-8 is inhibited byC. burnetii, coinciding with inhibition of apoptosis and increased susceptibility to necroptosis. Furthermore,C. burnetiireplication was increased in BMDMs lacking caspase-8, but not in those lacking RIPK1/3 kinase activity, corresponding with decreased TNFα production and reduced cell death. As TNFα is associated with the control ofC. burnetii, this lack of a TNFα response may allow for the unchecked bacterial growth we saw in caspase-8-/-BMDMs. This research identifies and explores caspase-8 as a key regulator ofC. burnetiiinfection, opening novel therapeutic doors.
Primary auditory cortex is necessary for the acquisition and expression of categorical behavior
Authors: Krall Rebecca F. , Chambers Callista N. , Arnold Megan P. , Brougher Lauren I. , Chen Justin , Deshmukh Rishi , King Hailey B. , Morford Harry J. , Wiemann John M. , Williamson Ross S.
Published: February 2024

The primary auditory cortex (ACtx) is critically involved in the association of sensory information with specific behavioral outcomes. Such sensory-guided behaviors are necessarily brain-wide endeavors, requiring a plethora of distinct brain areas, including those that are involved in aspects of decision making, motor planning, motor initiation, and reward prediction. ACtx comprises a number of distinct excitatory cell-types that allow for the brain-wide propagation of behaviorally-relevant sensory information. Exactly how ACtx involvement changes as a function of learning, as well as the functional role of distinct excitatory cell-types is unclear. Here, we addressed these questions by designing a two-choice auditory task in which water-restricted, head-fixed mice were trained to categorize the temporal rate of a sinusoidal amplitude modulated (sAM) noise burst and used transient cell-type specific optogenetics to probe ACtx necessity across the duration of learning. Our data demonstrate that ACtx is necessary for the ability to categorize the rate of sAM noise, and this necessity grows across learning. ACtx silencing substantially altered the behavioral strategies used to solve the task by introducing a fluctuating choice bias and increasing dependence on prior decisions. Furthermore, ACtx silencing did not impact the animal’s motor report, suggesting that ACtx is necessary for the conversion of sensation to action. Targeted inhibition of extratelencephalic projections on just 20% of trials had a minimal effect on task performance, but significantly degraded learning. Taken together, our data suggest that distinct cortical cell-types synergistically control auditory-guided behavior and that extratelencephalic neurons play a critical role in learning and plasticity.
Characterization and functional analysis ofToxoplasmaGolgi-associated proteins identified by proximity labelling
Authors: Pasquarelli Rebecca R. , Quan Justin J. , Cheng Emily S. , Yang Vivian , Britton Timmie A. , Sha Jihui , Wohlschlegel James A. , Bradley Peter J.
Published: February 2024

Toxoplasma gondiipossesses a highly polarized secretory pathway that contains both broadly conserved eukaryotic organelles and unique apicomplexan organelles which play essential roles in the parasite’s lytic cycle. As in other eukaryotes, theT. gondiiGolgi apparatus sorts and modifies proteins prior to their distribution to downstream organelles. Many of the typical trafficking factors found involved in these processes are missing from apicomplexan genomes, suggesting that these parasites have evolved unique proteins to fill these roles. Here we identify a novel Golgi-localizing protein (ULP1) which contains structural homology to the eukaryotic trafficking factor p115/Uso1. We demonstrate that depletion of ULP1 leads to a dramatic reduction in parasite fitness and replicative ability. Using ULP1 as bait for TurboID proximity labelling and immunoprecipitation, we identify eleven more novel Golgi-associated proteins and demonstrate that ULP1 interacts with theT. gondiiCOG complex. These proteins include both conserved trafficking factors and parasite-specific proteins. Using a conditional knockdown approach, we assess the effect of each of these eleven proteins on parasite fitness. Together, this work reveals a diverse set of novelT. gondiiGolgi-associated proteins that play distinct roles in the secretory pathway. As several of these proteins are absent outside of the Apicomplexa, they represent potential targets for the development of novel therapeutics against these parasites.

Importance

Apicomplexan parasites such asToxoplasma gondiiinfect a large percentage of the world’s population and cause substantial human disease. These widespread pathogens use specialized secretory organelles to infect their host cells, modulate host cell functions, and cause disease. While the functions of the secretory organelles are now better understood, the Golgi apparatus of the parasite remains largely unexplored, particularly regarding parasite-specific innovations that may help direct traffic intracellularly. In this work, we characterize ULP1, a protein that is unique to parasites but shares structural similarity to the eukaryotic trafficking factor p115/Uso1. We show that ULP1 plays an important role in parasite replication and demonstrate that it interacts with the conserved oligomeric Golgi (COG) complex. We then use ULP1 proximity labelling to identify eleven additional Golgi-associated proteins which we functionally analyze via conditional knockdown. This work expands our knowledge of theToxoplasmaGolgi apparatus and identifies potential targets for therapeutic intervention.
Niche exclusion of a lung pathogen in mice with designed probiotic communities
Authors: Hern Kelsey E , Phillips Ashlee M , Mageeney Catherine M. , Williams Kelly P. , Sinha Anupama , Carlson Hans K , Collette Nicole M , Branda Steven S , Arkin Adam P
Published: February 2024

For years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. While probiotic supplementation to prevent pathogen infiltration has been explored extensively in the gut, little has been done to study this phenomenon in the lower respiratory tract. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by a model bacterial pathogen (Burkholderia thailandensis) in mice. We demonstrate that understanding of antagonistic interactions between a pathogen and airway microbiotain vitrocan guide identification of probiotics with protective capabilitiesin vivo. While production of secondary metabolites appears to play a role in pathogen antagonism, exploitative competition appears to be the predominant mechanism by which the organisms studied here inhibitB. thailandensis. Specifically we show that niche overlap and resource competition between the probiotic and pathogen are predictive of probiotic performancein vivo. This work serves as a foundation for the rational design of probiotic communities for protection against and treatment of respiratory infections.
Conserved Pseudouridines in Helix 69 of the Ribosome are Important for Ribosome Dynamics in Translation
Authors: Jin Hong , Chen Xin
Published: February 2024

The widespread distribution of pseudouridine (Ψ), an isomer of the canonical uridine base, in RNA indicates its functional importance to the cell. In eukaryotes, it is estimated that around 2% of ribosomal RNA nucleotides are pseudouridines, most of which are located in functional regions of the ribosome. Defects in RNA pseudouridylation induce a range of detrimental effects from compromised cellular protein biosynthesis to disease phenotypes in humans. However, genome-wide changes to mRNA translation profiles by ribosomes lacking specific conserved pseudouridines have not been extensively studied. Here, using a new genomic method called 5P-Seq andin vitrobiochemistry, we investigated changes in ribosome dynamics and cellular translation profiles upon loss of Ψ2258 and Ψ2260 in helix 69, the two most conserved pseudouridines in the ribosomes. We found that inhibiting the formation of these two pseudouridines challenges ribosomes to maintain the correct open reading frame and causes generally faster ribosome dynamics in translation. Furthermore, mutant ribosomes are more prone to pause while translating a subset of GC-rich codons, especially rare codons such as Arg (CGA) and Arg (CGG). Our data suggest the presence of Ψ2258 and Ψ2260 contributes to the dynamics of the H69 RNA stem-loop, and helps to maintain functional interactions with the tRNAs as they move within the ribosome. The optimality of this ribosome-tRNA interaction is likely to be more critical for those limited tRNAs that decode rare codons. Consistent with the changes in ribosome dynamics, our data also show that IRES-mediated translation is compromised in the mutant ribosome. These results explain the importance of Ψ2258 and Ψ2260 in H69 to maintain cellular fitness. The strong conservation of Ψ2258 and Ψ2260 in the ribosomes from bacteria to humans indicates their functional significance in modulating ribosome functions. We anticipate that the identified functions of these covalent modifications will be conserved in other species.
Semi-synthetic glycoconjugate vaccine candidate againstCryptococcus neoformans
Authors: Crawford Conor J. , Liporagi-Lopes Livia , Coelho Carolina , Santos Junior Samuel R. , Nicola André Moraes , Wear Maggie P. , Vij Raghav , Oscarson Stefan , Casadevall Arturo
Published: February 2024

Cryptococcus neoformansis a fungus classified by the World Health Organization as a critically important pathogen, posing a significant threat to immunocompromised individuals. In this study, we present the chemical synthesis and evaluation of two semi-synthetic vaccine candidates targeting the capsular polysaccharide glucuronoxylomannan (GXM) ofC. neoformans.These semi-synthetic glycoconjugate vaccines contain the identical synthetic decasaccharide (M2 motif) antigen. This motif is present in serotype A strains, which constitute 95% of clinical cryptococcosis cases. This synthetic oligosaccharide was conjugated to two proteins (CRM197 and Anthrax 63 kDa PA) and tested for immunogenicity in mice. The conjugates elicited a specific antibody response that bound to the M2 motif but also exhibited additional cross-reactivity towards M1 and M4 GXM motifs. Both glycoconjugates produced antibodies that bound to GXM in ELISA assays and to live fungal cells. Mice immunized with the CRM197 glycoconjugate produced opsonic antibodies and displayed trends toward increased median survival relative to mice given a mock PBS injection (18 vs 15 days,p= 0.06). While these findings indicate promise, achieving a successful vaccine demands further optimization of the glycoconjugate. It could serve as a component in a multi-valent GXM motif vaccine, enhancing both strength and breadth of immune responses.
Quantifying association of early proteinuria and eGFR changes with long-term kidney failure hazard in C3G and IC-MPGN
Authors: Masoud Sherry , Wong Katie , Pitcher David , Downward Lewis , Proudfoot Clare , Webb Nicholas J.A. ,   RaDaR Consortium, Wong Edwin K.S. , Gale Daniel P.
Published: February 2024

Background

C3 glomerulopathy (C3G) and immune-complex membranoproliferative glomerulonephritis (IC-MPGN) are rare disorders that frequently result in kidney failure over the long-term. At present, there are no disease-specific treatments approved for these disorders, although there is much interest in the therapeutic potential of complement inhibition. However, the limited duration and necessarily small size of controlled trials means there is a need to quantify how well short-term changes in eGFR and proteinuria predict the clinically important outcome of kidney failure. We aimed to address this using longitudinal data from the UK National Registry of Rare Kidney Diseases (RaDaR).

Methods

RaDaR involves both retrospective and prospective data collection with linkage to hospital laboratories via automated feeds. 667 patients were included. Analyses of kidney survival were conducted using Kaplan–Meier and Cox regression. eGFR slope was estimated using linear mixed models.

Results

Over a median of 10.1 (IQR 6.9-14.3) years follow-up, 253/667 (38%) reached kidney failure. There was no difference in progression to kidney failure between C3G, IC-MPGN and Primary MPGN Not Otherwise Specified subgroups (p=0.75). Baseline urine protein creatinine ratio (UPCR), although high, was not associated with kidney failure risk. 2-year eGFR slope had a modest effect on kidney failure risk. In contrast, both 20-50% and 0.44g/g (50mg/mmol) reductions in time-averaged UPCR at 12 months were strongly associated with lower kidney failure risk (p≤0.002). Most notably, those with a UPCR <0.88g/g (<100mg/mmol) at 12 months had a substantially lower risk of kidney failure (HR 0.15 (95%CI 0.05-0.41).

Conclusions

We quantified the relationships between early changes in both eGFR and proteinuria with long-term kidney survival. We demonstrate that proteinuria a short time after diagnosis is a strong predictor of long-term outcome and that a UPCR <0.88g/g (<100mg/mmol) at 1 year is associated with a substantially lower kidney failure risk.
Geldof Expert Consensus Classification of Perianal Fistulizing Crohn’s Disease: A Real-World Application in a Serial Fistula MRI Cohort
Authors: Schroeder Matthew , Abushamma Suha , George Alvin T. , Balakrishna Ravella , Hickman John , Elumalai Anusha , Wise Paul , Zulfiqar Maria , Ludwig Daniel R , Shetty Anup , Viswanath Satish E. , Luo Chongliang , Sebastian Shaji , Ballard David H. , Deepak Parakkal
Published: February 2024

Background and Aims

Perianal fistulizing Crohn’s disease (CD-PAF) is an aggressive phenotype of Crohn’s disease (CD) defined by frequent relapses and disabling symptoms. A novel consensus classification system was recently outlined by Geldof et al. that seeks to unify disease severity with patient-centered goals but has not yet been validated. We aimed to apply this to a real-world cohort and identify factors that predict transition between classes over time.

Methods

We identified all patients with CD-PAF and at least one baseline and one follow-up pelvic (pMRI). Geldof Classification, disease characteristics, and imaging indices were collected retrospectively at time periods corresponding with respective MRIs.

Results

We identified 100 patients with CD-PAF of which 96 were assigned Geldof Classes 1 – 2c at baseline. Most patients (78.1%) started in Class 2b, but changes in classification were observed in 52.1% of all patients. Male sex (72.0%, 46.6%, 40.0%, p = 0.03) and prior perianal surgery (52.0% vs 44.6% vs 40.0%, p = 0.02) were more frequently observed in those with improved. Baseline pMRI indices were not associated with changes in classification, however, greater improvements in mVAI, MODIFI-CD, and PEMPAC were seen among those who improved. Linear mixed effect modeling identified only male sex (−0.31, 95% CI −0.60 to −0.02) with improvement in class.

Conclusion

Geldof classification highlights the dynamic nature of CD-PAF over time, however, our ability to predict transitions between classes remains limited and requires prospective assessment. Improvement in MRI index scores over time was associated with a transition to lower Geldof classification.
Selection of artemisinin partial resistance Kelch13 mutations in Uganda in 2016-22 was at a rate comparable to that seen previously in South-East Asia
Authors: Meier-Scherling Cecile P. G. , Watson Oliver J , Asua Victor , Ghinai Isaac , Katairo Thomas , Garg Shreeya , Conrad Melissa , Rosenthal Philip J. , Okell Lucy C , Bailey Jeffrey A.
Published: February 2024

Background

Artemisinin partial resistance, mediated by mutations in thePlasmodium falciparumKelch13 protein (K13), rapidly spread in South-East Asia (SEA), undermining antimalarial efficacies of artemisinin-based combination therapies (ACT). Validated K13 mutations have recently arisen in Africa, but rates of increase are not well characterized.

Methods

We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection coefficients using Bayesian mixed-effect linear models. We then tested whether SEA K13 mutation prevalence could have been forecast accurately using up to the first five years of available data and forecast future K13 mutation prevalence in Uganda.

Findings

The selection coefficient for the prevalence of relevant K13 mutations (441L, 469F/Y, 561H, 675V) was estimated at s=0·383 (95% CrI: 0·247 - 0·528) per year, a 38% relative prevalence increase. Selection coefficients across Uganda were s=0·968 (0·463 - 1·569) for 441L, s=0·153 (- 0·445 - 0·727) for 469F, s=0·222 (−0·011 - 0·398) for 469Y, and s=0·152 (−0·023 - 0·312) for 675V. In SEA, the selection coefficient was s=−0·005 (−0·852 - 0·814) for 539T, s=0·574 (−0·092 - 1·201) for 580Y, and s=0·308 (0·089 - 0·536) for all validated K13 mutations. Forecast prevalences for Uganda assuming constant selection neared fixation (>95% prevalence) within a decade (2028-2033) for combined K13 mutations.

Interpretation

The selection of K13 mutations in Uganda was at a comparable rate to that observed in SEA, suggesting K13 mutations may continue to increase quickly in Uganda.

Funding

NIH R01AI156267, R01AI075045, and R01AI089674.
Can machine learning or deep learning discover novel signatures of illness in continuous cardiorespiratory monitoring data?
Authors: Sullivan Brynne A. , Mesner Ian G. , Niestroy Justin , Lake Douglas E. , Fairchild Karen D. , Moorman J. Randall
Published: February 2024

Background

Cardiorespiratory deterioration due to sepsis is a leading cause of morbidity and mortality for extremely premature infants with very low birth weight (VLBW, birthweight <1500g). Abnormal heart rate (HR) patterns precede the clinical diagnosis of late-onset sepsis in this population. Decades ago, clinicians recognized a pattern of reduced HR variability and increased HR decelerations in electrocardiogram tracings of septic preterm infants. A predictive logistic regression model was developed from this finding using mathematical algorithms that detect this signature of illness. Display of this model as the fold increase in risk of imminent sepsis reduced mortality in a large randomized trial. Here, we sought to determine if machine learning or deep learning approaches would identify this uncommon but distinctive signature of sepsis in VLBW infants.

Methods

We studied VLBW infants admitted from 2012 to 2021 to a regional Level IV NICU. We collected one-hour HR time series data from bedside monitoring sampled at 0.5 Hz (n=300 HR values per series) throughout the NICU admission. First, we applied the principles of highly comparative time series analysis (HCTSA) to generate many mathematical time series features and combined them in a machine learning model. Next, we used deep learning in the form of a convolutional neural network on the raw data to learn the HR features. The output was a set of HR records determined by HCTSA or deep learning to be at high risk for imminent sepsis.

Results

We analyzed data from 566 infants with 61 episodes of sepsis. HCTSA and deep learning models predicted sepsis with high out-of-sample validation metrics. The riskiest records determined by both approaches demonstrated the previously identified HR signatures-reduced variability and increased decelerations.

Conclusions

We tested the ability of unguided machine learning approaches to detect the novel HR signature of sepsis in VLBW infants previously identified by human experts. Our main finding is that the computerized approach returned the same result - it identified heart rate characteristics of reduced variability and transient decelerations. We conclude that unguided machine learning can be as effective as human experts in identifying even a very rare phenotype in clinical data.
Personalized allele-specific CRISPR-Cas9 strategies for myofibrillar myopathy 6
Authors: Shin Jun Wan , Kim Kyung-Hee , Lee Yukyeong , Choi Doo Eun , Lee Jong-Min
Published: February 2024

Myofibrillar myopathy 6 (MFM6) is a rare childhood-onset myopathy characterized by myofibrillar disintegration, muscle weakness, and cardiomyopathy. The genetic cause of MFM6 is p.Pro209Leu mutation (rs121918312-T) in theBAG3gene, which generates the disease outcomes in a dominant fashion. Since the consequences of theBAG3mutation are strong and rapidly progressing, most MFM6 patients are due tode novomutation. There are no effective treatments for MFM6 despite its well-known genetic cause. Given p.Pro209Leu mutation is dominant, regenerative medicine approaches employing orthologous stem cells in which mutantBAG3is inactivated offer a promising avenue. Here, we developed personalized allele-specific CRISPR-Cas9 strategies capitalizing on PAM-altering SNP and PAM-proximal SNP. In order to identify the disease chromosome carrying thede novomutation in our two affected individuals, haplotype phasing through cloning-sequencing was performed. Based on the sequence differences between mutant and normalBAG3, we developed personalized allele-specific CRISPR-Cas9 strategies to selectively inactivate the mutant allele 1) by preventing the transcription of the mutantBAG3and 2) by inducing nonsense-mediated decay (NMD) of mutantBAG3mRNA. Subsequent experimental validation in patient-derived induced pluripotent stem cell (iPSC) lines showed complete allele specificities of our CRISPR-Cas9 strategies and molecular consequences attributable to inactivated mutantBAG3. In addition, mutant allele-specific CRISPR-Cas9 targeting did not alter the characteristics of iPSC or the capacity to differentiate into cardiomyocytes. Together, our data demonstrate the feasibility and potential of personalized allele-specific CRISPR-Cas9 approaches to selectively inactivate the mutantBAG3to generate cell resources for regenerative medicine approaches for MFM6.
COVID-19 Trends at The University of Tennessee: Predictive Insights from Raw Sewage SARS-CoV-2 Detection and Evaluation and PMMoV as an Indicator for Human Waste
Authors: Li Y. , Ash K. T. , Alamilla I. , Joyner D. C. , Williams D. E. , McKay P. J. , Green B. M. , DeBlander S. E. , North C. M. , Kara-Murdoch F. , Swift C. M. , Hazen T. C.
Published: February 2024

Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it’s not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage. This was done to investigate the correlations between SARS-CoV-2 concentrations, both with and without PMMoV normalization, and various parameters, including active COVID-19 cases, self-isolations, and their combination among all student residents. Significant positive correlations between SARS-CoV-2 concentrations a week prior, during the monitoring week, and the subsequent week with active cases. Despite these correlations, normalization by PMMoV does not enhance these associations. These findings suggest the potential utility of SARS-CoV-2 concentrations as an early warning indicator and provide valuable insights into the application and limitations of WBE for COVID-19 surveillance, specifically within the context of raw sewage on university campuses.
A functional genomic framework to elucidate novel causal non-alcoholic fatty liver disease genes
Authors: Saliba-Gustafsson Peter , Justesen Johanne M. , Ranta Amanda , Sharma Disha , Bielczyk-Maczynska Ewa , Li Jiehan , Najmi Laeya A. , Apodaka Maider , Aspichueta Patricia , Björck Hanna M. , Eriksson Per , Franco-Cereceda Anders , Gloudemans Mike , Mujica Endrina , Hoed Marcel den , Assimes Themistocles L. , Quertermous Thomas , Carcamo-Orive Ivan , Park Chong Y. , Knowles Joshua W.
Published: February 2024

Background & Aims

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver pathology in western countries, with serious public health consequences. Efforts to identify causal genes for NAFLD have been hampered by the relative paucity of human data from gold-standard magnetic resonance quantification of hepatic fat. To overcome insufficient sample size, genome-wide association studies using NAFLD surrogate phenotypes have been used, but only a small number of loci have been identified to date. In this study, we combined GWAS of NAFLD composite surrogate phenotypes with genetic colocalization studies followed by functional in vitro screens to identify bona fide causal genes for NAFLD.

Approach & Results

We used the UK Biobank to explore the associations of our novel NAFLD score, and genetic colocalization to prioritize putative causal genes forin vitrovalidation. We created a functional genomic framework to study NAFLD genesin vitrousing CRISPRi. Our data identifyVKORC1, TNKS, LYPLAL1andGPAMas regulators of lipid accumulation in hepatocytes and suggest the involvement ofVKORC1in the lipid storage related to the development of NAFLD.

Conclusions

Complementary genetic and genomic approaches are useful for the identification of NAFLD genes. Our data supportsVKORC1as abona fideNAFLD gene. We have established a functional genomic framework to study at scale putative novel NAFLD genes from human genetic association studies.
Outcomes and reinterventions following uterine artery embolization for the treatment of uterine leiomyomata
Authors: Martin Jonathan G. , Medema Alexis M.
Published: February 2024

Purpose

Uterine leiomyomas are common benign tumors that arise from smooth muscle and can significantly impact quality of life. Over the past two decades, uterine artery embolization has risen as a minimally invasive alternative treatment to hysterectomy or myomectomy for the management of leiomyomas. While prior work has established the safety of this procedure, there exist few reports quantifying sequelae, notably rates of subsequent treatment and primary ovarian insufficiency. The purpose of this study is to demonstrate the efficacy of uterine artery embolization as well as to investigate the frequency of gynecologic reintervention and primary ovarian insufficiency following treatment.

Methods

The study cohort consisted of patients (n=199) who presented with symptoms concerning for uterine pathology and with leiomyoma(s) confirmed by MRI. This cohort underwent embolization between January 2013 and December 2018 at a single academic institution. Data was collected from retrospective chart review and included demographics, symptomology, imaging, procedural details, and follow-up care. This data was subsequently analyzed to quantify the frequencies of various outcomes at 4–10 years following embolization.

Results

Of 199 symptomatic patients with confirmed leiomyomas, all underwent technically successful uterine artery embolization. At the time of follow-up, information was available for 188 (94.5%) patients, of which 145 (77.1%) reported significant symptomatic improvement while 34 required additional intervention—either medical (9%) or surgical (9%). The most common secondary medical management involved hormone therapy, while the most common subsequent gynecologic procedure was a hysterectomy. Additionally, there were seven (3.7%) cases of amenorrhea following embolization.

Conclusion

Given its minimally invasive nature, rapid recovery time, and uterine-sparing capability, uterine artery embolization should be considered a frontline therapy for symptomatic leiomyomas. This study supports an overall low complication rate, limited hospitalization time, near-complete resolution of symptoms, and low risk of ovarian dysfunction for a majority of patients. Following embolization, only 9% of patients required additional medical management, and only 9% required a second procedural intervention.
Perspectives of Osteopathic Medical Students on Preclinical Urology Exposure: A Single Institution Cross Sectional Survey
Authors: Wong Ryan , Mayrovitz Harvey N.
Published: February 2024

Context

There is an increasing number of medical school graduates opting for surgical specialties and the osteopathic applicant match rate for urology is lower than that of allopathic applicants. Factors influencing this may include a lack of interest, perceived challenges in matching into urology, insufficient urology mentorship, limited research opportunities, and inadequate osteopathic representation in urology.

Objective

To assess osteopathic medical students’ perspectives on pursuing urology and enhancing preclinical exposure to and knowledge of urology.

Methods

A 20-question survey addressing experiences and the factors influencing osteopathic medical students’ specialty selection and their interest in and perception of urology was designed by the investigators on Research Electronic Data Capture software. This survey was distributed via email listserv to all current osteopathic medical students attending Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine over two months. Responses were collected and analyzed using Fisher’s exact test.

Results

Of 150 respondents, 91% found mentors crucial in selecting a medical specialty, 95% emphasized the importance of early exposure, and 68% lacked familiarity with urology, with more M1 students unfamiliar compared to M2 (70.37% vs. 59.02%). A larger proportion of combined M1 and M2 (preclinical) students are considering urology as a specialty compared to M3 and M4 (clinical) students who are actively on rotations (56.52% vs. 28.57%;p= 0.0064). Also, a greater percentage of males are considering urology compared to females (64.15% vs. 42.71%;p= 0.0164). Among those considering urology (n = 75), 57.3% lack awareness of urology’s scope, and 84% report no preclinical discussions with urologists. Those students who report they are considering urology value early exposure significantly more than others (98.67% vs. 78.67%;p= 0.0001). They also express greater interest in having a core urology course (73.33% vs. 38.67%;p< 0.0001). More urology considering students are interested in extracurricular urology-related workshops, seminars, or conferences (61.33% vs. 17.33%;p<0.0001). Students who are considering urology as a specialty show greater interest in having a mentorship program (85.33% vs. 28%;p< 0.0001).

Conclusion

Results suggested that increased urology exposure during the preclinical years is important. Urology elective offerings and urology mentorship are of high interest among those considering urology. However, additional investigation is needed to determine the impact of preclinical urology curricula implementation on urology match outcomes.
Deep Learning Prediction of Glycopeptide Tandem Mass Spectra Powers Glycoproteomics
Authors: Zong Yu , Wang Yuxin , Qiu Xipeng , Huang Xuanjing , Qiao Liang
Published: February 2024

Protein glycosylation plays a significant role in numerous physiological and pathological cellular functions. Glycoproteomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) studies the protein glycosylation on a proteome-wide scale to get combinational information on glycosylation site, glycosylation level and glycan structure. However, the current sequence searching-based methods for glycoproteomics often fall short in glycan structure determination due to the limited occurrence of structure-determining ions. While spectral searching methods can utilize fragment intensity information to facilitate the identification of glycopeptides, its application is hindered by the difficulties in spectral library construction. In this work, we present DeepGP, a hybrid deep learning framework based on Transformer and graph neural network (GNN), for the prediction of MS/MS spectra and retention time of glycopeptides. Two GNN modules are utilized to capture the branched glycan structure and predict glycan ions intensity, respectively. Additionally, a pre-training strategy is implemented to alleviate the insufficiency of glycoproteomics data. Testing on multiple biological datasets, we demonstrate that DeepGP can predict MS/MS spectra and retention time of glycopeptides closely aligning with the experimental results. Comprehensive benchmarking of DeepGP on synthetic and biological datasets validates its effectiveness in distinguishing similar glycoforms. Remarkably, DeepGP can differentiate isomeric glycopeptides using MS/MS spectra without diagnostic ions. Based on various decoy methods, we demonstrated that DeepGP in combination with database searching can significantly increase the detection sensitivity of glycopeptides. We outlook that DeepGP can inspire extensive future work in glycoproteomics.
Structural insights into agonist binding and activation of succinate receptor 1
Authors: Liu Aijun , Liu Yezhou , Zhang Weijia , Ye Richard D.
Published: February 2024

Succinate is an intermediate of the citric acid cycle and serves important functions in energy homeostasis and metabolic regulation. Extracellular accumulation of succinate acts as a stress-induced signal through its G protein-coupled receptor, SUCNR1. Research on succinate signaling is hampered by the lack of high-resolution structures of the agonist-bound receptor. Here we present cryo-EM structures of SUCNR1-Gi complexes with the receptor bound to succinate and its non-metabolite derivative epoxysuccinate. Structural analysis of SUCNR1 identified key determinants for recognition of the dicarboxylate agonists incisconformation. R2817.39and Y832.64are critical to ligand binding, but Y301.39and R993.29also participate in binding of succinate and epoxysuccinate, respectively. The extracellular loop 2, through F175ECL2in its β-hairpin, forms a hydrogen bond with one of the carboxyl groups and serves as a lid to cap the binding pocket for succinate. At the receptor-Gi protein interface, agonist binding induces the rearrangement of a hydrophobic network on TM5 and TM6, leading to transmembrane signaling through TM3 and TM7. The agonist-bound SUCNR1 structures shed light on molecular recognition of succinate for receptor signaling, that may promote further development of novel agonists, antagonists and biased agonists targeting SUCNR1.
Attractor-like circuits improve visual decoding and behavior in zebrafish
Authors: Privat Martin , Hansen Enrique Carlos Arnoldo , Pietri Thomas , Marachlian Emiliano , Uribe-Arias Alejandro , Duchemin Auriane , Candat Virginie , Nourin Sarah , Sumbre Germán
Published: February 2024

Attractor networks are neural circuits with stable states that represent information or memories. They play a crucial role in memory retrieval, decision-making and integrating noisy cues. In zebrafish larvae, the spontaneous dynamics of the optic tectum is structured according to topographically organized neuronal assemblies exhibiting attractor-like behavior.

Here, we took advantage of the Methyl-CpG-binding protein 2 (MeCP2) deficient zebrafish mutant, which displays perturbed tectal dynamics, to study the functional role of the attractor-like circuits in visual processing.

In comparison to wild-type larvae, themecp2-mutant showed reduced functional connectivity in the optic tectum. This abnormal connectivity significantly affected the visual response, and the ability to discriminate between visual stimuli. Finally, the mutant larvae where less efficient in hunting paramecia. We argue that the attractor dynamics of the tectal assemblies improve stimulus discrimination, visual resolution, and increase the sensitivity to behaviorally relevant visual stimuli.
The co-receptor Tetraspanin12 directly captures Norrin to promote ligand-specific β-catenin signaling
Authors: Bruguera Elise S. , Mahoney Jacob P. , Weis William I.
Published: February 2024

Wnt/β-catenin signaling directs animal development and tissue renewal in a tightly controlled, cell- and tissue- specific manner. In the mammalian central nervous system, the atypical ligand Norrin controls angiogenesis and maintenance of the blood-brain barrier and blood-retina barrier through the Wnt/β-catenin pathway. Like Wnt, Norrin activates signaling by binding and heterodimerizing the receptors Frizzled (Fzd) and Low-density lipoprotein receptor-related protein 5 or 6 (LRP5/6), leading to membrane recruitment of the intracellular transducer Dishevelled (Dvl) and ultimately stabilizing the transcriptional coactivator β-catenin. Unlike Wnt, the cystine-knot ligand Norrin only signals through Fzd4 and additionally requires the co-receptor Tetraspanin12 (Tspan12); however, the mechanism underlying Tspan12-mediated signal enhancement is unclear. It has been proposed that Tspan12 integrates into the Norrin-Fzd4 complex to enhance Norrin-Fzd4 affinity or otherwise allosterically modulate Fzd4 signaling. Here, we measure direct, high-affinity binding between purified Norrin and Tspan12 in a lipid environment and use AlphaFold models to interrogate this interaction interface. We find that Tspan12 and Fzd4 can simultaneously bind Norrin and that a pre-formed Tspan12/Fzd4 heterodimer, as well as cells co-expressing Tspan12 and Fzd4, more efficiently capture low concentrations of Norrin than Fzd4 alone. We also show that Tspan12 competes with both heparan sulfate proteoglycans and LRP6 for Norrin binding and that Tspan12 does not impact Fzd4-Dvl affinity in the presence or absence of Norrin. Our findings suggest that Tspan12 does not allosterically enhance Fzd4 binding to Norrin or Dvl, but instead functions to directly capture Norrin upstream of signaling.