Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq.

Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

Projective light-sheet microscopy with flexible parameter selection.

Projection imaging accelerates volumetric interrogation in fluorescence microscopy, but for multi-cellular samples, the resulting images may lack contrast, as many structures and haze are summed up. Here, we demonstrate rapid projective light-sheet imaging with parameter selection (props) of imaging depth, position and viewing angle. This allows us to selectively image different sub-volumes of a sample, rapidly switch between them and exclude background fluorescence. Here we demonstrate the power of props by functional imaging within distinct regions of the zebrafish brain, monitoring calcium firing inside muscle cells of moving Drosophila larvae, super-resolution imaging of selected cell layers, and by optically unwrapping the curved surface of a Drosophila embryo. We anticipate that props will accelerate volumetric interrogation, ranging from subcellular to mesoscopic scales.

Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product.

The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and ß-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.

Mapping Changes in Glutamate with Glutamate-Weighted MRI in Forced Swim Test Model of Depression in Rats.

Chemical exchange saturation transfer with glutamate (GluCEST) imaging is a novel technique for the non-invasive detection and quantification of cerebral Glu levels in neuromolecular processes. Here we used GluCEST imaging and 1H magnetic resonance spectroscopy (1H MRS) to assess in vivo changes in Glu signals within the hippocampus in a rat model of depression induced by a forced swim test. The forced swimming test (FST) group exhibited markedly reduced GluCEST-weighted levels and Glu concentrations when examined using 1H MRS in the hippocampal region compared to the control group (GluCEST-weighted levels: 3.67 ± 0.81% vs. 5.02 ± 0.44%, p < 0.001; and Glu concentrations: 6.560 ± 0.292 µmol/g vs. 7.133 ± 0.397 µmol/g, p = 0.001). Our results indicate that GluCEST imaging is a distinctive approach to detecting and monitoring Glu levels in a rat model of depression. Furthermore, the application of GluCEST imaging may provide a deeper insight into the neurochemical involvement of glutamate in various psychiatric disorders.

HDPose: Post-Hierarchical Diffusion with Conditioning for 3D Human Pose Estimation.

Recently, monocular 3D human pose estimation (HPE) methods were used to accurately predict 3D pose by solving the ill-pose problem caused by 3D-2D projection. However, monocular 3D HPE still remains challenging owing to the inherent depth ambiguity and occlusions. To address this issue, previous studies have proposed diffusion model-based approaches (DDPM) that learn to reconstruct a correct 3D pose from a noisy initial 3D pose. In addition, these approaches use 2D keypoints or context encoders that encode spatial and temporal information to inform the model. However, they often fall short of achieving peak performance, or require an extended period to converge to the target pose. In this paper, we proposed HDPose, which can converge rapidly and predict 3D poses accurately. Our approach aggregated spatial and temporal information from the condition into a denoising model in a hierarchical structure. We observed that the post-hierarchical structure achieved the best performance among various condition structures. Further, we evaluated our model on the widely used Human3.6M and MPI-INF-3DHP datasets. The proposed model demonstrated competitive performance with state-of-the-art models, achieving high accuracy with faster convergence while being considerably more lightweight.

Alzheimer's disease transcriptional landscape in ex-vivo human microglia.

Microglia are resident immune cells of the brain and are implicated in the etiology of Alzheimer's Disease (AD) and other diseases. Yet the cellular and molecular processes regulating their function throughout the course of the disease are poorly understood. Here, we present the transcriptional landscape of primary microglia from 189 human postmortem brains, including 58 healthy aging individuals and 131 with a range of disease phenotypes, including 63 patients representing the full spectrum of clinical and pathological severity of AD. We identified transcriptional changes associated with multiple AD phenotypes, capturing the severity of dementia and neuropathological lesions. Transcript-level analyses identified additional genes with heterogeneous isoform usage and AD phenotypes. We identified changes in gene-gene coordination in AD, dysregulation of co-expression modules, and disease subtypes with distinct gene expression. Taken together, these data further our understanding of the key role of microglia in AD biology and nominate candidates for therapeutic intervention.

Early Prediction of Mortality for Septic Patients Visiting Emergency Room Based on Explainable Machine Learning: A Real-World Multicenter Study.

BACKGROUND: Worldwide, sepsis is the leading cause of death in hospitals. If mortality rates in patients with sepsis can be predicted early, medical resources can be allocated efficiently. We constructed machine learning (ML) models to predict the mortality of patients with sepsis in a hospital emergency department. METHODS: This study prospectively collected nationwide data from an ongoing multicenter cohort of patients with sepsis identified in the emergency department. Patients were enrolled from 19 hospitals between September 2019 and December 2020. For acquired data from 3,657 survivors and 1,455 deaths, six ML models (logistic regression, support vector machine, random forest, extreme gradient boosting [XGBoost], light gradient boosting machine, and categorical boosting [CatBoost]) were constructed using fivefold cross-validation to predict mortality. Through these models, 44 clinical variables measured on the day of admission were compared with six sequential organ failure assessment (SOFA) components (PaO2/FIO2 [PF], platelets (PLT), bilirubin, cardiovascular, Glasgow Coma Scale score, and creatinine). The confidence interval (CI) was obtained by performing 10,000 repeated measurements via random sampling of the test dataset. All results were explained and interpreted using Shapley's additive explanations (SHAP). RESULTS: Of the 5,112 participants, CatBoost exhibited the highest area under the curve (AUC) of 0.800 (95% CI, 0.756-0.840) using clinical variables. Using the SOFA components for the same patient, XGBoost exhibited the highest AUC of 0.678 (95% CI, 0.626-0.730). As interpreted by SHAP, albumin, lactate, blood urea nitrogen, and international normalization ratio were determined to significantly affect the results. Additionally, PF and PLTs in the SOFA component significantly influenced the prediction results. CONCLUSION: Newly established ML-based models achieved good prediction of mortality in patients with sepsis. Using several clinical variables acquired at the baseline can provide more accurate results for early predictions than using SOFA components. Additionally, the impact of each variable was identified.

Androgen deprivation induces double-null prostate cancer via aberrant nuclear export and ribosomal biogenesis through HGF and Wnt activation.

Androgen deprivation therapy (ADT) targeting androgen/androgen receptor (AR)- signaling pathways is the main therapy for advanced prostate cancer (PCa). However, ADT eventually fails in most patients who consequently develop castration-resistant prostate cancer (CRPC). While more potent AR antagonists and blockers for androgen synthesis were developed to improve clinical outcomes, they also show to induce more diverse CRPC phenotypes. Specifically, the AR- and neuroendocrine-null PCa, DNPC, occurs in abiraterone and enzalutamide-treated patients. Here, we uncover that current ADT induces aberrant HGF/MET signaling activation that further elevates Wnt/ß-catenin signaling in human DNPC samples. Co-activation of HGF/MET and Wnt/ß-catenin axes in mouse prostates induces DNPC-like lesions. Single-cell RNA sequencing analyses identify increased expression and activity of XPO1 and ribosomal proteins in mouse DNPC-like cells. Elevated expression of XPO1 and ribosomal proteins is also identified in clinical DNPC specimens. Inhibition of XPO1 and ribosomal pathways represses DNPC growth in both in vivo and ex vivo conditions, evidencing future therapeutic targets.

A Deep Learning-Based Approach for Prediction of Vancomycin Treatment Monitoring: Retrospective Study Among Patients With Critical Illness.

BACKGROUND: Vancomycin pharmacokinetics are highly variable in patients with critical illnesses, and clinicians commonly use population pharmacokinetic (PPK) models based on a Bayesian approach to dose. However, these models are population-dependent, may only sometimes meet the needs of individual patients, and are only used by experienced clinicians as a reference for making treatment decisions. To assist real-world clinicians, we developed a deep learning-based decision-making system that predicts vancomycin therapeutic drug monitoring (TDM) levels in patients in intensive care unit. OBJECTIVE: This study aimed to establish joint multilayer perceptron (JointMLP), a new deep-learning model for predicting vancomycin TDM levels, and compare its performance with the PPK models, extreme gradient boosting (XGBoost), and TabNet. METHODS: We used a 977-case data set split into training and testing groups in a 9:1 ratio. We performed external validation of the model using 1429 cases from Kangwon National University Hospital and 2394 cases from the Medical Information Mart for Intensive Care-IV (MIMIC-IV). In addition, we performed 10-fold cross-validation on the internal training data set and calculated the 95% CIs using the metric. Finally, we evaluated the generalization ability of the JointMLP model using the MIMIC-IV data set. RESULTS: Our JointMLP model outperformed other models in predicting vancomycin TDM levels in internal and external data sets. Compared to PPK, the JointMLP model improved predictive power by up to 31% (mean absolute error [MAE] 6.68 vs 5.11) on the internal data set and 81% (MAE 11.87 vs 6.56) on the external data set. In addition, the JointMLP model significantly outperforms XGBoost and TabNet, with a 13% (MAE 5.75 vs 5.11) and 14% (MAE 5.85 vs 5.11) improvement in predictive accuracy on the inner data set, respectively. On both the internal and external data sets, our JointMLP model performed well compared to XGBoost and TabNet, achieving prediction accuracy improvements of 34% and 14%, respectively. Additionally, our JointMLP model showed higher robustness to outlier data than the other models, as evidenced by its higher root mean squared error performance across all data sets. The mean errors and variances of the JointMLP model were close to zero and smaller than those of the PPK model in internal and external data sets. CONCLUSIONS: Our JointMLP approach can help optimize treatment outcomes in patients with critical illnesses in an intensive care unit setting, reducing side effects associated with suboptimal vancomycin administration. These include increased risk of bacterial resistance, extended hospital stays, and increased health care costs. In addition, the superior performance of our model compared to existing models highlights its potential to help real-world clinicians.

The effect of prescription drug insurance on the incidence of potentially inappropriate prescribing: Evidence from Medicare Part D.

The Medicare Part D program has been documented to increase the affordability and accessibility of drugs and improve the quality of prescription drug use; however, less is known about the equity impact of the Part D program on potentially inappropriate prescribing-specifically, incidences of polypharmacy and potentially inappropriate medication (PIM) use based on different racial/ethnic groups. Using a difference in the regression discontinuity design, we found that among Whites, Part D was associated with increases in polypharmacy and "broadly defined" PIM use, while the use of "always avoid" PIM remained unchanged. Conversely, Blacks and Hispanics reported no changes in such drug utilization patterns.

Geographic Isolation and Vulnerability Across Peru's Ecological Regions: The Influence of Regional Contexts of Extraction.

Geographically isolated places are often sites of exported environmental risks, intense resource extraction, exploitation and marginalization, and social policy neglect. These conditions create unique challenges related to vulnerability and adaptation that have direct disaster management implications. Our research investigates the relationship between geographic isolation and flood-related social vulnerability across Peru's ecological regions. Ecoregions have different relationships with colonialism and capitalism that shape vulnerability, and we hypothesize that the relationship between vulnerability and geographic isolation varies across ecoregions. Using mapping techniques and spatial regression analysis, we find that relationships between vulnerability and geographic isolation vary regionally, with differences that suggest alignment with regional contexts of extraction. We find notable differences in vulnerability related to public health infrastructure and access to services and between ecoregions with sharply contrasting histories of natural resource extraction and investment and disinvestment.

Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity.

Since the discovery of l-glutamate-producing Corynebacterium glutamicum, it has evolved to be an industrial workhorse. For biobased chemical production, suppling sufficient amounts of the NADPH cofactor is crucial. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme that converts glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate and produces NADH, is a major prospective solution for the cofactor imbalance issue. In this study, we determined the crystal structure of GAPDH from C. glutamicum ATCC13032 (CgGAPDH). Based on the structural information, we generated six CgGAPDH variants, CgGAPDHL36S, CgGAPDHL36S/T37K, CgGAPDHL36S/T37K/P192S, CgGAPDHL36S/T37K/F100V/P192S, CgGAPDHL36S/T37K/F100L/P192S, and CgGAPDHL36S/T37K/F100I/P192S, that can produce both NADH and NAPDH. The final CgGAPDHL36S/T37K/F100V/P192S variant showed a 212-fold increase in enzyme activity for NADP as well as 200% and 30% increased activity for the G3P substrate under NAD and NADP cofactor conditions, respectively. In addition, crystal structures of CgGAPDH variants in complex with NAD(P) permit the elucidation of differences between wild-type CgGAPDH and variants in relation to cofactor stabilization.

Medicaid Expansions and Access to Substance Abuse Treatment Services Among Limited English Proficiency Populations.

BACKGROUND: Although the myriad of provisions under the Affordable Care Act (ACA) have generally increased coverage and financial access to the health systems, language barriers represent a serious challenge to access to care among Limited English Proficiency (LEP) populations. OBJECTIVE: The aim of this study was to examine the effect of Medicaid expansions under the ACA on the availability of language services and Medicaid acceptance in substance abuse treatment (SAT) facilities. RESEARCH DESIGN: A quasi-experimental difference-in-differences design with multiple time periods was used to compare changes in the availability of language services and Medicaid as a payment source between Medicaid expansion and nonexpansion states. Facility-level observational data in the National Survey of Substance Abuse Treatment Services 2010-2019 was included. MEASURES: Availability of LEP services and Medicaid acceptance in the SAT facilities. RESULTS: The proportion of SAT facilities that provide LEP services increased from 40% in 2013 to 53% in 2019. The proportions by state are heterogeneous, ranging from approximately 20% to 70%. The ACA Medicaid expansions are not associated with changes in the availability of LEP services in the facilities. Moreover, Medicaid acceptance in the expansion states increased gradually following the expansion; however, the estimates are not statistically significant. CONCLUSION: The ACA Medicaid expansion had no impact on the availability of LEP services and the acceptance of Medicaid as a payment source in the SAT facilities.

Workman's compensation as exclusion criteria in rotator cuff repair literature - are we inadvertently excluding race?

OBJECTIVE: Despite an equal willingness to participate in clinical trials, there is evidence that several minority populations are systematically under-represented in studies. One potential cause and frequently used exclusionary criterion in orthopedic trials is patients with active workman's compensation (WC) insurance claims. The purpose of this study is to determine demographic differences in patients undergoing arthroscopic rotator cuff repair with commercial and government insurance vs workers compensation claims. METHODS: This was a retrospective review of patients who underwent primary arthroscopic rotator cuff repair at a single institution in the northeastern United States from 2018 to 2019. Patients undergoing revision cases were excluded. Chart review was used to extract demographic data such as age, gender, insurance, and reported race. RESULTS: A total of 4553 patient records were reviewed and included. There were 742 WC patients and 3811 non-WC patients. Two hundred and forty-four patients did not report their race. Overall, WC patients differed from non-WC with respect to race (P < 0.001). One hundred and eleven (15.0%) of WC and 293 (7.7%) non-WC patients reported being 'Black' or 'African American' (P = 0.002). This compares to 368 (49.6%) WC and 2788 (73.2%) non-WC patients who reported 'White' (P < 0.001). About 16.8% of WC patients were identified as 'Hispanic or Latino,' compared to 5.2% of non-WC (P < 0.001). CONCLUSION: African American and Hispanic/Latino patients are over-represented in workman's compensation patient populations relative to non-workman's compensation. Conversely, white patients are over-represented in non-WC patient populations, which serve as the basis for the majority of clinical study populations. Excluding workman's compensation patients from clinical trials may lead to an underrepresentation of African American and Hispanic/Latino patient populations in orthopedic clinical trials. In doing so, the generalizability of the results of rotator cuff repair clinical outcomes research to all races and ethnicities may be compromised.

Multi-omic profiling of the developing human cerebral cortex at the single-cell level.

The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that is mediated, in part, by the spatiotemporal activity of cis-regulatory elements (CREs). We simultaneously profiled gene expression and chromatin accessibility in 45,549 cortical nuclei across six broad developmental time points from fetus to adult. We identified cell type-specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectory analysis indicates that chromatin accessibility at CREs precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, we mapped cell type-specific and temporally specific genetic loci implicated in neuropsychiatric traits, including schizophrenia and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease.

Meet the authors: Ying Lu, Donghoon Lee, and Yanan Zhu.

We talk to co-first authors Donghoon Lee and Yanan Zhu and co-corresponding author Ying Lu about their paper "Molecular mechanism for activation of the 26S proteasome by ZFAND5" (this issue of Molecular Cell), the challenges of the project, their scientific pathways, and the late Dr. Alfred Goldberg.

Molecular mechanism for activation of the 26S proteasome by ZFAND5.

Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated proteins can increase, we studied mouse ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn-finger domain interacts with the Rpt5 ATPase and its C terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Upon proteasome binding, ZFAND5 widens the entrance of the substrate translocation channel, yet it associates only transiently with the proteasome. Dissociation of ZFAND5 then stimulates opening of the 20S proteasome gate. Using single-molecule microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.

Endocytosis gated by emergent properties of membrane-clathrin interactions.

Clathrin-mediated endocytosis (CME), the major cellular entry pathway, starts when clathrin assembles on the plasma membrane into clathrin-coated pits (CCPs). Two populations of CCPs are detected within the same cell: 'productive' CCPs that invaginate and pinch off, forming clathrin-coated vesicles (CCVs) [1, 2], and 'abortive' CCPs [3, 4, 5] that prematurely disassemble. The mechanisms of gating between these two populations and their relations to the functions of dozens of early-acting endocytic accessory proteins (EAPs) [5, 6, 7, 8, 9] have remained elusive. Here, we use experimentally-guided modeling to integrate the clathrin machinery and membrane mechanics in a single dynamical system. We show that the split between the two populations is an emergent property of this system, in which a switch between an Open state and a Closed state follows from the competition between the chemical energy of the clathrin basket and the mechanical energy of membrane bending. In silico experiments revealed an abrupt transition between the two states that acutely depends on the strength of the clathrin basket. This critical strength is lowered by membrane-bending EAPs [10, 11, 12]. Thus, CME is poised to be shifted between abortive and productive events by small changes in membrane curvature and/or coat stability. This model clarifies the workings of a putative endocytic checkpoint whose existence was previously proposed based on statistical analyses of the lifetime distributions of CCPs [4, 13]. Overall, a mechanistic framework is established to elucidate the diverse and redundant functions of EAPs in regulating CME progression.

HUWE1 Amplifies Ubiquitin Modifications to Broadly Stimulate Clearance of Proteins and Aggregates.

Selective breakdown of proteins and aggregates is crucial for maintaining normal cellular activities and is involved in the pathogenesis of diverse diseases. How the cell recognizes and tags these targets in different structural states for degradation by the proteasome and autophagy pathways has not been well understood. Here, we discovered that a HECT-family ubiquitin ligase HUWE1 is broadly required for the efficient degradation of soluble factors and for the clearance of protein aggregates/condensates. Underlying this capacity of HUWE1 is a novel Ubiquitin-Directed ubiquitin Ligase (UDL) activity which recognizes both soluble substrates and aggregates that carry a high density of ubiquitin chains and rapidly expand the ubiquitin modifications on these targets. Ubiquitin signal amplification by HUWE1 recruits the ubiquitin-dependent segregase p97/VCP to process these targets for subsequent degradation or clearance. HUWE1 controls the cytotoxicity of protein aggregates, mediates Targeted Protein Degradation and regulates cell-cycle transitions with its UDL activity.

Association of vaccine stockout with immunisation coverage in low-income and middle-income countries: a retrospective cohort study.

OBJECTIVES: This study investigated the association between vaccine stockout and immunisation coverage, and infant/under 5 mortality rates. DESIGN: A retrospective cohort study. SETTING: Low-income and middle-income countries. PARTICIPANTS: A cohort of 131 low-income and middle-income countries from 2004 to 2019. PRIMARY OUTCOME MEASURES: Main outcomes included immunisation coverages of (1) diphtheria-tetanus-pertussis containing vaccine (DTP), (2) measles containing vaccine (MCV), (3) BCG and (4) oral polio vaccine (OPV). We also included infant and under 5 mortality rates as secondary outcomes. RESULTS: The countries that experienced national-level stockouts of DTP and MCV had 3.7 and 4 percentage points lower coverage rates of DTP3 and MCV1, respectively, compared with the countries without the stockout events (p<0.01). Moreover, the statistically significant differences in the immunisation coverage rates across the countries with and without the stockout events are 2.4 percentage points and 2.6 percentage points for BCG and OPV, respectively (p<0.01). CONCLUSION: Our findings show that the incidence of vaccine stockout events is associated with the decreased immunisation coverages for children in low-income and middle-income countries. However, we did not observe a statistically significant association between the increasing frequency of vaccine stockout and infant and under 5 mortality rates.