The emerging importance of skull-brain interactions in traumatic brain injury.

The recent identification of skull bone marrow as a reactive hematopoietic niche that can contribute to and direct leukocyte trafficking into the meninges and brain has transformed our view of this bone structure from a solid, protective casing to a living, dynamic tissue poised to modulate brain homeostasis and neuroinflammation. This emerging concept may be highly relevant to injuries that directly impact the skull such as in traumatic brain injury (TBI). From mild concussion to severe contusion with skull fracturing, the bone marrow response of this local myeloid cell reservoir has the potential to impact not just the acute inflammatory response in the brain, but also the remodeling of the calvarium itself, influencing its response to future head impacts. If we borrow understanding from recent discoveries in other CNS immunological niches and extend them to this nascent, but growing, subfield of neuroimmunology, it is not unreasonable to consider the hematopoietic compartment in the skull may similarly play an important role in health, aging, and neurodegenerative disease following TBI. This literature review briefly summarizes the traditional role of the skull in TBI and offers some additional insights into skull-brain interactions and their potential role in affecting secondary neuroinflammation and injury outcomes.

Making Ends Meet: An Examination of Legal and Illegal Sources of Financial Support for Individuals Returning from Prison.

A fundamental challenge facing individuals returning from prison is securing income. Although there have been numerous studies on the relationship between post-release employment and reintegration, less is known about the extent to which returning individuals rely on other sources of financial support, such as the support from family members, public assistance, or earnings from illicit activities. There is also a knowledge gap around how these sources of financial support relate to one another. We use survey data from 385 men who were released from prison to two Chicago neighborhoods, collected as part of an evaluation of the Safer Return Demonstration. We found that 41% of men reported having a legal job since their release, 9% reported receiving income from illegal activities, 30% reported receiving monetary public assistance, 66% received non-monetary public assistance, and 60% were currently receiving financial support from their families. Results from logistic regression models indicate that individuals who were employed were less likely to be financially supported by their families or receive public benefits, but this had no impact on whether they received earning from illegal activities. We discuss the implications of these findings for policy, practice, and future research.

Venous thromboembolism testing practices after orthopaedic trauma: prophylaxis regimen does not influence testing patterns.

Objectives: To determine venous thromboembolism (VTE) testing patterns in an orthopaedic trauma population and to evaluate for differences in VTE surveillance by prophylaxis regimen through a secondary analysis of the ADAPT trial. Design: Prospective randomized trial. Setting: Level I trauma center. Patients: Three hundred twenty-nine adult (18 years and older) trauma patients presenting with an operative extremity fracture proximal to the metatarsals/carpals or any pelvic or acetabular fracture requiring VTE prophylaxis. Intervention: VTE imaging studies recorded within 90 days post injury. Main Outcome Measurements: Percentage of patients tested for VTE were compared between treatment groups using Fisher's exact test. Subsequently, multivariable regression was used to determine patient factors significantly associated with risk of receiving a VTE imaging study. Results: Sixty-seven patients (20.4%) had VTE tests ordered during the study period. Twenty (29.9%) of these 67 patients with ordered VTE imaging tests had a positive finding. No difference in proportion of patients tested for VTE by prophylaxis regimen (18.8% on aspirin vs. 22.0% on LMWH, P = 0.50) was observed. Factors associated with increased likelihood of VTE testing included White race (adjusted odds ratio [aOR]: 2.61, 95% CI: 1.26-5.42), increased Injury Severity Score (aOR for every 1-point increase: 1.10, 95% CI: 1.05-1.15), and lower socioeconomic status based on the Area Deprivation Index (aOR for every 10-point increase: 1.14, 95% CI: 1.00-1.30). Conclusions: VTE surveillance did not significantly differ by prophylaxis regimen. Patient demographic factors including race, injury severity, and socioeconomic status were associated with differences in VTE surveillance. Level of Evidence: Level I, Therapeutic.

The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure.

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.

Decarboxylative C-N Coupling of 2,2-Difluorobicyclo[1.1.1]pentane (BCP-F2) Building Blocks.

Described herein is our effort toward achieving the decarboxylative functionalization of 2,2-difluorobicyclo[1.1.1]pentane (BCP-F2) building blocks. When compared with the nonfluorinated bicyclo[1.1.1]pentane (BCP) analogues, we discovered divergent reactivities. This is the first successful decarboxylative coupling of BCP-F2 building blocks reported via the photoredox mechanism.

Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.

Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.

TrIP─Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias.

Accurate interatomic energies and forces enable high-quality molecular dynamics simulations, torsion scans, potential energy surface mappings, and geometry optimizations. Machine learning algorithms have enabled rapid estimates of the energies and forces with high accuracy. Further development of machine learning algorithms holds promise for producing universal potentials that support many different atomic species. We present the Transformer Interatomic Potential (TrIP): a chemically sound potential based on the SE(3)-Transformer. TrIP's species-agnostic architecture, which uses continuous atomic representation and homogeneous graph convolutions, encourages parameter sharing between atomic species for more general representations of chemical environments, maintains a reasonable number of parameters, serves as a form of regularization, and is a step toward accurate universal interatomic potentials. TrIP achieves state-of-the-art accuracies on the COMP6 benchmark with an energy prediction of just 1.02 kcal/mol MAE. We introduce physical bias in the form of Ziegler-Biersack-Littmark-screened nuclear repulsion and constrained atomization energies. An energy scan of a water molecule demonstrates that these changes improve long- and near-range interactions compared to other neural network potentials. TrIP also demonstrates stability in molecular dynamics simulations, demonstrating reasonable exploration of Ramachandran space.

Phosphorylated HP1α-Nucleosome Interactions in Phase Separated Environments.

In the nucleus, transcriptionally silent genes are sequestered into heterochromatin compartments comprising nucleosomes decorated with histone H3 Lys9 trimethylation and a protein called HP1α. This protein can form liquid-liquid droplets in vitro and potentially organize heterochromatin through a phase separation mechanism that is promoted by phosphorylation. Elucidating the molecular interactions that drive HP1α phase separation and its consequences on nucleosome structure and dynamics has been challenging due to the viscous and heterogeneous nature of such assemblies. Here, we tackle this problem by a combination of solution and solid-state NMR spectroscopy, which allows us to dissect the interactions of phosphorylated HP1α with nucleosomes in the context of phase separation. Our experiments indicate that phosphorylated human HP1α does not cause any major rearrangements to the nucleosome core, in contrast to the yeast homologue Swi6. Instead, HP1α interacts specifically with the methylated H3 tails and slows the dynamics of the H4 tails. Our results shed light on how phosphorylated HP1α proteins may regulate the heterochromatin landscape, while our approach provides an atomic resolution view of a heterogeneous and dynamic biological system regulated by a complex network of interactions and post-translational modifications.

In vitro comparison of methods for sampling copper-based antimicrobial surfaces.

IMPORTANCE: Self-sanitizing surfaces such as copper (Cu) are increasingly used on high-touch surfaces to prevent the spread of harmful viruses and bacteria. Being able to monitor the antimicrobial properties of Cu is fundamental in measuring its antimicrobial efficacy. Thorough investigations into reliable methods to enumerate bacteria from self-sanitizing surfaces are lacking in the literature. This study demonstrates that direct use of Petrifilm on Cu surfaces most likely revives stressed and dying bacteria, which induces increased bacterial counts. This phenomenon was not observed with indirect collection methods. Studies assessing time-kill kinetics or long-term efficacy of Cu should consider the impact of the collection method chosen.

The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure.

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 °C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape. Teaser: Pro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.

Dramatic improvement in the "Bulk" hyperpolarization of 131Xe via spin exchange optical pumping probed using in situ low-field NMR.

We report on hyperpolarization of quadrupolar (I=3/2) 131Xe via spin-exchange optical pumping. Observations of the 131Xe polarization dynamics via in situ low-field NMR show that the estimated alkali-metal/131Xe spin-exchange rates can be large enough to compete with 131Xe spin relaxation. 131Xe polarization up to 7.6±1.5% was achieved in ∼8.5×1020 spins-a ∼100-fold improvement in the total spin angular momentum-potentially enabling various applications, including: measurement of spin-dependent neutron-131Xe s-wave scattering; sensitive searches for time-reversal violation in neutron-131Xe interactions beyond the Standard Model; and surface-sensitive pulmonary MRI.

Dynamic Nuclear Polarization Illuminates Key Protein-Lipid Interactions in the Native Bacterial Cell Envelope.

Elucidating the structure and interactions of proteins in native environments is a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis. We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.

Dynamic nuclear polarization illuminates key protein-lipid interactions in the native bacterial cell envelope.

Elucidating the structure and interactions of proteins in native environments has become a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis . We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.

Lifetime and Jail-Specific Suicidal Ideation: Prevalence and Correlates in a Sample of People in Jail in the United States.

Despite high suicide mortality in U.S. jails, there is limited research into precursors for suicide in this population, such as suicidal ideation. The current study examined the prevalence and correlates of lifetime and jail-specific suicidal ideation among a sample of 196 individuals (137 men) in custody in a U.S. jail. Nearly half the sample had reported lifetime suicidal ideation (45%), whereas 30% had reported jail-specific suicidal ideation. Adjusted correlates of lifetime suicidal ideation included a history of mental illness (OR = 2.79) and drug use (OR = 2.70). Adjusted correlates of jail-specific suicidal ideation included a history of mental illness (OR = 2.74), drug use (OR = 3.16), and a dehumanizing custodial environment (OR = 3.74). Some theoretically and empirically relevant factors were not significantly associated with suicidal ideation. Both expected and unexpected findings are discussed within the context of suicide theory and research, and practical implications are explored.

Hyperpolarizing DNA Nucleobases via NMR Signal Amplification by Reversible Exchange.

The present work investigates the potential for enhancing the NMR signals of DNA nucleobases by parahydrogen-based hyperpolarization. Signal amplification by reversible exchange (SABRE) and SABRE in Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) of selected DNA nucleobases is demonstrated with the enhancement (ε) of 1H, 15N, and/or 13C spins in 3-methyladenine, cytosine, and 6-O-guanine. Solutions of the standard SABRE homogenous catalyst Ir(1,5-cyclooctadeine)(1,3-bis(2,4,6-trimethylphenyl)imidazolium)Cl ("IrIMes") and a given nucleobase in deuterated ethanol/water solutions yielded low 1H ε values (≤10), likely reflecting weak catalyst binding. However, we achieved natural-abundance enhancement of 15N signals for 3-methyladenine of ~3300 and ~1900 for the imidazole ring nitrogen atoms. 1H and 15N 3-methyladenine studies revealed that methylation of adenine affords preferential binding of the imidazole ring over the pyrimidine ring. Interestingly, signal enhancements (ε~240) of both 15N atoms for doubly labelled cytosine reveal the preferential binding of specific tautomer(s), thus giving insight into the matching of polarization-transfer and tautomerization time scales. 13C enhancements of up to nearly 50-fold were also obtained for this cytosine isotopomer. These efforts may enable the future investigation of processes underlying cellular function and/or dysfunction, including how DNA nucleobase tautomerization influences mismatching in base-pairing.

People in Custody With a Suicidal History: An Ideation-to-Action Perspective Involving Individuals Incarcerated in Two U.S. Jails.

OBJECTIVE: Despite high suicide mortality in U.S. jails, little is known about the cognitive (ideation) and behavioral (attempt) spectrum of suicide risk in this population. Identifying factors associated with the development of suicidal ideation, as well as the translation of thoughts to acts of suicide, is important for suicide prevention. METHOD: Using data from a cross-sectional study conducted in 2018-2019, we investigated suicidal ideation and attempt among 548 individuals incarcerated in jail in the United States. Specifically, we compared those with suicidal ideation (n = 212) to those without suicidal ideation (n = 336), as well as compared those who had experienced suicidal ideation and attempted suicide (n = 114) to those who thought about suicide without making an attempt (n = 98), on a range of sociodemographic and clinical factors. RESULTS: Over one-third (38.7%) of participants had a history of suicidal ideation, whereas 23.3% had attempted suicide. In the adjusted analyses, a family history of suicide (OR = 2.09), drug use (OR = 2.26), social support (OR = 0.61), and self-harm (OR = 24.93) were linked to suicidal ideation. No wish to live (OR = 5.26) and interpersonal violence while intoxicated (OR = 2.41) were associated with the progression from suicidal ideation to a suicide attempt. CONCLUSIONS: Consistent with extant theoretical and empirical work, findings suggest that factors linked to the development of suicidal cognitions differ from those underlying the progression from suicidal ideation to a (non-lethal) suicide attempt.HIGHLIGHTSSuicidal risk is particularly high among individuals who are incarcerated in jail.Factors linked to suicidal ideation differ from those underlying acts of suicide.Ideators and attempters possess a different set of targets for intervention.

Drug overdoses, geographic trajectories, and the influence of built environment and neighborhood characteristics.

Much research has analyzed the spatial patterns of drug overdose events and identified features of the environment associated with heightened overdose levels. Generally absent from the literature are studies that analyze how unique trajectories of overdoses vary over time. We address this gap in the literature through an analysis of drug overdoses occurring in Passaic County, New Jersey from 2015 through 2019. A group-based trajectory analysis classifies block groups according to their overdose trends. A mixed-effects panel negative binomial regression model then examines the built environment and neighborhood characteristics associated with overall overdose levels. Results indicate that Passaic County block groups can be classified across three groups based upon their overdose levels over the study period: low and stable, low with moderate increase, and elevated and increasing. While the largest effects were observed for concentrated disadvantage in the regression analysis, most variables positively associated with overdose levels were built environment measures.