Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry.

Many essential cellular processes, such as gene control, employ elaborate mechanisms involving the coordination of large, multi-component molecular assemblies. Few structural biology tools presently have the combined spatial-temporal resolution and molecular specificity required to capture the movement, conformational changes, and subunit association-dissociation kinetics, three fundamental elements of how such intricate molecular machines work. Here, we report a 3D single-molecule super-resolution imaging study using modulation interferometry and phase-sensitive detection that achieves <2 nm axial localization precision, well below the few-nanometer-sized individual protein components. To illustrate the capability of this technique in probing the dynamics of complex macromolecular machines, we visualize the movement of individual multi-subunit E. coli RNA polymerases through the complete transcription cycle, dissect the kinetics of the initiation-elongation transition, and determine the fate of σ70 initiation factors during promoter escape. Modulation interferometry sets the stage for single-molecule studies of several hitherto difficult-to-investigate multi-molecular transactions that underlie genome regulation.

Modeling direct air carbon capture and storage in a 1.5 °C climate future using historical analogs.

Limiting the rise in global temperature to 1.5 °C will rely, in part, on technologies to remove CO2 from the atmosphere. However, many carbon dioxide removal (CDR) technologies are in the early stages of development, and there is limited data to inform predictions of their future adoption. Here, we present an approach to model adoption of early-stage technologies such as CDR and apply it to direct air carbon capture and storage (DACCS). Our approach combines empirical data on historical technology analogs and early adoption indicators to model a range of feasible growth pathways. We use these pathways as inputs to an integrated assessment model (the Global Change Analysis Model, GCAM) and evaluate their effects under an emissions policy to limit end-of-century temperature change to 1.5 °C. Adoption varies widely across analogs, which share different strategic similarities with DACCS. If DACCS growth mirrors high-growth analogs (e.g., solar photovoltaics), it can reach up to 4.9 GtCO2 removal by midcentury, compared to as low as 0.2 GtCO2 for low-growth analogs (e.g., natural gas pipelines). For these slower growing analogs, unabated fossil fuel generation in 2050 is reduced by 44% compared to high-growth analogs, with implications for energy investments and stranded assets. Residual emissions at the end of the century are also substantially lower (by up to 43% and 34% in transportation and industry) under lower DACCS scenarios. The large variation in growth rates observed for different analogs can also point to policy takeaways for enabling DACCS.

Therapeutic plasma exchange for steroid refractory idiopathic inflammatory myopathies with interstitial lung disease.

BACKGROUND: Idiopathic inflammatory myopathies (IIMs) encompass many rheumatologic diseases characterized by inflammatory muscle disease, typically unified by proximal muscle weakness. A subset of patients with IIM present with interstitial lung disease (ILD) with identifiable antibodies such as in anti-synthetase syndrome (AS) with antibodies to aminoacyl-tRNA synthetases, and clinically amyopathic dermatomyositis (CADM) with anti-melanoma differentiation-associated protein 5 (MDA5). Recent case reports demonstrate response to therapeutic plasma exchange (TPE) or column filtration plasmapheresis in IIM with ILD resistant to medical management. We present our experience with eight patients with IIM with ILD undergoing TPE at a large US-based hospital system. PATIENT CHARACTERISTICS: Eight patients with IIM with ILD were treated with TPE over the last 10 years. The therapy consisted of 5-7 one plasma volume exchanges every other day to daily. Seven of eight patients had identifiable antibodies. RESULTS: Following completion of TPE, seven of eight demonstrated improvement in pulmonary function despite lack of improvement of pulmonary function with standard therapy. CONCLUSION: In antibody-mediated, treatment refractory IIM with ILD, TPE may be a viable intervention. This is a disease for which the role of apheresis is evolving. CLINICAL TRIAL REGISTRATION: Not application.

A specialized population of Periostin-expressing cardiac fibroblasts contributes to postnatal cardiomyocyte maturation and innervation.

During the postnatal period in mammals, the cardiac muscle transitions from hyperplasic to hypertrophic growth, the extracellular matrix (ECM) undergoes remodeling, and the heart loses regenerative capacity. While ECM maturation and crosstalk between cardiac fibroblasts (CFs) and cardiomyocytes (CMs) have been implicated in neonatal heart development, not much is known about specialized fibroblast heterogeneity and function in the early postnatal period. In order to better understand CF functions in heart maturation and postnatal cardiomyocyte cell-cycle arrest, we have performed gene expression profiling and ablation of postnatal CF populations. Fibroblast lineages expressing Tcf21 or Periostin were traced in transgenic GFP reporter mice, and their biological functions and transitions during the postnatal period were examined in sorted cells using RNA sequencing. Highly proliferative Periostin (Postn)+ lineage CFs were found from postnatal day 1 (P1) to P11 but were not detected at P30, due to a repression of Postn gene expression. This population was less abundant and transcriptionally different from Tcf21+ resident CFs. The specialized Postn+ population preferentially expresses genes related to cell proliferation and neuronal development, while Tcf21+ CFs differentially express genes related to ECM maturation at P7 and immune crosstalk at P30. Ablation of the Postn+ CFs from P0 to P6 led to altered cardiac sympathetic nerve patterning and a reduction in binucleation and hypertrophic growth with increased fetal troponin (TroponinI1) expression in CM. Thus, postnatal CFs are heterogeneous and include a transient proliferative Postn+ population required for cardiac nerve development and cardiomyocyte maturation soon after birth.

Classic indicators and diel dissolved oxygen versus trend analysis in assessing eutrophication of potable-water reservoirs.

Potable source-water reservoirs are the main water supplies in many urbanizing regions, yet their long-term responses to cultural eutrophication are poorly documented in comparison with natural lakes, creating major management uncertainties. Here, long-term discrete data (June 2006-June 2018) for classical eutrophication water quality indicators, continuous depth-profile data for dissolved oxygen (DO), and an enhanced hybrid statistical trend analysis model were used to evaluate the eutrophication status of a potable source-water reservoir. Based on classical indicators (nitrogen, N and phosphorus, P concentrations and ratios; phytoplankton biomass as chlorophyll a, chl a; and trophic state indices), the reservoir was eutrophic to hypereutrophic and stoichiometrically imbalanced. Anoxia/hypoxia occurred for 7-8 months annually systemwide, even throughout the water column for days to weeks in some years; and elevated total ammonia (up to ~900 µg tNH3 L-1 ) in surface waters from late summer/fall through late winter/early spring suggested substantial internal legacy nutrient loading. These surprising DO and tNH3 phenomena may characterize many reservoirs in urbanizing areas, and the associated cascade of negative impacts may increasingly affect them under global warming. Total organic carbon (TOC), seasonally influenced by phytoplankton biomass, commonly exceeded 6 mg L-1 , which is problematic for potable-water treatment, and significantly trended up over time. Wet-year inflow dilution influenced an apparent decreasing trend in nutrients within the hypereutrophic upper reservoir, which receives most tributary inputs. Nevertheless, significant reservoirwide trends (increasing total phosphorus [TP], phytoplankton chl a, TOC) and mid- and/or lower region trends (increasing total nitrogen [TN], tNH3 , decreasing TN:TP ratios) suggest that water quality degradation from eutrophication has worsened over time. These findings support broadly applicable recommendations to strengthen protection of potable source-water reservoirs in urbanizing watersheds: (1) protective numeric water quality criteria are needed for TOC as well as TN, TP, and chl a; (2) continuous diel data capture more realistic DO conditions than traditional sampling, and can provide important insights for water treatment managers; and (3) assessment of reservoir eutrophication status to track management progress over time should emphasize classic indicators equally as statistical trends, which are highly sensitive to short-term meteorological forcing.

Periostin-expressing Schwann cells and endoneurial cardiac fibroblasts contribute to sympathetic nerve fasciculation after birth.

BACKGROUND: The intracardiac nervous system (ICNS) is composed of neurons, in association with Schwann cells (SC) and endoneurial cardiac fibroblasts (ECF). Besides heart rhythm control, recent studies have implicated cardiac nerves in postnatal cardiac regeneration and cardiomyocyte size regulation, but cardiac SC and ECF remain understudied. During the postnatal period, the ICNS undergoes intense remodeling with nerve fasciculation and elongation throughout the myocardium, partially guided by the extracellular matrix (ECM). Here we report the origins, heterogeneity, and functions of SC and ECF that develop in proximity to neurons during postnatal ICNS maturation. METHODS AND RESULTS: Periostin lineage (Postn+) cells include cardiac Remak SC and ECF during the postnatal period in mice. The developmental origins of cardiac SC and ECF were examined using Rosa26eGFP reporter mice bred with Wnt1Cre, expressed in Neural crest (NC)-derived lineages, or tamoxifen-inducible Tcf21MerCreMer, expressed predominantly in epicardial-derived fibroblast lineages. ICNS components are NC-derived with the exceptions of the myelinating Plp1+ SC and the Tcf21+ lineage-derived intramural ventricular ECF. In addition, Postn+ lineage GFAP- Remak SC and ECF are present around the fasciculating cardiac nerves. Whole mount studies of the NC-derived cells confirmed postnatal maturation of the complex ICNS network from P0 to P30. Sympathetic, parasympathetic, and sensory neurons fasciculate from P0 to P7 indicated by co-staining with PSA-NCAM. Ablation of Postn+ cells from P0 to P6 or loss of Periostin leads to reduced fasciculation of cardiac sympathetic nerves. In addition, collagen remodeling surrounding maturing nerves of the postnatal heart is reduced in Postn-null mice. CONCLUSIONS: Postn+ cells include cardiac SC and ECF during postnatal nerve maturation, and these cells have different embryonic origins. At P7, the Postn+ cells associated with cardiac nerves are mainly Remak SC and ECF. Ablation of the Postn+ cells from P0 to P6 and also loss of Postn in Postn-null mice leads to reduced fasciculation of cardiac nerves at P7.

Leveraging historical data into oncology development programs: Two case studies of phase 2 Bayesian augmented control trial designs.

Leveraging historical data into the design and analysis of phase 2 randomized controlled trials can improve efficiency of drug development programs. Such approaches can reduce sample size without loss of power. Potential issues arise when the current control arm is inconsistent with historical data, which may lead to biased estimates of treatment efficacy, loss of power, or inflated type 1 error. Consideration as to how to borrow historical information is important, and in particular, adjustment for prognostic factors should be considered. This paper will illustrate two motivating case studies of oncology Bayesian augmented control (BAC) trials. In the first example, a glioblastoma study, an informative prior was used for the control arm hazard rate. Sample size savings were 15% to 20% by using a BAC design. In the second example, a pancreatic cancer study, a hierarchical model borrowing method was used, which enabled the extent of borrowing to be determined by consistency of observed study data with historical studies. Supporting Bayesian analyses also adjusted for prognostic factors. Incorporating historical data via Bayesian trial design can provide sample size savings, reduce study duration, and enable a more scientific approach to development of novel therapies by avoiding excess recruitment to a control arm. Various sensitivity analyses are necessary to interpret results. Current industry efforts for data transparency have meaningful implications for access to patient-level historical data, which, while not critical, is helpful to adjust for potential imbalances in prognostic factors.

Inhibition of fibronectin polymerization alleviates kidney injury due to ischemia-reperfusion.

Fibrosis is a common feature of chronic kidney disease; however, no clinical therapies effectively target the progression of fibrosis. Inhibition of fibronectin polymerization with the small peptide pUR4 attenuates fibrosis in the liver and heart. Here, we show that pUR4 decreases renal fibrosis and tissue remodeling using a clinically relevant model of kidney injury, unilateral ischemia-reperfusion. This work highlights the benefits of inhibiting matrix polymerization, alone or in conjunction with cell-based therapies, as a novel approach to diminish the maladaptive responses to ischemic kidney injury that lead to chronic renal failure.

Correction of frontal plane rotation of sesamoid apparatus during the Lapidus procedure: a novel approach.

The Lapidus procedure affords correction of a multitude of first ray pathologic entities. When reconstructing the first ray using the Lapidus procedure, the relocation of the first metatarsal over the sesamoid bones with frontal plane rotation should be considered one of the key components. In the present technical report, we have described a bunion correction with emphasis on sesamoid reduction through indirect frontal plane manipulation. Our technique, borne from applied basic anatomy of the first metatarsophalangeal joint, uses intact soft tissues about the first metatarsophalangeal joint to reduce subluxed or dislocated sesamoids.

Conservative management of spinal pathology with autologous conditioned serum: A systematic review of the literature.

BACKGROUND: Chronic inflammatory pain is associated with increased expression of interleukin (IL)-1, an inflammatory cytokine, and activity on its receptor (IL-1R). In response, the body produces IL-1R antagonist (IL-1Ra) to reduce this signaling. Autologous conditioned serum (ACS) is the only biologic therapy for spinal pathologies that enhances the action of endogenous IL-1Ra reserves to improve symptoms. This systematic review investigates the effectiveness of ACS in treating pain and disability caused by spinal pathologies. AIM: To evaluate the use of ACS as a conservative management option for spinal pathology. METHODS: A systematic review of PubMed/Medline was performed to identify studies investigating administration of ACS for treatment of any spinal pathology. RESULTS: Six articles were included, comprising 684 patients treated with epidural (n = 133) or transforaminal (n = 551) ACS injections. Patients had an average age of 54.0 years with slight female predominance (53.2%). The lumbar spine was most commonly treated, with 567 patients (82.9%) receiving injections for lumbar radiculopathy (n = 67), degenerative disc disease (DDD) (n = 372), or spinal stenosis (n = 128); cervical injections were performed in 109 patients (15.9%). Mean (SD) follow-up was 21.7 (4.8) weeks from first ACS injection. All studies investigating mechanical lumbar and lumbar or cervical radicular pain reported significant pain reduction at final follow-up compared to baseline. ACS achieved comparable or superior results to lumbar epidural steroid injections. Adverse events were reported in 21 patients (3.1%), with no serious adverse events. CONCLUSION: ACS injection is a safe and effective intervention for pain reduction in many spinal pathologies, including cervical and lumbar radiculopathies.

Use of femoral locking plate for salvage of failed ankle arthoplasty after trauma.

When total ankle arthroplasty fails, few good options are available for salvage. We report a case of total ankle arthroplasty displacement after trauma. The injury was initially repaired with an anterior ankle arthrodesis plate for ankle fusion. On the follow-up radiographs taken during the fourth postoperative week, internal fixation failure was noted. A second revision was undertaken, using a femoral locking plate to obtain tibiotalocalcaneal fusion. We present this case as an alternative method for developing a stable construct in revising total ankle take down.

The Golfer's Fore, Fore +, and Advanced Fore + Exercise Program: An Exercise Series and Injury Prevention Program for the Golfer.

Golf is increasing in popularity with 24.8 million golfers in the U.S. in 2020, a 2% increase from the previous year. This number increased to 37.5 million in 2021 which can be further broken down to 25.1 million on course and 12.4 million participating in off course activities. Playing golf does not come without risk of injury, with an annual incidence between 15.8% and 40.9% in amateurs and 31% in professional golfers. Most injuries in golf occur due to overuse (82.6%) and only a small percentage occur from a single traumatic event (17.4%). Injuries most commonly occur at the low back followed by the wrist. Injury prevention programs have shown to be successful in other sports however to date there are no studies assessing a golfer's specific program. The purpose of this clinical commentary is to describe three individualized and unsupervised golf exercise programs (The Golfer's Fore, Fore+, and Advanced Fore+), of varying difficultly, designed to reduce the risk of injury, improve strength/mobility, and optimize performance. Level of Evidence: 5.

The Need To Change Return to Play Testing in Athletes Following ACL Injury: A Theoretical Model.

The incidence of knee injuries in sport, particularly involving the ACL, appears to be increasing yearly, especially in younger age athletes. Even more concerning is the frequency of ACL reinjury also appears to be increasing year after year. Improving the objective criteria and testing methods used to determine return to play (RTP) readiness following ACL surgery is one aspect of the rehabilitation process that can significantly help in reducing reinjury rates. Currently, the majority of clinicians are still using post operative time frames as their number one criterion for clearance to RTP. This flawed method demonstrates an inadequate reflection of the true unpredictable, dynamic environment athletes are returning to participate in. In our clinical experience, objective testing to allow for clearance to sport participation following an ACL injury should incorporate neurocognitive and reactive testing due to the nature of the injury typically occurs because of failed control of unanticipated reactive movements. The purpose of this manuscript is to share a neurocognitive testing sequence we currently employ consisting of 8 tests in 3 categories: Blazepod tests, reactive shuttle run tests, and reactive hop tests. The use of a more dynamic reactive testing battery may decrease the reinjury rates when an athlete is cleared for participation by measuring readiness in chaotic circumstances that are more truly reflective of the sporting environment the athlete is working to return to and in the process give them a greater sense of confidence.

Neurocognitive and Reactive Return to Play Testing Protocol in Overhead Athletes Following Upper Extremity Injury.

The incidence of upper extremity (UE) injuries in sport, particularly with the shoulder and elbow in baseball/softball players, appears to be increasing yearly, especially in younger age athletes. Improving the objective criteria and testing methods used to determine return to play (RTP) readiness following non-operative or post-operative management of UE injuries is one aspect of the rehabilitation process that may significantly help in reducing reinjury rates. Currently, the majority of clinicians are still using post operative time frame and/or strength/range of motion as their main criteria for clearance to RTP following UE injury. This demonstrates an inadequate reflection of the actual unpredictable, dynamic environment athletes are returning to participate in. In our clinical experiences, objective testing to allow for clearance to sport participation should incorporate neurocognitive and reactive testing to promote improvements in the athlete's ability to dual task and focus/concentrate on the multi-dimensional tasks at hand. We know that neuroplastic changes occur following UE injury resulting in decreased proprioception and increased motor activation with simple UE tasks. Currently the research on UE return to play testing is limited. The purpose of this clinical commentary was to describe the utilization and provide reference values for a series of reactive neurocognitive UE tests, to assist with RTP, in high school and collegiate overhead athletes (baseball and softball) utilizing the Blaze Pod light system. The use of a more dynamic reactive testing battery may decrease the reinjury rates when an athlete is cleared for participation by measuring readiness in chaotic circumstances that are more reflective of the sporting environment the athlete is working to return to resulting in a greater sense of confidence, performance and prevention of reinjuries.

Scattering studies of hydrophobic monomers in liposomal bilayers: an expanding shell model of monomer distribution.

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.

BART Cancer: a web resource for transcriptional regulators in cancer genomes.

Dysregulation of gene expression plays an important role in cancer development. Identifying transcriptional regulators, including transcription factors and chromatin regulators, that drive the oncogenic gene expression program is a critical task in cancer research. Genomic profiles of active transcriptional regulators from primary cancer samples are limited in the public domain. Here we present BART Cancer (bartcancer.org), an interactive web resource database to display the putative transcriptional regulators that are responsible for differentially regulated genes in 15 different cancer types in The Cancer Genome Atlas (TCGA). BART Cancer integrates over 10000 gene expression profiling RNA-seq datasets from TCGA with over 7000 ChIP-seq datasets from the Cistrome Data Browser database and the Gene Expression Omnibus (GEO). BART Cancer uses Binding Analysis for Regulation of Transcription (BART) for predicting the transcriptional regulators from the differentially expressed genes in cancer samples compared to normal samples. BART Cancer also displays the activities of over 900 transcriptional regulators across cancer types, by integrating computational prediction results from BART and the Cistrome Cancer database. Focusing on transcriptional regulator activities in human cancers, BART Cancer can provide unique insights into epigenetics and transcriptional regulation in cancer, and is a useful data resource for genomics and cancer research communities.

Emergency Department Boarding of Non-Trauma Patients Adversely Affects Trauma Patient Length of Stay.

Introduction Emergency Department (ED) boarding delays initiation of time-sensitive protocols for trauma patients and makes them susceptible to increased mortality and morbidity. In this study, we compared the ED boarding times of non-trauma patients and ED length of stay (LOS) of trauma patients. Methods This was a single-center retrospective cohort study in a Level 1 trauma center. The median boarding time among non-trauma patients and ED LOS among trauma patients was determined by month between the period of April 2018 to March 2019. Linear regression and Pearson correlation coefficient were used to express the magnitude and direction of the relationship between these two variables. Results During the study period, the mean number of non-trauma patients admitted in our ED per month was 1,154 and trauma patients was 89. The mean of the median boarding time per month for non-trauma patients was 76 minutes, and the mean of the median ED LOS per month for trauma patients was 198 minutes. There was a significant positive correlation between boarding time for non-trauma patients and ED LOS for trauma patients (Pearson correlation coefficient: 0.73; p = 0.007). Conclusion The long boarding times for non-trauma patients is associated with ED LOS for trauma patients, indicating that the total patient volume in the hospital contributes to the trauma patient's stay in the ED. Thus, ED LOS of trauma patients can be minimized by improving overall ED and hospital flow, including non-trauma patients.

Technique Tip: Single-Incision Endoscopic Plantar Fasciotomy.

Two-incision endoscopic plantar fasciotomy (EPF) is an accepted surgical technique in the treatment of recalcitrant plantar fasciitis. Single-incision plantar fasciotomy is a relatively new technique in the surgeons' armamentarium; however, it is not without pitfalls, specifically poor visualization. This article aims to help the foot and ankle surgeon make a smooth transition from 2-incision EPF to single-incision EPF while maintaining optimum visualization. LEVELS OF EVIDENCE: Level V: Expert opinion.

Inhibitory deficits in prepulse inhibition, sensory gating, and antisaccade eye movement in schizotypy.

Schizotypy is a term that refers to a continuum of personality characteristics, emerging from mental states ranging from organized and normal to unorganized and disordered; with the latter tending to include individuals with high schizotypal scores as well as those diagnosed with schizotypal personality disorder. Evidence from psychophysiological studies has found a relative weakness in the inhibitory functioning, including prepulse inhibition (PPI), sensory gating (SG), and antisaccade eye movement (AEM) in schizotypy and schizophrenia. As schizotypy and schizophrenia are in the same spectrum, understanding the nature of sensory and motor inhibitory weakness associated with schizotypy will optimize the prevention and intervention for both schizotypy and schizophrenia populations. This review aims at examining the deficits of sensory gating, saccade control, and prepulse inhibition in schizotypy; examining the relationship between the three measures and schizotypal symptoms and traits; examining the effect of nicotine on the three measures; and examining the relevant brain regions to the three measures. We searched multiple databases (such as MEDLINE, Pubmed, PsychINFO, Google Scholar) using combinations of the keywords: schizotypy, schizotypal personality disorder, prepulse inhibition, sensory gating and antisaccade for articles published in English since 1980. We found that three measures (SG, PPI and AEM) are associated with major schizotypal symptoms, suggesting that three measures could be used to predict the disease etiology and prognosis. Secondly, the three measures are modulated by nicotine administration at a certain level, providing a potential tool to study the role of nicotine in the cognition and symptom improvement in schizotypy. Thirdly, brain-imaging studies have localized activity in brain regions associated with sensory gating, saccade control, and prepulse inhibition, narrowing the search for brain regions to target for the treatment and prevention of schizotypy. Overall, the three measures are suggested to be a valuable tool to study the inhibitory deficits in schizotypy, and maybe used as a tool for the prevention and treatment of schizotypy as well.