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BACKGROUND: Previous studies have identified TET1 as a potential key regulator of genes linked to asthma. TET1 has been shown to transcriptionally respond to house dust mite extract, an allergen known to directly cause allergic asthma development, and regulate the expression of genes involved in asthma. How TET1 regulates expression of these genes, however, is unknown. TET1 is a DNA demethylase; therefore, most prior research on TET1-based gene regulation has focused on how TET1 affects methylation. However, TET1 can also interact directly with transcription factors and histone modifiers to regulate gene expression. Understanding how TET1 regulates expression to contribute to allergic responses and asthma development thus requires a comprehensive approach. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. RESULTS: Throughout our analyses, we detected strong similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at largely the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. CONCLUSIONS: TET1 regulates gene expression through different mechanisms (DNA methylation and chromatin accessibility) in different parts of the genome in the airway epithelial cells, which mediates inflammatory responses to allergen. Collectively, our data suggest novel molecular mechanisms through which TET1 regulates critical pathways following allergen challenges and contributes to the development of asthma.

Within medical education, feedback is an invaluable tool to facilitate learning and growth throughout a physician’s training and beyond. Despite the importance of feedback, variations in practice indicate the need for evidence-based guidelines to inform best practices. Additionally, time constraints, variable acuity, and workflow in the emergency department (ED) pose unique challenges to providing effective feedback. This paper outlines expert guidelines for feedback in the ED setting from members of the Council of Residency Directors in Emergency Medicine Best Practices Subcommittee, based on the best evidence available through a critical review of the literature. We provide guidance on the use of feedback in medical education, with a focus on instructor strategies for giving feedback and learner strategies for receiving feedback, and we offer suggestions for fostering a culture of feedback.

Cardiff State Beach (CSB) in Encinitas, CA is a barrier bar, sandy beach in San Diego County along the west side of the San Elijo Lagoon. The beach has been nourished by sand placement several times over the past twenty years to enhance its width amidst erosive wave events. In addition, San Elijo Lagoon “bypassing” (dredging of sand from the inlet) has been routinely conducted and the resulting sand placed on the beach. CSB is also the location for a Living Shoreline project that built a vegetated dune system along the western edge of South Coast Highway 101. In the interplay between rising sea levels, changing wave climate and human management efforts, projecting beach width would enable an understanding of coastal sediment management practices needed to maintain beach width (“hold the line”). The objective of this capstone project was to use a sediment budget model created for Cardiff beach to project change in beach width for 2022-2050, assuming two strong El Nino winters and sea level rise scenarios outlined by the NOAA sea level rise technical report (2022). The model was then validated using a hindcast and then comparing to existing datasets from SIO and SANDAG surveys for the 2000-2020 period. Our preliminary results indicate a promising scenario of beach width increase for CSB during the period considered, even just with routine yearly bypassing. However, in the absence of human intervention in the form of added sand, El Niños and sea level rise take a toll on the beach width, decreasing it by ~25 m by the end of the three decades. The movement of sand between the dunes and the nearshore zone is a novel element of this model that needs to be assessed further during future El Niños or other highly energetic winter wave seasons. This work is intended to support the City of Encinitas and San Diego Association of Governments’ (SANDAG) beach monitoring program by providing future beach scenarios to enable decision-making around nourishment activities and coastal resilience.

Improving the recruitment, retention, and leadership advancement of faculty who are under-represented in medicine is a priority at many academic institutions to ensure excellence in patient care, research, and health equity. Here we provide a critical review of the literature and offer evidence-based guidelines for faculty recruitment, retention, and representation in leadership. Recommendations for recruitment include targeted recruitment to expand the candidate pool with diverse candidates, holistic review of applications, and incentivizing stakeholders for success with diversity efforts. Retention efforts should establish a culture of inclusivity, promote faculty develop-ment, and evaluate for biases in the promotion and tenure process. We believe this guide will be valuable for all leaders and faculty members seeking to advance diversity, equity, and inclusion in their institutions.

Improving the diversity and representation in the medical workforce requires intentional and deliberate efforts to improve the pipeline and pathway for underrepresented in medicine (UIM) applicants. Diversity enhances educational experiences and improves patient care and outcomes. Through a critical review of the literature, in this article we offer evidence-based guidelines for physician pipeline and pathway programs (PP). Recommendations are provided regarding considerations on the types of programs and surrounding implementation to ensure a sound infrastructure and framework. We believe this guide will be valuable for all leaders and faculty members seeking to grow the UIM applicant pool in our efforts to advance diversity, equity, and inclusion within medicine.

Advancement of diversity, equity, and inclusion (DEI) in emergency medicine can only occur with intentional recruitment of residency applicants underrepresented in medicine (UIM). Shared experiences from undergraduate and graduate medical education highlight considerations and practices that can contribute to improved diversity in the resident pool, such as holistic review and mitigating bias in the recruitment process. This review, written by members of the Council of Residency Directors in Emergency Medicine (CORD) Best Practices Subcommittee, offers best practice recommendations for the recruitment of UIM applicants. Recommendations address pre-interview readiness, interview approach, and post-interview strategies that residency leadership may use to implement holistic review and mitigate bias for recruitment of a diverse class.

IntroductionThe Academic Life in Emergency Medicine (ALiEM) Faculty Incubator program is a longitudinal, 1-year, virtual faculty development program for early- and mid-career faculty members that crosses specialties and institutions. This study sought to evaluate the outcomes among 3 years of participants.MethodsThis cross-sectional survey study evaluated postcourse and 1-year outcomes from three graduated classes of the ALiEM Faculty Incubator program. The program evaluation survey was designed to collect outcomes across multiple Kirkpatrick levels using pre/post surveys and tracking of abstracts, publications, speaking opportunities, new leadership positions, and new curricula.ResultsOver 3 years, 89 clinician educators participated in the program. Of those, 59 (66%) completed the initial survey and 33 (37%) completed the 1-year survey. Participants reported a significant increase in knowledge (4.1/9.0 vs. 7.0/9.0). The number of abstracts, publications, and invited presentations significantly increased after course completion and continued postcourse. A total of 37 of 59 (62.7%) developed a new curriculum during the course and 19 of 33 (57.6%) developed another new curriculum after the course. A total of 29 of 59 (49.2%) began a new leadership position upon course completion with 15 of 33 (45.5%) beginning another new leadership position 1 year later.DiscussionThe ALiEM Faculty Incubator program demonstrated an increase in perceived knowledge and documented academic productivity among early- and mid-career medical educators.

The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro, and in vivo analyses, we report that topoisomerase 1 (TOP1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of topotecan (TPT), an FDA-approved TOP1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as 4 days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of TOP1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing TOP1 inhibitors for severe coronavirus disease 2019 (COVID-19) in humans.

The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro, and in vivo analyses, we report that topoisomerase 1 (TOP1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of topotecan (TPT), an FDA-approved TOP1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as 4 days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of TOP1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing TOP1 inhibitors for severe coronavirus disease 2019 (COVID-19) in humans.

ObjectiveWhile the benefit of mechanical thrombectomy (MT) for patients with anterior circulation acute ischemic stroke with large-vessel occlusion (AIS-LVO) has been clearly established, difficult vascular access may make the intervention impossible or unduly prolonged. In this study, the authors evaluated safety as well as radiographic and functional outcomes in stroke patients treated with MT via direct carotid puncture (DCP) for prohibitive vascular access.MethodsThe authors retrospectively studied patients from their prospective AIS-LVO database who underwent attempted MT between 2015 and 2018. Patients with prohibitive vascular access were divided into two groups: 1) aborted MT (abMT) after failed transfemoral access and 2) attempted MT via DCP. Functional outcome was assessed using the modified Rankin Scale at 3 months. Associations with outcome were analyzed using ordinal logistic regression.ResultsOf 352 consecutive patients with anterior circulation AIS-LVO who underwent attempted MT, 37 patients (10.5%) were deemed to have prohibitive vascular access (mean age [± SD] 82 ± 11 years, mean National Institutes of Health Stroke Scale [NIHSS] score 17 ± 5, with females accounting for 75% of the patients). There were 20 patients in the DCP group and 17 in the abMT group. The two groups were well matched for the known predictors of clinical outcome: age, sex, and admission NIHSS score. Direct carotid access was successfully obtained in 19 of 20 patients. Successful reperfusion (thrombolysis in cerebral infarction score 2b or 3) was achieved in 16 (84%) of 19 patients in the DCP group. Carotid access complications included an inability to catheterize the carotid artery in 1 patient, neck hematomas in 4 patients, non-flow-limiting common carotid artery (CCA) dissections in 2 patients, and a delayed, fatal carotid blowout in 1 patient. The neck hematomas and non-flow-limiting CCA dissections did not require any subsequent interventions and remained clinically silent. Compared with the abMT group, patients in the DCP group had smaller infarct volumes (11 vs 48 ml, p = 0.04), a greater reduction in NIHSS score (-4 vs +2.9, p = 0.03), and better functional outcome (shift analysis for 3-month modified Rankin Scale score: adjusted OR 5.2, 95% CI 1.02-24.5; p = 0.048).ConclusionsDCP for emergency MT in patients with anterior circulation AIS-LVO and prohibitive vascular access is safe and effective and is associated with higher recanalization rates, smaller infarct volumes, and improved functional outcome compared with patients with abMT after failed transfemoral access. DCP should be considered in this patient population.

[This corrects the article DOI: 10.1371/journal.pmed.1003090.].

BACKGROUND:People living in sub-Saharan Africa (SSA) are disproportionately exposed to trauma and may be at increased risk for posttraumatic stress disorder (PTSD). However, a dearth of population-level representative data from SSA is a barrier to assessing PTSD. This manuscript sought to calculate pooled PTSD prevalence estimates from nationally and regionally representative surveys in SSA. METHODS AND FINDINGS:The search was conducted in PubMed, Embase, PsycINFO, and PTSDpubs and was last run between October 18, 2019, and November 11, 2019. We included studies that were published in peer-reviewed journals; used probabilistic sampling methods and systematic PTSD assessments; and included ≥ 450 participants who were current residents of an SSA country, at least 50% of whom were aged between 15 and 65 years. The primary outcomes were point prevalence estimates of PTSD across all studies, and then within subgroups. The protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42016029441). Out of 2,825 unique articles reviewed, 25 studies including a total of 58,887 eligible participants (54% female) in 10 out of the 48 countries in SSA were identified. Most studies enrolled any adult aged 18 years or older. However, some studies only enrolled specific age brackets or persons as young as 15 years old. Six studies were national surveys, and 19 were regional. There were 4 key findings in the meta-analysis: (1) the overall pooled prevalence of probable PTSD was 22% (95% CI 13%-32%), while the current prevalence-defined as 1 week to 1 month-was 25% (95% CI 16%-36%); (2) prevalence estimates were highly variable, ranging from 0% (95% CI 0%-0%) to 74% (95% CI 72%-76%); (3) conflict-unexposed regions had a pooled prevalence of probable PTSD of 8% (95% CI 3%-15%), while conflict-exposed regions had a pooled prevalence of probable PTSD of 30% (95% CI 21%-40%; p < 0.001); and (4) there was no significant difference in the pooled prevalence of PTSD for men and women. The primary limitations of our methodology are our exclusion of the following study types: those published in languages other than English, French, and Portuguese; smaller studies; those that focused on key populations; those that reported only on continuous measures of PTSD symptoms; and unpublished or non-peer-reviewed studies. CONCLUSIONS:In this study, PTSD symptoms consistent with a probable diagnosis were found to be common in SSA, especially in regions exposed to armed conflict. However, these studies only represent data from 10 of the 48 SSA countries, and only 6 studies provided national-level data. Given the enormous heterogeneity expected across the continent, and also within countries and regions, this review cannot speak to rates of PTSD in any regions not included in this review. Thus, substantial gaps in our knowledge of PTSD prevalence in SSA remain. More research on population-level prevalence is needed to determine the burden of trauma symptoms and PTSD in SSA and to identify acceptable and feasible approaches to address this burden given limited mental healthcare resources.

Background and Purpose- Loss of cerebral autoregulation in the acute phase of ischemic stroke leaves patients vulnerable to blood pressure (BP) changes. Effective BP management after endovascular thrombectomy may protect the brain from hypoperfusion or hyperperfusion. In this observational study, we compared personalized, autoregulation-based BP targets to static systolic BP thresholds. Methods- We prospectively enrolled 90 patients undergoing endovascular thrombectomy for stroke. Autoregulatory function was continuously measured by interrogating changes in near-infrared spectroscopy-derived tissue oxygenation (a cerebral blood flow surrogate) in response to changes in mean arterial pressure. The resulting autoregulatory index was used to trend the BP range at which autoregulation was most preserved. Percent time that mean arterial pressure exceeded the upper limit of autoregulation or decreased below the lower limit of autoregulation was calculated for each patient. Time above fixed systolic BP thresholds was computed in a similar fashion. Functional outcome was measured with the modified Rankin Scale at 90 days. Results- Personalized limits of autoregulation were successfully computed in all 90 patients (age 71.6±16.2, 47% female, mean National Institutes of Health Stroke Scale 13.9±5.7, monitoring time 28.0±18.4 hours). Percent time with mean arterial pressure above the upper limit of autoregulation associated with worse 90-day outcomes (odds ratio per 10% 1.84 [95% CI, 1.3-2.7] P=0.002), and patients with hemorrhagic transformation spent more time above the upper limit of autoregulation (10.9% versus 16.0%, P=0.042). Although there appeared to be a nonsignificant trend towards worse outcome with increasing time above systolic BP thresholds of 140 mm Hg and 160 mm Hg, the effect sizes were smaller compared with the personalized approach. Conclusions- Noninvasive determination of personalized BP thresholds for stroke patients is feasible. Deviation from these limits may increase risk of further brain injury and poor functional outcome. This approach may present a better strategy compared with the classical approach of maintaining systolic BP below a predetermined value, though a randomized trial is needed to determine the optimal approach for hemodynamic management.

Clinical teaching is the primary educational tool use to train learners from day one of medical school all the way to the completion of fellowship. However, concerns over time constraints and patient census have led to a decline in bedside teaching. This paper provides a critical review of the literature on clinical teaching with a focus on instructor teaching strategies, clinical teaching models, and suggestions for incorporating technology. Recommendations for instructor-related teaching factors include adequate preparation, awareness of effective teacher attributes, using evidence-based-knowledge dissemination strategies, ensuring good communication, and consideration of environmental factors. Proposed recommendations for potential teaching strategies include the Socratic method, the One-Minute Preceptor model, SNAPPS, ED STAT, teaching scripts, and bedside presentation rounds. Additionally, this article will suggest approaches to incorporating technology into clinical teaching, including just-in-time training, simulation, and telemedical teaching. This paper provides readers with strategies and techniques for improving clinical teaching effectiveness.

BACKGROUND:People living in sub-Saharan Africa (SSA) are disproportionately exposed to trauma and may be at increased risk for posttraumatic stress disorder (PTSD). However, a dearth of population-level representative data from SSA is a barrier to assessing PTSD. This manuscript sought to calculate pooled PTSD prevalence estimates from nationally and regionally representative surveys in SSA. METHODS AND FINDINGS:The search was conducted in PubMed, Embase, PsycINFO, and PTSDpubs and was last run between October 18, 2019, and November 11, 2019. We included studies that were published in peer-reviewed journals; used probabilistic sampling methods and systematic PTSD assessments; and included ≥ 450 participants who were current residents of an SSA country, at least 50% of whom were aged between 15 and 65 years. The primary outcomes were point prevalence estimates of PTSD across all studies, and then within subgroups. The protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42016029441). Out of 2,825 unique articles reviewed, 25 studies including a total of 58,887 eligible participants (54% female) in 10 out of the 48 countries in SSA were identified. Most studies enrolled any adult aged 18 years or older. However, some studies only enrolled specific age brackets or persons as young as 15 years old. Six studies were national surveys, and 19 were regional. There were 4 key findings in the meta-analysis: (1) the overall pooled prevalence of probable PTSD was 22% (95% CI 13%-32%), while the current prevalence-defined as 1 week to 1 month-was 25% (95% CI 16%-36%); (2) prevalence estimates were highly variable, ranging from 0% (95% CI 0%-0%) to 74% (95% CI 72%-76%); (3) conflict-unexposed regions had a pooled prevalence of probable PTSD of 8% (95% CI 3%-15%), while conflict-exposed regions had a pooled prevalence of probable PTSD of 30% (95% CI 21%-40%; p < 0.001); and (4) there was no significant difference in the pooled prevalence of PTSD for men and women. The primary limitations of our methodology are our exclusion of the following study types: those published in languages other than English, French, and Portuguese; smaller studies; those that focused on key populations; those that reported only on continuous measures of PTSD symptoms; and unpublished or non-peer-reviewed studies. CONCLUSIONS:In this study, PTSD symptoms consistent with a probable diagnosis were found to be common in SSA, especially in regions exposed to armed conflict. However, these studies only represent data from 10 of the 48 SSA countries, and only 6 studies provided national-level data. Given the enormous heterogeneity expected across the continent, and also within countries and regions, this review cannot speak to rates of PTSD in any regions not included in this review. Thus, substantial gaps in our knowledge of PTSD prevalence in SSA remain. More research on population-level prevalence is needed to determine the burden of trauma symptoms and PTSD in SSA and to identify acceptable and feasible approaches to address this burden given limited mental healthcare resources.

[This corrects the article DOI: 10.1371/journal.pmed.1003090.].

Background and Purpose- Optimal blood pressure (BP) management during the early stages of aneurysmal subarachnoid hemorrhage remains uncertain. Observational studies have found worse outcomes in patients with increased hemodynamic variability, suggesting BP optimization as a potential neuroprotective strategy. In this study, we calculated personalized BP targets at which cerebral autoregulation was best preserved. We analyzed how deviation from these limits correlates with functional outcome. Methods- We prospectively enrolled 31 patients with aneurysmal subarachnoid hemorrhage. Autoregulatory function was continuously measured by interrogating changes in near-infrared spectroscopy (NIRS)-derived tissue oxygenation-a surrogate for cerebral blood flow-as well as intracranial pressure (ICP) in response to changes in mean arterial pressure using time-correlation analysis. The resulting autoregulatory indices were used to identify the upper and lower limit of autoregulation. Percent time that mean arterial pressure exceeded limits of autoregulation was calculated for each patient. Functional outcome was assessed using the modified Rankin Scale at discharge and 90 days. Associations with outcome were analyzed using ordinal multivariate logistic regression. Results- Personalized limits of autoregulation were computed in all patients (age 57.5±13.4, 23F, mean World Federation of Neurological Surgeons 2±1, monitoring time 67.8±50.8 hours). Optimal BP and limits of autoregulation were calculated on average for 89.5±6.7% of the total monitoring period. ICP- and NIRS-derived optimal pressures strongly correlated with one another (P

Background and Purpose- After large-vessel intracranial occlusion, the fate of the ischemic penumbra, and ultimately final infarct volume, largely depends on tissue perfusion. In this study, we evaluated whether blood pressure reduction and sustained relative hypotension during endovascular thrombectomy are associated with infarct progression and functional outcome. Methods- We identified consecutive patients with large-vessel intracranial occlusion ischemic stroke who underwent mechanical thrombectomy at 2 comprehensive stroke centers. Intraprocedural mean arterial pressure (MAP) was monitored throughout the procedure. ΔMAP was calculated as the difference between admission MAP and lowest MAP during endovascular thrombectomy until recanalization. Sustained hypotension was measured as the area between admission MAP and continuous measurements of intraprocedural MAP (aMAP). Final infarct volume was measured using magnetic resonance imaging at 24 hours, and functional outcome was assessed using the modified Rankin Scale at discharge and 90 days. Associations with outcome were analyzed using linear and ordinal multivariable logistic regression. Results- Three hundred ninety patients (mean age 71±14 years, mean National Institutes of Health Stroke Scale score of 17) were included in the study; of these, 280 (72%) achieved Thrombolysis in Cerebral Infarction 2B/3 reperfusion. Eighty-seven percent of patients experienced MAP reductions during endovascular thrombectomy (mean 31±20 mm Hg). ΔMAP was associated with greater infarct growth ( P=0.036) and final infarct volume ( P=0.035). Mean ΔMAP among patients with favorable outcomes (modified Rankin Scale score, 0-2) was 20±21 mm Hg compared with 30±24 mm Hg among patients with poor outcome ( P=0.002). In the multivariable analysis, ΔMAP was independently associated with higher (worse) modified Rankin Scale scores at discharge (adjusted odds ratio per 10 mm Hg, 1.17; 95% CI, 1.04-1.32; P=0.009) and at 90 days (adjusted odds ratio per 10 mm Hg, 1.22; 95% CI, 1.07-1.38; P=0.003). The association between aMAP and outcome was also significant at discharge ( P=0.002) and 90 days ( P=0.001). Conclusions- Blood pressure reduction before recanalization is associated with larger infarct volumes and worse functional outcomes for patients affected by large-vessel intracranial occlusion stroke. These results underscore the importance of BP management during endovascular thrombectomy and highlight the need for further investigation of blood pressure management after large-vessel intracranial occlusion stroke.

Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.1 To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.2,3 Although high expression has been used to nominate drug targets for pediatric cancers,4,5 its utility has not been evaluated in a systematic way.6 We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.

Thermal fluctuations in cell membranes manifest as an excess area ([Formula: see text]) which governs a multitude of physical process at the sub-micron scale. We present a theoretical framework, based on an in silico tether pulling method, which may be used to reliably estimate [Formula: see text] in live cells. We perform our simulations in two different thermodynamic ensembles: (i) the constant projected area and (ii) the constant frame tension ensembles and show the equivalence of our results in the two. The tether forces estimated from our simulations compare well with our experimental measurements for tethers extracted from ruptured GUVs and HeLa cells. We demonstrate the significance and validity of our method by showing that all our calculations performed in the initial tether formation regime (i.e. when the length of the tether is comparable to its radius) along with experiments of tether extraction in 15 different cell types collapse onto two unified scaling relationships mapping tether force, tether radius, bending stiffness κ, and membrane tension σ. We show that [Formula: see text] is an important determinant of the radius of the extracted tether, which is equal to the characteristic length [Formula: see text] for [Formula: see text], and is equal to [Formula: see text] for [Formula: see text]. We also find that the estimated excess area follows a linear scaling behavior that only depends on the true value of [Formula: see text] for the membrane, based on which we propose a self-consistent technique to estimate the range of excess membrane areas in a cell.

Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.1 To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.2,3 Although high expression has been used to nominate drug targets for pediatric cancers,4,5 its utility has not been evaluated in a systematic way.6 We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.

Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.1 To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.2,3 Although high expression has been used to nominate drug targets for pediatric cancers,4,5 its utility has not been evaluated in a systematic way.6 We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.

We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.

We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.

Hydration free energy calculations in explicit solvent have become an integral part of binding free energy calculations and a valuable test of force fields. Most of these simulations follow the conventional norm of keeping edge length of the periodic solvent box larger than twice the Lennard-Jones (LJ) cutoff distance, with the rationale that this should be sufficient to keep the interactions between copies of the solute to a minimum. However, for charged solutes, hydration free energies can exhibit substantial box size-dependence even at typical box sizes. Here, we examine whether similar size-dependence affects hydration of neutral molecules. Thus, we focused on two strongly polar molecules with large dipole moments, where any size-dependence should be most pronounced, and determined how their hydration free energies vary as a function of simulation box size. In addition to testing a variety of simulation box sizes, we also tested two LJ cut-off distances, 0.65 and 1.0 nm. We show from these simulations that the calculated hydration free energy is independent of the box-size as well as the LJ cut-off distance, suggesting that typical hydration free energy calculations of neutral compounds indeed need not be particularly concerned with finite-size effects as long as standard good practices are followed.

Hydration free energy calculations in explicit solvent have become an integral part of binding free energy calculations and a valuable test of force fields. Most of these simulations follow the conventional norm of keeping edge length of the periodic solvent box larger than twice the Lennard-Jones (LJ) cutoff distance, with the rationale that this should be sufficient to keep the interactions between copies of the solute to a minimum. However, for charged solutes, hydration free energies can exhibit substantial box size-dependence even at typical box sizes. Here, we examine whether similar size-dependence affects hydration of neutral molecules. Thus, we focused on two strongly polar molecules with large dipole moments, where any size-dependence should be most pronounced, and determined how their hydration free energies vary as a function of simulation box size. In addition to testing a variety of simulation box sizes, we also tested two LJ cut-off distances, 0.65 and 1.0 nm. We show from these simulations that the calculated hydration free energy is independent of the box-size as well as the LJ cut-off distance, suggesting that typical hydration free energy calculations of neutral compounds indeed need not be particularly concerned with finite-size effects as long as standard good practices are followed.