Bellevue Hospital Center

The gem5 simulation infrastructure is the merger of the best aspects of the M5 [4] and GEMS [9] simulators. M5 provides a highly configurable simulation framework, multiple ISAs, and diverse CPU models. GEMS complements these features with a detailed and exible memory system, including support for multiple cache coherence protocols and interconnect models. Currently, gem5 supports most commercial ISAs (ARM, ALPHA, MIPS, Power, SPARC, and x86), including booting Linux on three of them (ARM, ALPHA, and x86). The project is the result of the combined efforts of many academic and industrial institutions, including AMD, ARM, HP, MIPS, Princeton, MIT, and the Universities of Michigan, Texas, and Wisconsin. Over the past ten years, M5 and GEMS have been used in hundreds of publications and have been downloaded tens of thousands of times. The high level of collaboration on the gem5 project, combined with the previous success of the component parts and a liberal BSD-like license, make gem5 a valuable full-system simulation tool.

Extracting governing equations from data is a central challenge in many diverse areas of science and engineering. Data are abundant whereas models often remain elusive, as in climate science, neuroscience, ecology, finance, and epidemiology, to name only a few examples. In this work, we combine sparsity-promoting techniques and machine learning with nonlinear dynamical systems to discover governing equations from noisy measurement data. The only assumption about the structure of the model is that there are only a few important terms that govern the dynamics, so that the equations are sparse in the space of possible functions; this assumption holds for many physical systems in an appropriate basis. In particular, we use sparse regression to determine the fewest terms in the dynamic governing equations required to accurately represent the data. This results in parsimonious models that balance accuracy with model complexity to avoid overfitting. We demonstrate the algorithm on a wide range of problems, from simple canonical systems, including linear and nonlinear oscillators and the chaotic Lorenz system, to the fluid vortex shedding behind an obstacle. The fluid example illustrates the ability of this method to discover the underlying dynamics of a system that took experts in the community nearly 30 years to resolve. We also show that this method generalizes to parameterized systems and systems that are time-varying or have external forcing.

Since the publication of Paper 5 of this series the so-called "Linear Formula" has been used in the study of a large number of individuals.Practically all of the subjects of respiration experiments in the Sage calorimeter have been measured in this way, and in addition Means1of Boston has used it as a factor in determining his normal base line of metabolism and the extent of the pathological variations.Means has found that the range of normal variation from the average is smaller and that the apparent depression of metabolism in obesity is much less marked when the linear formula, instead of Meeh's formula, is used to determine surface area.The accuracy of the linear formula has been shown in Paper 9 of this series.In order to correct the slight error in the factor for the arms, and also in order to clear up a few points in the measurements which may cause confusion, it seems best to repeat the formula and show the bony landmarks by diagram (Fig. 1).Some difficulty has been experienced in locating the superior border of the great trochanter in fat subjects.This landmark is the starting point of the measure¬ ment "O" which represents the length of the thighs.If we employ another factor we can use the new measurement "W," the distance from lower border of the patella to the upper border of the pubes, a point already located in the measurement "L."In taking this measure¬ ment, however, one must be careful to have the legs straight and the knees, heels and great toes touching.It is better to take all measure¬ ments from a footboard with the subject lying down,2 determining dis¬ tance from soles of feet to lower border of patella, to upper border of

Since the year 2000, a concerted campaign against malaria has led to unprecedented levels of intervention coverage across sub-Saharan Africa. Understanding the effect of this control effort is vital to inform future control planning. However, the effect of malaria interventions across the varied epidemiological settings of Africa remains poorly understood owing to the absence of reliable surveillance data and the simplistic approaches underlying current disease estimates. Here we link a large database of malaria field surveys with detailed reconstructions of changing intervention coverage to directly evaluate trends from 2000 to 2015, and quantify the attributable effect of malaria disease control efforts. We found that Plasmodium falciparum infection prevalence in endemic Africa halved and the incidence of clinical disease fell by 40% between 2000 and 2015. We estimate that interventions have averted 663 (542–753 credible interval) million clinical cases since 2000. Insecticide-treated nets, the most widespread intervention, were by far the largest contributor (68% of cases averted). Although still below target levels, current malaria interventions have substantially reduced malaria disease incidence across the continent. Increasing access to these interventions, and maintaining their effectiveness in the face of insecticide and drug resistance, should form a cornerstone of post-2015 control strategies. In this study, the authors present an analysis of the malaria burden in sub-Saharan Africa between 2000 and 2015, and quantify the effects of the interventions that have been implemented to combat the disease; they find that the prevalence of Plasmodium falciparum infection has been reduced by 50% since 2000 and the incidence of clinical disease by 40%, and that interventions have averted approximately 663 million clinical cases since 2000, with insecticide-treated bed nets being the largest contributor. In one of the largest public health campaigns in history, a concerted malaria control campaign has been under way in sub-Saharan Africa for the past 15 years. Billions of dollars have been invested to provide interventions such as bed nets and antimalarial drugs but the overall effect on malaria burden remains unclear. This study uses field data from 30,000 population clusters in a sophisticated space–time modelling framework to quantify the changing Plasmodium falciparum risk (a 40% decline in case incidence since 2000) and the role of malaria interventions (around 700 million cases averted). Although below target levels, the current campaign has substantially reduced the incidence of malaria across the continent. Continued success will depend upon increasing access to these interventions, and maintaining their effectiveness in the face of insecticide and drug resistance.

(1945). A Standardized Memory Scale for Clinical Use. The Journal of Psychology: Vol. 19, No. 1, pp. 87-95.

BACKGROUND: The scope of the terrorist attacks of September 11, 2001, was unprecedented in the United States. We assessed the prevalence and correlates of acute post-traumatic stress disorder (PTSD) and depression among residents of Manhattan five to eight weeks after the attacks. METHODS: We used random-digit dialing to contact a representative sample of adults living south of 110th Street in Manhattan. Participants were asked about demographic characteristics, exposure to the events of September 11, and psychological symptoms after the attacks. RESULTS: Among 1008 adults interviewed, 7.5 percent reported symptoms consistent with a diagnosis of current PTSD related to the attacks, and 9.7 percent reported symptoms consistent with current depression (with "current" defined as occurring within the previous 30 days). Among respondents who lived south of Canal Street (i.e., near the World Trade Center), the prevalence of PTSD was 20.0 percent. Predictors of PTSD in a multivariate model were Hispanic ethnicity, two or more prior stressors, a panic attack during or shortly after the events, residence south of Canal Street, and loss of possessions due to the events. Predictors of depression were Hispanic ethnicity, two or more prior stressors, a panic attack, a low level of social support, the death of a friend or relative during the attacks, and loss of a job due to the attacks. CONCLUSIONS: There was a substantial burden of acute PTSD and depression in Manhattan after the September 11 attacks. Experiences involving exposure to the attacks were predictors of current PTSD, and losses as a result of the events were predictors of current depression. In the aftermath of terrorist attacks, there may be substantial psychological morbidity in the population.

BACKGROUND: The efficacy and safety of vena caval filters in the prevention of pulmonary embolism in patients with proximal deep-vein thrombosis is still a matter of debate. METHODS: Using a two-by-two factorial design, we randomly assigned 400 patients with proximal deep-vein thrombosis who were at risk for pulmonary embolism to receive a vena caval filter (200 patients) or no filter (200 patients), and to receive low-molecular-weight heparin (enoxaparin, 195 patients) or unfractionated heparin (205 patients). The rates of recurrent venous thromboembolism, death, and major bleeding were analyzed at day 12 and at two years. RESULTS: At day 12, two patients assigned to receive filters (1.1 percent), as compared with nine patients assigned to receive no filters (4.8 percent), had had symptomatic or asymptomatic pulmonary embolism (odds ratio, 0.22; 95 percent confidence interval, 0.05 to 0.90). At two years, 37 patients assigned to the filter group (20.8 percent), as compared with 21 patients assigned to the no-filter group (11.6 percent), had had recurrent deep-vein thrombosis (odds ratio, 1.87; 95 percent confidence interval, 1.10 to 3.20). There were no significant differences in mortality or the other outcomes. At day 12, three patients assigned to low-molecular-weight heparin (1.6 percent), as compared with eight patients assigned to unfractionated heparin (4.2 percent), had had symptomatic or asymptomatic pulmonary embolism (odds ratio, 0.38; 95 percent confidence interval, 0.10 to 1.38). CONCLUSIONS: In high-risk patients with proximal deep-vein thrombosis, the initial beneficial effect of vena caval filters for the prevention of pulmonary embolism was counterbalanced by an excess of recurrent deep-vein thrombosis, without any difference in mortality. Our data also confirmed that low-molecular-weight heparin was as effective and safe as unfractionated heparin for the prevention of pulmonary embolism.

BACKGROUND: Clinically significant anxiety and depression are common in patients with cancer, and are associated with poor psychiatric and medical outcomes. Historical and recent research suggests a role for psilocybin to treat cancer-related anxiety and depression. METHODS: In this double-blind, placebo-controlled, crossover trial, 29 patients with cancer-related anxiety and depression were randomly assigned and received treatment with single-dose psilocybin (0.3 mg/kg) or niacin, both in conjunction with psychotherapy. The primary outcomes were anxiety and depression assessed between groups prior to the crossover at 7 weeks. RESULTS: Prior to the crossover, psilocybin produced immediate, substantial, and sustained improvements in anxiety and depression and led to decreases in cancer-related demoralization and hopelessness, improved spiritual wellbeing, and increased quality of life. At the 6.5-month follow-up, psilocybin was associated with enduring anxiolytic and anti-depressant effects (approximately 60-80% of participants continued with clinically significant reductions in depression or anxiety), sustained benefits in existential distress and quality of life, as well as improved attitudes towards death. The psilocybin-induced mystical experience mediated the therapeutic effect of psilocybin on anxiety and depression. CONCLUSIONS: In conjunction with psychotherapy, single moderate-dose psilocybin produced rapid, robust and enduring anxiolytic and anti-depressant effects in patients with cancer-related psychological distress. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT00957359.

BACKGROUND: Carotid stenting is less invasive than endarterectomy, but it is unclear whether it is as safe in patients with symptomatic carotid-artery stenosis. METHODS: We conducted a multicenter, randomized, noninferiority trial to compare stenting with endarterectomy in patients with a symptomatic carotid stenosis of at least 60%. The primary end point was the incidence of any stroke or death within 30 days after treatment. RESULTS: The trial was stopped prematurely after the inclusion of 527 patients for reasons of both safety and futility. The 30-day incidence of any stroke or death was 3.9% after endarterectomy (95% confidence interval [CI], 2.0 to 7.2) and 9.6% after stenting (95% CI, 6.4 to 14.0); the relative risk of any stroke or death after stenting as compared with endarterectomy was 2.5 (95% CI, 1.2 to 5.1). The 30-day incidence of disabling stroke or death was 1.5% after endarterectomy (95% CI, 0.5 to 4.2) and 3.4% after stenting (95% CI, 1.7 to 6.7); the relative risk was 2.2 (95% CI, 0.7 to 7.2). At 6 months, the incidence of any stroke or death was 6.1% after endarterectomy and 11.7% after stenting (P=0.02). There were more major local complications after stenting and more systemic complications (mainly pulmonary) after endarterectomy, but the differences were not significant. Cranial-nerve injury was more common after endarterectomy than after stenting. CONCLUSIONS: In this study of patients with symptomatic carotid stenosis of 60% or more, the rates of death and stroke at 1 and 6 months were lower with endarterectomy than with stenting. (ClinicalTrials.gov number, NCT00190398 [ClinicalTrials.gov].).

High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.

Abstract The purpose of this review paper is to present the technical basis for establishing sediment quality criteria using equilibrium partitioning (EqP). Equilibrium partitioning is chosen because it addresses the two principal technical issues that must be resolved: the varying bioavailability of chemicals in sediments and the choice of the appropriate biological effects concentration. The data that are used to examine the question of varying bioavailability across sediments are from toxicity and bioaccumulation experiments utilizing the same chemical and test organism but different sediments. It has been found that if the different sediments in each experiment are compared, there is essentially no relationship between sediment chemical concentrations on a dry weight basis and biological effects. However, if the chemical concentrations in the pore water of the sediment are used (for chemicals that are not highly hydrophobic) or if the sediment chemical concentrations on an organic carbon basis are used, then the biological effects occur at similar concentrations (within a factor of two) for the different sediments. In addition, the effects concentrations are the same as, or they can be predicted from, the effects concentration determined in water- only exposures. The EqP methodology rationalizes these results by assuming that the partitioning of the chemical between sediment organic carbon and pore water is at equilibrium. In each of these phases, the fugacity or activity of the chemical is the same at equilibrium. As a consequence, it is assumed that the organism receives an equivalent exposure from a water-only exposure or from any equilibrated phase, either from pore water via respiration, from sediment carbon via ingestion; or from a mixture of the routes. Thus, the pathway of exposure is not significant. The biological effect is produced by the chemical activity of the single phase or the equilibrated system. Sediment quality criteria for nonionic organic chemicals are based on the chemical concentration in sediment organic carbon. For highly hydrophobic chemicals this is necessary because the pore water concentration is, for those chemicals, no longer a good estimate of the chemical activity. The pore water concentration is the sum of the free chemical concentration, which is bioavailable and represents the chemical activity, and the concentration of chemical complexed to dissolved organic carbon, which, as the data presented below illustrate, is not bioavailable. Using the chemical concentration in sediment organic carbon eliminates this ambiguity. Sediment quality criteria also require that a chemical concentration be chosen that is sufficiently protective of benthic organisms. The final chronic value (FCV) from the U.S. Environmental Protection Agency (EPA) water quality criteria is proposed. An analysis of the data compiled in the water quality criteria documents demonstrates that benthic species, defined as either epibenthic or infaunal species, have a similar sensitivity to water column species. This is the case if the most sensitive species are compared and if all species are compared. The results of benthic colonization experiments also support the use of the FCV. Equilibrium partitioning cannot remove all the variation in the experimentally observed sediment- effects concentration and the concentration predicted from water-only exposures. A variation of approximately a factor of two to three remains. Hence, it is recognized that a quantification of this uncertainty should accompany the sediment quality criteria. The derivation of sediment quality criteria requires the octanol/water partition coefficient of the chemical. It should be measured with modern experimental techniques, which appear to remove the large variation in reported values. The derivation of the final chronic value should also be updated to include the most recent toxicological information.

BACKGROUND: Moderate-to-severe asthma remains poorly treated. We evaluated the efficacy and safety of dupilumab (SAR231893/REGN668), a fully human monoclonal antibody to the alpha subunit of the interleukin-4 receptor, in patients with persistent, moderate-to-severe asthma and elevated eosinophil levels. METHODS: We enrolled patients with persistent, moderate-to-severe asthma and a blood eosinophil count of at least 300 cells per microliter or a sputum eosinophil level of at least 3% who used medium-dose to high-dose inhaled glucocorticoids plus long-acting beta-agonists (LABAs). We administered dupilumab (300 mg) or placebo subcutaneously once weekly. Patients were instructed to discontinue LABAs at week 4 and to taper and discontinue inhaled glucocorticoids during weeks 6 through 9. Patients received the study drug for 12 weeks or until a protocol-defined asthma exacerbation occurred. The primary end point was the occurrence of an asthma exacerbation; secondary end points included a range of measures of asthma control. Effects on various type 2 helper T-cell (Th2)-associated biomarkers and safety and tolerability were also evaluated. RESULTS: A total of 52 patients were assigned to the dupilumab group, and 52 patients were assigned to the placebo group. Baseline characteristics were similar in the two groups. Three patients had an asthma exacerbation with dupilumab (6%) versus 23 with placebo (44%), corresponding to an 87% reduction with dupilumab (odds ratio, 0.08; 95% confidence interval, 0.02 to 0.28; P<0.001). Significant improvements were observed for most measures of lung function and asthma control. Dupilumab reduced biomarkers associated with Th2-driven inflammation. Injection-site reactions, nasopharyngitis, nausea, and headache occurred more frequently with dupilumab than with placebo. CONCLUSIONS: In patients with persistent, moderate-to-severe asthma and elevated eosinophil levels who used inhaled glucocorticoids and LABAs, dupilumab therapy, as compared with placebo, was associated with fewer asthma exacerbations when LABAs and inhaled glucocorticoids were withdrawn, with improved lung function and reduced levels of Th2-associated inflammatory markers. (Funded by Sanofi and Regeneron Pharmaceuticals; ClinicalTrials.gov number, NCT01312961.).

BACKGROUND: Oral contraceptives are rarely prescribed for women with systemic lupus erythematosus, because of concern about potential negative side effects. In this double-blind, randomized, noninferiority trial, we prospectively evaluated the effect of oral contraceptives on lupus activity in premenopausal women with systemic lupus erythematosus. METHODS: A total of 183 women with inactive (76 percent) or stable active (24 percent) systemic lupus erythematosus at 15 U.S. sites were randomly assigned to receive either oral contraceptives (triphasic ethinyl estradiol at a dose of 35 microg plus norethindrone at a dose of 0.5 to 1 mg for 12 cycles of 28 days each; 91 women) or placebo (92 women) and were evaluated at months 1, 2, 3, 6, 9, and 12. Subjects were excluded if they had moderate or high levels of anticardiolipin antibodies, lupus anticoagulant, or a history of thrombosis. RESULTS: The primary end point, a severe lupus flare, occurred in 7 of 91 subjects receiving oral contraceptives (7.7 percent) as compared with 7 of 92 subjects receiving placebo (7.6 percent). The 12-month rates of severe flare were similar: 0.084 for the group receiving oral contraceptives and 0.087 for the placebo group (P=0.95; upper limit of the one-sided 95 percent confidence interval for this difference, 0.069, which is within the prespecified 9 percent margin for noninferiority). Rates of mild or moderate flares were 1.40 flares per person-year for subjects receiving oral contraceptives and 1.44 flares per person-year for subjects receiving placebo (relative risk, 0.98; P=0.86). In the group that was randomized to receive oral contraceptives, there was one deep venous thrombosis and one clotted graft; in the placebo group, there was one deep venous thrombosis, one ocular thrombosis, one superficial thrombophlebitis, and one death (after cessation of the trial). CONCLUSIONS: Our study indicates that oral contraceptives do not increase the risk of flare among women with systemic lupus erythematosus whose disease is stable.

PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science.

We develop a new method which extends dynamic mode decomposition (DMD) to incorporate the effect of control to extract low-order models from high-dimensional, complex systems. DMD finds spatial-temporal coherent modes, connects local-linear analysis to nonlinear operator theory, and provides an equation-free architecture which is compatible with compressive sensing. In actuated systems, DMD is incapable of producing an input-output model; moreover, the dynamics and the modes will be corrupted by external forcing. Our new method, dynamic mode decomposition with control (DMDc), capitalizes on all of the advantages of DMD and provides the additional innovation of being able to disambiguate between the underlying dynamics and the effects of actuation, resulting in accurate input-output models. The method is data-driven in that it does not require knowledge of the underlying governing equations---only snapshots in time of observables and actuation data from historical, experimental, or black-box simulations. We demonstrate the method on high-dimensional dynamical systems, including a model with relevance to the analysis of infectious disease data with mass vaccination (actuation).

Transformers have achieved superior performances in many tasks in natural language processing and computer vision, which also triggered great interest in the time series community. Among multiple advantages of Transformers, the ability to capture long-range dependencies and interactions is especially attractive for time series modeling, leading to exciting progress in various time series applications. In this paper, we systematically review Transformer schemes for time series modeling by highlighting their strengths as well as limitations. In particular, we examine the development of time series Transformers in two perspectives. From the perspective of network structure, we summarize the adaptations and modifications that have been made to Transformers in order to accommodate the challenges in time series analysis. From the perspective of applications, we categorize time series Transformers based on common tasks including forecasting, anomaly detection, and classification. Empirically, we perform robust analysis, model size analysis, and seasonal-trend decomposition analysis to study how Transformers perform in time series. Finally, we discuss and suggest future directions to provide useful research guidance.

The classical optimal power flow problem with a nonseparable objective function can be solved by an explicit Newton approach. Efficient, robust solutions can be obtained for problems of any practical size or kind. Solution effort is approximately proportional to network size, and is relatively independent of the number of controls or binding inequalities. The key idea is a direct simultaneous solution for all of the unknowns in the Lagrangian function on each iteration. Each iteration minimizes a quadratic approximation of the Lagrangian. For any given set of binding constraints the process converges to the Kuhn-Tucker conditions in a few iterations. The challenge in algorithm development is to efficiently identify the binding inequalities.

ST-Segment Elevation in Covid-19 Eighteen patients with Covid-19 presented with ST-segment elevation on ECG or had it develop during hospitalization. Eight patients received a diagnosis of acute my...

Treatment of patients with acute pancreatitis is based on the initial assessment of disease severity. Severe pancreatitis occurs in 20%-30% of all patients with acute pancreatitis and is characterized by a protracted clinical course, multiorgan failure, and pancreatic necrosis. Early staging is based on the presence and degree of systemic failure (cardiovascular, pulmonary, renal) and on the presence and extent of pancreatic necrosis. Individual laboratory indexes (markers of pancreatic injury, markers of inflammatory response), while promising, have not yet gained clinical acceptance. Numeric grading systems with sensitivities of about 70% are commonly used today as indicators of organ failure and disease severity. Contrast material-enhanced computed tomography is used in addition to help evaluate local pancreatic morphology and the presence and extent of pancreatic necrosis. Advantages and limitations of the clinical, laboratory, and imaging prognostic indexes are analyzed and discussed.

Evidence-based guidelines for the management of persons infected with human immunodeficiency virus (HIV) were prepared by an expert panel of the HIV Medicine Association of the Infectious Diseases Society of America. These updated guidelines replace those published in 2004. The guidelines are intended for use by health care providers who care for HIV-infected patients or patients who may be at risk for acquiring HIV infection. Since 2004, new antiretroviral drugs and classes have become available, and the prognosis of persons with HIV infection continues to improve. However, with fewer complications and increased survival, HIV-infected persons are increasingly developing common health problems that also affect the general population. Some of these conditions may be related to HIV infection itself and its treatment. HIV-infected persons should be managed and monitored for all relevant age- and gender-specific health problems. New information based on publications from the period 2003-2008 has been incorporated into this document.