Nonadherence to primary prophylaxis against Pneumocystis jirovecii pneumonia.

BackgroundDespite the effectiveness of prophylaxis, Pneumocystis jirovecii pneumonia (PCP) continues to be the most common serious opportunistic infection among HIV-infected persons. We describe factors associated with nonadherence to primary PCP prophylaxis.Methodology/principal findingsWe used 2000-2004 data from the Supplement to HIV/AIDS Surveillance (SHAS) project, a cross-sectional interview project of HIV-infected persons >or=18 years conducted in 18 states. We limited the analysis to persons who denied having prior PCP, reported having a current prescription to prevent PCP, and answered the question "In the past 30 days, how often were you able to take the PCP medication(s) exactly the way your doctor told you to take them?" We used multivariable logistic regression to describe factors associated with nonadherence. Of 1,666 subjects prescribed PCP prophylaxis, 305 (18.3%) were nonadherent. Persons were more likely to be nonadherent if they reported using marijuana (adjusted odds ratio [aOR] = 1.6, 95% confidence interval [CI] = 1.1-2.4), non-injection drugs other than marijuana (aOR = 1.5, 95% CI = 1.0-2.1), or injection drugs (aOR = 2.3, 95% CI = 1.3-4.1) in the past year; their mental health was "not good" for >or=1 day during the past month (aOR = 1.6, 95% CI = 1.2-2.2); their most recent CD4 count was <200 cells/microL (aOR = 1.6, 95% CI = 1.1-2.2); or taking ART usually (aOR = 9.6, 95% CI = 6.7-13.7) or sometimes/rarely/never (aOR = 18.4, 95% CI = 11.1-30.4), compared with always, as prescribed.Conclusion/significanceProviders should inquire about and promote strategies to improve adherence to PCP prophylaxis, particularly among persons who use illicit drugs, have mental health issues, and who are not compliant with ART to reduce the occurrence of PCP

Genomes to life project : quarterly report October 2003.

This SAND report provides the technical progress through October 2003 of the Sandia-led project, 'Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,' funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project, including a copy of the original proposal, can be found at www.genomes-to-life.or

Genomes to life project quarterly report June 2004.

This SAND report provides the technical progress through June 2004 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO{sub 2} are important terms in the global environmental response to anthropogenic atmospheric inputs of CO{sub 2} and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort

Genomes to life project quarterly report February 2003.

This SAND report provides the technical progress for the first quarter (through February 2003) of the Sandia-led project, 'Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,' funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project, including a copy of the original proposal, can be found at www.genomes-to-life.or

Shotgun protein sequencing.

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins

Phase behavior and molecular scale dynamics of confined fluids using new atomistic simulation techniques: CRADA No. 1140 close-out report

The Mobil-nCUBE-Sandia CRADA No. 1140 was aimed at developing the tools and capabilities to model fluid phase behavior and flow in pores--ultimately leading to a better understanding of these phenomena. In this CRADA close-out report the collaboration`s original goals are revisited, the course of the CRADA is traced, and the technical accomplishments of the CRADA are presented

Fat Graft for Parotidectomy Defect Reconstruction in the Setting of Malignant Disease

Objectives: Currently, limited data examines the safety of utilizing fat transfers in the setting of malignant parotid disease. Here we evaluate the safety of fat graft reconstruction of parotidectomy defects in the setting of malignant disease. Study Design: Retrospective cohort study Methods: Electronic chart review of patients who underwent parotidectomy from 2012-2020 were reviewed. Results: Three hundred and sixty-one patients were identified at a single institution who underwent parotidectomy, and 113 (31.3%) were for malignancy. One hundred and thirty-two patients underwent fat graft reconstruction (49.2%, n=65 for umbilical, 50.8%, n=67 for dermal). One-third of patients had malignant pathology (34.8%, n=46). The most common malignant tumors were squamous cell carcinoma (n=15), acinic cell carcinoma (n=9), and mucoepidermoid carcinoma (n=6). Twenty patients (45.5%) received postoperative radiation therapy. Complications included: surgical site necrosis (13%), hematoma (4.3%), and infection (2.2%). Overall incidence of malignant recurrence was 4.4% with a mean time of follow-up of 10.3 (range 0 – 77.3) months. Incidence of malignant recurrence in the fat graft reconstruction subset was 0% with a mean follow-up of 9.8 (range 0.2 – 49.3) months. There was no association with use of fat graft and recurrence (p\u3e0.05). Conclusion: Parotidectomy defects for malignant neoplasms can be reconstructed with fat graft transfers with no impact on surveillance for disease recurrence.https://jdc.jefferson.edu/otoposters/1010/thumbnail.jp

Intraoperative Evaluation of Nasal Valve Repair Interventions: A Prospective Analysis

Objectives: To allow for early identification and treatment of inadequate nasal valve repair interventions in the intraoperative setting, based on degree of nasal valve collapse quantified by suction-assisted pressure readings. Patient outcomes were measured by comparison of pre- and post-operative Nasal Obstruction Symptom Evaluation (NOSE) surveys. Study Design: Prospective study. Methods: All enrolled patients undergo suction-assisted evaluation of nasal valve collapse before surgical intervention. Patients randomized into the experimental group underwent repeat assessment after various nasal valve interventions, compared to a control group where adequacy of interventions was assessed by palpation of the nasal ala. Results: 20 patients who underwent nasal valve repair were first randomized into control (10) or experimental (10) groups. Two patients in the control group did not receive nasal valve work due to pre-operative readings and were excluded from further analysis. Nasal valve interventions included alar rim grafts (5), spreader grafts (10), batten grafts (2), and nasal valve suture suspension (8). After nasal valve interventions, average suction reading at first sign of collapse increased by 92% (p \u3c 0.0001) and average suction reading at maximal collapse increased by 16% (p \u3c 0.0001). Pre-operative NOSE scores decreased by 55% (p \u3c 0.0001) at the first follow-up visit at 9.3±3.5 days. No patients in the experimental group required additional nasal valve interventions after repeat suction-assisted evaluations intraoperatively. Conclusion: Intraoperative suction-assisted evaluation of nasal valve collapse can help assess adequacy of nasal valve interventions and determine whether additional interventions are necessary to improve nasal valve integrity.https://jdc.jefferson.edu/otoposters/1011/thumbnail.jp