Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version)

Traditional mathematical models of photosynthesis are based on mass action kinetics of light reactions. This approach requires the modeller to enumerate all the possible state combinations of the modelled chemical species. This leads to combinatorial explosion in the number of reactions although the structure of the model could be expressed more compactly. We explore the use of rule-based modelling, in particular, a simplified variant of Kappa, to compactly capture and automatically reduce existing mathematical models of photosynthesis. Finally, the reduction procedure is implemented in BioNetGen language and demonstrated on several ODE models of photosynthesis processes. This is an extended version of the paper published in proceedings of 5th International Workshop on Static Analysis and Systems Biology (SASB) 2014.Comment: SASB 2014 full pape

Is there a well-tested tool to detect drug-seeking behaviors in chronic pain patients?

There is no well-tested, easily administered screening tool to detect drug-seeking behaviors in primary care patients taking long-term opioids or being considered for such therapy (strength of recommendation [SOR]: C, studies of intermediate outcomes)

Screening Mammography for Reducing Breast Cancer Mortality

Screening mammography reduces breast cancer mortality in women 40 to 49 years of age who have an average risk of breast cancer. (Strength of Recommendation: A, based on eight randomized controlled trials [RCTs].) The relative risk reduction in this age group is 15 percent, similar to that of women 50 years and older (14 percent). To prevent one breast cancer death, 1,904 women 40 to 49 years of age must be screened annually for 10 years, compared with 1,339 women 50 to 59 years of age. Although both age groups appear to have a similar relative risk reduction from routine screening, women 40 to 49 years of age have a smaller absolute risk reduction and may experience greater harms from screening compared with older women. These potential harms include false-positive results, diagnosis and treatment for cancer that would not have become clinically evident during the woman's lifetime, false-negative results (i.e., false reassurance), radiation exposure, biopsies, and anxiety

An Accurate Model of Beam Ion Instability with Nonlinear Space Charge, Realistic Beam Optics and Multiple Gas Species Vacuum Abstract

The previous analyses of beam ion instability have been performed for single gas species only. However, there are multiple gas species in the vacuum chambers of an accelerator. The superposition rule doesn’t apply in general and it overestimates the instability. Therefore, it is important to use multiple gas species model. On the other hand, the variation of beam size along the accelerator ring or linac provides Landau damping to the instability. In previous studies, the effect of beam optics has been represented by a frequency spread and a quality factor. In practice, it could be difficult to accurately estimate the frequency spread and quality factor for general beam optics because the variation of the beam size along the ring usually doesn’t have simple distribution. This paper provides a more accurate method to analyze beam ion instability with arbitrary vacuum component and arbitrary beam optics where the variation of the beam size along the accelerator ring or linac can be arbitrary. Meanwhile, the nonlinear space charge effect is also included and the general beam filling pattern can be easily modeled. Our analyses agree well with expensive simulations. PACS numbers: 29.27.Bd, 29.20.db I

How safe and effective is ondansetron for nausea and vomiting in pregnancy?

Q: How safe and effective is ondansetron for nausea and vomiting in pregnancy? Evidence-based answer: oral ondansetron is more effective than a combination of pyridoxine and doxylamine for outpatient treatment of nausea and vomiting in pregnancy (strength of recommendation [SOR]: B, randomized controlled trial [RCT]). For moderate to severe nausea and vomiting, intravenous (IV) ondansetron is at least as effective as IV metoclopramide and may cause fewer adverse reactions (SOR: B, RCTs). Disease registry, case-control, and cohort studies report a slight increase in the risk of cardiac defects with ondansetron use in first-trimester pregnancies, but no major or other birth defects are associated with ondansetron exposure (SOR: B, a systematic review of observational trials and a single retrospective cohort study). A specialty society guideline recommends weighing the risks and benefits of ondansetron use before 10 weeks' gestational age and suggests reserving ondansetron for patients who have persistent nausea and vomiting unresponsive to first- and second-line treatments (SOR: C, expert opinion).Kimberly L. Collins, MD; Megan Wilson, MD; E. Chris Vincent, MD, University of Washington, Seattle ; Sarah Safranek, MLIS, University of Washington, SeattleIncludes bibliographical reference

Adverse Childhood Experiences and Adult Smoking, Nebraska, 2011

Introduction Smoking is a public health risk; the prevalence of smoking among adults in Nebraska is 18-4%. Studies indicate that maltreatment of children alters their brain development, possibly increasing risk for tobacco use. Previous studies have documented associations between childhood maltreatment and adult health behaviors, demonstrating the influence of adverse experiences on tobacco use. We examined prevalence and associations between adverse childhood experiences and smoking among Nebraskans. Methods We analyzed 2011 Nebraska Behavioral Risk Factor Surveillance System (Adverse Childhood Experience module) data, defining adverse childhood experience exposures as physical, sexual, and verbal abuse (ie, direct exposures), and household dysfunction associated with mental illness, substance abuse, divorce, domestic violence, and living with persons with incarceration histories (ie, environmental exposures). We estimated prevalence of exposures, taking into account the complex survey design. We used logistic regression with predicted margins to estimate adjusted relative risk for smoking by direct or environmental exposure. Results Approximately 51% of Nebraskans experienced 1 or more adverse childhood events; 7% experienced 5 or more. Prevalence of environmental exposures (42%) was significantly higher than that of direct exposures (31%). Prevalence of individual exposures ranged from 6% (incarceration of a household member) to 25% (verbal abuse). Adjusted relative risks of smoking for direct and environmental exposures were 1.5 and 1.8, respectively. Conclusion We present a new method of evaluating adverse childhood experience data. Prevalence of adverse childhood experiences is high among Nebraskans, and these exposures are associated with smoking. State-specific strategies to monitor adverse events among children and provide interventions might help to decrease the smoking rate in this population

Adverse Childhood Experiences and Adult Smoking, Nebraska, 2011

Introduction Smoking is a public health risk; the prevalence of smoking among adults in Nebraska is 18-4%. Studies indicate that maltreatment of children alters their brain development, possibly increasing risk for tobacco use. Previous studies have documented associations between childhood maltreatment and adult health behaviors, demonstrating the influence of adverse experiences on tobacco use. We examined prevalence and associations between adverse childhood experiences and smoking among Nebraskans. Methods We analyzed 2011 Nebraska Behavioral Risk Factor Surveillance System (Adverse Childhood Experience module) data, defining adverse childhood experience exposures as physical, sexual, and verbal abuse (ie, direct exposures), and household dysfunction associated with mental illness, substance abuse, divorce, domestic violence, and living with persons with incarceration histories (ie, environmental exposures). We estimated prevalence of exposures, taking into account the complex survey design. We used logistic regression with predicted margins to estimate adjusted relative risk for smoking by direct or environmental exposure. Results Approximately 51% of Nebraskans experienced 1 or more adverse childhood events; 7% experienced 5 or more. Prevalence of environmental exposures (42%) was significantly higher than that of direct exposures (31%). Prevalence of individual exposures ranged from 6% (incarceration of a household member) to 25% (verbal abuse). Adjusted relative risks of smoking for direct and environmental exposures were 1.5 and 1.8, respectively. Conclusion We present a new method of evaluating adverse childhood experience data. Prevalence of adverse childhood experiences is high among Nebraskans, and these exposures are associated with smoking. State-specific strategies to monitor adverse events among children and provide interventions might help to decrease the smoking rate in this population

Multistate product traceforward investigation to link imported romaine lettuce to a US cyclosporiasis outbreak – Nebraska, Texas, and Florida, June–August 2013

During June–August 2013, 25 US states reported 631 cyclosporiasis cases including Nebraska and Iowa where a regional investigation implicated common-source imported salad mix served in two chain restaurants. At least two common-origin growing fields were likely sources of contaminated romaine lettuce. Using producer- and distributor-provided data, we conducted a grower-specific traceforward investigation to reveal exposures of ill US residents elsewhere who reported symptom onset during 11 June–1 July 2013, the time period established in the Nebraska and Iowa investigation. Romaine lettuce shipped on 2–6 June from one of these Mexico-origin growing fields likely caused cyclosporiasis in 78 persons reporting illness onsets from 11 June to 1 July in Nebraska, Texas, and Florida. Nationwide, 97% (314/324) of persons confirmed with cyclosporiasis with symptom onset from 11 June to 1 July 2013 resided in 11 central and eastern US states receiving approximately two-thirds of romaine lettuce from this field. This grower’s production practices should be investigated to determine potential sources of contamination and to develop recommendations to prevent future illnesses