Unified tumor growth mechanisms from multimodel inference and dataset integration.

Mechanistic models of biological processes can explain observed phenomena and predict responses to a perturbation. A mathematical model is typically constructed using expert knowledge and informal reasoning to generate a mechanistic explanation for a given observation. Although this approach works well for simple systems with abundant data and well-established principles, quantitative biology is often faced with a dearth of both data and knowledge about a process, thus making it challenging to identify and validate all possible mechanistic hypothesis underlying a system behavior. To overcome these limitations, we introduce a Bayesian multimodel inference (Bayes-MMI) methodology, which quantifies how mechanistic hypotheses can explain a given experimental datasets, and concurrently, how each dataset informs a given model hypothesis, thus enabling hypothesis space exploration in the context of available data. We demonstrate this approach to probe standing questions about heterogeneity, lineage plasticity, and cell-cell interactions in tumor growth mechanisms of small cell lung cancer (SCLC). We integrate three datasets that each formulated different explanations for tumor growth mechanisms in SCLC, apply Bayes-MMI and find that the data supports model predictions for tumor evolution promoted by high lineage plasticity, rather than through expanding rare stem-like populations. In addition, the models predict that in the presence of cells associated with the SCLC-N or SCLC-A2 subtypes, the transition from the SCLC-A subtype to the SCLC-Y subtype through an intermediate is decelerated. Together, these predictions provide a testable hypothesis for observed juxtaposed results in SCLC growth and a mechanistic interpretation for tumor treatment resistance.

SBbadger: biochemical reaction networks with definable degree distributions.

MOTIVATION: An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. RESULTS: In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. AVAILABILITY AND IMPLEMENTATION: SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective.

Dysregulation of iron metabolism in cancer is well documented and it has been suggested that there is interdependence between excess iron and increased cancer incidence and progression. In an effort to better understand the linkages between iron metabolism and breast cancer, a predictive mathematical model of an expanded iron homeostasis pathway was constructed that includes species involved in iron utilization, oxidative stress response and oncogenic pathways. The model leads to three predictions. The first is that overexpression of iron regulatory protein 2 (IRP2) recapitulates many aspects of the alterations in free iron and iron-related proteins in cancer cells without affecting the oxidative stress response or the oncogenic pathways included in the model. This prediction was validated by experimentation. The second prediction is that iron-related proteins are dramatically affected by mitochondrial ferritin overexpression. This prediction was validated by results in the pertinent literature not used for model construction. The third prediction is that oncogenic Ras pathways contribute to altered iron homeostasis in cancer cells. This prediction was validated by a combination of simulation experiments of Ras overexpression and catalase knockout in conjunction with the literature. The model successfully captures key aspects of iron metabolism in breast cancer cells and provides a framework upon which more detailed models can be built.

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Lipid identification from data produced with high-throughput technologies is essential to the elucidation of the roles played by lipids in cellular function and disease. Software tools for identifying lipids from tandem mass (MS/MS) spectra have been developed, but they are often costly or lack the sophistication of their proteomics counterparts. We have developed Greazy, an open source tool for the automated identification of phospholipids from MS/MS spectra, that utilizes methods similar to those developed for proteomics. From user-supplied parameters, Greazy builds a phospholipid search space and associated theoretical MS/MS spectra. Experimental spectra are scored against search space lipids with similar precursor masses using a peak score based on the hypergeometric distribution and an intensity score utilizing the percentage of total ion intensity residing in matching peaks. The LipidLama component filters the results via mixture modeling and density estimation. We assess Greazy's performance against the NIST 2014 metabolomics library, observing high accuracy in a search of multiple lipid classes. We compare Greazy/LipidLama against the commercial lipid identification software LipidSearch and show that the two platforms differ considerably in the sets of identified spectra while showing good agreement on those spectra identified by both. Lastly, we demonstrate the utility of Greazy/LipidLama with different instruments. We searched data from replicates of alveolar type 2 epithelial cells obtained with an Orbitrap and from human serum replicates generated on a quadrupole-time-of-flight (Q-TOF). These findings substantiate the application of proteomics derived methods to the identification of lipids. The software is available from the ProteoWizard repository: http://tiny.cc/bumbershoot-vc12-bin64 .

Fundoplication versus medical management of gastroesophageal reflux disease: systematic review and meta-analysis.

BACKGROUND: Medical, endoscopic, and open/laparoscopic surgical methods are used to treat gastroesophageal reflux disease (GERD). This study aimed to perform a systematic review of randomized controlled trials comparing medical and surgical treatments of GERD in adult patients. METHODS: For the study, MEDLINE and EMBASE (1980-2012) were searched. Two reviewers independently assessed methodologic aspects and extracted data from eligible studies, focusing on patient-relevant outcomes. The primary outcomes were health-related and GERD-specific quality-of-life aspects. Standardized mean differences (SMDs) between treatment groups were calculated and combined using random-effect meta-analysis. RESULTS: The study identified 11 publications reporting on 7 trials comparing surgical (open or laparoscopic) and medical treatment of GERD. Meta-analysis of both quality-of-life aspects showed a pooled-effect estimate in favor of fundoplication (SMD 0.18; 95 % confidence interval [CI] 0.01-0.35; SMD 0.33; 95 % CI 0.13-0.54). Heartburn and regurgitation were less frequent after surgical intervention. However, a considerable proportion of patients still needed antireflux medication after fundoplication. Nevertheless, the surgical patients were significantly more satisfied with their symptom control and showed higher satisfaction with the treatment received. CONCLUSIONS: This systematic review showed that surgical management of GERD is more effective than medical management with respect to patient-relevant outcomes in the short and medium term. However, long-term studies still are needed to determine whether antireflux surgery is an equivalent alternative to lifelong medical treatment.

Antibiotics for community-acquired pneumonia in adult outpatients.

BACKGROUND: Lower respiratory tract infection (LRTI) is the third leading cause of death worldwide and the first leading cause of death in low-income countries. Community-acquired pneumonia (CAP) is a common condition that causes a significant disease burden for the community, particularly in children younger than five years, the elderly and immunocompromised people. Antibiotics are the standard treatment for CAP. However, increasing antibiotic use is associated with the development of bacterial resistance and side effects for the patient. Several studies have been published regarding optimal antibiotic treatment for CAP but many of these data address treatments in hospitalised patients. This is an update of our 2009 Cochrane Review and addresses antibiotic therapies for CAP in outpatient settings. OBJECTIVES: To compare the efficacy and safety of different antibiotic treatments for CAP in participants older than 12 years treated in outpatient settings with respect to clinical, radiological and bacteriological outcomes. SEARCH METHODS: We searched CENTRAL (2014, Issue 1), MEDLINE (January 1966 to March week 3, 2014), EMBASE (January 1974 to March 2014), CINAHL (2009 to March 2014), Web of Science (2009 to March 2014) and LILACS (2009 to March 2014). SELECTION CRITERIA: We looked for randomised controlled trials (RCTs), fully published in peer-reviewed journals, of antibiotics versus placebo as well as antibiotics versus another antibiotic for the treatment of CAP in outpatient settings in participants older than 12 years of age. However, we did not find any studies of antibiotics versus placebo. Therefore, this review includes RCTs of one or more antibiotics, which report the diagnostic criteria and describe the clinical outcomes considered for inclusion in this review. DATA COLLECTION AND ANALYSIS: Two review authors (LMB, TJMV) independently assessed study reports in the first publication. In the 2009 update, LMB performed study selection, which was checked by TJMV and MMK. In this 2014 update, two review authors (SP, SM) independently performed and checked study selection. We contacted trial authors to resolve any ambiguities in the study reports. We compiled and analysed the data. We resolved differences between review authors by discussion and consensus. MAIN RESULTS: We included 11 RCTs in this review update (3352 participants older than 12 years with a diagnosis of CAP); 10 RCTs assessed nine antibiotic pairs (3321 participants) and one RCT assessed four antibiotics (31 participants) in people with CAP. The study quality was generally good, with some differences in the extent of the reporting. A variety of clinical, bacteriological and adverse events were reported. Overall, there was no significant difference in the efficacy of the various antibiotics. Studies evaluating clarithromycin and amoxicillin provided only descriptive data regarding the primary outcome. Though the majority of adverse events were similar between all antibiotics, nemonoxacin demonstrated higher gastrointestinal and nervous system adverse events when compared to levofloxacin, while cethromycin demonstrated significantly more nervous system side effects, especially dysgeusia, when compared to clarithromycin. Similarly, high-dose amoxicillin (1 g three times a day) was associated with higher incidence of gastritis and diarrhoea compared to clarithromycin, azithromycin and levofloxacin. AUTHORS' CONCLUSIONS: Available evidence from recent RCTs is insufficient to make new evidence-based recommendations for the choice of antibiotic to be used for the treatment of CAP in outpatient settings. Pooling of study data was limited by the very low number of studies assessing the same antibiotic pairs. Individual study results do not reveal significant differences in efficacy between various antibiotics and antibiotic groups. However, two studies did find significantly more adverse events with use of cethromycin as compared to clarithromycin and nemonoxacin when compared to levofloxacin. Multi-drug comparisons using similar administration schedules are needed to provide the evidence necessary for practice recommendations. Further studies focusing on diagnosis, management, cost-effectiveness and misuse of antibiotics in CAP and LRTI are warranted in high-, middle- and low-income countries.

First-order ultrasensitivity in phosphorylation cycles.

Cellular signal transduction takes place through a network of phosphorylation cycles. These pathways take the form of a multi-layered cascade of cycles. This work focuses on the sensitivity of single, double and n length cycles. Cycles that operate in the zero-order regime can become sensitive to changes in signal, resulting in zero-order ultrasensitivity (ZOU). Using frequency analysis, we confirm previous efforts that cascades can act as noise filters by computing the bandwidth. We show that n length cycles display what we term first-order ultrasensitivity which occurs even when the cycles are not operating in the zero-order regime. The magnitude of the sensitivity, however, has an upper bound equal to the number of cycles. It is known that ZOU can be significantly reduced in the presence of retroactivity. We show that the first-order ultrasensitivity is immune to retroactivity and that the ZOU and first-order ultrasensitivity can be blended to create systems with constant sensitivity over a wider range of signal. We show that the ZOU in a double cycle is only modestly higher compared with a single cycle. We therefore speculate that the double cycle has evolved to enable amplification even in the face of retroactivity.

Signal integration and integral feedback control with biochemical reaction networks.

Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it enables a system's output to respond to changing inputs, but to then return exactly back to some pre-determined setpoint value afterward. To gain a deeper understanding of how biochemical networks are able to both integrate signals and perform integral feedback control, we investigated these abilities for several simple reaction networks. We found imperfect overlap between these categories, with some networks able to perform both tasks, some able to perform integration but not integral feedback control, and some the other way around. Nevertheless, networks that could either integrate or perform integral feedback control shared key elements. In particular, they included a chemical species that was neutrally stable in the open loop system (no feedback), meaning that this species does not have a unique stable steady-state concentration. Neutral stability could arise from zeroth order decay reactions, binding to a partner that was produced at a constant rate (which occurs in antithetic control), or through a long chain of covalent cycles. Mathematically, it arose from rate equations for the reaction network that were underdetermined when evaluated at steady-state.

Sensitivity and Frequency Response of Biochemical Cascades.

Signal transduction from a cell's surface to cytoplasmic and nuclear targets takes place through a complex network of interconnected pathways. Phosphorylation cycles are common components of many pathways and may take the form of a multi-layered cascade of cycles or incorporate species with multiple phosphorylation sites that effectively create a sequence of cycles with increasing states of phosphorylation. This work focuses on the frequency response and sensitivity of such systems, two properties that have not been thoroughly examined. Starting with a singularly phosphorylated single-cycle system, we compare the sensitivity to perturbation at steady-state across a range of input signal strengths. This is followed by a frequency response analysis focusing on the gain and associated bandwidth. Next, we consider a two-layer cascade of single phosphorylation cycles and focus on how the two cycles interact to produce various effects on the bandwidth and damping properties. Then we consider the (ultra)sensitivity of a doubly phosphorylated system, where we describe in detail first-order ultrasensitivity, a unique property of these systems, which can be blended with zero-order ultrasensitivity to create systems with relatively constant gain over a range of signal input. Finally, we give an in-depth analysis of the sensitivity of an n-phosphorylated system.

Immediate versus conditional treatment of uncomplicated urinary tract infection - a randomized-controlled comparative effectiveness study in general practices.

BACKGROUND: Uncomplicated urinary tract infections (UTI) are usually treated with antibiotics as recommended by primary care guidelines. Antibiotic treatment supports clinical cure in individual patients but also leads to emerging resistance rates in the population. We designed a comparative effectiveness study to investigate whether the use of antibiotics for uncomplicated UTI could be reduced by initial treatment with ibuprofen, reserving antibiotic treatment to patients who return due to ongoing or recurrent symptoms. METHODS/DESIGN: This is a randomized-controlled, double-blind, double dummy multicentre trial assessing the comparative effectiveness of immediate vs. conditional antibiotic therapy in uncomplicated UTI. Women > 18 and < 65 years, presenting at general practices with at least one of the typical symptoms dysuria or frequency/urgency of micturition, will be screened and enrolled into the trial. During an 18- months recruitment period, a total of 494 patients will have to be recruited in 45 general practices in Lower Saxony. Participating patients receive either immediate antibiotic therapy with fosfomycin-trometamol 1x3g or initial symptomatic treatment with ibuprofen 3x400mg for 3 days. The ibuprofen group will be provided with antibiotic therapy only if needed, i.e. for persistent or worsening symptoms. For a combined primary endpoint, we choose the number of all antibiotic prescriptions regardless of the medical indication day 0-28 and the "disease burden", defined as a weighted sum of the daily total symptom scores from day 0 to day 7. The study is considered positive if superiority of conditional antibiotic treatment with respect to the first primary endpoint and non-inferiority of conditional antibiotic treatment with respect to the second primary endpoint is proven. DISCUSSION: This study aims at investigating whether the use of antibiotics for uncomplicated UTI could be reduced by initial treatment with ibuprofen. The comparative effectiveness design was chosen to prove the effectiveness of two therapeutic strategies instead of the pure drug efficacy.

Recommendations for the Outpatient Drug Treatment of Patients With COVID-19.

BACKGROUND: One of the purposes of outpatient treatment for COVID-19 patients is to prevent severe disease courses and hospitalization. There is a need for evidence-based recommendations to be applied in primary care and specialized outpatient settings. METHODS: This guideline was developed on the basis of publications that were retrieved by a systematic search for randomized controlled trials in the Cochrane COVID-19 trial registry. The quality of evidence was assessed with GRADE, and structured consensus generation was carried out with MAGICapp. RESULTS: Unvaccinated COVID-19 outpatients with at least one risk factor for a severe disease course may be treated in the early phase of the disease with sotrovimab, remdesivir, or nirmatrelvir/ritonavir. Molnupiravir may also be used for such patients if no other clinically appropriate treatment options are available. Immunosuppressed persons with COVID-19 who are at high risk, and whose response to vaccination is expected to be reduced, ought to be treated with sotrovimab. It should be noted, however, that the clinical efficacy of sotrovimab against infections with the omicron subtype BA.2 is uncertain at the currently used dose, as the drug has displayed reduced activity against this subtype in vitro. COVID-19 patients at risk of a severe course may be offered budesonide inhalation, according to an off-label recommendation of the German College of General Practitioners and Family Physicians (other medical societies do not recommend either for or against this treatment). Thrombo - embolism prophylaxis with low-molecular-weight heparin may be given to elderly patients or those with a pre-existing illness. No recommendation is made concerning fluvoxamine or colchicine. Acetylsalicylic acid, azithromycin, ivermectin, systemic steroids, and vitamin D should not be used for the outpatient treatment of COVID-19. CONCLUSION: Drug treatment is now available for outpatients with COVID-19 in the early phase. Nearly all of the relevant trials have been conducted in unvaccinated subjects; this needs to be kept in mind in patient selection.

Dynamics and Sensitivity of Signaling Pathways.

Purpose of Review: Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets. In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer. An achievement that would facilitate the use of such models is their ability to identify controlling biochemical parameters in signaling pathways, such as molecular abundances and chemical reaction rates, because this would help determine effective points of attack by therapeutics. Recent Findings: We summarize the current state of understanding the sensitivity of phosphorylation cycles with and without sequestration. We also describe some basic properties of regulatory motifs including feedback and feedforward regulation. Summary: Although much recent work has focused on understanding the dynamics and particularly the sensitivity of signaling networks in eukaryotic systems, there is still an urgent need to build more scalable models of signaling networks that can appropriately represent their complexity across different cell types and tumors.

The association between a journal's source of revenue and the drug recommendations made in the articles it publishes.

BACKGROUND: There is evidence to suggest that pharmaceutical companies influence the publication and content of research papers. Most German physicians rely on journals for their continuing medical education. We studied the influence of pharmaceutical advertising on the drug recommendations made in articles published in 11 German journals that focus on continuing medical education. METHODS: We conducted a cross-sectional study of all of the issues of 11 journals published in 2007. Only journals frequently read by general practitioners were chosen. Issues were screened for pharmaceutical advertisements and recommendations made in the editorial content for a specified selection of drugs. Each journal was rated on a five-point scale according to the strength with which it either recommended or discouraged the use of these drugs. We looked for differences in these ratings between free journals (i.e., those financed entirely by pharmaceutical advertising), journals with mixed sources of revenue and journals financed solely by subscription fees. The journals were also screened for the simultaneous appearance of advertisements and recommendations for the same drug within a certain period, which was adjusted for both journal and class of drug. RESULTS: We identified 313 issues containing at least one advertisement for the selected drugs and 412 articles in which drug recommendations were made. Free journals were more likely to recommend the specified drugs than journals with sources of revenue that were mixed or based solely on subscriptions. The simultaneous appearance of advertisements and recommendations for the same drug in the same issue of a journal showed an inconsistent association. INTERPRETATION: Free journals almost exclusively recommended the use of the specified drugs, whereas journals financed entirely with subscription fees tended to recommend against the use of the same drugs. Doctors should be aware of this bias in their use of material published in medical journals that focus on continuing medical education.

Sensitivity to change of the Neck Pain and Disability Scale.

The Neck Pain and Disability Scale (NPAD) is a 20-item instrument to measure neck pain and related disability. The aim of this study was to assess sensitivity to change of the NPAD. A total of 411 participants from 15 general practices in the middle of Germany completed a multidimensional questionnaire including the German version of the NPAD and self-reported demographic and clinical information. Sensitivity to change was analysed by linear regression analysis of the NPAD at follow-up and educational level, age class, depression, anxiety, and deficits in social support, respectively, and by Pearson's correlation analyses between mean change in NPAD at follow-up and mean change in prognostic markers. Those having more than basic education (regression coefficient -7.2, p < 0.001) and/or being in a younger age class (-2.9, p = 0.020) consistently reported significantly lower average NPAD scores at follow-up compared to those with basic education and/or a older age class. In contrast, those who were classified to be depressed (regression coefficient 2.1, p < 0.001), anxious (1.9, p < 0.001), or having deficits in social support (5.5, p = 0.004) reported significantly higher NPAD scores. Change in depression, anxiety, and social support scale between baseline and follow-up was significantly correlated with change in the NPAD score. Hence, these data are in the direction anticipated across all baseline factors investigated. In conclusion, the NPAD seems to be a sensitive measure for use in clinical practice and future studies of neck pain and related disability.

Serum levels of interleukin-6 and interleukin-10 in relation to depression scores in patients with cardiovascular risk factors.

It is currently unknown whether elevated cytokine levels in depression are confined to any specific subgroup of depressive patients. In this study, medical out-patients presenting with cardiovascular risk factors (N = 356) were assessed for both cognitive-affective and physical symptoms of depression using the Hospital Anxiety and Depression Scale (HADS) and the Maastricht questionnaire (MQ), respectively. In study participants assigned to the highest (≥21) and lowest (≤5) quartile for the MQ score, serum levels of cytokines were measured. We found highly significant associations between cognitive-affective symptoms of depression and elevated serum levels of interleukin-6 (IL-6; ρ = .231; p = .002) and interleukin-10 (IL-10; ρ = .370; p < .001), respectively. In multiple regression models elevated IL-10 serum concentration was independently related to cognitive-affective symptoms of depression (ρ = .165; p = .002). When all cytokines were included in one model, elevated IL-10 serum concentrations remained a significant predictor for depressive mood (ρ = .157; p = .009). In patients with cardiovascular risk factors and extreme scores for vital exhaustion, elevated serum IL-6 and even more IL-10 concentrations are linked to the presence of depressive mood. Future studies will have to test whether the so far unreported association of IL-10 with depressive mood represents a causal pathway involved in the pathogenesis or in the prognostic effect of depressive mood in cardiac patients.

Symptomatic treatment (ibuprofen) or antibiotics (ciprofloxacin) for uncomplicated urinary tract infection?--results of a randomized controlled pilot trial.

BACKGROUND: Uncomplicated lower urinary tract infections (UTI) are usually treated with antibiotics. However, there is little evidence for alternative therapeutic options.This pilot study was set out 1) to make a rough estimate of the equivalence of ibuprofen and ciprofloxacin for uncomplicated urinary tract infection with regard to symptom resolution, and 2) to demonstrate the feasibility of a double-blind, randomized controlled drug trial in German general practices. METHODS: We performed a double-blind, randomized controlled pilot trial in 29 German general practices. Eighty otherwise healthy women aged 18 to 85 years, presenting with at least one of the main UTI symptoms dysuria and frequency and without any complicating factors, were randomly assigned to receive either ibuprofen 3 x 400 mg oral or ciprofloxacin 2 x 250 mg (+1 placebo) oral, both for three days.Intensity of main symptoms--dysuria, frequency, low abdominal pain--was recorded at inclusion and after 4, 7 and 28 days, scoring each symptom from 0 (none) to 4 (very strong). The primary endpoint was symptom resolution on Day 4. Secondary outcomes were the burden of symptoms on Days 4 and 7 (based on the sum score of all symptoms), symptom resolution on Day 7 and frequency of relapses. Equivalence margins for symptom burden on Day 4 were pre-specified as +/- 0.5 sum score points. Data analysis was done by intention to treat and per protocol. Randomization was carried out on patient level by computer programme in blocks of six. RESULTS: Seventy-nine patients were analyzed (ibuprofen n = 40, ciprofloxacin n = 39). On Day 4, 21/36 (58.3%) of patients in the ibuprofen-group were symptom-free versus 17/33 (51.5%) in the ciprofloxacin-group. On Day 4, ibuprofen patients reported fewer symptoms in terms of total sum score (1; SD 1,42) than ciprofloxacin patients (1,3; SD 1,9), difference -0,33 (95% CI (-1,13 to +0,47)), PP (per protocol) analysis. During Days 0 and 9, 12/36 (33%) of patients in the ibuprofen-group received secondary antibiotic treatment due to ongoing or worsening symptoms, compared to 6/33 (18%) in the ciprofloxacin-group (non significant). A total of 58 non-serious adverse events were reported, 32 in the ibuprofen group versus 26 in the ciprofloxacin group (non significant). CONCLUSIONS: Our results support the assumption of non-inferiority of ibuprofen compared to ciprofloxacin for treatment of symptomatic uncomplicated UTI, but need confirmation by further trials. TRIAL REGISTRATION NUMBER: ISRCTN00470468. See Commentary http://www.biomedcentral.com/1471-2296/11/42.

Elevated serum levels of interleukin-10 and tumor necrosis factor α [corrected] are both associated with vital exhaustion in patients with cardiovascular risk factors.

BACKGROUND: Vital exhaustion, a psychological state characterized by unusual fatigue, irritability, and feelings of demoralization, has been identified as a risk factor for cardiovascular diseases and linked to elevated levels of pro-inflammatory cytokines. OBJECTIVE: The purpose of this study was to investigate the relationship between vital exhaustion and cytokine levels in patients with cardiovascular risk factors. METHOD: The entire cohort consisted of 356 primary-care patients with cardiovascular risk factors who participated in a study of early recognition of heart failure. All participants completed the Maastricht questionnaire (MQ) for assessing vital exhaustion. Cytokine serum levels were measured in all those subjects (N=178) who were assigned to the highest and lowest quartiles of the MQ, respectively. RESULTS: We found that elevated serum concentrations of IL-6, TNFα, and IL-10, but not IL-1ß or natriuretic peptides were associated with high MQ scores indicative of vital exhaustion. Using logistic regression analyses controlling for clinical variables and Type D personality, both TNFα (multivariate odds ratio [OR] =1.86; 95%-confidence interval [CI] =1.30-2.68; p=0.001) and IL-10(OR=1.62; 95%-CI=1.15-2.28; p=0.006), but not other cytokines significantly predicted vital exhaustion independently of other clinical and laboratory parameters examined [corrected]. CONCLUSION: The subjective state of vital exhaustion is linked to a substantial alteration in the pattern of secreted cytokines. Data suggest that a disturbance in the levels of both pro-inflammatory and anti-inflammatory mediators, rather than isolated stimulation by pro-inflammatory cytokines, is associated with the mental and physical changes of vital exhaustion.

Appropriateness of treatment recommendations for PPI in hospital discharge letters.

PURPOSE: The reasons for the dramatic increase in proton pump inhibitors (PPI) prescriptions remain unclear and cannot be explained solely by increased morbidity, new indications or a decrease in alternative medication. Inappropriate use and discharge recommendations in hospitals are considered to be possible explanations. As the quality of PPI recommendations in hospital discharge letters in Germany has not been investigated to date, we have studied the appropriateness of these referrals. METHODS: Hospital discharge letters with recommendations for PPI medication from 35 primary care practices in the county of Mecklenburg-Western Pomerania (MV; North-east Germany) were collected and analysed, and the appropriateness of the PPI indication was rated. RESULTS: No information justifying the recommendation for continuous PPI medication could be identified in 54.5% of the discharge letters; in 12.7%, the indication was uncertain, and in 32.7%, we found an evidence-based indication for PPI medication. The most common indication for adequate PPI use was nonsteroidal anti-inflammatory drug-prophylaxis in high-risk patients. CONCLUSIONS: Inadequate recommendations for PPIs in discharge letters are frequent. This may lead to a continuation of this therapy in primary care, thereby unnecessarily increasing polypharmacy and the risk of adverse events as well as burdening the public health budget. Hospitals should therefore critically review recommendations for PPI medication and the dosage thereof in their discharge letters and clearly document the reason for PPI use and the need for continuous prescription in primary care.

A Probabilistic Approach to Explore Signal Execution Mechanisms With Limited Experimental Data.

Mathematical models of biochemical reaction networks are central to the study of dynamic cellular processes and hypothesis generation that informs experimentation and validation. Unfortunately, model parameters are often not available and sparse experimental data leads to challenges in model calibration and parameter estimation. This can in turn lead to unreliable mechanistic interpretations of experimental data and the generation of poorly conceived hypotheses for experimental validation. To address this challenge, we evaluate whether a Bayesian-inspired probability-based approach, that relies on expected values for quantities of interest calculated from available information regarding the reaction network topology and parameters can be used to qualitatively explore hypothetical biochemical network execution mechanisms in the context of limited available data. We test our approach on a model of extrinsic apoptosis execution to identify preferred signal execution modes across varying conditions. Apoptosis signal processing can take place either through a mitochondria independent (Type I) mode or a mitochondria dependent (Type II) mode. We first show that in silico knockouts, represented by model subnetworks, successfully identify the most likely execution mode for specific concentrations of key molecular regulators. We then show that changes in molecular regulator concentrations alter the overall reaction flux through the network by shifting the primary route of signal flow between the direct caspase and mitochondrial pathways. Our work thus demonstrates that probabilistic approaches can be used to explore the qualitative dynamic behavior of model biochemical systems even with missing or sparse data.