Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization

The overdetermination of the mathematical problem underlying ptychography is reduced by a host of experimentally more desirable settings. Furthermore, reconstruction of the sample-induced phase shift is typically limited by uncertainty in the experimental parameters and finite sample thicknesses. Presented is a conjugate gradient descent algorithm, regularized optimization for ptychography (ROP), that recovers the partially known experimental parameters along with the phase shift, improves resolution by incorporating the multislice formalism to treat finite sample thicknesses, and includes regularization in the optimization process, thus achieving reliable results from noisy data with severely reduced and underdetermined information.Comment: 18 pages, 7 figures, 3 table

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

<p>Abstract</p> <p>Background</p> <p>Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on transcriptional regulation. Steady-state chemostat cultures, which do enable accurate control, measurement and manipulation of individual cultivation parameters (e.g. specific growth rate, temperature, identity of the growth-limiting nutrient) appear to provide a promising experimental platform for such a combinatorial analysis.</p> <p>Results</p> <p>A microarray compendium of 170 steady-state chemostat cultures of the yeast <it>Saccharomyces cerevisiae </it>is presented and analyzed. The 170 microarrays encompass 55 unique conditions, which can be characterized by the combined settings of 10 different cultivation parameters. By applying a regression model to assess the impact of (combinations of) cultivation parameters on the transcriptome, most <it>S. cerevisiae </it>genes were shown to be influenced by multiple cultivation parameters, and in many cases by combinatorial effects of cultivation parameters. The inclusion of these combinatorial effects in the regression model led to higher explained variance of the gene expression patterns and resulted in higher function enrichment in subsequent analysis. We further demonstrate the usefulness of the compendium and regression analysis for interpretation of shake-flask-based transcriptome studies and for guiding functional analysis of (uncharacterized) genes and pathways.</p> <p>Conclusion</p> <p>Modeling the combinatorial effects of environmental parameters on the transcriptome is crucial for understanding transcriptional regulation. Chemostat cultivation offers a powerful tool for such an approach.</p

Thiopurine metabolite levels in patients with atopic dermatitis and/or chronic hand/foot eczema treated with azathioprine

Background: Azathioprine is frequently used in severe eczema. It is converted in the liver into active metabolites, including 6-thioguanine nucleotide (6-TGN) and methylated 6-methylmercaptopurine (6-MMP). In the past, the therapeutic potential of azathioprine may have not been fully utilized. Recent investigations on inflammatory bowel disease have led to a better understanding of azathioprine metabolism and optimizing treatment. Objective: To investigate whether measuring thiopurine metabolites in circulation can improve the effectiveness and safety of azathioprine treatment in patients with atopic dermatitis and/or chronic hand/foot eczema. Methods: Azathioprine metabolite levels were measured in eczema patients during maintenance treatment (Part I) and dose escalation (Part II). Clinical effectiveness, hepatotoxicity, and bone marrow suppression were analyzed and TPMT genotype was assessed. Results: A wide variation in metabolite levels in all dose groups was observed. In Part I (32 patients), there were no significant differences in 6-TGN levels between clinical responders and non-responders (p = .806). No hepatoxicity or myelotoxicity was observed. In Part II, all 6-TGN and 6-MMP levels increased during dose escalation. Hypermethylation was observed in 2/8 patients. Conclusion: For individual eczema patients treated with azathioprine, routinely measuring 6-TGN and 6-MMP can be helpful in optimizing azathioprine dose, improving clinical effectiveness, and preventing side effects

Extravasation of an antibody-drug conjugate: A case report of epidermal necrosis after trastuzumab-emtansine extravasation

WHAT IS KNOWN AND OBJECTIVE: Trastuzumab-emtansine is an antibody-drug conjugate developed to decrease off-target toxicity. According to the product label, reactions secondary to extravasation are mild or moderate. CASE SUMMARY: We report on a 51-year-old woman who developed epidermal necrosis after extravasation of trastuzumab-emtansine, which required surgical intervention. Six weeks later, the lesions were healed with residual hyperpigmentation. WHAT IS NEW AND CONCLUSION: We describe the course of a case of severe toxicity following trastuzumab-emtansine extravasation. We provide treatment recommendations and recommend amending the information on the product label on extravasation

Predicting therapy response to mycophenolic acid using UGT1A9 genotyping: towards personalized medicine in atopic dermatitis

Atopic dermatitis (AD) is a very common chronic inflammatory skin disease requiring long-term treatment. Mycophenolic acid (MPA) is used off-label in treatment of patients with severe AD failing Cyclosporin A (CsA) treatment, however clinical efficacy is observed in only half of the AD patients. In blood, MPA levels are known to have a large interindividual variability. Low MPA exposure and increased enzyme activity correlates with the presence of UGT1A9 polymorphisms. In this retrospective study, 65 adult AD patients treated with MPA were classified as responder or non-responder to MPA treatment. UGT1A9 polymorphisms were determined using PCR. A significantly higher number of UGT1A9 polymorphisms was found in the group that did not respond to MPA treatment. Of the patients that carried a UGT1A9 polymorphism, 85.7% were non-responsive to MPA treatment. This implies that non-responsiveness in AD patients is more likely to occur in carriers of a UGT1A9 polymorphism. In a binary logistic regression analysis the odds ratio (OR) was 8.65 (95% confidence interval: 0.93–80.17). Our results show that UGT1A9 polymorphisms can be used to identify patients with non-responsiveness to MPA. Patients with UGT1A9 polymorphisms might benefit from higher MPA dosage

Mixed volatility in a single device: memristive non-volatile and threshold switching in SmNiO3/BaTiO3 devices

Analog neuromorphic circuits use a range of volatile and non-volatile memristive effects to mimic the functionalities of neurons and synapses. Creating devices with combined effects is important for reducing the footprint and power consumption of neuromorphic circuits. This work presents an epitaxial SmNiO3/BaTiO3 electrical device that displays non-volatile memristive switching to either allow or block access to a volatile threshold switching regime. This behavior arises from coupling the BaTiO3 ferroelectric polarization to SmNiO3 metal–insulator transition; the polarization in the BaTiO3 layer that is in contact with the SmNiO3 layer modifies the device resistance continuously in a controllable, non-volatile manner. Additionally, the polarization state varies the threshold voltage at which the Joule-heating-driven insulator-to-metal phase transition occurs in the nickelate, which results in a negative differential resistance curve and produces a sharp, volatile threshold switch. Reliable current oscillations with stable frequencies, large amplitude, and a relatively low driving voltage are demonstrated when the device is placed in a Pearson–Anson-like circuit

Phenobarbital, Midazolam Pharmacokinetics, Effectiveness, and Drug-Drug Interaction in Asphyxiated Neonates Undergoing Therapeutic Hypothermia

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Unintentional guideline deviations in hospitalized patients with two or more antithrombotic agents:an intervention study

Purpose Treatment schedules for antithrombotic therapy are complex, and there is a risk of inappropriate prescribing or continuation of antithrombotic therapy beyond the intended period of time. The primary aim of this study was to determine the frequency of unintentional guideline deviations in hospitalized patients. Secondary aims were to determine whether the frequency of unintentional guideline deviations decreased after intervention by a pharmacist, to determine the acceptance rate of the interventions and to determine the type of interventions. Methods We performed a non-controlled prospective intervention study in three teaching hospitals in the Netherlands. We examined whether hospitalized patients who used the combination of an anticoagulant plus at least one other antithrombotic agent had an unintentional guideline deviation. In these cases, the hospital pharmacist contacted the physician to assess whether this deviation was intentional. If the deviation was unintentional, a recommendation was provided how to adjust the antithrombotic regimen according to guideline recommendations. Results Of the 988 included patients, 407 patients had an unintentional guideline deviation (41.2%). After intervention, this was reduced to 22 patients (2.2%) (p < 0.001). The acceptance rate of the interventions was 96.6%. The most frequently performed interventions were discontinuation of an low molecular weight heparin in combination with a direct oral anticoagulant and discontinuation of an antiplatelet agent when there was no indication for the combination of an antiplatelet agent and an anticoagulant. Conclusion A significant number of hospitalized patients who used an anticoagulant plus one other antithrombotic agent had an unintentional guideline deviation. Intervention by a pharmacist decreased unintentional guideline deviations

Artificial intelligence exceeds humans in epidemiological job coding

BACKGROUND: Work circumstances can substantially negatively impact health. To explore this, large occupational cohorts of free-text job descriptions are manually coded and linked to exposure. Although several automatic coding tools have been developed, accurate exposure assessment is only feasible with human intervention. METHODS: We developed OPERAS, a customizable decision support system for epidemiological job coding. Using 812,522 entries, we developed and tested classification models for the Professions et Catégories Socioprofessionnelles (PCS)2003, Nomenclature d'Activités Française (NAF)2008, International Standard Classifications of Occupation (ISCO)-88, and ISCO-68. Each code comes with an estimated correctness measure to identify instances potentially requiring expert review. Here, OPERAS' decision support enables an increase in efficiency and accuracy of the coding process through code suggestions. Using the Formaldehyde, Silica, ALOHA, and DOM job-exposure matrices, we assessed the classification models' exposure assessment accuracy. RESULTS: We show that, using expert-coded job descriptions as gold standard, OPERAS realized a 0.66-0.84, 0.62-0.81, 0.60-0.79, and 0.57-0.78 inter-coder reliability (in Cohen's Kappa) on the first, second, third, and fourth coding levels, respectively. These exceed the respective inter-coder reliability of expert coders ranging 0.59-0.76, 0.56-0.71, 0.46-0.63, 0.40-0.56 on the same levels, enabling a 75.0-98.4% exposure assessment accuracy and an estimated 19.7-55.7% minimum workload reduction. CONCLUSIONS: OPERAS secures a high degree of accuracy in occupational classification and exposure assessment of free-text job descriptions, substantially reducing workload. As such, OPERAS significantly outperforms both expert coders and other current coding tools. This enables large-scale, efficient, and effective exposure assessment securing healthy work conditions

Fourth Human Parechovirus Serotype

We identified a novel human parechovirus (HPeV) type (K251176-02) from a neonate with fever. Analysis of the complete genome showed K251176-02 to be a new HPeV genotype. Since K251176-02 could not be neutralized with antibodies against known HPeV serotypes 1–3, it should be classified as a fourth HPeV serotype