Jan Willem Bikker

Targeted therapy aims to block tumor-driving signaling pathways and is generally based on analysis of one primary tumor (PT) biopsy. Tumor heterogeneity within PT and between PT and metastatic breast lesions may, however, impact the effect of a chosen therapy. Whereas studies are available that investigate genetic heterogeneity, we present results on phenotypic heterogeneity by analyzing the variation in the functional activity of signal transduction pathways, using an earlier developed platform to measure such activity from mRNA measurements of pathways’ direct target genes. Statistical analysis comparing macro-scale variation in pathway activity on up to five spatially distributed PT tissue blocks (n = 35), to micro-scale variation in activity on four adjacent samples of a single PT tissue block (n = 17), showed that macro-scale variation was not larger than micro-scale variation, except possibly for the PI3K pathway. Simulations using a “checkerboard clone-size” model showed that multiple small clones could explain the higher micro-scale variation in activity found for the TGFβ and Hedgehog pathways, and that intermediate/large clones could explain the possibly higher macro-scale variation of the PI3K pathway. While within PT, pathway activities presented a highly positive correlation, correlations weakened between PT and lymph node metastases (n = 9), becoming even worse for PT and distant metastases (n = 9), including a negative correlation for the ER pathway. While analysis of multiple sub-samples of a single biopsy may be sufficient to predict PT response to targeted therapies, metastatic breast cancer treatment prediction requires analysis of metastatic biopsies. Our findings on phenotypic intra-tumor heterogeneity are compatible with emerging ideas on a Big Bang type of cancer evolution in which macro-scale heterogeneity appears not dominant.

It is known that quantitative measures for the reliability of software systems can be derived from software reliability models, and, as such, support the product development process. Over the past four decades, research activities in this area have been performed. As a result, many software reliability models have been proposed. It was shown that, once these models reach a certain level of convergence, it can enable the developer to release the software and stop software testing accordingly. Criteria to determine the optimal testing time include the number of remaining errors, failure rate, reliability requirements, or total system cost. In this paper, we present our results in predicting the reliability of software for agile testing environments. We seek to model this way of working by extending the Jelinski–Moranda model to a “stack” of feature-specific models, assuming that the bugs are labeled with the features they belong to. In order to demonstrate the extended model, two use cases are presented. The questions to be answered in these two cases are: how many software bugs remain in the software and should one decide to stop testing the software?

Aims: To assess the impact of periodontal treatment on systemic inflammation in type 2 diabetes.Materials and Methods: Adults with type 2 diabetes (n = 83) and without diabetes (controls, n = 75) were recruited, and participants with periodontitis received periodontal treatment and 12 months’ follow‐up. Biomarkers for periodontal inflammation (gingival crevicular fluid interleukin‐6, tumour necrosis factor‐α, interleukin‐1β, interferon‐γ, matrix metalloproteinase‐8, matrix metalloproteinase‐9, adiponectin) and serum markers of inflammation and diabetes control (glycated haemoglobin, high sensitivity C‐reactive protein, interleukin‐6, tumour necrosis factor‐α, interleukin‐1β, interferon‐γ, leptin, adiponectin) were measured. Structural equation modelling was used to evaluate periodontal treatment effects on oral and systemic inflammation.Results: Periodontal treatment resulted in significant improvements in clinical status and reductions in gingival crevicular fluid biomarkers from baseline to month 12. Structural equation modelling identified that, at baseline, individuals with diabetes and periodontitis had significantly higher systemic inflammation than non‐diabetic controls with periodontitis (Δ = 0.20, p = .002), with no significant differences between groups for oral inflammation. There was a greater reduction in systemic inflammation following periodontal treatment in individuals with diabetes and periodontitis compared to those with periodontitis but not diabetes (Δ = −0.25, p = .01).Conclusions: Diabetes and periodontitis together appear to increase systemic inflammation, with evidence of reductions following periodontal treatment.

Analyzing heart rate variability (HRV) in preterm infants can help track maturational changes and subclinical signatures of disease. We conducted an observational study to characterize the effect of demographic and cardiorespiratory factors on three features of HRV using a linear mixed-effects model. HRV-features were tailored to capture the unique physiology of preterm infants, including the contribution of transient pathophysiological heart rate (HR) decelerations. Infants were analyzed during stable periods in the incubator and subsequent sessions of Kangaroo care (KC) – an intervention that increases comfort. In total, 957 periods in the incubator and during KC were analyzed from 66 preterm infants. Our primary finding was that gestational age (GA) and postmenstrual age (PMA) have the largest influence on HRV while the HR and breathing rate have a considerably smaller effect. Birth weight and gender do not affect HRV. We identified that with increasing GA and PMA, overall HRV decreased and increased respectively. Potentially these differences can be attributed to distinct trajectories of intra- and extrauterine development. With increasing GA, the propensity towards severe HR decelerations decreases, thereby reducing overall variability, while with increasing PMA, the ratio of decelerations and accelerations approaches unity, increasing overall HRV.

589 Background: Treatment with targeted drugs aims to block tumor driving signaling pathway(s). Drug choice is often based on a single preoperative primary breast cancer biopsy. It is important that biopsied cancer tissue is representative for the primary tumor (PT) or metastases to treat. Little is known about pathway heterogeneity within the PT, and between PT and metastatic tumors. A novel analysis method was developed to identify and quantify activity of signal transduction pathways in cancer tissue, based on Bayesian models that infer a pathway activity score from transcription factor target gene mRNA levels (Cancer Res 2014;74:2936-45). Methods: Pathway analysis, originally developed for AffymetrixU133Plus2.0, was adapted to RT-qPCR for use on formalin fixed paraffin embedded tissue. Estrogen (ER) and androgen (AR) receptor, PI3K, Hedgehog (HH), TGFβ and Wnt pathway activities were analyzed. Samples were from multiple locations (“quadrants”) in 15 luminal A, 9 luminal B, and 8 ER-negative primary breast cancers; from subdivided quadrant samples (4 “subquadrants”) of respectively 9, 4, and 4 PTs; and from 13 distant and 24 lymph node (LN) metastases of respectively 9 and 7 matched luminal PTs. Analysis of pathway activity score (PAS) variance was performed with linear mixed models with subgroup-dependent standard deviations. Results: In primary breast cancer intra-tumor PAS variance was not larger at macroscale (“quadrant”) than at microscale (“subquadrant”). For ER, AR, HH, and Wnt pathways, PAS variation was higher between distant metastases and PT than within the PT (p < 0.0002). For HH and Wnt pathways, PAS variation was higher between LN metastases than within the PT (p < 0.002). Correlation between primary and metastatic pathway activities ranged from -0.34 for ER to 0.47/0.50 for TGFβ/HH pathways. Conclusions: A single location tissue sample was representative for the whole primary tumor with respect to signaling pathway activity, suggesting one biopsy as generally sufficient for (neo)adjuvant therapy choice. Pathway activities varied between primary cancer and metastases, indicating the necessity of metastatic sample analysis (biopsies or liquid biopsy) to improve therapy choice.

Light sources attract nocturnal flying insects, but some lamps attract more insects than others. The relation between the properties of a light source and the number of attracted insects is, however, poorly understood. We developed a model to quantify the attractiveness of light sources based on the spectral output. This model is fitted using data from field experiments that compare a large number of different light sources. We validated this model using two additional datasets, one for all insects and one excluding the numerous Diptera. Our model facilitates the development and application of light sources that attract fewer insects without the need for extensive field tests and it can be used to correct for spectral composition when formulating hypotheses on the ecological impact of artificial light. In addition, we present a tool allowing the conversion of the spectral output of light sources to their relative insect attraction based on this model.

Interactive Journal of Medical Research

Background and Objective: Though devices for hair growth based on low levels of light have shown encouraging results, further improvements of their efficacy is impeded by a lack of knowledge on the exact molecular targets that mediate physiological response in skin and hair follicle. The aim of this study was to investigate the expression of selected light‐sensitive receptors in the human hair follicle and to study the impact of UV‐free blue light on hair growth ex vivo.Material and Methods: The expression of Opsin receptors in human skin and hair follicles has been characterized using RT‐qPCR and immunofluorescence approaches. The functional significance of Opsin 3 was assessed by silencing its expression in the hair follicle cells followed by a transcriptomic profiling. Proprietary LED‐based devices emitting two discrete visible wavelengths were used to access the effects of selected optical parameters on hair growth ex vivo and outer root sheath cells in vitro.Results: The expression of OPN2 (Rhodopsin) and OPN3 (Panopsin, Encephalopsin) was detected in the distinct compartments of skin and anagen hair follicle. Treatment with 3.2 J/cm² of blue light with 453 nm central wavelength significantly prolonged anagen phase in hair follicles ex vivo that was correlated with sustained proliferation in the light‐treated samples. In contrast, hair follicle treatment with 3.2 J/cm² of 689 nm light (red light) did not significantly affect hair growth ex vivo. Silencing of OPN3 in the hair follicle outer root sheath cells resulted in the altered expression of genes involved in the control of proliferation and apoptosis, and abrogated stimulatory effects of blue light (3.2 J/cm²; 453 nm) on proliferation in the outer root sheath cells.Conclusions: We provide the first evidence that (i) OPN2 and OPN3 are expressed in human hair follicle, and (ii) A 453 nm blue light at low radiant exposure exerts a positive effect on hair growth ex vivo, potentially via interaction with OPN3. Lasers Surg. Med. 49:705–718, 2017.

BACKGROUND Many preterm infants require enteral feeding as they cannot coordinate sucking, swallowing, and breathing. In enteral feeding, milk feeds are delivered through a small feeding tube passed via the nose or mouth into the stomach. Intermittent milk feeds may either be administered using a syringe to gently push milk into the infant’s stomach (push feed) or milk can be poured into a syringe attached to the tube and allowed to drip in by gravity (gravity feed). This practice of enteral feeding is common in neonatal intensive care units. There is, however, no evidence in the literature to recommend the use of one method of feeding over the other. OBJECTIVE The aim of this study was to investigate which of the two methods of feeding is physiologically better tolerated by infants, as measured by the incidence of critical cardiorespiratory alarms during and immediately after feeding. METHODS We conducted a prospectively designed observational study with records of all feeding episodes in infants of gestational age less than 30 weeks at birth and with a minimum enteral intake of 100 mL/kg/day. In total, 2140 enteral feeding episodes were noted from 25 infants over 308 infant-days with records for several characteristics of the infants (eg, gestational age), feeding (eg, the position of infants), and of nursing-care events before feeding (eg, diapering). Logistic regression with mixed effects was used to model cardiorespiratory alarms for the push and gravity methods of feeding. RESULTS After adjustments were made for all confounding variables, the position of infants was found to be statistically significant in changing the outcome of critical alarms for the two methods of feeding (P=.02). For infants in the lateral position, push feeds led to 40% more instances of one or more critical cardiorespiratory alarms in comparison with the gravity method. Both methods of feeding created a statistically comparable number of alarms for infants in the prone position. CONCLUSIONS This study provides objective data that may assist in optimizing enteral feeding protocols for premature infants. The incidence of critical cardiorespiratory alarms for infants in the lateral position can be lowered by the use of gravity instead of push feeding. No differences were observed between the two types of feeding when infants were in the prone position.

Evaluate the short-term clinical efficacy of high-frequency, high-amplitude sonic powered toothbrushes compared to manual toothbrushes on plaque removal and gingivitis reduction in everyday use through a meta-analysis of randomized controlled trials. Embase, MEDLINE, BIOSIS, Inspec, PQ SciTech, Compendex, SciSearch and IADR abstracts databases were searched. Eligible were clinical trials comparing at least one manual to one sonic powered toothbrush on plaque or gingivitis reduction over four weeks to three months in subjects without disability that could affect tooth brushing. Two authors selected and extracted data from eligible studies. When insufficient information was available, researchers were contacted. Data were pooled using random-effects models to compute standardized mean differences (SMD) and 95% confidence intervals (95% CI) quantifying differences in plaque or gingivitis reduction. Risk for bias and sources of heterogeneity were assessed. The combined results of 18 studies comprising 1,870 subjects showed that sonic powered toothbrushes had statistically significantly greater plaque removal (SMD = -0.89, 95%CI = [-1.27, -0.51]) and gingivitis reduction (-0.67, [-1.01, -0.32]). Heterogeneity was large and bias was not apparent. High-frequency, high-amplitude sonic powered toothbrushes decreased plaque and gingivitis significantly more effectively than manual toothbrushes in everyday use in studies lasting up to three months.