Effects of 1,25 Dihydroxyvitamin D3 and Calcium on Growth and Differentiation and on c-fos and p53 Gene Expression in Normal Human Keratinocytes

Calcium enhances keratinocyte differentiation, and 1,25 dihydroxyvitamin D3 (1,25(OH)2D3) is both antiproliferative and prodifferentiative in many cell types, including normal human keratinocytes. In the present study, we examined the combined effects of calcium and 1,25(OH)2D3 on parameters of growth and differentiation and on c-fos and p53 gene expression in normal human keratinocytes. Exposure of normal human keratinocytes to 1,25(OH)2D3 markedly reduced [3H] thymidine incorporation and cell number at low and high medium Ca++ concentrations. Simultaneously, cells in the G0/G1 phase of the cell cycle increased significantly and those in the S phase fell precipitously. l,25(OH)2D3 and calcium also induced keratinocyte differentiation independently, as assessed by iminuno- cytochemistry and by induction of involucrin mRNA. Both Ca++ and 1,25(OH)2D3 were shown, by nuclear run-on assays, to increase involucrin gene transcription. A rapid, transient elevation in c-fos protooncogene expression preceded these effects when epidermal growth factor was present alone. When 1,25(OH)2D3 was added to quiescent keratinocytes, there was a marked augmentation of c-fos mRNA accumulation at low and high medium Ca++ concentrations. Varying medium Ca++ concentrations had no effect on c-fos mRNA levels. Increasing medium Ca++ concentrations from 0.15 to 2.0mM produced marked elevations of p53 mRNA accumulation and of the rate of p53 gene transcription, whereas 1,25(OH)2D3 had no effect.These results, therefore, suggest that 1,25(OH)2D3 and calcium act in concert to modulate the expression of two important cell-cycle-associated genes, which may be important components in the initial programming of growth and differentiation of normal human keratinocytes

Collaborative hyperparameter tuning

International audienceHyperparameter learning has traditionally been a manual task because of the limited number of trials. Today's computing infrastructures allow bigger evaluation budgets, thus opening the way for algorithmic approaches. Recently, surrogate-based optimization was successfully applied to hyperparameter learning for deep belief networks and to WEKA classifiers. The methods combined brute force computational power with model building about the behavior of the error function in the hyperparameter space, and they could significantly improve on manual hyperparameter tuning. What may make experienced practitioners even better at hyperparameter optimization is their ability to generalize across similar learning problems. In this paper, we propose a generic method to incorporate knowledge from previous experiments when simultaneously tuning a learning algorithm on new problems at hand. To this end, we combine surrogate-based ranking and optimization techniques for surrogate-based collaborative tuning (SCoT). We demonstrate SCoT in two experiments where it outperforms standard tuning techniques and single-problem surrogate-based optimization

Extreme compass and Dynamic Multi-Armed Bandits for Adaptive Operator Selection

The goal of adaptive operator selection is the on-line control of the choice of variation operators within evolutionary algorithms. The control process is based on two main components, the credit assignment, that defines the reward that will be used to evaluate the quality of an operator after it has been applied, and the operator selection mechanism, that selects one operator based on some operators qualities. Two previously developed adaptive operator selection methods are combined here: Compass evaluates the performance of operators by considering not only the fitness improvements from parent to offspring, but also the way they modify the diversity of the population, and their execution time; dynamic multi-armed bandit proposes a selection strategy based on the well-known UCB algorithm, achieving a compromise between exploitation and exploration, while nevertheless quickly adapting to changes. Tests with the proposed method, called ExCoDyMAB, are carried out using several hard instances of the satisfiability problem (SAT). Results show the good synergetic effect of combining both approaches

Investigating the association of rs2910164 with cancer predisposition in an Irish cohort.

IntroductionMicroRNAs (miRNAs) are small noncoding RNA molecules that exert post-transcriptional effects on gene expression by binding with cis-regulatory regions in target messenger RNA (mRNA). Polymorphisms in genes encoding miRNAs or in miRNA-mRNA binding sites confer deleterious epigenetic effects on cancer risk. miR-146a has a role in inflammation and may have a role as a tumour suppressor. The polymorphism rs2910164 in the MIR146A gene encoding pre-miR-146a has been implicated in several inflammatory pathologies, including cancers of the breast and thyroid, although evidence for the associations has been conflicting in different populations. We aimed to further investigate the association of this variant with these two cancers in an Irish cohort.MethodsThe study group comprised patients with breast cancer (BC), patients with differentiated thyroid cancer (DTC) and unaffected controls. Germline DNA was extracted from blood or from saliva collected using the DNA Genotek Oragene 575 collection kit, using crystallisation precipitation, and genotyped using TaqMan-based PCR. Data were analysed using SPSS, v22.ResultsThe total study group included 1516 participants. This comprised 1386 Irish participants; 724 unaffected individuals (controls), 523 patients with breast cancer (BC), 136 patients with differentiated thyroid cancer (DTC) and three patients with dual primary breast and thyroid cancer. An additional cohort of 130 patients with DTC from the South of France was also genotyped for the variant. The variant was detected with a minor allele frequency (MAF) of 0.19 in controls, 0.22 in BC and 0.27 and 0.26 in DTC cases from Ireland and France, respectively. The variant was not significantly associated with BC (per allele odds ratio = 1.20 (0.98-1.46), P  = 0.07), but was associated with DTC in Irish patients (per allele OR = 1.59 (1.18-2.14), P = 0.002).ConclusionThe rs2910164 variant in MIR146A is significantly associated with DTC, but is not significantly associated with BC in this cohort

Scaling Analysis of Affinity Propagation

We analyze and exploit some scaling properties of the Affinity Propagation (AP) clustering algorithm proposed by Frey and Dueck (2007). First we observe that a divide and conquer strategy, used on a large data set hierarchically reduces the complexity ${\cal O}(N^2)$ to ${\cal O}(N^{(h+2)/(h+1)})$, for a data-set of size $N$ and a depth $h$ of the hierarchical strategy. For a data-set embedded in a $d$-dimensional space, we show that this is obtained without notably damaging the precision except in dimension $d=2$. In fact, for $d$ larger than 2 the relative loss in precision scales like $N^{(2-d)/(h+1)d}$. Finally, under some conditions we observe that there is a value $s^*$ of the penalty coefficient, a free parameter used to fix the number of clusters, which separates a fragmentation phase (for $s<s^*$) from a coalescent one (for $s>s^*$) of the underlying hidden cluster structure. At this precise point holds a self-similarity property which can be exploited by the hierarchical strategy to actually locate its position. From this observation, a strategy based on \AP can be defined to find out how many clusters are present in a given dataset.Comment: 28 pages, 14 figures, Inria research repor

A phase I/II study of irinotecan when added to 5-fluorouracil and leucovorin and pelvic radiation in locally advanced rectal cancer: a Colorectal Clinical Oncology Group Study

The objective of this study was to evaluate the maximum tolerated dose (MTD) and recommended dose of irinotecan administered as a 5-day schedule synchronously with 5-fluorouracil (5FU), leucovorin (LV) and preoperative pelvic radiation (45 Gy) for primary borderline/unresectable, locally advanced rectal cancer. The study used escalating doses of intravenous irinotecan (6, 8, 10, 12, 14, 16, 18, and 20 mg m−2) administered on days 1–5 and 29–33 followed by low dose LV (20 mg m−2) and 5FU (350 mg m−2 over 1 h) in sequential cohorts. Preoperative pelvic radiotherapy using a three- or four-field technique and megavoltage photons comprised 45 Gy given in 25 fractions, 1.8 Gy per fraction. Surgery in the form of mesorectal excision was performed 6–10 weeks later. Histopathological examination of the resected specimen was performed according to techniques of Quirke, and compared with clinical staging. A distance of 1 mm or less between the peripheral extent of the tumour and the radial resection margin defined an involved circumferential resection margin (CRM). The MTD was determined as the dose causing more than a third of patients to have a dose-limiting toxicity (DLT) defined as specific grade 3 or 4 toxicities. Once the MTD was reached, a further 14 patients were treated at the dose level below the MTD. In total, 57 patients received irinotecan at the eight dose levels. The final cohort reached DLT after only four patients had been enrolled. The median age was 62 years (range 26–75), 37 male and 20 female subjects. The MTD of irinotecan in this schedule was 20 mg m−2 when three out of four patients experienced DLT. Dose limiting grade 3 or 4 diarrhoea was reported in seven out of 57 patients, three at the 20 mg m−2 dose level. Serious haematological toxicity (grade 3) was minimal and reported in only three patients; one grade 3 neutropaenia, one grade 4 neutropaenia and one grade 3 febrile neutropaenia and anaemia. Compliance was good with 93 and 89% of patients completing radiotherapy and chemotherapy, respectively. The remaining patients had only minor deviations from protocol therapy. Eight patients did not proceed to surgery, in six cases because they remained unresectable or had developed metastatic disease, one patient was unfit for surgery and one died as a result of complications from radiotherapy. Forty-nine patients underwent a potentially curative surgical resection. Histopathological examination of the resected specimen demonstrated pCR 12 out of 49 (24%) and 12 out of 57 (21%) overall. A histologically confirmed clear circumferential resection margin (CRM) was achieved in 39 out of 49 (80%) of those resected, and 39 out of 57 (68%) overall. In conclusion, MTD with this scheduled regimen of irinotecan is 20 mg m−2 (days 1–5 and 29–33). The acceptable toxicity and compliance at 18 mg m−2 recommend testing this dose in future phase III studies. The tumour downstaging and complete resection rates (negative CRM) are encouragingly high for this very locally advanced group

Factors predictive of lymph node metastasis in the follicular variant of papillary thyroid carcinoma

BACKGROUND: The treatment of papillary thyroid carcinomas larger than 1 cm usually consists of total thyroidectomy and central lymph node dissection (LND). In patients with the follicular variant of papillary thyroid carcinoma (FVPTC), preoperative cytology and intraoperative frozen-section analysis cannot always establish the diagnosis. The aim of this study was to evaluate predictive factors for lymph node metastasis in patients with FVPTC and to identify patients who might benefit from LND. METHODS: The study included patients with FVPTC treated by total thyroidectomy and LND between 2000 and 2010 in four departments. When fewer than six non-involved lymph nodes were removed, the patient was excluded from the analysis. RESULTS: Some 199 patients were included. The median tumour size was 17 (range 1-85) mm, and tumours were classified as T1a in 28 patients, T1b in 40, T2 in 53, and T3 in 78. Eighty-one patients (40·7 per cent) had lymph node metastasis (51 classified as N1a and 30 as N1b). Four risk factors were predictive of lymph node metastasis in the multivariable analysis: multifocality (odds ratio (OR) 2·36, 95 per cent confidence interval 1·15 to 4·86), angiolymphatic invasion (OR 3·67, 1·01 to 13·36), absence of tumour capsule (OR 3·00, 1·47 to 6·14) and tumour involvement of perithyroid tissue (OR 3·89, 1·85 to 8·18). The rate of lymph node metastasis varied between 14 and 94 per cent depending on the presence of risk factors. CONCLUSION: The rate of lymph node metastasis in patients with FVPTC varies widely according to the presence or absence of predictive risk factors