Methylation data imputation performances under different representations and missingness patterns.

BACKGROUND: High-throughput technologies enable the cost-effective collection and analysis of DNA methylation data throughout the human genome. This naturally entails missing values management that can complicate the analysis of the data. Several general and specific imputation methods are suitable for DNA methylation data. However, there are no detailed studies of their performances under different missing data mechanisms -(completely) at random or not- and different representations of DNA methylation levels (ß and M-value). RESULTS: We make an extensive analysis of the imputation performances of seven imputation methods on simulated missing completely at random (MCAR), missing at random (MAR) and missing not at random (MNAR) methylation data. We further consider imputation performances on the popular ß- and M-value representations of methylation levels. Overall, ß-values enable better imputation performances than M-values. Imputation accuracy is lower for mid-range ß-values, while it is generally more accurate for values at the extremes of the ß-value range. The MAR values distribution is on the average more dense in the mid-range in comparison to the expected ß-value distribution. As a consequence, MAR values are on average harder to impute. CONCLUSIONS: The results of the analysis provide guidelines for the most suitable imputation approaches for DNA methylation data under different representations of DNA methylation levels and different missing data mechanisms.

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform.

INTRODUCTION: Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability. MATERIAL AND METHODS: To systematically investigate the effect of pre-processing on meta-analysis, we analysed four different collections of DNA methylation samples (datasets), each composed of two subsets, for which raw data from controls (i.e. healthy subjects) and cases (i.e. patients) are available. We pre-processed the data from each dataset with nine among the most common pipelines found in literature. Moreover, we evaluated the performance of regRCPqn, a modification of the RCP algorithm that aims to improve data consistency. For each combination of pre-processing (9 × 9), we first evaluated the between-sample variability among control subjects and, then, we identified genomic positions that are differentially methylated between cases and controls (differential analysis). RESULTS AND CONCLUSION: The pre-processing of DNA methylation data affects both the between-sample variability and the loci identified as differentially methylated, and the effects of pre-processing are strongly dataset-dependent. By contrast, application of our renormalization algorithm regRCPqn: (i) reduces variability and (ii) increases agreement between meta-analysed datasets, both critical components of data harmonization.

The gender gap in Italian academic medicine from 2005 to 2015: still a glass ceiling.

BACKGROUND: Although women make up half of the population of medical students and residents, they are still under-represented in prominent leadership positions in academia. The disparity is greatest at the highest levels and represents a loss of talent for academic health centers, showing that women must choose between career advancement and personal life. OBJECTIVES: The aim of this study was to analyze gender distribution in Italian medical academia in all hierarchical roles (researchers in tenure track positions, associate and full professors) in different disciplinary scientific fields (SSD) in 2015 compared to 2005. METHODS: Medical faculties were considered at 31/12/2005 and 30/09/2015, and analyzed using Excel data sheet (Office for Windows 2007). Database was analyzed using STATA software (Texas, Inc. 2014). RESULTS: Women are under-represented in all careers: in 2005 they made up 36.2% of researchers, 21.7% of associate professors and only 9.4% of full professors. The percentage of women researchers increased significantly (p<0.0001) in 2015 to 41.9%, but the percentages of female associate professors (25.3%) and full professors (14.2%) were still extremely low. DISCUSSION: Our study shows that women are under-represented in Italian academia, with only a slight increase in presence in 2015 compared to ten years before. More action is needed to create a supportive environment, increase awareness and monitor potential discrimination.

Missing value estimation methods for DNA methylation data.

MOTIVATION: DNA methylation is a stable epigenetic mark with major implications in both physiological (development, aging) and pathological conditions (cancers and numerous diseases). Recent research involving methylation focuses on the development of molecular age estimation methods based on DNA methylation levels (mAge). An increasing number of studies indicate that divergences between mAge and chronological age may be associated to age-related diseases. Current advances in high-throughput technologies have allowed the characterization of DNA methylation levels throughout the human genome. However, experimental methylation profiles often contain multiple missing values that can affect the analysis of the data and also mAge estimation. Although several imputation methods exist, a major deficiency lies in the inability to cope with large datasets, such as DNA methylation chips. Specific methods for imputing missing methylation data are therefore needed. RESULTS: We present a simple and computationally efficient imputation method, metyhLImp, based on linear regression. The rationale of the approach lies in the observation that methylation levels show a high degree of inter-sample correlation. We performed a comparative study of our approach with other imputation methods on DNA methylation data of healthy and disease samples from different tissues. Performances have been assessed both in terms of imputation accuracy and in terms of the impact imputed values have on mAge estimation. In comparison to existing methods, our linear regression model proves to perform equally or better and with good computational efficiency. The results of our analysis provide recommendations for accurate estimation of missing methylation values. AVAILABILITY AND IMPLEMENTATION: The R-package methyLImp is freely available at https://github.com/pdilena/methyLImp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Sensitization to Rubber Accelerators in Northeastern Italy: The Triveneto Patch Test Database.

BACKGROUND: Natural and synthetic rubbers containing rubber accelerators are well-known causes of occupational skin disease. Allergic contact dermatitis caused by rubber gloves is frequent and has almost exclusively been attributed to contact sensitization to accelerators. OBJECTIVE: This study aimed to evaluate the frequency of rubber accelerators sensitization in the population living in northeastern Italy, to find time trend and a correlation with occupations, and to investigate co-sensitization between rubber accelerators. METHODS: A population of 23,774 subjects was patch tested in 6 cities in northeastern Italy in the years 1996 to 2012 using carba mix 3%, thiuram mix 1%, benzothiazole (MBT) mix 1%, and isopropyl phenyl paraphenylamine diamine (IPPD) mix 0.6%. RESULTS: The overall frequency of carbamates, MBT, thiurams, and IPPD mix sensitization was 3.4%, 0.65%, 1.75%, and 0.83%, respectively. On a logistic regression analysis (control group: white-collar workers), we found a statistically significant association to carbamates (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.03-1.7) and thiurams (OR, 1.6; 95% CI, 1.1-2.3) for health care workers. Thiuram sensitivity was also significantly associated with dermatitis in maids and restaurant workers (OR, 2.2; 95% CI, 1.4-3.6), hairdressers (OR, 3.6; 95% CI, 1.8-7.1), shop assistants (OR, 2.9; 95% CI, 1.2-6.8), construction workers (OR, 2.7; 95% CI, 1.7-4.1), mechanics (OR, 2.1; 95% CI, 1.3-3.4), and professional drivers (OR, 2.6; 95% CI, 1.2-5.9). CONCLUSIONS: In conclusion, our results demonstrated that rubber accelerators have an important role in allergic contact dermatitis in the northeast of Italy and their sensitization is associated significantly with occupations that wear gloves or use chemical substances. Between rubber accelerators tested, carbamates sensitization is prevalent and increasing during considered years.

A longitudinal study of neck and upper limb musculoskeletal disorders and alternative measures of vibration exposure.

OBJECTIVE: To investigate the exposure-response relationships between alternative frequency weightings of hand-transmitted vibration (HTV) and neck and upper limb musculoskeletal disorders (MSDs) in a cohort of HTV workers. METHODS: In a three-year longitudinal study, the occurrence of neck and upper limb MSDs was investigated in 249 HTV workers and 138 control men. In the HTV workers, MSDs were related to measures of daily vibration exposure expressed in terms of 8-h energy-equivalent frequency-weighted acceleration magnitude [A(8)]. To calculate A(8), the acceleration magnitudes of vibration were weighted by means of four alternative frequency weightings of HTV. The associations between MSDs, individual characteristics, physical work load other than vibration, and psychological strain were also investigated. RESULTS: The occurrence of upper limb MSDs was greater in the HTV workers than in the controls. After adjustment for potential confounders, the occurrence of elbow/forearm and wrist/hand MSDs increased with the increase in vibration exposure. A measure of model selection did not reveal any substantial difference in the performance of the alternative frequency weightings of HTV for the prediction of neck and upper limb MSDs. In the study population, age, hard physical work load, and poor psychological well-being were associated with both neck and upper limb MSDs. CONCLUSIONS: In this study, there was evidence for significant exposure-response relationships between HTV exposure and MSDs in the distal sites of the upper limbs. There were no differences in the prediction of neck and upper limb MSDs between measures of daily vibration exposure calculated with alternative frequency weightings of acceleration magnitude.

Sensitization to Formaldehyde in Northeastern Italy, 1996 to 2012.

BACKGROUND: Formaldehyde is a widely used organic compound, used in several applications (hard thermoset resins, adhesives, disinfectants, tissue fixatives, etc), in its free form or released by formaldehyde releaser products. Its use is under control due to its toxic, carcinogenic, and allergenic properties. OBJECTIVE: The aim of this study was to investigate the frequency of formaldehyde sensitization, time trend, and correlation to occupations. METHODS: This study is a cross-sectional study on a population of 23,774 patients tested from 1996 to 2012 in Northeastern Italy. RESULTS: Frequency of sensitization was 3.3%, without any significant time trend. Hands (39.8% overall) and face (25.6% females, 15.5% males) were mainly involved. We found a trend toward decrease by age in females (3.11% in first quintile [14-26 years], 2.29% in fifth quintile [59-97 years], P < 0.01). On a logistic regression analysis (control group: white-collar workers), we found associations in health care (odds ratio [OR], 1.37; 95% confidence interval [CI], 1.04-1.81), wood (OR, 2.14; 95% CI, 1.30-3.51), and textile (OR, 1.79; 95% CI, 1.14-2.79) sectors and professional drivers (OR, 1.94; 95% CI, 1.05-3.60). We found a high rate of cosensitization to formaldehyde in patients with positive patch test reactions to quaternium-15 (OR, 18.7; 95% CI, 12.6-27.7). CONCLUSIONS: Sensitization to formaldehyde is relevant in our population, especially in the health care sector, wood and textile industries, and professional drivers. No significant time trend was found.

Titanium Dioxide Nanoparticle Penetration into the Skin and Effects on HaCaT Cells.

Titanium dioxide nanoparticles (TiO2NPs) suspensions (concentration 1.0 g/L) in synthetic sweat solution were applied on Franz cells for 24 h using intact and needle-abraded human skin. Titanium content into skin and receiving phases was determined. Cytotoxicity (MTT, AlamarBlue(®) and propidium iodide, PI, uptake assays) was evaluated on HaCat keratinocytes after 24 h, 48 h, and seven days of exposure. After 24 h of exposure, no titanium was detectable in receiving solutions for both intact and damaged skin. Titanium was found in the epidermal layer after 24 h of exposure (0.47 ± 0.33 µg/cm(2)) while in the dermal layer, the concentration was below the limit of detection. Damaged skin, in its whole, has shown a similar concentration (0.53 ± 0.26 µg/cm(2)). Cytotoxicity studies on HaCaT cells demonstrated that TiO2NPs induced cytotoxic effects only at very high concentrations, reducing cell viability after seven days of exposure with EC50s of 8.8 × 10(-4) M (MTT assay), 3.8 × 10(-5) M (AlamarBlue(®) assay), and 7.6 × 10(-4) M (PI uptake, index of a necrotic cell death). Our study demonstrated that TiO2NPs cannot permeate intact and damaged skin and can be found only in the stratum corneum and epidermis. Moreover, the low cytotoxic effect observed on human HaCaT keratinocytes suggests that these nano-compounds have a potential toxic effect at the skin level only after long-term exposure.

Primin sensitization in north-eastern Italy: a temporal trend from 1996 to 2012.

BACKGROUND: Primin is the main contact allergen found in the ornamental plant Primula obconica Hance. OBJECTIVE: To analyse the temporal trend of sensitivity to primin in north-eastern Italy and to evaluate the associations with occupations in our geographical area. METHODOLOGY: From 1996 to 2012, 24 052 consecutive patients with suspected allergic contact dermatitis were patch tested in north-eastern Italy. Individual characteristics were collected through a standardized questionnaire in eight departments of dermatology or occupational medicine. RESULTS: The overall prevalence of primin sensitization was 1.9%; the prevalence was significantly higher in women (2.6%) than in men (0.5%). The Pordenone area had the higher prevalence of sensitization, which reached 6% in 1999-2001. We found a significant association between primin sensitization and household workers [odds ratio (OR) 2.3; 95% confidence interval (CI): 1.61-3.35], retired people (OR 1.8; 95%CI: 1.22-2.81), woodworkers (OR 2.1; 95%CI: 1.10-6.18), and chemical industry workers (OR 2.9; 95%CI: 1.05-8.29). CONCLUSION: Our study showed that contact allergy to primin is still relevant in north-eastern Italy. The frequency of sensitization is decreasing, but for retired and household workers it is still >4%. Our results suggest the need to promote the use of primin-free P. obconica in Italy.

Relationships of neurosensory disorders and reduced work ability to alternative frequency weightings of hand-transmitted vibration.

OBJECTIVE: This cohort study aims to compare the performance of alternative frequency weightings of hand-transmitted vibration (HTV) for the assessment of the exposure-response relationships for neurosensory disorders and reduced work ability among HTV-exposed workers. METHODS: In a 3-year follow up study, the occurrence of neurosensory symptoms and reduced work ability, and the response to quantitative sensory testing (grip force, manipulative dexterity, touch sensation) were investigated in 249 HTV-exposed workers and 138 healthy controls. Among the HTV-exposed workers, the sensory outcomes were related to measures of daily vibration exposure expressed in terms of 8-hour energy-equivalent frequency-weighted acceleration magnitude [A(8)]. To calculate A(8), the acceleration magnitudes of vibration were weighted by means of four alternative frequency weightings of HTV. RESULTS: The occurrence of neurosensory symptoms, reduced work ability, and abnormalities of sensory tests was greater among the HTV-exposed workers than the controls. Among the HTV-exposed workers, the deterioration of neurosensory outcomes and the reduction of work ability increased on par with the measures of vibration exposure. Exposure-response models revealed that the four alternative frequency weightings of HTV provided the same predictions for the probability of finger numbness among the exposed workers (observed 36% versus predicted 32%). CONCLUSIONS: The findings of this study revealed significant dose-response relationships between measures of vibration exposure, sensory disorders, and reduced work ability among the HTV-exposed workers. There were no differences in the prediction of finger numbness between measures of vibration exposure calculated with alternative frequency weightings of HTV.

Occupational sensitization to epoxy resins in Northeastern Italy (1996-2010).

BACKGROUND: One of the main health concerns of epoxy resins is their role as skin sensitizer. This sensitization is not uncommon, because the prevalence ranges around 1-12% of the general population. OBJECTIVES: Perform a cross sectional study in a patch test population from Northeastern Italy to investigate the prevalence of epoxy resins sensitization among patients with suspected contact dermatitis. Subsequently, relate findings to patients' occupation and evaluate time trend of prevalence. METHODS: The final study database included 19 088 consecutive patients, tested from 1996 to 2010 in Northeastern Italy. RESULTS: The overall prevalence of epoxy resins sensitization was 0·89%. Dermatitis most frequently involved hands (40·25%). In both sexes, we find a significant correlation in mechanics, woodworkers, and chemical industry workers; and in males only, among farmers and fishers, construction workers, and unemployed. We found significant increase of sensitization in construction workers in the analyzed period. CONCLUSIONS: The overall prevalence of sensitization to epoxy resins in Northeastern Italy is in line with other European countries, but we found an increased risk of sensitization in some professions and an increasing trend of prevalence in construction workers. Better preventive actions are strongly advised in higher risk professions, with particular attentions towards building sector.

Relationships of low back outcomes to internal spinal load: a prospective cohort study of professional drivers.

PURPOSE: To investigate the relationships between low back symptoms and alternative measures of external dose and internal spinal dose in professional drivers exposed to whole body vibration (WBV). METHODS: The occurrence of low back symptoms was investigated in a cohort of 537 drivers over a 2-year follow-up period. Low back pain (LBP), individual characteristics, and work-related risk factors were investigated with a structured questionnaire. Exposure to WBV was evaluated by means of measures of external dose (daily vibration exposure in terms of either equivalent continuous acceleration over an 8-h period (A(8)) or vibration dose value according to the EU Directive on mechanical vibration) and measures of internal lumbar load (daily compressive dose S ed and risk factor R according to ISO/CD 2631-5 2014). RESULTS: In the drivers' cohort, the cumulative incidence of 12-month low back outcomes was 16.8% for LBP, 9.3% for chronic LBP, and 21.8% for sciatic pain. The measures of internal spinal load were better predictors of the occurrence of low back symptoms than the measures of daily vibration exposure. A twofold increase in the risk estimates for low back outcomes was found in the upper quartile of the R factor (0.41-0.72 units) compared to the lower one (0.07-0.19 units). CONCLUSIONS: In this prospective cohort study, measures of internal spinal dose performed better than measures of daily vibration exposure (external dose) for the prediction of low back outcomes in professional drivers. The ISO boundary values of the risk factor R for low and high probabilities of adverse health effects on the lumbar spine tend to underestimate the health risk in professional drivers.

Nickel, chromium and cobalt sensitization in a patch test population in north-eastern Italy (1996-2010).

BACKGROUND: Sensitization to nickel, cobalt and chromium is frequent in patch test populations. The prevalence is affected by geographical and socio-cultural factors. OBJECTIVES: To investigate the temporal trend of nickel, cobalt and chromium contact sensitization between 1996 and 2010 in north-eastern Italy. PATIENTS/METHODS: Nineteen thousand and eighty-eight patients (67.2% women and 32.8% men) with suspected allergic dermatitis underwent patch testing with the European baseline series. The associations between nickel, cobalt and chromium sensitization and patient age (in quintiles) and year of patch testing were investigated by means of multivariate logistic regression analysis. RESULTS: The prevalence of nickel sensitization decreased significantly among younger women (≤26 years), from 38.3% (1996-1998) to 31.9% (2002-2004), 28.3% (2005-2007) and 29.0% (2008-2010), whereas an increase was observed in the 36-45-year and 46-58-year age groups. The overall prevalence of chromium sensitization dropped from 10.2% (1996-1998) to 4.6% (2008-2010) among women, and from 11.3% (1996-1998) to 5.9% (2008-2010) among men. The prevalence of cobalt sensitization increased among younger men (≤26 years), from 2.7% (1996-1998) to 7.3% (1999-2001), 9.6% (2002-2004), and 6.6% (2005-2007). CONCLUSIONS: Our study showed a decreasing trend of nickel sensitization (only among younger women) and of chromium sensitization in both sexes.

Concurrent sensitization to metals and occupation.

BACKGROUND: Cosensitization to nickel, cobalt and chromium occurs in the general population and in some occupational groups. OBJECTIVES: To estimate the isolated and concurrent occurrence of nickel, cobalt and chromium contact sensitization and their association with individual and occupational risk factors. PATIENTS/METHODS: Twelve thousand four hundred and ninety-two patients were patch tested with the European baseline series between 1997 and 2004 in north-eastern Italy. The associations between patch test results and patient characteristics and occupations were investigated by means of multinomial logistic regression analysis. RESULTS: Of the patients, 34.7% (4334 patients) had one or more positive patch test reactions to metals. As compared with those with negative reactions to all three metals, nickel sensitization was significantly higher in females than in males, not only as monosensitization, but also as cosensitization with cobalt, with chromium, or with both metals. Building and related trades workers showed positive reactions to chromium + nickel [odds ratio (OR) 1.99; 95% confidence interval (CI) 1.05-3.76) and chromium + cobalt (OR 2.61; 95% CI 1.46-4.67]. Cleaning workers showed a high prevalence of nickel, chromium, nickel + chromium and nickel + cobalt + chromium cosensitization (ORs 1.29, 1.66, 2.11, and 1.79, respectively). An excess risk for cosensitization to all three metals was found in textile and leather workers (OR 2.19; 95% CI 1.10-4.33), and in bartenders (OR 2.10; 95% CI 1.03-4.26). CONCLUSIONS: Some occupational groups are more likely to develop nickel, cobalt and chromium cosensitization.

Job strain, effort-reward imbalance and ambulatory blood pressure: results of a cross-sectional study in call handler operators.

OBJECTIVES: To examine the association between two job stress models-the job strain (JDC) and the effort-reward imbalance (ERI) model-and ambulatory blood pressure monitoring in call handler operators. METHODS: Participants included 74 women (age, 34.9 ± 9.9 years) and 26 men (age 36.0 ± 10.8 years) who were monitored on 2 workdays for ambulatory blood pressure. Measures of both job stress models were related to blood pressure by the generalized estimating equations (GEE) method while adjusting for potential confounders (gender, age, cigarette smoking, alcohol consumption, educational level, marital status, time of day, and work schedule). RESULTS: Workshifts were associated with an increase of 3-4 and 14 mmHg in mean arterial pressure (MAP) compared with diurnal activities out of work and sleeping period, respectively (P < 0.001). Ambulatory blood pressure was also significantly related with work schedule preference: unpleasant work schedule was associated with an increase of 2 mmHg in MAP compared with pleasant work schedule (P = 0.013). In the ERI model, subjects scoring high in work stress have higher ambulatory blood pressure at work, at home, and during sleep. Work stress by time interaction was not longer significant when controlling for potential confounders: generalized estimating equations revealed that MAP was influenced by BMI (>25 vs. <25: 0.7 (0.2-1.1) mmHg), workshift preference (unpleasant vs. pleasant: 2 (0.4-3.6) mmHg), and time of day. Weak not significant relation was found between ABP and psychosocial factors evaluated by the JDC and ERI models. CONCLUSION: These results do not support work stress as a significant factor influencing ABP in a homogeneous group of call-handlers. Complementary information independently obtained from the two work stress models could provide more exhaustive explanations on the stress-related effects on blood pressure.

Site specific X-ray anomalous dispersion of the geometrically frustrated kagomé magnet, herbertsmithite, ZnCu(3)(OH)(6)Cl(2).

Structural characterization, exploiting X-ray scattering differences at elemental absorption edges, is developed to quantitatively determine crystallographic site-specific metal disorder. We apply this technique to the problem of Zn-Cu chemical disorder in ZnCu(3)(OH)(6)Cl(2). This geometrically frustrated kagomé antiferromagnet is one of the best candidates for a spin-liquid ground state, but chemical disorder has been suggested as a mundane explanation for its magnetic properties. Using anomalous scattering at the Zn and Cu edges, we determine that there is no Zn occupation of the intralayer Cu sites within the kagomé layer; however there is Cu present on the Zn intersite, leading to a structural formula of (Zn(0.85)Cu(0.15))Cu(3)(OH)(6)Cl(2). The lack of Zn mixing onto the kagomé lattice sites lends support to the idea that the electronic ground state in ZnCu(3)(OH)(6)Cl(2) and its relatives is nontrivial.

Nickel, cobalt and chromate sensitization and occupation.

BACKGROUND: Exposure to nickel, cobalt and chromate are important causes of occupational contact dermatitis. OBJECTIVES: To estimate the prevalence of nickel, cobalt and chromate allergy in a population of consecutive patients and to investigate the possible association with individual and occupational risk factors. PATIENTS/METHODS: A total of 14 464 patients (67.6% women and 32.4% men) with suspected allergic dermatitis underwent patch tests. The associations between patch test results and occupations were studied by multivariate logistic regression analysis. RESULTS: About 24.6% of the patients reacted positively to nickel sulphate, 10.2% to cobalt chloride and 8.7% to potassium dichromate. Nickel sensitization was higher in women aged 26-35 years in comparison with the youngest group (15-25 years) and the older group (> 45 years). In women, the prevalence of positive reactions to nickel was positively associated with metal and mechanical work (OR 1.54; 95%, CI 1.16-2.05). Chromate sensitization was more prevalent in building trade workers for both women (OR 1.58; 95% CI 1.00-2.49) and men (OR 2.24; 95% CI 1.55-3.22). Cobalt sensitization was associated with textile and leather work in women (OR 1.52; 95% CI 1.09-2.12) and with cleaning work in men (OR 1.86; 95% CI 1.18-2.93). CONCLUSIONS: Our study showed interesting associations between some occupations and nickel, chromate and cobalt allergy.