MaxSkew and MultiSkew: Two R Packages for Detecting, Measuring and Removing Multivariate Skewness

Skewness plays a relevant role in several multivariate statistical techniques. Sometimes it is used to recover data features, as in cluster analysis. In other circumstances, skewness impairs the performances of statistical methods, as in the Hotelling's one-sample test. In both cases, there is the need to check the symmetry of the underlying distribution, either by visual inspection or by formal testing. The R packages MaxSkew and MultiSkew address these issues by measuring, testing and removing skewness from multivariate data. Skewness is assessed by the third multivariate cumulant and its functions. The hypothesis of symmetry is tested either nonparametrically, with the bootstrap, or parametrically, under the normality assumption. Skewness is removed or at least alleviated by projecting the data onto appropriate linear subspaces. Usages of MaxSkew and MultiSkew are illustrated with the Iris dataset

Pneumocystosis as a Complication of H1N1 Influenza A Infection in an HIV-Positive Patient on Effective cART

H1N1 influenza A virus can affect the immune system, causing lymphopenia. This might be of great concern for HIV individuals undergoing effective antireroviral therapy (cART). We report the first confirmed case of H1N1-induced AIDS and Pneumocystis jiroveci pneumonia in an HIV-positive woman on effective cART since 2006

Changing in the post-surgery infective complications following the shortening of the antibiotic prophylaxis in the patients undergoing skin dermal substitutes reconstruction

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue, both in massive deep burns, extensive full-thickness wounds, and reconstruction after cancer resection. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material & Methods: Infective complications at the site of SDS were compared in two groups of patients: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a >24h-antibiotic prophylaxis, and subjects undergoing surgical reconstruction between May 2016 and June 2017 (PERIOD B) who received a ≤24h-antibiotic prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Univariate linear regression analysis was performed to evaluate the risk factors for infection (sex, age, ASA code, perioperative antibiotic prophylaxis, site of SDS intervention, type of SDS, dimensions of surgical area, chronic renal impairment, and diabetes mellitus). Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The 66.4% (n=77) of the study population was male, and the mean age was 73 years (22-92 years). Seventy-eight patients (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were former or current smokers, and 45 (38.8%) had an ASA code ≥3. In the 94.8% of the patients (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the arm or the hand in 9 (7.8%), the leg in 12 (10.3%) and the foot in 12 (10.3%). Among 116 patients undergoing SDS surgical reconstruction, 62 (53.4%) received a >24h-prophylaxis and 54 (46.6%) received a ≤24h-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limb/foot had higher infection rate in comparison with those undergoing SDS reconstruction in chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received >24h or ≤24h-antibiotic prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. No significant differences in pathogen prevalence were found (p=0.692). Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed to reduce of 6 days-per-patient the antibiotic exposure

Infective complications in patients undergoing surgical reconstruction with dermal matrix: the Modena experience

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue1,2,3. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material & Methods: Infective complications at the site of SDS were compared in 2 groups: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a >24H-antibiotic-prophylaxis, and between May 2016 and June 2017 (PERIOD B) who received a ≤24H-antibiotic-prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The mean age was 73-years, 77 were male (66.4%), 78 (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were smokers, and 45 (38.8%) had an ASA score ≥3. In the 94.8% (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the limbs in 33 (28.5%). Among 116 patients, 62 (53.4%) received >24H-antibiotic and 54 (46.6%) ≤24H-antibiotic-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limbs had higher infection rate in comparison with chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received >24H or ≤24H-antibiotic-prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. Discussion: As far as we know, this is the first study that compared two perioperative antibiotic prophylaxis regimes in patients undergoing SDS reconstruction. Comparing the two patient groups (≤24-hour and >24-hour prophylaxis), no differences in the rate of infection were found. The result is very important: it shows that prolongation of prophylaxis in this type of surgical patients does not reduce the rate of infection. Shortening of antibiotic prophylaxis allowed to reduce of 6 days-per-patient the antibiotic exposure. It was surprising that only the reconstruction of the limbs, in comparison with other sites, was associated with a higher risk of infection (33.3 and 15.7 respectively). Nor the most critical patients (with an ASA score ≥3), nor patients undergoing major surgical reconstructions (surgical area >60 cm2) resulted associated with a higher risk. Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed a reduction of 6 days-per-patient the antibiotic exposure. Randomized and controlled trials, with greater population, could give a more accurate response on the duration of antibiotic prophylaxis in patients undergoing surgical SDS reconstruction

Epidemiology and Outcomes of Bloodstream Infections in HIV-Patients during a 13-Year Period

No data on antibiotic resistance in bloodstream infection (BSI) in people living with HIV (PLWH) exist. The objective of this study was to describe BSI epidemiology in PLWH focusing on multidrug resistant (MDR) organisms. A retrospective, single-center, observational study was conducted including all positive blood isolates in PLWH from 2004 to 2017. Univariable and multivariable GEE models using binomial distribution family were created to evaluate the association between MDR and mortality risk. In total, 263 episodes (299 isolates) from 164 patients were analyzed; 126 (48%) BSI were community-acquired, 137 (52%) hospital-acquired. At diagnosis, 34.7% of the patients had virological failure, median CD4 count was 207/μL. Thirty- and 90-day mortality rates were 24.2% and 32.4%, respectively. Thirty- and 90-day mortality rates for MDR isolates were 33.3% and 46.9%, respectively (p < 0.05). Enterobacteriaceae were the most prevalent microorganisms (29.8%), followed by Coagulase-negative staphylococci (21.4%), and S. aureus (12.7%). In BSI due to MDR organisms, carbapenem-resistant K. pneumoniae and methicillin-resistant S. aureus were associated with mortality after adjustment for age, although this correlation was not confirmed after further adjustment for CD4 < 200/μL. In conclusion, BSI in PLWH is still a major problem in the combination antiretroviral treatment era and it is related to a poor viro-immunological status, posing the question of whether it should be considered as an AIDS-defining event

Bitter Is Better: Wild Greens Used in the Blue Zone of Ikaria, Greece

The current study reports an ethnobotanical field investigation of traditionally gathered and consumed wild greens (Chorta) in one of the five so-called Blue Zones in the world: Ikaria Isle, Greece. Through 31 semi-structured interviews, a total of 56 wild green plants were documented along with their culinary uses, linguistic labels, and locally perceived tastes. Most of the gathered greens were described as bitter and associated with members of Asteraceae and Brassicaceae botanical families (31%), while among the top-quoted wild greens, species belonging to these two plant families accounted for 50% of the wild vegetables, which were consumed mostly cooked. Cross-cultural comparison with foraging in other areas of the central-eastern Mediterranean and the Near East demonstrated a remarkable overlapping of Ikarian greens with Cretan and Sicilian, as well as in the prevalence of bitter-tasting botanical genera. Important differences with other wild greens-related food heritage were found, most notably with the Armenian and Kurdish ones, which do not commonly feature many bitter greens. The proven role of extra-oral bitter taste receptors in the modulation of gastric emptying, glucose absorption and crosstalk with microbiota opens new ways of looking at these differences, in particular with regard to possible health implications. The present study is also an important attempt to preserve and document the bio-cultural gastronomic heritage of Chorta as a quintessential part of the Mediterranean diet. The study recommends that nutritionists, food scientists, and historians, as well as policymakers and practitioners, pay the required attention to traditional rural dietary systems as models of sustainable health

A genome-wide association study of early menopause and the combined impact of identified variants

Early menopause (EM) affects up to 10% of the female population, reducing reproductive lifespan considerably. Currently, it constitutes the leading cause of infertility in the western world, affecting mainly those women who postpone their first pregnancy beyond the age of 30 years. The genetic aetiology of EM is largely unknown in the majority of cases. We have undertaken a meta-analysis of genome-wide association studies (GWASs) in 3493 EM cases and 13 598 controls from 10 independent studies. No novel genetic variants were discovered, but the 17 variants previously associated with normal age at natural menopause as a quantitative trait (QT) were also associated with EM and primary ovarian insufficiency (POI). Thus, EM has a genetic aetiology which overlaps variation in normal age at menopause and is at least partly explained by the additive effects of the same polygenic variants. The combined effect of the common variants captured by the single nucleotide polymorphism arrays was estimated to account for ∼30% of the variance in EM. The association between the combined 17 variants and the risk of EM was greater than the best validated non-genetic risk factor, smokin

Rare coding variants and X-linked loci associated with age at menarche.

More than 100 loci have been identified for age at menarche by genome-wide association studies; however, collectively these explain only ∼3% of the trait variance. Here we test two overlooked sources of variation in 192,974 European ancestry women: low-frequency protein-coding variants and X-chromosome variants. Five missense/nonsense variants (in ALMS1/LAMB2/TNRC6A/TACR3/PRKAG1) are associated with age at menarche (minor allele frequencies 0.08-4.6%; effect sizes 0.08-1.25 years per allele; P<5 × 10(-8)). In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P=9.4 × 10(-13)) and FAAH2 (rs5914101, P=4.9 × 10(-10)). Highlighted genes implicate cellular energy homeostasis, post-transcriptional gene silencing and fatty-acid amide signalling. A frequently reported mutation in TACR3 for idiopathic hypogonatrophic hypogonadism (p.W275X) is associated with 1.25-year-later menarche (P=2.8 × 10(-11)), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively, these novel variants explain ∼0.5% variance, indicating that these overlooked sources of variation do not substantially explain the 'missing heritability' of this complex trait.UK sponsors (see article for overseas ones): This work made use of data and samples generated by the 1958 Birth Cohort (NCDS). Access to these resources was enabled via the 58READIE Project funded by Wellcome Trust and Medical Research Council (grant numbers WT095219MA and G1001799). A full list of the financial, institutional and personal contributions to the development of the 1958 Birth Cohort Biomedical resource is available at http://www2.le.ac.uk/projects/birthcohort. Genotyping was undertaken as part of the Wellcome Trust Case-Control Consortium (WTCCC) under Wellcome Trust award 076113, and a full list of the investigators who contributed to the generation of the data is available at www.wtccc.org.uk ... The Fenland Study is funded by the Wellcome Trust and the Medical Research Council, as well as by the Support for Science Funding programme and CamStrad. ... SIBS - CRUK ref: C1287/A8459 SEARCH - CRUK ref: A490/A10124 EMBRACE is supported by Cancer Research UK Grants C1287/A10118, C1287/A16563 and C1287/A17523. Genotyping was supported by Cancer Research - UK grant C12292/A11174D and C8197/A16565. Gareth Evans and Fiona Lalloo are supported by an NIHR grant to the Biomedical Research Centre, Manchester. The Investigators at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust are supported by an NIHR grant to the Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust. Ros Eeles and Elizabeth Bancroft are supported by Cancer Research UK Grant C5047/A8385. ... Generation Scotland - Scottish Executive Health Department, Chief Scientist Office, grant number CZD/16/6. Exome array genotyping for GS:SFHS was funded by the Medical Research Council UK. 23andMe - This work was supported in part by NIH Award 2R44HG006981-02 from the National Human Genome Research Institute.This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/ncomms875