DaMiRseq—an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification

Abstract Summary RNA-Seq is becoming the technique of choice for high-throughput transcriptome profiling, which, besides class comparison for differential expression, promises to be an effective and powerful tool for biomarker discovery. However, a systematic analysis of high-dimensional genomic data is a demanding task for such a purpose. DaMiRseq offers an organized, flexible and convenient framework to remove noise and bias, select the most informative features and perform accurate classification. Availability and implementation DaMiRseq is developed for the R environment (R ≥ 3.4) and is released under GPL (≥2) License. The package runs on Windows, Linux and Macintosh operating systems and is freely available to non-commercial users at the Bioconductor open-source, open-development software project repository (https://bioconductor.org/packages/DaMiRseq/). In compliance with Bioconductor standards, the authors ensure stable package maintenance through software and documentation updates. Supplementary information Supplementary data are available at Bioinformatics online

The psychophysical impact that COVID-19 has on children must not be underestimated

Italy has been one of the European countries that has been most affected by the COVID\u201019 pandemic. By 16 April 2020, 159,107 Italian residents had tested positive for COVID\u201019 and these included 1,123 children, up to nine years of age (0.7%) and 1,804 adolescents, aged between 10 and 19 years old (1.1%) (1). These data were in line with the case studies reported for the Chinese population, where the respective percentage (proportion) was 0.9% and 1.2% respectively (2). A five\u2010year\u2010old Italian child, who had been affected by many previous and unspecified pathologies, died after testing positive for COVID\u201019 infection (1). The lower vulnerability of the paediatric population to COVID\u201019 seems eviden

CMB Polarization Systematics, Cosmological Birefringence and the Gravitational Waves Background

Cosmic Microwave Background experiments must achieve very accurate calibration of their polarization reference frame to avoid biasing the cosmological parameters. In particular, a wrong or inaccurate calibration might mimic the presence of a gravitational wave background, or a signal from cosmological birefringence, a phenomenon characteristic of several non-standard, symmetry breaking theories of electrodynamics that allow for \textit{in vacuo} rotation if the polarization direction of the photon. Noteworthly, several authors have claimed that the BOOMERanG 2003 (B2K) published polarized power spectra of the CMB may hint at cosmological birefringence. Such analyses, however, do not take into account the reported calibration uncertainties of the BOOMERanG focal plane. We develop a formalism to include this effect and apply it to the BOOMERanG dataset, finding a cosmological rotation angle $\alpha=-4.3^\circ\pm4.1^\circ$. We also investigate the expected performances of future space borne experiment, finding that an overall miscalibration larger then $1^\circ$ for Planck and $0.2\circ$ for EPIC, if not properly taken into account, will produce a bias on the constraints on the cosmological parameters and could misleadingly suggest the presence of a GW background.Comment: 10 pages, 3 figure

Vitamin D Supplementation in the Assessment of Cardiovascular Risk Factors in Overweight and Obese Children

Childhood obesity is associated with cardiovascular-disease (CVD) risk factors, an unfavorable lipid profile and reduced levels of 25(OH)D. The aim of our study is to evaluate whether vitamin D supplementation may play a role in the assessment of the CVD risk factors in overweight/obese children and adolescents

Massive thymic hyperplasia in a 15-month-old boy: Case report and literature review

Key Clinical Message A surgical approach is the choice in young infants with MTH, who are furthest from the time of physiological involution of the thymus, and when the thymus achieves the largest relative size, a surgical approach is the choice. Steroid therapy has been shown to be ineffective (4, 9, 16, 18-20). No surgical complications have been reported, and the outcome is excellent. Recurrence has been seen in only one case

Inflammatory myofibroblastic lung tumor: its birth, its bleeding growth, its difficult diagnosis and its surgical end in a child

The diagnosis of inflammatory myofibroblastic tumor is based on radiology and histology. The treatment is surgical, and the prognosis is good. For this reason, although this lung disease is rare, when a child show up at hospital with an unknown hemoptysis, this medical condition should not be underestimated

Insights into Pediatric Sleep Disordered Breathing: Exploring Risk Factors, Surgical Interventions, and Physical and Scholastic Performance at Follow-Up

: (1) Background: Sleep-disordered breathing represents a growing public health concern, especially among children and adolescents. The main risk factors for pediatric sleep-disordered breathing in school-age children are tonsillar and adenoid hypertrophy. Adenoidectomy, often in combination with tonsillectomy, is the primary treatment modality for pediatric sleep-disordered breathing. This study aims to comprehensively investigate various risk and protective factors in children with sleep-disordered breathing undergoing adenotonsillar or adenoidal surgeries. We also aim to explore the differences in neuropsychological profiles. (2) Methods: This is an observational, retrospective cohort study. We collected information on adenoidectomy or adenotonsillectomy in children referred to our center. We reviewed the clinical history and preoperative visits and collected data through a telephone questionnaire. The Pediatric Sleep Questionnaire (PSQ) and the Pediatric Quality of Life Inventory (PedsQL) screen sleep-disordered breathing and quality of life, respectively. The data were statistically analyzed using SPSS version 22.0 for Windows (SPSS Inc., Chicago, IL, USA). (3) Results: The study involved 138 patients, but only 100 children participated. A higher percentage of patients with sleep-disordered breathing were observed to have mothers who smoked during pregnancy. A smaller proportion of patients with sleep-disordered breathing habitually used a pacifier. A rise in physical score was associated with a reduced PSQ at follow-up (p = 0.051). An increase in the overall academic score was related to a decrease in the PSQ at follow-up (p < 0.001). A more significant proportion of patients undergoing adenotonsillectomy were observed to have a history of prematurity and cesarean birth. (4) This comprehensive study delves into the intricate interplay of risk and protective factors impacting children with sleep-disordered breathing undergoing adenotonsillectomy and adenoidectomy

Neoadjuvant treatments in triple-negative breast cancer patients: where we are now and where we are going

Abstract: Triple-negative breast cancer (TNBC) remains the poorest-prognosis breast cancer (BC) subtype. Gene expression profiling has identified at least six different triple-negative subtypes with different biology and sensitivity to therapies. The heterogeneous nature of TN tumors may justify the difficulty in treating this BC subtype. Several targeted agents have been investigated in clinical trials without demonstrating a clear survival benefit. Therefore, systemic chemotherapy remains the cornerstone of current clinical practice. Improving the knowledge of tumor biology is mandatory for patient management. In stages II and III, neoadjuvant systemic treatment is an effective option of care. The achievement of a pathological complete response represents an optimal surrogate for survival outcome as well as a test for tumor drug sensitivity. In this review, we provide a brief description of the main predictive biomarkers for tumor response to systemic treatment. Moreover, we review the treatment strategies investigated for TNBCs in neoadjuvant settings focusing on experimental drugs such as immunotherapy and poly [ADP-ribose] polymerase inhibitors that hold promise in the treatment of this aggressive disease. Therefore, the management of TNBC represents an urgent, current, unmet need in daily clinical practice. A key recommendation is to design biology-driven clinical trials wherein TNBC patients may be treated on the basis of tumor molecular profile