Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq). We applied ChIP-seq to map the chromosomal binding sites for two ISWI-containing nucleosome remodeling factors, ACF and RSF, in Drosophila embryos. Employing several polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF-1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters. Further validation included controls using chromatin of mutant embryos that do not express ACF1 or RSF-1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and appear as 'Phantom Peaks'. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin. Mining the modENCODE ChIP-seq profiles identifies potential Phantom Peaks in many profiles of epigenetic regulators. These profiles and other ChIP-seq data featuring prominent Phantom Peaks must be validated with chromatin from cells in which the protein of interest has been depleted

A study of the core of the Shapley Concentration: VI. Spectral properties of galaxies

We present the results of a study of the spectral properties of galaxies in the central part of the Shapley Concentration, covering an extremely wide range of densities, from the rich cluster cores to the underlying supercluster environment. Our sample is homogeneous, in a well defined magnitude range (17=<b_J=<18.8) and contains ~1300 spectra of galaxies at the same distance, covering an area of ~26 sq.deg. These characteristics allowed an accurate spectral classification, that we performed using a Principal Components Analysis technique. This spectral classification, together with the [OII] equivalent widths and the star formation rates, has been used to study the properties of galaxies at different densities: cluster, intercluster (i.e. galaxies in the supercluster but outside clusters) and field environment. No significant differences are present between samples at low density regimes (i.e. intercluster and field galaxies). Cluster galaxies, instead, not only have values significantly different from the field ones, but also show a dependence on the local density. Moreover, a well defined morphology-density relation is present in the cluster complexes, although these structures are known to be involved in major merging events. Also the mean equivalent width of [OII] shows a trend with the local environment, decreasing at increasing densities, even if it is probably induced by the morphology-density relation. Finally we analyzed the mean star formation rate as a function of the density, finding again a decreasing trend (at ~ 3sigma significance level). Our analysis is consistent with the claim of Balogh et al. (1998) that the star formation in clusters is depressed.Comment: 13 pages with encapsulated figures; MNRAS in pres

Male Oxidative Stress Infertility (MOSI): Proposed Terminology and Clinical Practice Guidelines for Management of Idiopathic Male Infertility

Despite advances in the field of male reproductive health, idiopathic male infertility, in which a man has altered semen characteristics without an identifiable cause and there is no female factor infertility, remains a challenging condition to diagnose and manage. Increasing evidence suggests that oxidative stress (OS) plays an independent role in the etiology of male infertility, with 30% to 80% of infertile men having elevated seminal reactive oxygen species levels. OS can negatively affect fertility via a number of pathways, including interference with capacitation and possible damage to sperm membrane and DNA, which may impair the sperm’s potential to fertilize an egg and develop into a healthy embryo. Adequate evaluation of male reproductive potential should therefore include an assessment of sperm OS. We propose the term Male Oxidative Stress Infertility, or MOSI, as a novel descriptor for infertile men with abnormal semen characteristics and OS, including many patients who were previously classified as having idiopathic male infertility. Oxidation-reduction potential (ORP) can be a useful clinical biomarker for the classification of MOSI, as it takes into account the levels of both oxidants and reductants (antioxidants). Current treatment protocols for OS, including the use of antioxidants, are not evidence-based and have the potential for complications and increased healthcare-related expenditures. Utilizing an easy, reproducible, and cost-effective test to measure ORP may provide a more targeted, reliable approach for administering antioxidant therapy while minimizing the risk of antioxidant overdose. With the increasing awareness and understanding of MOSI as a distinct male infertility diagnosis, future research endeavors can facilitate the development of evidence-based treatments that target its underlying cause

Standards in semen examination:publishing reproducible and reliable data based on high-quality methodology

Biomedical science is rapidly developing in terms of more transparency, openness and reproducibility of scientific publications. This is even more important for all studies that are based on results from basic semen examination. Recently two concordant documents have been published: the 6th edition of the WHO Laboratory Manual for the Examination and Processing of Human Semen, and the International Standard ISO 23162:2021. With these tools, we propose that authors should be instructed to follow these laboratory methods in order to publish studies in peer-reviewed journals, preferable by using a checklist as suggested in an Appendix to this article.Peer reviewe

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Energy dissipation measurements in stirred vessels with particle image velocimetry

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq). We applied ChIP-seq to map the chromosomal binding sites for two ISWI-containing nucleosome remodeling factors, ACF and RSF, in Drosophila embryos. Employing several polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF-1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters. Further validation included controls using chromatin of mutant embryos that do not express ACF1 or RSF-1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and appear as 'Phantom Peaks'. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin. Mining the modENCODE ChIP-seq profiles identifies potential Phantom Peaks in many profiles of epigenetic regulators. These profiles and other ChIP-seq data featuring prominent Phantom Peaks must be validated with chromatin from cells in which the protein of interest has been depleted

L’utilizzo di dispositivi ad alto flusso durante le manovre assistenziali nei pazienti (adulti ricoverati) con infezione da SARS-CoV-2: uno studio di coorte retrospettivo.

INTRODUCTION 14% of patients with SARS-cov-2 infection progress to hypoxia respiratory failure requiring oxygen therapy. The objective of the study is to assess the effectiveness and safety of high-flow nasal oxygen (HFNC) during assistive maneuvers (personal hygiene, self-care and nutrition) in patients with SARS-cov-2 infection. MATERIALS AND METHODS With a retrospective cohort study design with a statistical analysis of inferential type, in three subintensive departments of the Local Health Authority of Asti from 8 November 2020 to 20 January 2021, the documentation of patients from 41 to 100 years old with SARS-cov-2 infection who used HFNCs during assistive maneuvers alternating with the CPAP helmet/mask was examined. For the research of the sample was used the program Dshop®, in which the ages, the percentages of FiO2 and the cmh2o of PEEP administered to the patients were collected and ventilation parameters were detected. RESULTS Analysis of 536 medical records 114 were included in the study. There was a significant reduction in po2 and po2/FiO2 ratio and a decrease in spo2 in the oldest age group in the sample [91-100] when using HFNC. With regard to FiO2, a significant reduction in spo2 and P/F was shown with the administration of FiO2 by 90-100%. Finally, with the HFNC the values of HCO3 and lactates are contained in the optimal values of the EGA unlike the helmet/ mask CPAP with PEEP of 15 cmh2o. DISCUSSION AND CONCLUSIONS The HFNC is associated with increased comfort in fact the patient can hydrate, feed, perform hygiene and self-care independently. The CPAP ventilatory mode, on the other hand, requires a strong human-device collaboration, the patients often turn out to be anxious, claustrophobic and not adherent.INTRODUZIONE Il 14% dei pazienti con infezione da SARS-CoV-2 progredisce verso l'insufficienza respiratoria ipossiemica che richiede ossigenoterapia. L’obiettivo dello studio è quello di valutare l’efficacia e la sicurezza dell’ossigeno nasale ad alto flusso (HFNC) durante le manovre assistenziali (igiene personale, cura del sé e alimentazione) nei pazienti con infezione da SARS-CoV-2. MATERIALI E METODI Con disegno di studio coorte retrospettiva in tre reparti subintensivi dell’Azienda Sanitaria Locale di Asti dal 8 Novembre 2020 al 20 Gennaio 2021, è stata esaminata la documentazione di pazienti dai 41 ai 100 anni con infezione da SARS-CoV-2 che utilizzavano gli HFNC durante le manovre assistenziali alternati al casco/maschera CPAP. Per la ricerca del campione è stato utilizzato il programma Dshop® in cui sono state raccolte le età, le percentuali di FiO2 e i cmH2O di PEEP somministrate alle persone assistite e sono stati rilevati i parametri di ventilazione. È stata effettuata un’analisi statistica di tipo inferenziale. RISULTATI Dall’analisi di 536 cartelle cliniche 114 sono state inserite nello studio. È emersa una riduzione significativa della pO2 e del rapporto pO2/FiO2 e una diminuzione della SpO2 nella fascia di età più anziana del campione [91-100] durante l’utilizzo di HFNC. Per quanto riguarda la FiO2 è stata mostrata una riduzione significativa della SpO2 e del P/F con la somministrazione di FiO2 del 90-100%. Infine, con l’HFNC i valori di HCO3 e lattati sono contenuti nei valori ottimali dell’EGA a differenza del casco/maschera CPAP con PEEP di 15 cmH2O. DISCUSSIONE E CONCLUSIONI L'HFNC è associato ad un maggiore comfort infatti il paziente può idratarsi, alimentarsi, eseguire l’igiene e la cura del sé in autonomia. La modalità ventilatoria CPAP richiede, invece, una spiccata collaborazione uomo-dispositivo, i pazienti spesso risultano essere ansiosi, claustrofobici e non aderenti