Peak shape clustering reveals biological insights

Background: ChIP-seq experiments are widely used to detect and study DNA-protein interactions, such as transcription factor binding and chromatin modifications. However, downstream analysis of ChIP-seq data is currently restricted to the evaluation of signal intensity and the detection of enriched regions (peaks) in the genome. Other features of peak shape are almost always neglected, despite the remarkable differences shown by ChIP-seq for different proteins, as well as by distinct regions in a single experiment. Results: We hypothesize that statistically significant differences in peak shape might have a functional role and a biological meaning. Thus, we design five indices able to summarize peak shapes and we employ multivariate clustering techniques to divide peaks into groups according to both their complexity and the intensity of their coverage function. In addition, our novel analysis pipeline employs a range of statistical and bioinformatics techniques to relate the obtained peak shapes to several independent genomic datasets, including other genome-wide protein-DNA maps and gene expression experiments. To clarify the meaning of peak shape, we apply our methodology to the study of the erythroid transcription factor GATA-1 in K562 cell line and in megakaryocytes. Conclusions: Our study demonstrates that ChIP-seq profiles include information regarding the binding of other proteins beside the one used for precipitation. In particular, peak shape provides new insights into cooperative transcriptional regulation and is correlated to gene expression

The Role of Dietary Intake in the Weight Loss Outcomes of Roux-en-Y Gastric Bypass and Sleeve Gastrectomy: A Systematic Review and Meta-analysis

The relationship between postoperative dietary intake and weight loss after bariatric surgery remains unclear. We performed a systematic review and meta-analysis of studies published between January 2000 and May 2023, reporting weight loss outcomes, and dietary intake before and after Roux-en-Y gastric bypass and sleeve gastrectomy. A total of 42 studies were included. There was no detectable difference in dietary intake between the two procedures. Roux-en-Y gastric bypass induced an average decrease in energy intake of 886 kcal/day at 12-month post-surgery; however, there was no correlation between daily energy intake and weight loss. These findings show a substantial reduction of energy intake in the first year after bariatric surgery but do not support a link between lower energy intake and greater weight loss

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Antenatal predictors of maternal bonding for adolescent mothers

Research studies have found that pregnant adolescents and adolescent mothers differ from their older counterparts on a number of psychological factors. Differences have been noted in the level of antenatal bonding to the foetus, the presence of depressive and/or anxious symptomatology during the pregnancy, the woman’s own attachment experiences and the amount of social support received. These variables have also been found to influence the development of maternal bonding after the baby is born. The primary aim of this research was to examine these antenatal factors and to assess their relative contribution to maternal bonding at six weeks postpartum. A further aim was to explore how different cultural and religious beliefs held by the adolescent and her family impact on the adolescent. The sample comprised pregnant adolescents aged between 13 and 19 years who attended either the Women’s Clinic at Sunshine Hospital or the Young Mothers’ Clinic at the Royal Women’s Hospital in Melbourne, Australia. The participants completed a number of standardised questionnaires during their pregnancy to measure antenatal bonding, retrospective perceptions of their own experiences of being parented by their mother (care and control), depression, anxiety and social support. The adolescents also participated in a semi-structured interview regarding religious and cultural beliefs. At six weeks and three months postpartum the adolescents completed another set of questionnaires to measure postnatal bonding, depression and anxiety. The proposed model to predict post-natal bonding was tested using hierarchical multiple regression. Results of the multivariate analyses indicated that the proposed regression model did not fit the data. Antenatal bonding was the only antenatal factor that was significantly related to postnatal bonding at six weeks. There were other significant correlations noted among the antenatal factors of care, control, depression, anxiety and social support received, but none of these appeared to be significantly related to postnatal bonding in this sample. However, strong relationships were noted between all postnatal factors (postnatal bonding, postnatal anxiety and postnatal depression) at both six weeks and three months postpartum. Information from the interviews on the influence of cultural and religious beliefs was presented and case studies were provided to highlight some of the experiences of these young women. The results of this research were compared and contrasted to the limited number of previous studies that have been carried out in the area. The lack of support for some hypotheses was discussed in the context of the limitations of the study. Other hypotheses were generated and discussed with recommendations made for future research

Functional data analysis of "Omics" data : how does the genomic landscape influence integration and fixation of endogenous retroviruses?

 We consider thousands of endogenous retrovirus detected in the human and mouse genomes, and quantify a large number of genomic landscape features at high resolution around their integration sites and in control regions. We propose to analyze this data employing a recently developed functional inferential procedure and functional logistic regression, with the aim of gaining insights on the effects of genomic landscape features on the integration and fixation of endogenous retroviruses.</p

La tomografia a emissione di positroni (PET) con F-18 FDG nello studio delle formazioni espansive a sede surrenalica: confronto tra lesioni benigne e maligne

In this study, 15 patients (4 men and 11 women, mean age: 50 +/- 13 years) with unilateral adrenal masses detected on ultrasound (US), Computed Tomography (CT) and/or Magnetic Resonance (MR) studies were submitted to positron emission tomography (PET) with fluorine-18 deoxyglucose (FDG). Histology demonstrated 3 adenomas, 1 myelolipoma, 1 angiolipoma, 1 neurinoma, 1 cyst, 1 malignant pheochromocytoma, 4 carcinomas and 3 metastases. The patient population was divided into two groups. Group 1 (n = 7) consisted of benign adrenal lesions. Group 2 consisted of malignant adrenal tumors. Lesion measurements were performed on the basis of the results of US, CT and/or MR images. In Group 1, no FDG uptake was observed in adrenal masses. Conversely, in Group 2 adrenal lesions showed abnormally increased FDG uptake, suggesting high glucose tumor metabolism. No significant difference in lesion size was observed between Groups 1 and 2 (5.6 +/- 4.0 vs 6.3 +/- 3.0 cm). Furthermore, in 6 patients of Group 2, total body PET images showed abnormal FDG uptake in extra-adrenal locations, such as chest (n = 2) and abdominal (n = 5) lymph nodes, lungs (n = 6), liver (n = 5), pancreas (n = 1), bone (n = 1) and muscle (n = 1) tissues. In conclusion, the results of this study suggest that PET imaging with FDG can characterize adrenal masses. In particular, abnormally increased FDG uptake in adrenal malignancies allows to differentiate these abnormalities from benign lesions. Furthermore, total body imaging PET can identify extra-adrenal tumor sites in patients with malignant tumor

La Vigie marocaine

21 juin 19341934/06/21 (A25,N8280)-1934/06/21

Additional file 4: of Peak shape clustering reveals biological insights

ChIP-seq data. (XLSX 14 kb