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

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

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 2: of Peak shape clustering reveals biological insights

Random forest analysis. (XLSX 74 kb

IWTomics: testing high-resolution sequence-based "Omics" data at multiple locations and scales

With increased generation of high-resolution sequence-based "Omics" data, detecting statistically significant effects at different genomic locations and scales has become key to addressing several scientific questions. IWTomics is an R/Bioconductor package (integrated in Galaxy) that, exploiting sophisticated Functional Data Analysis techniques (i.e. statistical techniques that deal with the analysis of curves), allows users to pre-process, visualize and test these data at multiple locations and scales. The package provides a friendly, flexible and complete workflow that can be employed in many genomic and epigenomic applications

Agriculture adaptation in climate change : adaptation report

There is the need for a legal instrument that would first and foremost establish the executive powers of a new entity with overarching responsibilities and powers over all the authorities that have sectoral responsibilities for climate change. Such a legal instrument should also identify these sectoral authorities and their responsibilities, preferably within an Annex which could be amended and adjusted in a flexible manner. This instrument should be managed by a new unit on climate change within MRA and it should ensure integration without causing fragmentation between the sectors. At the same time, retaining the sectoral input would ensure that there is no duplication of roles, that the institutions are specialised within their own field and that the overarching institution does not becomes a bottle neck. In other words, different competent authorities responsible for the different sectoral policies and obligations should remain, but these must be answerable to an institution that has executive powers to ensure compliance and to coordinate long and short term planning with respect to climate change targets and impacts. By way of recommendation therefore, a legal instrument of this sort should seek to intervene as little as possible in the daily running of the sectoral policies and only apply its powers in situations of emergency when non compliance by the different sectors stalls the fulfilment of Malta’s obligations. Its main role should be to ensure implementation of a National Strategy on Mitigation and Adaptation. This legal instrument would not duplicate the role of public institutions that are already regulators for various sectors on climate change. It would however empower the new entity to take enforcement measures against the said institutions if they fail to do so. It would also ensure the implementation and enforcement of existing legislation that regulates the various sectors in order to rationalize their sustainable use and provide for conservation measures. This would benefit both the implementation of mitigation and adaptation measures. An entity entrusted with the overall responsibility for climate change law and policy must be legally empowered to ensure the implementation of national adaptation programmes. It must also coordinate the various sectors to carry out the necessary research to adopt and implement mitigation and adaptation measures. It must necessarily be supported by a parallel capacity building process in the various entities that run the day-to- day implementation functions. On an administrative level, without necessarily being included in a legal instrument, memoranda of understanding and stakeholder dialogue are indispensable tools to ensure cooperation. This will facilitate reaching mitigation and adaptation targets within the stipulated time frames. The mainstreaming of climate change impacts in national policies ensures the adoption of mitigation and adaptation measures and guarantees synergy and linkages amongst various public plans and programmes. Response to climate change should take place at a strategic level to assess beforehand the socio-economic impacts of any mitigation and adaptation measures adopted as a consequence prior to mainstreaming into national policy making. The existing Regulations on the Strategic Environment Assessment already include climate change impacts as one of the issues that needs to be taken into consideration in an SEA. Furthermore, for all those situations where an SEA is not required, Maltese authorities should promote pro-active adaptation measures such as, for example, in development planning, rather than take reactive adaptation measures. The new climate change legal instrument must ensure effective monitoring and stakeholder engagement, particularly the involvement of NGOS and Local Councils which increases public awareness on climate change issues. The new law should also take into consideration national security issues relating to climate change when formulating mitigation and adaptation strategies. The new law should also target the development of a research programme for climate change, including access to funding programmes. It is vital that Investment in research and development in all sectors should not remain on a voluntary basis. It will provide local industry with the necessary technology and it will generate specialised local expertise in a rapidly growing sector that is assuming a tremendous economic potential. Procrastination is detrimental on two main fronts. First because Malta will miss out in securing a place in this niche-market and second because we will keep relying upon foreign technology and expertise. Since Malta can rely on and pool from the scientific and technical advice of the European Environmental agency, it is best to concentrate on investing in scientific and technical research that addresses the local scenario. This should be earmarked as a priority for EU funded projects and care should be taken not to duplicate research conducted by EU agencies to which Malta has access, but rather to build upon it and apply it at the local level. It is also essential to include as a legal obligation the publication to civil society of information acquired as a result of research conducted at the EU level or carried out locally. It must be ensured that all sectors surmount the constraints due to the lack of a sound knowledge base on local ecosystem dynamics. Filling such a gap would serve to build local scientific evidence that would identify to what extent marine, terrestrial and aquatic flora and fauna groups are vulnerable to the impacts of climate change. Emphasis should be placed on minor and already vulnerable groups. All sectors should be legally bound to maintain a Geographic Information System to integrate data related to climate change, and any other data required apart from spatial information. Adopting and implementing the recommendations suggested by the National Sustainable Development Strategy for Malta would greatly enhance the implementation of adaptation measures relating to climate change, both on a cross-sectoral and sectoral level. At present it is envisaged that the government is currently preparing a new Bill on sustainable development, in the meantime the applicable provisions of the EPA by virtue of which the sustainable development strategy was published should continue to apply. Malta should also endeavour to promote more regional cooperation in the Mediterranean under the Barcelona Convention framework and Euro Med, to identify the adaptation needs of the Mediterranean littoral to the impacts of climate change. Authorities should initiate immediately, even at the regional Mediterranean level, studies to assess vulnerability due to climate change, how new opportunities may be tapped, how to meet with the negative consequences of climate change in the sector, how to ensure that local operators adapt to the shift in tourism trends as a result of climate change. There is the need of systematic and sustained awareness building programmes to educate all. This will intensify awareness and promote a change in behavioural patterns to improve adaptation to climate change. Increasing awareness of climate change impacts within the government, industry, and community sectors will support cultural change transitions that are required for the adoption of more climate change friendly technologies, designs, and operations by public and private operators. The new climate change law should also obligate the various sectors to formulate contingency plans. This serves to: address the negative impacts envisaged as a result of climate change particularly upon vulnerable groups. assess socio-economic implications, with increased insurance covers for risks resulting from the likely impacts of climate change. identify financial guarantees and incentives amongst the various stakeholders in all sectors.peer-reviewe