Tackling aspecific side reactions during histone propionylation: the promise of reversing overpropionylation

Histone proteins are essential elements for DNA packaging. Moreover, the PTMs that are extremely abundant on these proteins, contribute in modeling chromatin structure and recruiting enzymes involved in gene regulation, DNA repair and chromosome condensation. This fundamental aspect, together with the epigenetic inheritance of histone PTMs, underlines the importance of having biochemical techniques for their characterization. Over the past two decades, significant improvements in mass accuracy and resolution of mass spectrometers have made LC-coupled MS the strategy of choice for accurate identification and quantification of protein PTMs. Nevertheless, in previous work we disclosed the limitations and biases of the most widely adopted sample preparation protocols for histone propionylation, required prior to bottom-up MS analysis. In this work, however, we put forward a new specific and efficient propionylation strategy by means of propionic anhydride. In this method, aspecific overpropionylation at serine (S), threonine (T) and tyrosine (Y) is reversed by adding hydroxylamine (HA). We recommend using this method for future analysis of histones through bottom-up MS

The Development of a Screening Tool for Childcare Professionals to Detect and Refer Infant and Toddler Maltreatment and Trauma: A Tale of Four Countries

Abstract: Child maltreatment is considered a pressing social question, compromising the present and future mental and physical health of one in four children in Europe. While children younger than three years of age are especially vulnerable, few screening instruments are available for the detection of risk in this age group. The purpose of this research was to develop a screening tool for childcare professionals working in public and private daycare settings to support them in the early identification and referral of infants and toddlers exposed to emotional and physical abuse and neglect by primary caregivers, to be used in different settings across four European countries: Belgium, Italy, Latvia, and Hungary. Method: A stratified process was used to create the screening tool: We started by using Living lab methodology to co-create the screening tool with its final users, which was followed by testing the tool with a total of 120 childcare professionals from the four participating countries. Results: During the Living Lab phase, a screening tool with three layers was developed. The initial layer includes five “red flags” that signal particular concern and require immediate action. The second layer is a quick screener with twelve items focused on four areas: neglect of basic needs, delays in development, unusual behaviors, and interaction with caregivers. The third layer is an in-depth questionnaire that aids in formalizing a thorough observation of twenty-five items within the same four areas as the quick screener. After a one-day training session, 120 childcare professionals caring for children aged 0–3 from four countries assessed the screening tool and their overall training experience. Childcare professionals reported great satisfaction with the three-layered structure, which made the tool versatile, and agreed on its content, which was considered helpful in the daycare setting for the regular evaluation of the behavior of children and their primary caregivers, thus improving the early observation of change from the normal behavior of the infant or toddler. Conclusion: The three-layered screening tool was reported as feasible, practical, and with great content validity by childcare professionals working in four European countries

CMB-S4: Forecasting Constraints on Primordial Gravitational Waves

CMB-S4---the next-generation ground-based cosmic microwave background (CMB) experiment---is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the Universe, from the highest energies at the dawn of time through the growth of structure to the present day. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semi-analytic projection tool, targeted explicitly towards optimizing constraints on the tensor-to-scalar ratio, $r$, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2--3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments given a desired scientific goal. To form a closed-loop process, we couple this semi-analytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for $r > 0.003$ at greater than $5\sigma$, or, in the absence of a detection, of reaching an upper limit of $r < 0.001$ at $95\%$ CL.Comment: 24 pages, 8 figures, 9 tables, submitted to ApJ. arXiv admin note: text overlap with arXiv:1907.0447

CMB-S4: Forecasting Constraints on Primordial Gravitational Waves

Abstract: CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL

Carbon-ion radiotherapy monitoring in depth using secondary-ion tracking

The advantages of carbon-ion pencil beam radiotherapy imply an increased sensitivity of the dose distribution in the patient to any changes in the patient geometry, such as internal anatomical changes or patient misalignment. This can lead to a deterioration of the dose distribution within the patient. Monitoring methods of the internal patient’s dose distribution for carbon-ion beam radiotherapy are therefore of great importance to early detect possible under- or over-dosage in the patient, eventually, reduce the tumor safety margins applied around targeted tumor volumes and thus decrease the delivered dose in healthy tissues. Up to now, several non-invasive in-vivo ion-beam monitoring methods have been developed. These are mostly based on the detection of different kinds of secondary radiation, such as annihilation-photons from β+ emitters, prompt photons, or prompt charged nuclear fragments, emitted from a patient during the treatment delivery. These secondary radiations are the results of nuclear interactions of the primary treatment beam with the irradiated tissue. They potentially carry valuable information about the primary treatment beam range, position, or intensity in the patient. However, so far none of the monitoring methods has reached sufficient maturity for a wide application in clinical routine. This thesis aimed to develop methods for detection and localization of therapy-relevant geometry variations of 2 mm in head models, mimicking possible inter-fractional changes on the surface or inside patients’ heads. In contrast to previous research which concentrated on single stationary pencil beams, this thesis was focused on entire therapy-like treatment plans composed of thousands of single pencil beams with low numbers of primary-ions and irradiated under clinic-like conditions in terms of dose, dose rate, and tumor volume. In this thesis, methods were based on the detection and tracking of charged secondary nuclear fragments (secondary ions) emitted from the patient during carbon ion radiotherapy delivery. Subsequently, methods for analysis and interpretation of the measured secondary-ion paths (tracks) were developed. The developed radiation detection methods exploited the capabilities of a novel mini-tracker, based on the Timepix3 technology developed at CERN and positioned behind the patient. The deadtime-free data acquisition enabled a gapless recording of all impacting secondary ion tracks. Moreover, it enabled synchronization of the data with the beam application monitoring system, and thus assign each measured secondary ion with its respective pencil beam, opening entirely new research possibilities. The experiments were performed at the Heidelberg Ion-Beam Therapy Center (HIT), closely mimicking clinic-like conditions. Single fields of carbon-ion treatment plans with a prescribed fraction dose of 3 Gy (RBE) were used to simulate treatments of spherical tumor volumes in the used head models. Two types of head models were used: a homogeneous plastic cylinder and an anthropomorphic head phantom composed of real bones and tissue-equivalent materials. Secondary ions exiting the head models during irradiation were detected with a mini-tracker composed of two small (2cm²) parallel Timepix3 detectors placed downstream of the head with a certain angle with respect to the beam axis. Inter-fractional changes were modeled by adding or removing 2-mm-thick slabs positioned in front or inside the targeted head models. Within the thesis, it was demonstrated that the developed method for the analysis of the measured track distributions, taking into account the actual time-dependent position of the pencil beam, approximated the measured position of the secondary ion creation in the head model significantly better than the methods developed up to now. By using this method, surface changes down to 1 mm were found to be detectable even for the anatomical head phantom. Internal changes of 2-mm-thickness extending over the whole lateral tumor dimension (wide changes) were found to be detectable for all investigated positions between the dose plateau and the distal end of the tumor. The significance was at least 3 standard deviations for a single mini-tracker and of at least 9 standard deviations when using 8 mini-trackers at 30°, as it is planned for the future. Correct localization of all the studied changes was achieved within 6.3 mm of their actual position. This is sufficient to provide information to the clinicians about the part of the dose distribution which is affected. The detection of 2-mm-thick changes affecting only a part of the tumor (narrow changes), required the development of a new method based on the additional information on the lateral pencil beam positions. With this technique, internal 2-mm-thick changes as small as 10 mm in diameter placed in front of the tumor, were demonstrated to be detectable with a significance of almost 2 standard deviations. This technique makes the developed monitoring method sensitive to the lateral position of the cavity and thus reaches the third dimension. Positions of the mini-tracker closer to the beam axis were found to provide higher detection efficiencies due to the larger amount of data, but also lead to larger geometrical uncertainties and lower localization accuracies. At larger angles, the accuracy of the change localization was found to be better. For future measurements, multi-angle detection systems are recommended to maximize both detectability and localization accuracy. Finally, the applicability of the monitoring of carbon-ion pencil beam delivery in a real patient treatment was demonstrated by designing a patient-friendly measurement system that was shown to be safely used in a clinical environment. After investigating the influence of the developed system on the beam delivery, and with the fulfillment of all clinical and safety requirements, the integration of this system into the clinical workflow of the HIT facility was achieved. With this detection system, the first measurement of a real patient irradiation fraction was performed. The amount of measured data was sufficient to determine a secondary-ion emission profile along the depth of the patient’s head. And a differentiation between pencil beams with a 1 cm range difference was demonstrated. In conclusion, this thesis presents novel methods for carbon ion treatment monitoring of external and internal patient geometry changes in the head based on secondary ion tracking, allowing detection changes down to the clinically desired 2 mm. The designed monitoring system was proven to be well incorporable into a clinical workflow. Thus, the presented work paves the way towards monitoring inter-fractional changes along the beam direction during carbon-ion beam therapy and builds the basis for the upcoming clinical trial at the HIT facility

Outcomes of reverse total shoulder arthroplasty with postoperative scapular fracture

status: accepte

Optimal staging of lymphoma during pregnancy is crucial

status: publishe

EnTIRE: Mapping Normative Frameworks for EThics and Integrity of REsearch

Background: The areas of Research Ethics and Research Integrity (RE+RI) are rapidly evolving. In the EU and internationally, new legislation, codes of conduct and good practices are constantly being developed. New technologies (e.g. gene editing), complex statistical methods (e.g. biostatistics), pressure to publish and obtain grants, and growing emphasis on stakeholder driven science (e.g. public-private partnerships) increase the complexity of conducting science. In this complex and dynamic environment, researchers cannot easily identify the correct rules and best tools for responsible conduct of research. This also increasingly constitutes a challenge for RE+RI experts.Aim: Our aim is to create a platform that makes the normative framework governing RE+RI easily accessible, supports application in research and evaluation, and involves all stakeholders in a participatory way, thus achieving sustainability. The platform will foster uptake of ethical standards and responsible conduct of research, and ultimately support research excellence and strengthen society’s confidence in research and its findings.Vision: Our vision is that in order to make the normative framework governing RE+RI accessible, a dynamic online Wiki-platform, owned by the community of RE+RI stakeholders, is needed. The value of this platform will lie in the availability of practical information on how to comply with EU, national and discipline-specific RE+RI standards and legislation, including information on rules and procedures, educational materials, and illustrative cases and scenarios. Adopting open science (open source and open data) approaches, the platform will be easy to use, by applying novel techniques for data collection and comparison, enabling users to navigate quickly and intuitively to appropriate content. In order to keep the platform up-to-date and sustainable, it will be based upon active involvement of the RE+RI community, and will contribute to further development of this community by providing a podium for reflection and dialogue on RE+RI norms and practices.Objectives: EnTIRE’s work packages (WP) will: undertake an in-depth stakeholder consultation across EU countries exploring RE+RI experiences and practices in order to define the boundaries of data to be collected, and developing a mapping structure adapted to user needs (WP 2); assemble the relevant normative elements, including RE+RI rules and procedures, educational materials, and illustrative casuistry, and identify relevant institutions across EU countries (WP 3-5); develop a user-friendly Wiki-platform and online resources to foster and facilitate responsible research practices and to promote compliance amongst European researchers with RE+RI standards and pertinent legislation and regulations (WP 6); and foster further development of the RE+RI community, that will support the platform and be supported by it, will keep the information up-to-date, disseminate the project’s findings and develop innovative strategies for maintaining the platform and building relationships to relevant organisations for further dissemination, including sustainable funding (WP 7).Relevance to the work programme: The proposed project responds directly to the core requirement of call SwafS-16-2016 to ‘provide a dynamic mapping of the RE+RI normative framework which applies to scientific research conducted in the EU and beyond’. Our proposal does this by using a participatory approach, stimulating knowledge transfer regarding codes and regulations, resources and institutions, and cases, by applying innovative ICT solutions and open science approaches, and by further developing a community of active users, to enable sustainability after the end of the project

Controlling T cells spreading, mechanics and activation by micropatterning

International audienceAbstract We designed a strategy, based on a careful examination of the activation capabilities of proteins and antibodies used as substrates for adhering T cells, coupled to protein microstamping to control at the same time the position, shape, spreading, mechanics and activation state of T cells. Once adhered on patterns, we examined the capacities of T cells to be activated with soluble anti CD3, in comparison to T cells adhered to a continuously decorated substrate with the same density of ligands. We show that, in our hand, adhering onto an anti CD45 antibody decorated surface was not affecting T cell calcium fluxes, even adhered on variable size micro-patterns. Aside, we analyzed the T cell mechanics, when spread on pattern or not, using Atomic Force Microscopy indentation. By expressing MEGF10 as a non immune adhesion receptor in T cells we measured the very same spreading area on PLL substrates and Young modulus than non modified cells, immobilized on anti CD45 antibodies, while retaining similar activation capabilities using soluble anti CD3 antibodies or through model APC contacts. We propose that our system is a way to test activation or anergy of T cells with defined adhesion and mechanical characteristics, and may allow to dissect fine details of these mechanisms since it allows to observe homogenized populations in standardized T cell activation assays