Group theoretical and topological analysis of the quantum spin Hall effect in silicene

Silicene consists of a monolayer of silicon atoms in a buckled honeycomb structure. It was recently discovered that the symmetry of such a system allows for interesting Rashba spin-orbit effects. A perpendicular electric field is able to couple to the sublattice pseudospin, making it possible to electrically tune and close the band gap. Therefore, external electric fields may generate a topological phase transition from a topological insulator to a normal insulator (or semimetal) and vice versa. The contribution of the present article to the study of silicene is twofold: First, we perform a group theoretical analysis to systematically construct the Hamiltonian in the vicinity of the $K$ points of the Brillouin zone and discover a new, but symmetry allowed term. Subsequently, we identify a tight binding model that corresponds to the group theoretically derived Hamiltonian near the $K$ points. Second, we start from this tight binding model to analyze the topological phase diagram of silicene by an explicit calculation of the $Z_2$ topological invariant of the band structure. To this end, we calculate the $Z_2$ topological invariant of the honeycomb lattice in a manifestly gauge invariant way which allows us to include $S_z$ symmetry breaking terms -- like Rashba spin orbit interaction -- into the topological analysis. Interestingly, we find that the interplay of two Rashba terms can generate a non-trivial quantum spin Hall phase in silicene. This is in sharp contrast to the more extensively studied honeycomb system graphene where Rashba spin orbit interaction is known to compete with the quantum spin Hall effect in a potentially detrimental way.Comment: 24 pages, 6 figure

EUPATI: Collaboration between patients, academia and industry to champion the informed patient in the research and development of medicines

The value of collaborations and partnerships between different stakeholders to achieve optimum outcomes in the medicines research and development process is being recognised. Historically, there has been a lack of collaboration with patients and many research consortiums consisting mainly of academia and/or industry partners. Although patient experts are able to bring valuable first-hand experience and insights, they might not possess detailed knowledge about medicines research and development to actively participate in the collaboration process. The European Patients’ Academy on Therapeutic Innovation (EUPATI) was established to deliver training to patient experts, and education resourcesto patient advocates and members of the health-interested public across Europe. EUPATI was launched in February 2012 and is a patient-led Innovative Medicines Initiative (IMI) project, with a multi-stakeholder consortium of patient advocates, academia, industry and not-for-profit organisations. Training and educational materials will be used for capacity building among patients, for educating patient advocates and for informing the health-interested public. The successful uptake of EUPATI’s materials will hopefully translate into a new paradigm of increased patient involvement across the entire medicines research and development process, bringing mutual benefits, including better medicines, to all stakeholders

Artificial intelligence based deconvolving on megavoltage photon beam profiles for radiotherapy applications

Objective. The aim of this work is an AI based approach to reduce the volume effect of ionization chambers used to measure high energy photon beams in radiotherapy. In particular for profile measurements, the air-filled volume leads to an inaccurate measurement of the penumbra. Approach. The AI-based approach presented in this study was trained with synthetic data intended to cover a wide range of realistic linear accelerator data. The synthetic data was created by randomly generating profiles and convolving them with the lateral response function of a Semiflex 3D ionization chamber. The neuronal network was implemented using the open source tensorflow.keras machine learning framework and a U-Net architecture. The approach was validated on three accelerator types (Varian TrueBeam, Elekta VersaHD, Siemens Artiste) at FF and FFF energies between 6 MV and 18 MV at three measurement depths. For each validation, a Semiflex 3D measurement was compared against a microDiamond measurement, and the AI processed Semiflex 3D measurement was compared against the microDiamond measurement. Main results. The AI approach was validated with dataset containing 306 profiles measured with Semiflex 3D ionization chamber and microDiamond. In 90% of the cases, the AI processed Semiflex 3D dataset agrees with the microDiamond dataset within 0.5 mm/2% gamma criterion. 77% of the AI processed Semiflex 3D measurements show a penumbra difference to the microDiamond of less than 0.5 mm, 99% of less than 1 mm. Significance. This AI approach is the first in the field of dosimetry which uses synthetic training data. Thus, the approach is able to cover a wide range of accelerators and the whole specified field size range of the ionization chamber. The application of the AI approach offers an quality improvement and time saving for measurements in the water phantom, in particular for large field size

An Early Transcriptional Analysis of Fracture Hematoma in Rat

Among other stressors, age and mechanical constraints significantly influence regeneration cascades in bone healing. Here, our aim was to identify genes and, through their functional annotation, related biological processes that are influenced by an interaction between the effects of mechanical fixation stability and age. Therefore, at day three post-osteotomy, chip-based whole- genome gene expression analyses of fracture hematoma tissue were performed for four groups of Sprague-Dawley rats with a 1.5-mm osteotomy gap in the femora with varying age (12 vs. 52 weeks - biologically challenging) and external fixator stiffness (mechanically challenging). From 31099 analysed genes, 1103 genes were differentially expressed between the six possible combinations of the four groups and from those 144 genes were identified as statistically significantly influenced by the interaction between age and fixation stability. Functional annotation of these differentially expressed genes revealed an association with extracellular space, cell migration or vasculature development. The chip-based whole-genome gene expression data was validated by q-RT-PCR at days three and seven post-osteotomy for MMP-9 and MMP-13, members of the mechanosensitive matrix metalloproteinase family and key players in cell migration and angiogenesis. Furthermore, we observed an interaction of age and mechanical stimuli in vitro on cell migration of mesenchymal stromal cells. These cells are a subpopulation of the fracture hematoma and are known to be key players in bone regeneration. In summary, these data correspond to and might explain our previously described biomechanical healing outcome after six weeks in response to fixation stiffness variation. In conclusion, our data highlight the importance of analysing the influence of risk factors of fracture healing (e.g. advanced age, suboptimal fixator stability) in combination rather than alone

Biobanking from the patient perspective

Biobanks and biobanking research plays an increasingly important role in healthcare research and delivery as health systems become more patient-centred and medicine becomes more personalised. There is also growing acceptance and appreciation of the value that patients, patient advocacy organisations and the public can bring as stakeholders in biobanking and more generally in research. Therefore, the importance of active, early and sustained engagement and involvement of patient and public representatives in biobanks will become increasingly relevant. Organising and facilitating patient and public involvement in biobanking takes considerable time and effort for all stakeholders involved. Therefore, for any biobank operator considering involving patients and the public in their biobanking activities, consideration of best practices, current guidance, ethical issues and evaluation of involvement will be important. In this article, we demonstrate that patients are much more than donors to biobanks—they are collaborators at the heart of biobanking with an important voice to identify perspective, which can be an extremely valuable resource for all biobanks to utilise. The case studies herein provide examples of good practice of patient involvement in biobanking as well as outcomes from these practices, and lessons learned. Our aim is to provide useful insights from these efforts and potential future strategies for the multiple stakeholders that work with patients and the public involved in biobank-based research

Amundsen Sea Mollusca from the BIOPEARL II expedition

Information regarding the molluscs in this dataset is based on the epibenthic sledge (EBS) samples collected during the cruise BIOPEARL II / JR179 RRS James Clark Ross in the austral summer 2008. A total of 35 epibenthic sledge deployments have been performed at five locations in the Amundsen Sea at Pine Island Bay (PIB) and the Amundsen Sea Embayment (ASE) at depths ranging from 476 to 3501m. This presents a unique and important collection for the Antarctic benthic biodiversity assessment as the Amundsen Sea remains one of the least known regions in Antarctica. Indeed the work presented in this dataset is based on the first benthic samples collected with an EBS in the Amundsen Sea. However we assume that the data represented are an underestimation of the real fauna present in the Amundsen Sea. In total 9261 specimens belonging to 6 classes 55 families and 97 morphospecies were collected. The species richness per station varied between 6 and 43. Gastropoda were most species rich 50 species followed by Bivalvia (37), Aplacophora (5), Scaphopoda (3) and one from each of Polyplacophora and Monoplacophora

An Approach to Solving the Complex Clinicogenomic Data Landscape in Precision Oncology: Learnings From the Design of WAYFIND-R, a Global Precision Oncology Registry

Oncología de precisión; Datos clinicogenómicosOncologia de precisió; Dades clinicogenòmiquesPrecision oncology; Clinicogenomic dataPrecision oncology, where patients are given therapies based on their genomic profile and disease trajectory, is rapidly evolving to become a pivotal part of cancer management, supported by regulatory approvals of biomarker-matched targeted therapies and cancer immunotherapies. However, next-generation sequencing (NGS)–based technologies have revealed an increasing number of molecular-based cancer subtypes with rare patient populations, leading to difficulties in executing/recruiting for traditional clinical trials. Therefore, approval of novel therapeutics based on traditional interventional studies may be difficult and time consuming, with delayed access to innovative therapies. Real-world data (RWD) that describe the patient journey in routine clinical practice can help elucidate the clinical utility of NGS-based genomic profiling, multidisciplinary case discussions, and targeted therapies. We describe key learnings from the setup of WAYFIND-R (NCT04529122), a first-of-its-kind global cancer registry collecting RWD from patients with solid tumors who have undergone NGS-based genomic profiling. The meaning of ‘generalizability’ and ‘high quality’ for RWD across different geographic areas was revisited, together with patient recruitment processes, and data sharing and privacy. Inspired by these learnings, WAYFIND-R’s design will help physicians discuss patient treatment plans with their colleagues, improve understanding of the impact of treatment decisions/cancer care processes on patient outcomes, and provide a platform to support the design and conduct of further clinical/epidemiologic research. WAYFIND-R demonstrates user-friendly, electronic case report forms, standardized collection of molecular tumor board-based decisions, and a dashboard providing investigators with access to local cohort-level data and the ability to interact with colleagues or search the entire registry to find rare populations. Overall, WAYFIND-R will inform on best practice for NGS-based treatment decisions by clinicians, foster global collaborations between cancer centers and enable robust conclusions regarding outcome data to be drawn, improve understanding of disparities in patients’ access to advanced diagnostics and therapies, and ultimately drive advances in precision oncology

Unraveling local tissue changes within severely injured skeletal muscles in response to MSC-based intervention using MALDI Imaging mass spectrometry

Pre-clinical and clinical studies are now beginning to demonstrate the high potential of cell therapies in enhancing muscle regeneration. We previously demonstrated functional benefit after the transplantation of autologous bone marrow mesenchymal stromal cells (MSC-TX) into a severe muscle crush trauma model. Despite our increasing understanding of the molecular and cellular mechanisms underlying MSC's regenerative function, little is known about the local molecular alterations and their spatial distribution within the tissue after MSC-TX. Here, we used MALDI imaging mass spectrometry (MALDI-IMS) in combination with multivariate statistical strategies to uncover previously unknown peptide alterations within severely injured skeletal muscles. Our analysis revealed that very early molecular alterations in response to MSC-TX occur largely in the region adjacent to the trauma and only to a small extent in the actual trauma region. Using "bottom up" mass spectrometry, we subsequently identified the proteins corresponding to the differentially expressed peptide intensity distributions in the specific muscle regions and used immunohistochemistry to validate our results. These findings extend our current understanding about the early molecular processes of muscle healing and highlights the critical role of trauma adjacent tissue during the early therapeutic response upon treatment with MSC

A prospective, non-randomized phase II trial of Trastuzumab and Capecitabine in patients with HER2 expressing metastasized pancreatic cancer

Background: Pancreatic cancer is the fourth most common cause of cancer related death in Western countries. Advantages in surgical techniques, radiation and chemotherapy had almost no impact on the long term survival of affected patients. Therefore, the need for better treatment strategies is urgent. HER2, a receptor tyrosine kinase of the EGFR family, involved in signal transduction pathways leading to cell growth and differentiation is overexpressed in a number of cancers, including breast and pancreatic cancer. While in breast cancer HER2 has already been successfully used as a treatment target, there are only limited data evaluating the effects of inhibiting HER2 tyrosine kinases in patients with pancreatic cancer. Methods: Here we report the design of a prospective, non-randomized multi-centered Phase II clinical study evaluating the effects of the Fluoropyrimidine-carbamate Capecitabine (Xeloda (R)) and the monoclonal anti-HER2 antibody Trastuzumab (Herceptin (R)) in patients with non-resectable, HER2 overexpressing pancreatic cancer. Patients eligible for the study will receive Trastuzumab infusions on day 1, 8 and 15 concomitant to the oral intake of Capecitabine from day 1 to day 14 of each three week cylce. Cycles will be repeated until tumor progression. A total of 37 patients will be enrolled with an interim analysis after 23 patients. Discussion: Primary end point of the study is to determine the progression free survival after 12 weeks of bimodal treatment with the chemotherapeutic agent Capecitabine and the anti-HER2 antibody Trastuzumab. Secondary end points include patient's survival, toxicity analysis, quality of life, the correlation of HER2 overexpression and clinical response to Trastuzumab treatment and, finally, the correlation of CA19-9 plasma levels and progression free intervals