Fidelity enhancement by logical qubit encoding

We demonstrate coherent control of two logical qubits encoded in a decoherence free subspace (DFS) of four dipolar-coupled protons in an NMR quantum information processor. A pseudo-pure fiducial state is created in the DFS, and a unitary logical qubit entangling operator evolves the system to a logical Bell state. The four-spin molecule is partially aligned by a liquid crystal solvent, which introduces strong dipolar couplings among the spins. Although the system Hamiltonian is never fully specified, we demonstrate high fidelity control over the logical degrees of freedom. In fact, the DFS encoding leads to higher fidelity control than is available in the full four-spin Hilbert space.Comment: 10 pages, 2 figure

Foundations and scaffolding: exploring literature and practice to build a new curriculum framework for TU Dublin

The IMPACT project at TU Dublin has been informed in part by the outcomes of the Co-CREATE project in 2019-20. Co-CREATE was a Team Teaching Fellowship project to support and underpin the building of a quality curriculum framework for the new technological university. A number of IMPACT projects (for example, NorthStar) have continued the work started within the Co-CREATE project to make it sustainable and embedded within the university. We present findings from one element of the Co-CREATE project which has informed a range of initiatives in IMPACT. This is the review of literature and practice undertaken to underpin the Co-CREATE project. The review addresses student voice and agency in curriculum design, enhancing sustainability in curriculum design, and identifies the importance of interdisciplinary approaches in the development of new programmes and provision. Curriculum in higher education has been discussed in educational literature as a fluid and contested concept. It relates to product, often described as content and syllabus, but also process, socially and politically embedded with the potential for change in positive or less positive directions. We present our findings and insights, and the recommendations we have made to stakeholders in our institution. We reflect on the purposes of higher education in the 21st century, and consider the UN Sustainable Development Goals and how they relate to TU Dublin’s mission and vision. We consider the place of graduate attributes, innovation, global citizenship and the impact of new technologies. We report on the development of curriculum frameworks and design at other technological universities, and how our experiences might be more diverse than those of traditional universities. We consider the impact of “connected” approaches to curriculum in research-intensive universities, and how these might be translated to the technological university context. We conclude with recommendations arising from the review of literature and practice which underpinned further work in Co-CREATE, and which may also be of value to others commencing this kind of work or reviewing curricula

Improved functional overview of protein complexes using inferred epistatic relationships

<p>Abstract</p> <p>Background</p> <p>Epistatic Miniarray Profiling(E-MAP) quantifies the net effect on growth rate of disrupting pairs of genes, often producing phenotypes that may be more (negative epistasis) or less (positive epistasis) severe than the phenotype predicted based on single gene disruptions. Epistatic interactions are important for understanding cell biology because they define relationships between individual genes, and between sets of genes involved in biochemical pathways and protein complexes. Each E-MAP screen quantifies the interactions between a logically selected subset of genes (e.g. genes whose products share a common function). Interactions that occur between genes involved in different cellular processes are not as frequently measured, yet these interactions are important for providing an overview of cellular organization.</p> <p>Results</p> <p>We introduce a method for combining overlapping E-MAP screens and inferring new interactions between them. We use this method to infer with high confidence 2,240 new strongly epistatic interactions and 34,469 weakly epistatic or neutral interactions. We show that accuracy of the predicted interactions approaches that of replicate experiments and that, like measured interactions, they are enriched for features such as shared biochemical pathways and knockout phenotypes. We constructed an expanded epistasis map for yeast cell protein complexes and show that our new interactions increase the evidence for previously proposed inter-complex connections, and predict many new links. We validated a number of these in the laboratory, including new interactions linking the SWR-C chromatin modifying complex and the nuclear transport apparatus.</p> <p>Conclusion</p> <p>Overall, our data support a modular model of yeast cell protein network organization and show how prediction methods can considerably extend the information that can be extracted from overlapping E-MAP screens.</p

Preparation and Crystal Structure of a Platinum(II) Complex of [CH2N(CH2COOH)CH2CONH2]2, the Hydrolysis Product of an Anti-Tumour Bis(3,5-Dioxopiperazin-1-YL)Alkane

The synthesis and crystal and molecular structures of the platinum(II) complex Pt(HL)Cl where H2L is the diacid diamide –[CH2N(CH2COOH)CH2CONH2]2, a hydrolytic metabolite of an antitumour active bis(3,5-dioxopiperazin-1-yl)alkane are reported. The complex is square planar and contains HL– as a tridentate 2N (amino), O (carboxylate) donor. The metal to ligand bond distances are Pt-Cl 2.287(1) Å, Pt-O 2.002 (1) Å, Pt-Ntrans Cl 2.014(1) Å and Pt-Ntrans O 2.073 Å. There is extensive hydrogen bonding, each molecule of Pt(HL)Cl being intermolecularly hydrogen bonded to ten others giving a 3-dimensional network. There is also one intramolecular H-bond

A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events

Protein complexes are responsible for the bulk of activities within the cell, but how their behavior and abundance varies across tumors remains poorly understood. By combining proteomic profiles of breast tumors with a large-scale protein-protein interaction network, we have identified a set of 285 high-confidence protein complexes whose subunits have highly correlated protein abundance across tumor samples. We used this set to identify complexes that are reproducibly under- or overexpressed in specific breast cancer subtypes. We found that mutation or deletion of one subunit of a co-regulated complex was often associated with a collateral reduction in protein expression of additional complex members. This collateral loss phenomenon was typically evident from proteomic, but not transcriptomic, profiles, suggesting post-transcriptional control. Mutation of the tumor suppressor E-cadherin (CDH1) was associated with a collateral loss of members of the adherens junction complex, an effect we validated using an engineered model of E-cadherin loss. Ryan et al. develop an approach to identify co-regulated protein complexes from breast tumor proteomic profiles and demonstrate that genomic loss of one subunit is often associated with a reduction in the protein expression of an entire complex.European Commission - Seventh Framework Programme (FP7)Science Foundation IrelandWellcome TrustHealth Research BoardCancer Research UKBreast Cancer No

In vitro dissolution models for the prediction of in vivo performance of an oral mesoporous silica formulation

Drug release from mesoporous silica systems has been widely investigated in vitro using USP Type II (paddle) dissolution apparatus. However, it is not clear if the observed enhanced in vitro dissolution can forecast drug bioavailability in vivo. In this study, the ability of different in vitro dissolution models to predict in vivo oral bioavailability in a pig model was examined. The fenofibrate-loaded mesoporous silica formulation was compared directly to a commercial reference product, Lipantil Supra®. Three in vitro dissolution methods were considered; USP Type II (paddle) apparatus, USP Type IV (flow-through cell) apparatus and a USP IV Transfer model (incorporating a SGF to FaSSIF-V2 media transfer). In silico modelling, using a physiologically based pharmacokinetic modelling and simulation software package (Gastroplus™), to generate in vitro/in vivo relationships was also investigated. The study demonstrates that the in vitro dissolution performance of a mesoporous silica formulation varies depending on the dissolution apparatus utilised and experimental design. The findings show that the USP IV transfer model was the best predictor of in vivo bioavailability. The USP Type II (paddle) apparatus was not effective at forecasting in vivo behaviour. This observation is likely due to hydrodynamic differences between the two apparatus and the ability of the transfer model to better simulate gastrointestinal transit. The transfer model is advantageous in forecasting in vivo behaviour for formulations which promote drug supersaturation and as a result are prone to precipitation to a more energetically favourable, less soluble form. The USP IV transfer model could prove useful in future mesoporous silica formulation development. In silico modelling has the potential to assist in this process. However, further investigation is required to overcome the limitations of the model for solubility enhancing formulations