"Smoking gun" signatures of topological milestones in trivial materials by measurement fine-tuning and data postselection

Exploring the topology of electronic bands is a way to realize new states of matter with possible implications for information technology. Because bands cannot always be observed directly, a central question is how to tell that a topological regime has been achieved. Experiments are often guided by a prediction of a unique signal or a pattern, called "the smoking gun". Examples include peaks in conductivity, microwave resonances, and shifts in interference fringes. However, many condensed matter experiments are performed on relatively small, micron or nanometer-scale, specimens. These structures are in the so-called mesoscopic regime, between atomic and macroscopic physics, where phenomenology is particularly rich. In this paper, we demonstrate that the trivial effects of quantum confinement, quantum interference and charge dynamics in nanostructures can reproduce accepted smoking gun signatures of triplet supercurrents, Majorana modes, topological Josephson junctions and fractionalized particles. The examples we use correspond to milestones of topological quantum computing: qubit spectroscopy, fusion and braiding. None of the samples we use are in the topological regime. The smoking gun patterns are achieved by fine-tuning during data acquisition and by subsequent data selection to pick non-representative examples out of a fluid multitude of similar patterns that do not generally fit the "smoking gun" designation. Building on this insight, we discuss ways that experimentalists can rigorously delineate between topological and non-topological effects, and the effects of fine-tuning by deeper analysis of larger volumes of data.Comment: Data are available through Zenodo at DOI: 10.5281/zenodo.834930

Integrative transcriptomic analysis in human and mouse model of anaphylaxis identifies gene signatures associated with cell movement, migration and neuroinflammatory signalling

Background: Anaphylaxis is an acute life-threatening allergic reaction and a concern at a global level; therefore, further progress in understanding the underlying mechanisms and more effective strategies for diagnosis, prevention and management are needed. Objective: We sought to identify the global architecture of blood transcriptomic features of anaphylaxis by integrating expression data from human patients and mouse model of anaphylaxis. Methods: Bulk RNA-sequencings of peripheral whole blood were performed in: i) 14 emergency department (ED) patients with acute anaphylaxis, predominantly to Hymenoptera venom, ii) 11 patients with peanut allergy undergoing double-blind, placebo-controlled food challenge (DBPCFC) to peanut, iii) murine model of IgE-mediated anaphylaxis. Integrative characterisation of differential gene expression, immune cell-type-specific gene expression profiles, and functional and pathway analysis was undertaken. Results: 1023 genes were commonly and significantly dysregulated during anaphylaxis in ED and DBPCFC patients; of those genes, 29 were also dysregulated in the mouse model. Cell-type-specific gene expression profiles showed a rapid downregulation of blood basophil and upregulation of neutrophil signature in ED and DBPCFC patients and the mouse model, but no consistent and/or significant differences were found for other blood cells. Functional and pathway analysis demonstrated that human and mouse blood transcriptomic signatures of anaphylaxis follow trajectories of upregulation of cell movement, migration and neuroinflammatory signalling, and downregulation of lipid activating nuclear receptors signalling. Conclusion: Our study highlights the matched and extensive blood transcriptomic changes and suggests the involvement of discrete cellular components and upregulation of migration and neuroinflammatory pathways during anaphylaxis

Planar Josephson Junctions Templated by Nanowire Shadowing

More and more materials, with a growing variety of properties, are built into electronic devices. This is motivated both by increased device performance and by the studies of materials themselves. An important type of device is a Josephson junction based on the proximity effect between a quantum material and a superconductor, useful for fundamental research as well as for quantum and other technologies. When both junction contacts are placed on the same surface, such as a two-dimensional material, the junction is called ``planar". One outstanding challenge is that not all materials are amenable to the standard planar junction fabrication. The device quality, rather than the intrinsic characteristics, may be defining the results. Here, we introduce a technique in which nanowires are placed on the surface and act as a shadow mask for the superconductor. The advantages are that the smallest dimension is determined by the nanowire diameter and does not require lithography, and that the junction is not exposed to chemicals such as etchants. We demonstrate this method with an InAs quantum well, using two superconductors - Al and Sn, and two semiconductor nanowires - InAs and InSb. The junctions exhibit critical current levels consistent with transparent interfaces and uniform width. We show that the template nanowire can be operated as a self-aligned electrostatic gate. Beyond single junctions, we create SQUIDs with two gate-tunable junctions. We suggest that our method can be used for a large variety of quantum materials including van der Waals layers, topological insulators, Weyl semimetals and future materials for which proximity effect devices is a promising research avenue.Comment: Written using The Block Method. Data on Zenodo DOI: https://doi.org/10.5281/zenodo.641608

Generic nano-imprint process for fabrication of nanowire arrays

A generic process has been developed to grow nearly defect free arrays of (heterostructured) InP and GaP nanowires. Soft nanoimprint lithography has been used to pattern gold particle arrays on full 2 inch substrates. After lift-off organic residues remain on the surface, which induce the growth of additional undesired nanowires. We show that cleaning of the samples before growth with piranha solution in combination with a thermal anneal at 550 C for InP and 700 C for GaP results in uniform nanowire arrays with 1% variation in nanowire length, and without undesired extra nanowires. Our chemical cleaning procedure is applicable to other lithographic techniques such as e-beam lithography, and therefore represents a generic process.Comment: 12 pages, 4 figures, 2 table

Постать Тараса Шевченка в рецепції Ліни Костенко

У статті розглядається поетика творення Ліною Костенко образу Кобзаря крізь призму власного "я", через пережиті відчуття поета-шістдесятника, що своєю проекцією нагадують душевні терзання великого поета.В статье рассмотрена поэтика создания Линой Костенко образа Тараса Шевченко сквозь призму собственного "я", через пережитые ощущения поэта-шестидесятника, своей проекцией напоминающие душевные терзания великого поэта.The article deals with the problem of the poetics creation by Lina Kostenko Taras Shevchenko’ image through a prism her own mind, through sensations of the poet-sixtier, by the projection reminding sincere torments the great poet is considered

Local Network Topology in Human Protein Interaction Data Predicts Functional Association

The use of high-throughput techniques to generate large volumes of protein-protein interaction (PPI) data has increased the need for methods that systematically and automatically suggest functional relationships among proteins. In a yeast PPI network, previous work has shown that the local connection topology, particularly for two proteins sharing an unusually large number of neighbors, can predict functional association. In this study we improved the prediction scheme by developing a new algorithm and applied it on a human PPI network to make a genome-wide functional inference. We used the new algorithm to measure and reduce the influence of hub proteins on detecting function-associated protein pairs. We used the annotations of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as benchmarks to compare and evaluate the function relevance. The application of our algorithms to human PPI data yielded 4,233 significant functional associations among 1,754 proteins. Further functional comparisons between them allowed us to assign 466 KEGG pathway annotations to 274 proteins and 123 GO annotations to 114 proteins with estimated false discovery rates of <21% for KEGG and <30% for GO. We clustered 1,729 proteins by their functional associations and made functional inferences from detailed analysis on one subcluster highly enriched in the TGF-β signaling pathway (P<10−50). Analysis of another four subclusters also suggested potential new players in six signaling pathways worthy of further experimental investigations. Our study gives clear insight into the common neighbor-based prediction scheme and provides a reliable method for large-scale functional annotation in this post-genomic era