Classification using distance nearest neighbours

This paper proposes a new probabilistic classification algorithm using a Markov random field approach. The joint distribution of class labels is explicitly modelled using the distances between feature vectors. Intuitively, a class label should depend more on class labels which are closer in the feature space, than those which are further away. Our approach builds on previous work by Holmes and Adams (2002, 2003) and Cucala et al. (2008). Our work shares many of the advantages of these approaches in providing a probabilistic basis for the statistical inference. In comparison to previous work, we present a more efficient computational algorithm to overcome the intractability of the Markov random field model. The results of our algorithm are encouraging in comparison to the k-nearest neighbour algorithm.Comment: 12 pages, 2 figures. To appear in Statistics and Computin

Magnetic domain evolution in permalloy mesoscopic dots

Permalloy (Ni80Fe20) squares (30 nm thick and w mu m wide; 1 less than or equal to w less than or equal to 200 mu m) and circular disks (30 nm thick and r mu m diameter; 1 less than or equal to r less than or equal to 200 mu m) prepared on a GaAs (100) substrate were observed in both their demagnetized and remanent states by magnetic force microscopy (MFM) associated with non-contact atomic force microscopy (NC-AFM). The squares (2 less than or equal to w mu m) exhibited conventional closure domains and the corner plays a very important role in creating new walls. The circular disks, on the other hand, formed either vortex domain (5 less than or equal to r less than or equal to 20 mu m) or multi-domain (50 less than or equal to r mu m) states, The magnetization rotation is observed by MFM to change according to the size and shape of the elements, The MFM observations are supported by micromagnetic calculations which confirm the effect of the corner on the domain wall formation

The Shallow Geological Model: mapping and monitoring the marine landscape

Managing our seas without a sound knowledge of the sea-bed environment and the processes that shape the sea-bed characteristics makes it difficult to conserve key areas, maintain biodiversity and economically develop our marine resources in an efficient and sustainable way. Recent developments in marine landscape mapping, visualisation techniques and instant data access provide timely, proven technologies that are now in widespread use

Encrypted accelerated least squares regression.

Information that is stored in an encrypted format is, by definition, usually not amenable to statistical analysis or machine learning methods. In this paper we present detailed analysis of coordinate and accelerated gradient descent algorithms which are capable of fitting least squares and penalised ridge regression models, using data encrypted under a fully homomorphic encryption scheme. Gradient descent is shown to dominate in terms of encrypted computational speed, and theoretical results are proven to give parameter bounds which ensure correctness of decryption. The characteristics of encrypted computation are empirically shown to favour a non-standard acceleration technique. This demonstrates the possibility of approximating conventional statistical regression methods using encrypted data without compromising privacy

Definition of valid proteomic biomarkers: a bayesian solution

Clinical proteomics is suffering from high hopes generated by reports on apparent biomarkers, most of which could not be later substantiated via validation. This has brought into focus the need for improved methods of finding a panel of clearly defined biomarkers. To examine this problem, urinary proteome data was collected from healthy adult males and females, and analysed to find biomarkers that differentiated between genders. We believe that models that incorporate sparsity in terms of variables are desirable for biomarker selection, as proteomics data typically contains a huge number of variables (peptides) and few samples making the selection process potentially unstable. This suggests the application of a two-level hierarchical Bayesian probit regression model for variable selection which assumes a prior that favours sparseness. The classification performance of this method is shown to improve that of the Probabilistic K-Nearest Neighbour model

Evolution of Antarctic Sea Ice Ahead of the Record Low Annual Maximum Extent in September 2023

The 2023 Antarctic sea ice extent (SIE) maximum on 7 September was the lowest annual maximum in the satellite era (16.98 × 106 km2), with the largest contributions to the anomaly coming from the Ross (37.7%, −0.57 × 106 km2) and Weddell (32.9%, −0.49 × 106 km2) Seas. The SIE was low due to anomalously warm (>0.3°C) upper-ocean temperatures combined with anomalously strong northerly winds impeding the ice advance during the fall and winter. Northerly winds of >12 ms−1 in the Weddell Sea occurred because of negative pressure anomalies over the Antarctic Peninsula, while those in the Ross Sea were associated with extreme blocking episodes off the Ross Ice Shelf. The Ross Sea experienced an unprecedented SIE decrease of −1.08 × 103 km2 d−1 from 1 June till the annual maximum. The passage of quasi-stationary and explosive polar cyclones contributed to periods of southward ice-edge shift in both sectors

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

The cohesin complex plays an essential role in chromosome maintenance and transcriptional regulation. Recurrent somatic mutations in the cohesin complex are frequent genetic drivers in cancer including myelodysplatic syndromes (MDS) and acute myeloid leukemia (AML). Here, using genetic dependency screens of STAG2-mutant AML, we identified DNA damage repair and replication as genetic dependencies in cohesin-mutant cells. We demonstrated increased levels of DNA damage and sensitivity of cohesin-mutant cells to PARP inhibition. We developed a mouse model of MDS in which Stag2 mutations arise as clonal secondary lesions in the background of clonal hematopoiesis driven by Tet2 mutations, and demonstrated selective depletion of cohesin-mutant cells with PARP inhibition in vivo. Finally, we demonstrated a shift from STAG2- to STAG1-containing cohesin complexes in cohesin-mutant cells, which is associated with longer DNA loop extrusion, more intermixing of chromatin compartments, and increased interaction with PARP and RPA proteins. Our findings inform the biology and therapeutic opportunities for cohesin-mutant malignancies

Record low Antarctic sea ice cover in February 2022

On 25 February 2022 Antarctic sea ice extent (SIE) dropped to a satellite-era record low level of 1.92 × 106 km2, 0.92 × 106 km2 below the long-term mean. The area of sea ice was also at a record low level of 1.24 × 106 km2. Although no individual sector was at a record low, at the minimum there were negative sea ice anomalies in all sectors of the Southern Ocean, with the largest in the Ross (contributing 46%) and Weddell Seas (26%). The Amundsen Sea Low had a record low depth in October/November 2021, with a series of very deep depressions giving strong offshore winds. These accelerated ice loss during the melt season, creating a 1.00 × 106 km2 coastal polynya in the Ross Sea. In the northern Weddell Sea, westerly winds of record strength led to ice export from the region

Early subretinal allograft rejection is characterized by innate immune activity

Successful subretinal transplantation is limited by considerable early graft loss, despite pharmacological suppression of adaptive immunity. We postulated that early innate immune activity is a dominant factor in determining graft survival and chose a non-immunosuppressed mouse model of retinal pigment epithelial (RPE) cell transplantation to explore this. Expression of almost all measured cytokines by DH01 RPE cells increased significantly following graft preparation and the neutrophil chemoattractant, KC/GRO/CINC, was most significantly increased. Subretinal allografts of DH01 cells (C57BL/10 origin) into healthy, non-immunosuppressed C57BL/6 murine eyes were harvested and fixed at 1, 3, 7 and 28 days post-operatively and subsequently cryosectioned and stained. Graft cells were detected using SV40 large T antigen (SV40T) immunolabeling and apoptosis/necrosis by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL). Sections were also immunolabeled for macrophage (CD11b & F4/80), neutrophil (Gr1 Ly-6G), and T-lymphocyte (CD3-ε) infiltration. Images captured with an Olympus FV1000 confocal microscope were analyzed using Imaris software. The proportion of the subretinal bolus comprising graft cells (SV40T+) was significantly (p<0.001) reduced between post-operative day (POD) 3 (90% ± 4%) and POD 7 (20% ± 7%). CD11b+, F4/80+ and Gr1 Ly-6G+ cells increased significantly (p<0.05) from POD 1 and predominated over SV40T+ cells by POD 7. Co-labeling confocal microscopic analysis demonstrated graft engulfment by neutrophils and macrophages at POD 7 and reconstruction of z-stacked confocal images confirmed SV40T inside Gr1 Ly-6G+ cells. Expression of CD3-ε was low and did not differ significantly between time-points. By POD 28, no graft cells were detectable and few inflammatory cells remained. These studies reveal for the first time a critical role for innate immune mechanisms early in subretinal graft rejection. The future success of subretinal transplantation will require more emphasis on techniques to limit innate immune-mediated graft loss, rather than focusing exclusively on suppression of the adaptive immune response

Quantitative comparison of single- and two-particle properties in the cuprates

We explore the strong variations of the electronic properties of copper-oxygen compounds across the doping phase diagram in a quantitative way. To this end we calculate the electronic Raman response on the basis of results from angle-resolved photoemission spectroscopy (ARPES). In the limits of our approximations we find agreement on the overdoped side and pronounced discrepancies at lower doping. In contrast to the successful approach for the transport properties at low energies, the Raman and the ARPES data cannot be reconciled by adding angle-dependent momentum scattering. We discuss possible routes towards an explanation of the suppression of spectral weight close to the $(\pi,0)$ points which sets in abruptly close to 21% doping.Comment: 7 pages, 4 figure