Recovering the Imperfect: Cell Segmentation in the Presence of Dynamically Localized Proteins

Deploying off-the-shelf segmentation networks on biomedical data has become common practice, yet if structures of interest in an image sequence are visible only temporarily, existing frame-by-frame methods fail. In this paper, we provide a solution to segmentation of imperfect data through time based on temporal propagation and uncertainty estimation. We integrate uncertainty estimation into Mask R-CNN network and propagate motion-corrected segmentation masks from frames with low uncertainty to those frames with high uncertainty to handle temporary loss of signal for segmentation. We demonstrate the value of this approach over frame-by-frame segmentation and regular temporal propagation on data from human embryonic kidney (HEK293T) cells transiently transfected with a fluorescent protein that moves in and out of the nucleus over time. The method presented here will empower microscopic experiments aimed at understanding molecular and cellular function.Comment: Accepted at MICCAI Workshop on Medical Image Learning with Less Labels and Imperfect Data, 202

The number of metastable states in the generalized random orthogonal model

We calculate the number of metastable states in the generalized random orthogonal model. The results obtained are verified by exact numerical enumeration for small systems sizes but taking into account finite size effects. These results are compared with those for Hopfield model in order to examine the effect of strict orthonormality of neural network patterns on the number of metastable states.Comment: 12 pages, 4 EPS figure

Reduced receptor editing in lupus-prone MRL/lpr mice

The initial B cell repertoire contains a considerable proportion of autoreactive specificities. The first major B cell tolerance checkpoint is at the stage of the immature B cell, where receptor editing is the primary mode of eliminating self-reactivity. The cells that emigrate from the bone marrow have a second tolerance checkpoint in the transitional compartment in the spleen. Although it is known that the second checkpoint is defective in lupus, it is not clear whether there is any breakdown in central B cell tolerance in the bone marrow. We demonstrate that receptor editing is less efficient in the lupus-prone strain MRL/lpr. In an in vitro system, when receptor-editing signals are given to bone marrow immature B cells by antiidiotype antibody or after in vivo exposure to membrane-bound self-antigen, MRL/lpr 3-83 transgenic immature B cells undergo less endogenous rearrangement and up-regulate recombination activating gene messenger RNA to a lesser extent than B10 transgenic cells. CD19, along with immunoglobulin M, is down-regulated in the bone marrow upon receptor editing, but the extent of down-regulation is fivefold less in MRL/lpr mice. Less efficient receptor editing could allow some autoreactive cells to escape from the bone marrow in lupus-prone mice, thus predisposing to autoimmunity

Magnitudes of submarine groundwater discharge from marine and terrestrial sources: Indian River Lagoon, Florida

Magnitudes of terrestrial (fresh) and marine (saline) sources of submarine groundwater discharge (SGD) are estimated for a transect across Indian River Lagoon, Florida. Two independent techniques (seepage meters and pore water Cl- concentrations) show terrestrial SGD decreases linearly to around 22 m offshore, and these techniques, together with a model based on the width of the outflow face, indicate a cumulative discharge of between 0.02 and 0.9 m3/d per meter of shoreline. Seepage meters and models of the deficiencies in 222Rn activity in shallow sediments indicate marine SGD discharges of roughly 117 m3/d per meter of shoreline across the entire 1800-m-wide transect. Two surface streams nearest the transect have an average discharge of about 28 m3/d per meter of shoreline. Marine SGD is thus 4 times greater then surface water discharge and more than 2 orders of magnitude greater than terrestrial SGD. The magnitude of the terrestrial SGD is limited by the amount of regional precipitation, evaporation, recharge, and groundwater usage, while marine SGD is limited only by processes circulating marine water into and out of the sediments. The large magnitude of marine SGD means that it could be important for estuarine cycling of reactive components such as nutrients and metals with only slight modification from estuarine water compositions. The small magnitude of terrestrial SGD means that large differences from estuarine water composition would be required to affect chemical cycling

Magnitudes of submarine groundwater discharge from marine and terrestrial sources: Indian River lagoon

[1] Magnitudes of terrestrial (fresh) and marine (saline) sources of submarine groundwater discharge (SGD) are estimated for a transect across Indian River Lagoon, Florida. Two independent techniques (seepage meters and pore water Cl À concentrations) show terrestrial SGD decreases linearly to around 22 m offshore, and these techniques, together with a model based on the width of the outflow face, indicate a cumulative discharge of between 0.02 and 0.9 m 3 /d per meter of shoreline. Seepage meters and models of the deficiencies in 222 Rn activity in shallow sediments indicate marine SGD discharges of roughly 117 m 3 /d per meter of shoreline across the entire 1800-m-wide transect. Two surface streams nearest the transect have an average discharge of about 28 m 3 /d per meter of shoreline. Marine SGD is thus 4 times greater then surface water discharge and more than 2 orders of magnitude greater than terrestrial SGD. The magnitude of the terrestrial SGD is limited by the amount of regional precipitation, evaporation, recharge, and groundwater usage, while marine SGD is limited only by processes circulating marine water into and out of the sediments. The large magnitude of marine SGD means that it could be important for estuarine cycling of reactive components such as nutrients and metals with only slight modification from estuarine water compositions. The small magnitude of terrestrial SGD means that large differences from estuarine water composition would be required to affect chemical cycling

LSD1 cooperates with CTIP2 to promote HIV-1 transcriptional silencing

Microglial cells are the main HIV-1 targets in the central nervous system (CNS) and constitute an important reservoir of latently infected cells. Establishment and persistence of these reservoirs rely on the chromatin structure of the integrated proviruses. We have previously demonstrated that the cellular cofactor CTIP2 forces heterochromatin formation and HIV-1 gene silencing by recruiting HDAC and HMT activities at the integrated viral promoter. In the present work, we report that the histone demethylase LSD1 represses HIV-1 transcription and viral expression in a synergistic manner with CTIP2. We show that recruitment of LSD1 at the HIV-1 proximal promoter is associated with both H3K4me3 and H3K9me3 epigenetic marks. Finally, our data suggest that LSD1-induced H3K4 trimethylation is linked to hSET1 recruitment at the integrated provirus

A compactness theorem for scalar-flat metrics on manifolds with boundary

Let (M,g) be a compact Riemannian manifold with boundary. This paper is concerned with the set of scalar-flat metrics which are in the conformal class of g and have the boundary as a constant mean curvature hypersurface. We prove that this set is compact for dimensions greater than or equal to 7 under the generic condition that the trace-free 2nd fundamental form of the boundary is nonzero everywhere.Comment: 49 pages. Final version, to appear in Calc. Var. Partial Differential Equation

An Exploratory Study into the Factors Impeding Ethical Consumption

Although consumers are increasingly engaged with ethical factors when forming opinions about products and making purchase decisions, recent studies have highlighted significant differences between consumers’ intentions to consume ethically, and their actual purchase behaviour. This article contributes to an understanding of this “ethical purchasing gap” through a review of existing literature, and the inductive analysis of focus group discussions. A model is suggested which includes exogenous variables such as moral maturity and age which have been well covered in the literature, together with further impeding factors identified from the focus group discussions. For some consumers, inertia in purchasing behaviour was such that the decision-making process was devoid of ethical considerations. Several manifested their ethical views through post-purchase dissonance and retrospective feelings of guilt. Others displayed a reluctance to consume ethically due to personal constraints, a perceived negative impact on image or quality, or an outright negation of responsibility. Those who expressed a desire to consume ethically often seemed deterred by cynicism, which caused them to question the impact they, as an individual, could achieve. These findings enhance the understanding of ethical consumption decisions and provide a platform for future research in this area