Structured learning of assignment models for neuron reconstruction to minimize topological errors

© 20xx IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Structured learning provides a powerful framework for empirical risk minimization on the predictions of structured models. It allows end-to-end learning of model parameters to minimize an application specific loss function. This framework is particularly well suited for discrete optimization models that are used for neuron reconstruction from anisotropic electron microscopy (EM) volumes. However, current methods are still learning unary potentials by training a classifier that is agnostic about the model it is used in. We believe the reason for that lies in the difficulties of (1) finding a representative training sample, and (2) designing an application specific loss function that captures the quality of a proposed solution. In this paper, we show how to find a representative training sample from human generated ground truth, and propose a loss function that is suitable to minimize topological errors in the reconstruction. We compare different training methods on two challenging EM-datasets. Our structured learning approach shows consistently higher reconstruction accuracy than other current learning methods.Peer ReviewedPostprint (author's final draft

The feasibility of radiolabeling for human serum albumin (HSA) adsorption studies

Human serum albumin (HSA) was labeled in various ways and with different radioactive labels (Technetium-99m and Iodine-125). Characterization with electrophoresis on polyacryl gel and immunoelectrophoresis did not reveal differences between labeled and nonlabeled HSA. The release of the label from labeled proteins in phosphate buffer (pH 7.4) was studied as a function of time. 125I-labeled proteins were stable and 99mTc-labeled proteins showed different stabilities depending on the labeling method which was used. The adsorption behavior of labeled HSA and HSA onto polystyrene (PS) and silicon rubber (SR) was studied by using two methods. It appeared that all labeled HSA compounds showed a preferential adsorption onto PS (and SR) substrates. The 99mTc-labeled HSA showed a high value of the preferential adsorption factor (φ 1). The φ value for 125I-labeled HSA was about 1.4. It was also shown that φ was dependent on the kind of substrate used. The methods developed to determine preferential adsorption of labeled proteins compared to their nonlabeled analogs are also generally applicable for different types of compounds

Estimating Fiscal Multipliers by Combining Statistical Identification with Potentially Endogenous Proxies

Different proxy variables used in fiscal policy SVARs lead to contradicting conclusions regarding the size of fiscal multipliers. In this paper, we show that the conflicting results are due to violations of the exogeneity assumptions, i.e. the commonly used proxies are endogenously related to the structural shocks. We propose a novel approach to include proxy variables into a Bayesian non-Gaussian SVAR, tailored to accommodate potentially endogenous proxy variables. Using our model, we show that increasing government spending is a more effective tool to stimulate the economy than reducing taxes. We construct new exogenous proxies that can be used in the traditional proxy VAR approach resulting in similar estimates compared to our proposed hybrid SVAR model.Comment: 10 figure

TED: a tolerant edit distance for segmentation evaluation

© . This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/In this paper, we present a novel error measure to compare a computer-generated segmentation of images or volumes against ground truth. This measure, which we call Tolerant Edit Distance (TED), is motivated by two observations that we usually encounter in biomedical image processing: (1) Some errors, like small boundary shifts, are tolerable in practice. Which errors are tolerable is application dependent and should be explicitly expressible in the measure. (2) Non-tolerable errors have to be corrected manually. The effort needed to do so should be reflected by the error measure. Our measure is the minimal weighted sum of split and merge operations to apply to one segmentation such that it resembles another segmentation within specified tolerance bounds. This is in contrast to other commonly used measures like Rand index or variation of information, which integrate small, but tolerable, differences. Additionally, the TED provides intuitive numbers and allows the localization and classification of errors in images or volumes. We demonstrate the applicability of the TED on 3D segmentations of neurons in electron microscopy images where topological correctness is arguable more important than exact boundary locations. Furthermore, we show that the TED is not just limited to evaluation tasks. We use it as the loss function in a max-margin learning framework to find parameters of an automatic neuron segmentation algorithm. We show that training to minimize the TED, i.e., to minimize crucial errors, leads to higher segmentation accuracy compared to other learning methods.Peer ReviewedPostprint (author's final draft

Quantized Anomalous Hall Effect in Two-Dimensional Ferromagnets - Quantum Hall Effect from Metal -

We study the effect of disorder on the anomalous Hall effect (AHE) in two-dimensional ferromagnets. The topological nature of AHE leads to the integer quantum Hall effect from a metal, i.e., the quantization of $\sigma_{xy}$ induced by the localization except for the few extended states carrying Chern number. Extensive numerical study on a model reveals that Pruisken's two-parameter scaling theory holds even when the system has no gap with the overlapping multibands and without the uniform magnetic field. Therefore the condition for the quantized AHE is given only by the Hall conductivity $\sigma_{xy}$ without the quantum correction, i.e., $|\sigma_{xy}| > e^2/(2h)$.Comment: 5 pages, 4 figures, REVTe

Health and wealth in the Roman Empire

Ancient Rome was the largest and most populous empire of its time, and the largest pre-industrial state in European history. Recent though not universally accepted research suggests that at least for the most populous central periods of its history standard of living was also rather higher than before or after. To trace whether this is also reflected in Roman biological standard of living, we present the first large and more or less comprehensive dataset, based on skeletal data for some 10,000 individuals, covering all periods of Roman history, and all regions (even if inevitably unequally). We discuss both the methodologies that we developed and the historical results. Instead of reconstructing heights from the long bones assuming fixed body proportions or from one individual long bone, we apply exploratory factor analysis and calculate factor scores for 50-year periods. Our measure of the biological standard of living declined during the last two centuries B.C. and started to improve again, slowly at first, from the second century A.D. It correlated negatively with population, but also with other aspects of standard of living such as wages or diets

Auditory information processing during adequate propofol anesthesia monitored by electroencephalogram bispectral index

Memory for intraoperative events may arise from inadequate anesthesia when the hypnotic state is not continuously monitored. Electroencephalogram bispectral index (BIS) enables monitoring of the hypnotic state and titration of anesthesia to an adequate level (BIS 40 to 60). At this level, preserved memory function has been observed in trauma patients. We investigated memory formation in elective surgical outpatients during target-controlled propofol anesthesia supplemented with alfentanil. While BIS remained between 40 and 60, patients listened to a tape with either familiar instances (exemplars) from two categories (Experimental [E] group, n = 41) or bird sounds (Control [C] group, n = 41). After recovery, memory was tested directly and indirectly. BIS during audio presentation was on average (+/- SD) 44 +/- 5 and 46 +/- 5 for Groups E and C, respectively. No patient consciously recalled the intraoperative period, nor were presented words recognized reliably (Group E, 0.9 +/- 0.8 hits; Group C, 0.8 +/- 0.8 hits) (P = 0.7). When asked to generate category exemplars, Group E named 2.10 +/- 1.0 hits versus 1.98 +/- 1.0 in Group C (P = 0.9). We found no explicit or implicit memory effect of familiar words presented during adequate propofol anesthesia at BIS levels between 40 and 60 in elective surgical patients. IMPLICATIONS: This study suggests that stable levels of adequate hypnosis may prevent information processing and memory formation during general anesthesia and supports the feasibility of electroencephalogram bispectral index as a monitor of adequate anesthesia

The Significance of Vascular Alterations in Acute and Chronic Rejection for Vascularized Composite Allotransplantation.

Vascularized composite allotransplantation (VCA) has emerged as a useful reconstructive option for patients suffering from major tissue defects and functional deficits. While the technical feasibility has been optimized and more than 130 VCAs have been performed during the last two decades, hurdles such as acute and chronic allograft rejection, graft deterioration, and eventual functional impairment need to be addressed. Recently, chronic graft rejection and progressive failure have been linked to vascular alterations observed in the allografts. Graft vasculopathy (GV) may play a pivotal role in long-term graft deterioration. The understanding of the underlying pathophysiological processes and their initial triggers is of utmost importance in the prevention, attenuation, and therapy of GV. While there are reports on the etiology and development of GV in solid organ transplantation, there are limited data with respect to chronic rejection and GV in the realm of VCA. Nevertheless, recent reports from long-term VCA recipients suggest that GV could truly jeopardize allografts in the follow-up evaluation. Chronic rejection and GV include different entities and might have different pathways in distinct organs. Herein, we reviewed the current literature on vascular changes during both acute and chronic allograft rejection, with a focus on their clinical and translational significance for VCA