Probit models for capture-recapture data subject to imperfect detection, individual heterogeneity and misidentification

As noninvasive sampling techniques for animal populations have become more popular, there has been increasing interest in the development of capture-recapture models that can accommodate both imperfect detection and misidentification of individuals (e.g., due to genotyping error). However, current methods do not allow for individual variation in parameters, such as detection or survival probability. Here we develop misidentification models for capture-recapture data that can simultaneously account for temporal variation, behavioral effects and individual heterogeneity in parameters. To facilitate Bayesian inference using our approach, we extend standard probit regression techniques to latent multinomial models where the dimension and zeros of the response cannot be observed. We also present a novel Metropolis-Hastings within Gibbs algorithm for fitting these models using Markov chain Monte Carlo. Using closed population abundance models for illustration, we re-visit a DNA capture-recapture population study of black bears in Michigan, USA and find evidence of misidentification due to genotyping error, as well as temporal, behavioral and individual variation in detection probability. We also estimate a salamander population of known size from laboratory experiments evaluating the effectiveness of a marking technique commonly used for amphibians and fish. Our model was able to reliably estimate the size of this population and provided evidence of individual heterogeneity in misidentification probability that is attributable to variable mark quality. Our approach is more computationally demanding than previously proposed methods, but it provides the flexibility necessary for a much broader suite of models to be explored while properly accounting for uncertainty introduced by misidentification and imperfect detection. In the absence of misidentification, our probit formulation also provides a convenient and efficient Gibbs sampler for Bayesian analysis of traditional closed population capture-recapture data.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS783 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Controls-structures-electromagnetics interaction program

A technology development program is described involving Controls Structures Electromagnetics Interaction (CSEI) for large space structures. The CSEI program was developed as part of the continuing effort following the successful kinematic deployment and RF tests of the 15 meter Hoop/Column antenna. One lesson learned was the importance of making reflector surface adjustment after fabrication and deployment. Given are program objectives, ground based test configuration, Intelsat adaptive feed, reflector shape prediction model, control experiment concepts, master schedule, and Control Of Flexible Structures-II (COFS-II) baseline configuration

The Pros and Cons of the Small Business Reorganization Act of 2019

Effective February 19, 2020, Congress enacted new bankruptcy legislation granting debtors the option to elect a new subchapter V of chapter 11 of the bankruptcy code (Subchapter V). This was made possible by the bipartisan legislation known as the Small Business Reorganization Act of 2019 (SBRA). 1 The SBRA was enacted to provide small business debtors 2 the opportunity to reorganize in a cost-effective manner. This Article addresses certain pros and cons of these amendments to the Bankruptcy Code (Code), which will depend upon the eyes of the beholder

FIMO: scanning for occurrences of a given motif

Summary: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

Our current understanding of how DNA is packed in the nucleus is most accurate at the fine scale of individual nucleosomes and at the large scale of chromosome territories. However, accurate modeling of DNA architecture at the intermediate scale of ∼50 kb-10 Mb is crucial for identifying functional interactions among regulatory elements and their target promoters. We describe a method, Fit-Hi-C, that assigns statistical confidence estimates to mid-range intra-chromosomal contacts by jointly modeling the random polymer looping effect and previously observed technical biases in Hi-C data sets. We demonstrate that our proposed approach computes accurate empirical null models of contact probability without any distribution assumption, corrects for binning artifacts, and provides improved statistical power relative to a previously described method. High-confidence contacts identified by Fit-Hi-C preferentially link expressed gene promoters to active enhancers identified by chromatin signatures in human embryonic stem cells (ESCs), capture 77% ofRNA polymerase II-mediated enhancer-promoter interactions identified using ChIA-PET in mouse ESCs, and confirm previously validated, cell line-specific interactions in mouse cortex cells. We observe that insulators and heterochromatin regions are hubs for high-confidence contacts, while promoters and strong enhancers are involved in fewer contacts. We also observe that binding peaks of master pluripotency factors such as NANOG and POU5F1 are highly enriched in high-confidence contacts for human ESCs. Furthermore, we show that pairs of loci linked by high-confidence contacts exhibit similar replication timing in human and mouse ESCs and preferentially lie within the boundaries of topological domains for human and mouse cell lines

Quantifying similarity between motifs

A common question within the context of de novo motif discovery is whether a newly discovered, putative motif resembles any previously discovered motif in an existing database. To answer this question, we define a statistical measure of motif-motif similarity, and we describe an algorithm, called Tomtom, for searching a database of motifs with a given query motif. Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs

Opportunities for Self-Evaluation Increase Student Calibration in an Introductory Biology Course

Accurate self-evaluation is critical for learning. Calibration describes the relationship between learners’ perception of their performance and their actual performance on a task. Here, we describe two studies aimed at assessing and improving student calibration in a first-semester introductory biology course at a 4-year public institution. Study 1 investigated students’ (n = 310) calibration (the difference between estimated and actual exam performance) across one semester. Students were significantly miscalibrated for the first exam: their predicted scores were, on average, significantly higher than their actual scores. The lowest-performing students had the most inaccurate estimates. Calibration improved with each exam. By the final exam, students underestimated their scores. We initiated a second study in the following semester to examine whether explicitly teaching students about self-evaluation strategies would improve their calibration and performance. Instruction in the experimental section (n = 290) focused on students’ tendency to overestimate their abilities and provided retrieval-practice opportunities. Students in the experimental section showed better calibration and performance on the first exam compared with students in a control section taught by a different instructor during the same semester (n = 251). These findings suggest that simple instructional strategies can increase students’ metacognitive awareness and improve their performance

Surface electronic properties of undoped InAlN alloys

The variation in surface electronic properties of undoped c-plane InxAl1−xN alloys has been investigated across the composition range using a combination of high-resolution x-ray photoemission spectroscopy and single-field Hall effect measurements. For the In-rich alloys, electron accumulation layers, accompanied by a downward band bending, are present at the surface, with a decrease to approximately flatband conditions with increasing Al composition. However, for the Al-rich alloys, the undoped samples were found to be insulating with approximate midgap pinning of the surface Fermi level observed

The 15-meter antenna performance optimization using an interdisciplinary approach

A 15-meter diameter deployable antenna has been built and is being used as an experimental test system with which to develop interdisciplinary controls, structures, and electromagnetics technology for large space antennas. The program objective is to study interdisciplinary issues important in optimizing large space antenna performance for a variety of potential users. The 15-meter antenna utilizes a hoop column structural concept with a gold-plated molybdenum mesh reflector. One feature of the design is the use of adjustable control cables to improve the paraboloid reflector shape. Manual adjustment of the cords after initial deployment improved surface smoothness relative to the build accuracy from 0.140 in. RMS to 0.070 in. Preliminary structural dynamics tests and near-field electromagnetic tests were made. The antenna is now being modified for further testing. Modifications include addition of a precise motorized control cord adjustment system to make the reflector surface smoother and an adaptive feed for electronic compensation of reflector surface distortions. Although the previous test results show good agreement between calculated and measured values, additional work is needed to study modelling limits for each discipline, evaluate the potential of adaptive feed compensation, and study closed-loop control performance in a dynamic environment