Unsupervised Bilingual POS Tagging with Markov Random Fields

In this paper, we give a treatment to the problem of bilingual part-of-speech induction with parallel data. We demonstrate that naïve optimization of log-likelihood with joint MRFs suffers from a severe problem of local maxima, and suggest an alternative – using contrastive estimation for estimation of the parameters. Our experiments show that estimating the parameters this way, using overlapping features with joint MRFs performs better than previous work on the 1984 dataset.

A Dynamin-3 Spliced Variant Modulates the Actin/Cortactin-Dependent Morphogenesis of Dendritic Spines

Immature dendrites extend many actin-rich filopodial structures that can be replaced by synapse-containing dendritic spines as the neuron matures. The large GTPase dynamin-3 (Dyn3) is a component of the postsynapse in hippocampal neurons but its function is undefined. Here, we demonstrate that a specific Dyn3 variant (Dyn3baa) promotes the formation of immature dendritic filopodia in cultured neurons. This effect is dependent upon Dyn3 GTPase activity and a direct interaction with the F-actin-binding protein cortactin. Consistent with these findings, Dyn3baa binds to cortactin with a 200% higher affinity than Dyn3aaa, a near identical isoform that does not induce dendritic filopodia when expressed in cultured neurons. Finally, levels of Dyn3baa-encoding mRNA are tightly regulated during neuronal maturation and are markedly upregulated during synaptogenesis. Together, these findings provide the first evidence that an enhanced interaction between a specific Dyn3 splice variant and cortactin modulate actin-membrane dynamics in developing neurons to regulate the morphogenesis of dendritic spines. Supplementary material available online at http://jcs.biologists.org/cgi/content/full/118/6/1279/DC

Labor Market Density and Increasing Returns to Scale: How Strong is the Evidence?

Models of economic geography posit that the density of economic activity has two e¤ects that oppose each other in equilibrium: decreasing returns to productive activities due to congestion e¤ects and increasing returns that result from information spillovers and local demand externalities. In an in�uential paper, Ciccone and Hall (1996) looked at the effect of county level labor market concentration on per-worker Gross State Product in a cross section of US States, and observed that on net, the increasing returns/agglomeration effect dominates. We extend their analysis and re-examine the relationship between density and productivity across industries and over both states and time. Through careful identi�cation of the source and nature of productivity shocks, we show that the evidence for agglomeration effects is indeed quite robust, even within industries, providing evidence for the presence of Marshallian externalities. As for the balance of agglomeration and congestion e¤ects found in previous literature, what we call �net increasing returns to scale", the evidence is much weaker.

Dynamic Social Balance and Convergent Appraisals via Homophily and Influence Mechanisms

Social balance theory describes allowable and forbidden configurations of the topologies of signed directed social appraisal networks. In this paper, we propose two discrete-time dynamical systems that explain how an appraisal network \textcolor{blue}{converges to} social balance from an initially unbalanced configuration. These two models are based on two different socio-psychological mechanisms respectively: the homophily mechanism and the influence mechanism. Our main theoretical contribution is a comprehensive analysis for both models in three steps. First, we establish the well-posedness and bounded evolution of the interpersonal appraisals. Second, we fully characterize the set of equilibrium points; for both models, each equilibrium network is composed by an arbitrary number of complete subgraphs satisfying structural balance. Third, we establish the equivalence among three distinct properties: non-vanishing appraisals, convergence to all-to-all appraisal networks, and finite-time achievement of social balance. In addition to theoretical analysis, Monte Carlo validations illustrates how the non-vanishing appraisal condition holds for generic initial conditions in both models. Moreover, numerical comparison between the two models indicate that the homophily-based model might be a more universal explanation for the formation of social balance. Finally, adopting the homophily-based model, we present numerical results on the mediation and globalization of local conflicts, the competition for allies, and the asymptotic formation of a single versus two factions

HID-1 controls formation of large dense core vesicles by influencing cargo sorting and trans-Golgi network acidification

Large dense core vesicles (LDCVs) mediate the regulated release of neuropeptides and peptide hormones. They form at the trans-Golgi network (TGN), where their soluble content aggregates to form a dense core, but the mechanisms controlling biogenesis are still not completely understood. Recent studies have implicated the peripheral membrane protein HID-1 in neuropeptide sorting and insulin secretion. Using CRISPR/Cas9, we generated HID-1 KO rat neuroendocrine cells, and we show that the absence of HID-1 results in specific defects in peptide hormone and monoamine storage and regulated secretion. Loss of HID-1 causes a reduction in the number of LDCVs and affects their morphology and biochemical properties, due to impaired cargo sorting and dense core formation. HID-1 KO cells also exhibit defects in TGN acidification together with mislocalization of the Golgi-enriched vacuolar H+-ATPase subunit isoform a2. We propose that HID-1 influences early steps in LDCV formation by controlling dense core formation at the TGN.</jats:p

Interactive Image Analysis in Age-related Macular Degeneration (AMD) and Stargardt Disease (STGD)

The literature of the last three decades is replete with automatic methods for retinal image analysis. Acceptance has been limited due to post-processing or tuning requirements that may be just as time consuming as the original manual methods. The point of view herein is that by taking advantage of the human visual system and expert knowledge from the outset, the promised efficiencies of digital methods can be achieved in practice as well as in theory. Thus, simple labeling of regions of interest that is accepted and easily performed in a few moments by the human can provide enormous advantage to an already well-developed algorithm. Three examples are provided: drusen segmentation, image registration, and geographic atrophy segmentation, with applications to disease understanding

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription

Existing climate change will lead to pronounced shifts in the diversity of soil prokaryotes

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 3 (2018): e00167-18, doi:10.1128/mSystems.00167-18.Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.This work was supported by the Strategic Priority Research Program (XDB15010101, XDA05050404) of the Chinese Academy of Sciences, the National Program on Key Basic Research Project (2014CB954002, 2014CB954004), the National Natural Science Foundation of China (41701298, 41371254), the “135” Plan and Frontiers Projects of Institute of Soil Science (ISSASIP1641), and the National Science and Technology Foundation project (2015FY110100). J.A.G. was supported by the U.S. Dept. of Energy under contract DE-AC02-06CH11357. N.F. was supported by a grant from the National Science Foundation (DEB-0953331). K.S.P. and J.L. were supported by the National Science Foundation (DMS-1069303), the Gordon and Betty Moore Foundation (grant no. 3300), the Gladstone Institutes, and a gift from the San Simeon Fund

Nodal dynamics, not degree distributions, determine the structural controllability of complex networks

Structural controllability has been proposed as an analytical framework for making predictions regarding the control of complex networks across myriad disciplines in the physical and life sciences (Liu et al., Nature:473(7346):167-173, 2011). Although the integration of control theory and network analysis is important, we argue that the application of the structural controllability framework to most if not all real-world networks leads to the conclusion that a single control input, applied to the power dominating set (PDS), is all that is needed for structural controllability. This result is consistent with the well-known fact that controllability and its dual observability are generic properties of systems. We argue that more important than issues of structural controllability are the questions of whether a system is almost uncontrollable, whether it is almost unobservable, and whether it possesses almost pole-zero cancellations.Comment: 1 Figures, 6 page