Information Storage in the Stochastic Ising Model

Most information systems store data by modifying the local state of matter, in the hope that atomic (or sub-atomic) local interactions would stabilize the state for a sufficiently long time, thereby allowing later recovery. In this work we initiate the study of information retention in locally-interacting systems. The evolution in time of the interacting particles is modeled via the stochastic Ising model (SIM). The initial spin configuration $X_0$ serves as the user-controlled input. The output configuration $X_t$ is produced by running $t$ steps of the Glauber chain. Our main goal is to evaluate the information capacity $I_n(t)\triangleq\max_{p_{X_0}}I(X_0;X_t)$ when the time $t$ scales with the size of the system $n$. For the zero-temperature SIM on the two-dimensional $\sqrt{n}\times\sqrt{n}$ grid and free boundary conditions, it is easy to show that $I_n(t) = \Theta(n)$ for $t=O(n)$. In addition, we show that on the order of $\sqrt{n}$ bits can be stored for infinite time in striped configurations. The $\sqrt{n}$ achievability is optimal when $t\to\infty$ and $n$ is fixed. One of the main results of this work is an achievability scheme that stores more than $\sqrt{n}$ bits (in orders of magnitude) for superlinear (in $n$) times. The analysis of the scheme decomposes the system into $\Omega(\sqrt{n})$ independent Z-channels whose crossover probability is found via the (recently rigorously established) Lifshitz law of phase boundary movement. We also provide results for the positive but small temperature regime. We show that an initial configuration drawn according to the Gibbs measure cannot retain more than a single bit for $t\geq e^{cn^{\frac{1}{4}+\epsilon}}$. On the other hand, when scaling time with $\beta$, the stripe-based coding scheme (that stores for infinite time at zero temperature) is shown to retain its bits for time that is exponential in $\beta$

Similarity Search Over Graphs Using Localized Spectral Analysis

This paper provides a new similarity detection algorithm. Given an input set of multi-dimensional data points, where each data point is assumed to be multi-dimensional, and an additional reference data point for similarity finding, the algorithm uses kernel method that embeds the data points into a low dimensional manifold. Unlike other kernel methods, which consider the entire data for the embedding, our method selects a specific set of kernel eigenvectors. The eigenvectors are chosen to separate between the data points and the reference data point so that similar data points can be easily identified as being distinct from most of the members in the dataset.Comment: Published in SampTA 201

Hawks to Doves: The Role of Personality in Foreign Policy Decision-Making

Why do some hawkish leaders become doves, and what determines whether these leaders' views affect dramatic change in a state's foreign policy? Structural and domestic political explanations of foreign policy change tend to overlook the importance of leaders in such change. Political psychologists offer important insight into how and why certain leaders are inclined to revise their beliefs. Two psychological factors in particular hold great promise for explaining leaders' foreign policy shifts: cognitive openness and cognitive complexity. Cognitively open leaders are receptive to new information and are thus more prone to changing their beliefs than cognitively closed leaders. Similarly, cognitively complex leaders recognize that distinct situations possess multiple dimensions, and so are more likely to engage in adaptive behavior than their cognitively simple counterparts. The primary case explored in this dissertation is that of Shimon Peres, who began his political career as a tough-minded hawk and, in mid-career, transformed into a leading dove. Peres is found to possess particularly high levels of cognitive openness and complexity, thus explaining why his dovish shift was more expansive and occurred sooner than did Yitzhak Rabin's dovish turn. Begin and Shamir, by contrast, are found to be more cognitively closed and simple than either Peres or Rabin, thus explaining why these hawks remained hawks despite having witnessed the same systemic-structural and domestic political events as Peres and Rabin. While cognitive structure is seen as the key causal variable for the leader's dovish turn, systemic-structural and domestic political factors serve as the permissive conditions and/or triggering events for this phenomenon. In the case of Peres, his cognitive structure also helps to explain why he was able to wield disproportionate influence on Israeli foreign policy during periods in which he was a secondary political actor. His high degree of cognitive openness enabled him to seek out domestic and international partners in an effort to build coalitions of support for his political agenda. His high degree of cognitive complexity facilitated an understanding of the intricate needs of the many political and bureaucratic actors with whom he dealt, enabling him to win over the necessary support for his agenda

Biological interaction networks are conserved at the module level

<p>Abstract</p> <p>Background</p> <p>Orthologous genes are highly conserved between closely related species and biological systems often utilize the same genes across different organisms. However, while sequence similarity often implies functional similarity, interaction data is not well conserved even for proteins with high sequence similarity. Several recent studies comparing high throughput data including expression, protein-protein, protein-DNA, and genetic interactions between close species show conservation at a much lower rate than expected.</p> <p>Results</p> <p>In this work we collected comprehensive high-throughput interaction datasets for four model organisms (<it>S. cerevisiae, S. pombe, C. elegans</it>, and <it>D. melanogaster</it>) and carried out systematic analyses in order to explain the apparent lower conservation of interaction data when compared to the conservation of sequence data. We first showed that several previously proposed hypotheses only provide a limited explanation for such lower conservation rates. We combined all interaction evidences into an integrated network for each species and identified functional modules from these integrated networks. We then demonstrate that interactions that are part of functional modules are conserved at much higher rates than previous reports in the literature, while interactions that connect between distinct functional modules are conserved at lower rates.</p> <p>Conclusions</p> <p>We show that conservation is maintained between species, but mainly at the module level. Our results indicate that interactions within modules are much more likely to be conserved than interactions between proteins in different modules. This provides a network based explanation to the observed conservation rates that can also help explain why so many biological processes are well conserved despite the lower levels of conservation for the interactions of proteins participating in these processes.</p> <p>Accompanying website: <url>http://www.sb.cs.cmu.edu/CrossSP</url></p

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

Background: Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species- Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis- over time following fluconazole exposure. Results: Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles- Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions: We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey

Conduction delays across the specialized conduction system of the heart: Revisiting atrioventricular node (AVN) and Purkinje-ventricular junction (PVJ) delays

Background and significanceThe specialized conduction system (SCS) of the heart was extensively studied to understand the synchronization of atrial and ventricular contractions, the large atrial to His bundle (A-H) delay through the atrioventricular node (AVN), and delays between Purkinje (P) and ventricular (V) depolarization at distinct junctions (J), PVJs. Here, we use optical mapping of perfused rabbit hearts to revisit the mechanism that explains A-H delay and the role of a passive electrotonic step-delay at the boundary between atria and the AVN. We further visualize how the P anatomy controls papillary activation and valve closure before ventricular activation.MethodsRabbit hearts were perfused with a bolus (100–200 µl) of a voltage-sensitive dye (di4ANEPPS), blebbistatin (10–20 µM for 20 min) then the right atrial appendage and ventricular free-wall were cut to expose the AVN, P fibers (PFs), the septum, papillary muscles, and the endocardium. Fluorescence images were focused on a CMOS camera (SciMedia) captured at 1K-5 K frames/s from 100 × 100 pixels.ResultsAP propagation across the AVN-His (A-H) exhibits distinct patterns of delay and conduction blocks during S1–S2 stimulation. Refractory periods were 81 ± 9, 90 ± 21, 185 ± 15 ms for Atrial, AVN, and His, respectively. A large delay (&gt;40 ms) occurs between atrial and AVN activation that increased during rapid atrial pacing contributing to the development of Wenckebach periodicity followed by delays within the AVN through slow or blocked conduction. The temporal resolution of the camera allowed us to identify PVJs by detecting doublets of AP upstrokes. PVJ delays were heterogeneous, fastest in PVJ that immediately trigger ventricular APs (3.4 ± 0.8 ms) and slow in regions where PF appear insulated from the neighboring ventricular myocytes (7.8 ± 2.4 ms). Insulated PF along papillary muscles conducted APs (&gt;2 m/s), then triggered papillary muscle APs (&lt;1 m/s), followed by APs firing of septum and endocardium. The anatomy of PFs and PVJs produced activation patterns that control the sequence of contractions ensuring that papillary contractions close the tricuspid valve 2–5 ms before right ventricular contractions.ConclusionsThe specialized conduction system can be accessed optically to investigate the electrical properties of the AVN, PVJ and activation patterns in physiological and pathological conditions

Pervasive Rise of Small-scale Deforestation in Amazonia

Understanding forest loss patterns in Amazonia, the Earth’s largest rainforest region, is critical for effective forest conservation and management. Following the most detailed analysis to date, spanning the entire Amazon and extending over a 14-year period (2001–2014), we reveal significant shifts in deforestation dynamics of Amazonian forests. Firstly, hotspots of Amazonian forest loss are moving away from the southern Brazilian Amazon to Peru and Bolivia. Secondly, while the number of new large forest clearings (>50 ha) has declined significantly over time (46%), the number of new small clearings (<1 ha) increased by 34% between 2001–2007 and 2008–2014. Thirdly, we find that small-scale low-density forest loss expanded markedly in geographical extent during 2008–2014. This shift presents an important and alarming new challenge for forest conservation, despite reductions in overall deforestation rates

Making landscape Decisions to Meet Net Zero Carbon: Pathways that consider ethics, socio-ecological diversity, and landscape functions.

Landscapes are an integral part of the net-zero challenge; not only are they carbon stores but they constitute the environments upon which humans develop their livelihoods, interact and shape their cultures. This report focuses on three key landscape types (agricultural, peatlands and forests), and the associated practices and impacts with particular relevance to the net zero carbon agenda. We have brought together perspectives from natural and social science, humanities, and the arts to understand and evaluate how modern landscapes can absorb the impact of potential zero-carbon policies

What makes an operational Farm Soil Carbon Code? Insights from a global comparison of existing soil carbon codes using a structured analytical framework

Soils have the potential to sequester and store significant amounts of carbon, contributing towards climate change mitigation. Soil carbon markets are now emerging to pay farmers for changes in land use or management that absorb carbon from the atmosphere, governed by codes that ensure additionality, permanence and non-leakage whilst protecting against unintentional reversals. This paper represents the first global comparative analysis of agricultural soil carbon codes, providing new insights into the wide range of approaches currently used to govern these emerging markets internationally. To do this, the paper first develops an analytical framework for the systematic comparison of codes, which could be applied to the analysis of codes in other land uses and habitats. This framework was then used to identify commonalities and differences in methods, projects, administration and commercialisation and associated code documents for 12 publicly available codes from the UK, France, Australia, USA and international bodies. Codes used a range of mechanisms to manage: additionality (including legal, adoption, financial viability and investment tests); uncertainty and risks around soil carbon sequestration (including minimum permanence periods, carbon buffers, contractual arrangements and/or insurance policies); leakage (including restriction of eligible practices and monitoring to subtract leakage from verified sequestration); baselines (including multi-year and variable buffers based on empirical data or models); measurement, reporting and verification methods (stipulating time intervals, methods, data sources and assessments of uncertainty); auditing; resale of carbon units; stakeholder engagement; and approaches to ensure market integrity (such as buyer checks). The paper concludes by discussing existing MRV methods and codes that could be adapted for use in the UK and evaluates the need for an over-arching standard for soil carbon codes in the UK, to which existing codes and other schemes already generating soil carbon credits could be assessed and benchmarked