Regional surname affinity: A spatial network approach.

OBJECTIVE: We investigate surname affinities among areas of modern-day China, by constructing a spatial network, and making community detection. It reports a geographical genealogy of the Chinese population that is result of population origins, historical migrations, and societal evolutions. MATERIALS AND METHODS: We acquire data from the census records supplied by China's National Citizen Identity Information System, including the surname and regional information of 1.28 billion registered Chinese citizens. We propose a multilayer minimum spanning tree (MMST) to construct a spatial network based on the matrix of isonymic distances, which is often used to characterize the dissimilarity of surname structure among areas. We use the fast unfolding algorithm to detect network communities. RESULTS: We obtain a 10-layer MMST network of 362 prefecture nodes and 3,610 edges derived from the matrix of the Euclidean distances among these areas. These prefectures are divided into eight groups in the spatial network via community detection. We measure the partition by comparing the inter-distances and intra-distances of the communities and obtain meaningful regional ethnicity classification. DISCUSSION: The visualization of the resulting communities on the map indicates that the prefectures in the same community are usually geographically adjacent. The formation of this partition is influenced by geographical factors, historic migrations, trade and economic factors, as well as isolation of culture and language. The MMST algorithm proves to be effective in geo-genealogy and ethnicity classification for it retains essential information about surname affinity and highlights the geographical consanguinity of the population.

Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization.

The liquid-liquid critical point scenario of water hypothesizes the existence of two metastable liquid phases--low-density liquid (LDL) and high-density liquid (HDL)--deep within the supercooled region. The hypothesis originates from computer simulations of the ST2 water model, but the stability of the LDL phase with respect to the crystal is still being debated. We simulate supercooled ST2 water at constant pressure, constant temperature, and constant number of molecules N for N ≤ 729 and times up to 1 µs. We observe clear differences between the two liquids, both structural and dynamical. Using several methods, including finite-size scaling, we confirm the presence of a liquid-liquid phase transition ending in a critical point. We find that the LDL is stable with respect to the crystal in 98% of our runs (we perform 372 runs for LDL or LDL-like states), and in 100% of our runs for the two largest system sizes (N = 512 and 729, for which we perform 136 runs for LDL or LDL-like states). In all these runs, tiny crystallites grow and then melt within 1 µs. Only for N ≤ 343 we observe six events (over 236 runs for LDL or LDL-like states) of spontaneous crystallization after crystallites reach an estimated critical size of about 70 ± 10 molecules.

The role of the dynamic crossover temperature and the arrest in glass-forming fluids.

We discuss the role of the dynamic glass-forming fragile-to-strong crossover (FSC) in supercooled liquids. In the FSC, significant dynamic changes such as the decoupling (the violation of the Stokes-Einstein relation) of homologous transport parameters, e.g., the density relaxation time τ and the viscosity η, occur at a characteristic temperature T(c). We study the FSC using a scaling law approach. In particular, we use both forms of the mode-coupling theory (MCT): the original (ideal) and the extended form, which explicitly describes energy hopping processes. We demonstrate that T(c) plays the most important physical role in understanding dynamic arrest processes.

The size variance relationship of business firm growth rates.

The relationship between the size and the variance of firm growth rates is known to follow an approximate power-law behavior sigma(S) approximately S(-beta(S)) where S is the firm size and beta(S) approximately 0.2 is an exponent that weakly depends on S. Here, we show how a model of proportional growth, which treats firms as classes composed of various numbers of units of variable size, can explain this size-variance dependence. In general, the model predicts that beta(S) must exhibit a crossover from beta(0) = 0 to beta(infinity) = 1/2. For a realistic set of parameters, beta(S) is approximately constant and can vary from 0.14 to 0.2 depending on the average number of units in the firm. We test the model with a unique industry-specific database in which firm sales are given in terms of the sum of the sales of all their products. We find that the model is consistent with the empirically observed size-variance relationship.

NMR evidence of a sharp change in a measure of local order in deeply supercooled confined water.

Using NMR, we measure the proton chemical shift delta, of supercooled nanoconfined water in the temperature range 195 K < T < 350 K. Because delta is directly connected to the magnetic shielding tensor, we discuss the data in terms of the local hydrogen bond geometry and order. We argue that the derivative -( partial differential ln delta/ partial differentialT)(P) should behave roughly as the constant pressure specific heat C(P)(T), and we confirm this argument by detailed comparisons with literature values of C(P)(T) in the range 290-370 K. We find that -( partial differential ln delta/ partial differentialT)(P) displays a pronounced maximum upon crossing the locus of maximum correlation length at approximately 240 K, consistent with the liquid-liquid critical point hypothesis for water, which predicts that C(P)(T) displays a maximum on crossing the Widom line.

Towards design principles for optimal transport networks.

We investigate the navigation problem in lattices with long-range connections and subject to a cost constraint. Our network is built from a regular two-dimensional (d=2) square lattice to be improved by adding long-range connections (shortcuts) with probability P(ij) approximately r(ij)(-alpha), where r(ij) is the Manhattan distance between sites i and j, and alpha is a variable exponent. We introduce a cost constraint on the total length of the additional links and find optimal transport in the system for alpha=d+1 established here for d=1 and d=2. Remarkably, this condition remains optimal, regardless of the strategy used for navigation, being based on local or global knowledge of the network structure, in sharp contrast with the results obtained for unconstrained navigation using global or local information, where the optimal conditions are alpha=0 and alpha=d, respectively. The validity of our results is supported by data on the U.S. airport network.

Age-related reduction in microcolumnar structure correlates with cognitive decline in ventral but not dorsal area 46 of the rhesus monkey.

The age-related decline in cognitive function that is observed in normal aging monkeys and humans occurs without significant loss of cortical neurons. This suggests that cognitive impairment results from subtle, sub-lethal changes in the cortex. Recently, changes in the structural coherence in mini- or microcolumns without loss of neurons have been linked to loss of function. Here we use a density map method to quantify microcolumnar structure in both banks of the sulcus principalis (prefrontal cortical area 46) of 16 (ventral) and 19 (dorsal) behaviorally tested female rhesus monkeys from 6 to 33 years of age. While total neuronal density does not change with age in either of these banks, there is a significant age-related reduction in the strength of microcolumns in both regions on the order of 40%. This likely reflects a subtle but definite loss of organization in the structure of the cortical microcolumn. The reduction in strength in ventral area 46 correlates with cognitive impairments in learning and memory while the reduction in dorsal area 46 does not. This result is congruent with published data attributing cognitive functions to ventral area 46 that are similar to our particular cognitive battery which does not optimally tap cognitive functions attributed to dorsal area 46. While the exact mechanisms underlying this loss of microcolumnar organization remain to be determined, it is plausible that they reflect age-related alterations in dendritic and/or axonal organization which alter connectivity and may contribute to age-related declines in cognitive performance.

Hemoglobin kinetics and the effect of organic phosphates.

A kinetic model based on allosteric mechanisms of cooperativity fits the experimentally observed phosphate dependence of hemoglobin reactions. Subunit inequivalence is found to be important in analyzing hemoglobin kinetics. The observed increase in the rate of deoxygenation in the presence of organic phosphates is primarily related to the increased rate of dissociation of the second oxygen molecule.

Raman spectroscopic investigation of gramicidin A' conformations.

Gramicidin A' is believed to form transmembrane channels in lipid bilayers and biological membranes. The first Raman spectroscopic study of gramicidin A' is presented. Evidence is found for two types of conformation. One type is found in the powder and has a Raman spectrum similar to that of model polypeptides with beta hydrogen bonding. The second type is found when gramicidin A' is dissolved in dimethyl sulfoxide.

Laser raman spectroscopy--new probe of myosin substructure.

Laser Raman spectroscopy is used to probe the heterogeneous substructure of the large contractile protein myosin. Some peaks are assigned to specific chemical groups of the molecule; others, notably the conformationally sensitive amide III vibrations, provide information on the structurally distinct regions of the molecule. Deuteration of the NH groups is instrumental in the assignment of these vibrational modes. The relative intensities of bands typical of alpha-helical conformations (near 1265 and 1304 cm-1) and bands associated with nonhelical structure (near 1244 cm-1) are sensitive indicators of myosin substructure and represent potentially useful probes of conformational changes.

Electrostatic and steric effects in the selective complexation of cations in nonactin.

The ester carbonyl stretch frequencies of complexes of the macrotetrolide nonactin with Na(+), K(+), Rb(+), Cs(+), Tl(+), NH(4)(+), NH(3)OH(+), and (NH(2))(2)CNH(2)(+) have been measured. For the larger alkali cations and the polyatomic cations, the ester carbonyl stretch frequency is linearly proportional to the cation-ester carbonyl electrostatic interaction energy. This constitutes direct evidence that the cation-nonactin interaction is primarily electrostatic, rather than mechanical (steric).

Raman spectroscopic evidence for two conformations of uncomplexed valinomycin in the solid state.

Raman spectroscopy is applied for the first time to elucidate the different conformations of the carrier transport molecule, valinomycin. Splitting of the ester and amide carbonyl stretch vibrations is observed in the Raman spectrum of crystals of valinomycin grown from both n-octane and acetone. These observations support the contention that some ester carbonyl groups are intramolecularly hydrogen bonded. The Raman spectrum of valinomycin grown from o-dichlorobenzene does not display this feature.

Opsin structure probed by raman spectroscopy of photoreceptor membranes.

The first nonresonance Raman spectra of photoreceptor membranes are presented. Information about the membrane protein, opsin, and the membrane phospholipids can be deduced. Opsin appears to contain alpha-helical structure but little beta structure. The tyrosine residues are predominantly hydrogen bonded, and disulfide bonds, if they are present, are not in the normal gauche-gauche configuration.

Effects of the Arctic (E22-->G) mutation on amyloid beta-protein folding: discrete molecular dynamics study.

The 40-42 residue amyloid beta-protein (Abeta) plays a central role in the pathogenesis of Alzheimer's disease (AD). Of the two main alloforms, Abeta40 and Abeta42, the longer Abeta42 is linked particularly strongly to AD. Despite the relatively small two amino acid length difference in primary structure, in vitro studies demonstrate that Abeta40 and Abeta42 oligomerize through distinct pathways. Recently, a discrete molecular dynamics (DMD) approach combined with a four-bead protein model recapitulated the differences in Abeta40 and Abeta42 oligomerization and led to structural predictions amenable to in vitro testing. Here, the same DMD approach is applied to elucidate folding of Abeta40, Abeta42, and two mutants, [G22]Abeta40 and [G22]Abeta42, which cause a familial ("Arctic") form of AD. The implicit solvent in the DMD approach is modeled by amino acid-specific hydropathic and electrostatic interactions. The strengths of these effective interactions are chosen to best fit the temperature dependence of the average beta-strand content in Abeta42 monomer, as determined using circular dichroism (CD) spectroscopy. In agreement with these CD data, we show that at physiological temperatures, the average beta-strand content in both alloforms increases with temperature. Our results predict that the average beta-strand propensity should decrease in both alloforms at temperatures higher than approximately 370 K. At physiological temperatures, both Abeta40 and Abeta42 adopt a collapsed-coil conformation with several short beta-strands and a small (<1%) amount of alpha-helical structure. At slightly above physiological temperature, folded Abeta42 monomers display larger amounts of beta-strand than do Abeta40 monomers. At increased temperatures, more extended conformations with a higher amount of beta-strand (approximately < 30%) structure are observed. In both alloforms, a beta-hairpin at A21-A30 is a central folding region. We observe three additional folded regions: structure 1, a beta-hairpin at V36-A42 that exists in Abeta42 but not in Abeta40; structure 2, a beta-hairpin at R5-H13 in Abeta42 but not in Abeta40; and structure 3, a beta-strand A2-F4 in Abeta40 but not Abeta42. At physiological temperatures, the Arctic mutation, E22G, disrupts contacts in the A21-A30 region of both [G22]Abeta peptides, resulting in a less stable main folding region relative to the wild type peptides. The Arctic mutation induces a significant structural change at the N-terminus of [G22]Abeta40 by preventing the formation of structure 3 observed in Abeta40 but not Abeta42, thereby reducing the structural differences between [G22]Abeta40 and [G22]Abeta42 at the N-terminus. [G22]Abeta40 is characterized by a significantly increased amount of average beta-strand relative to the other three peptides due to an induced beta-hairpin structure at R5-H13, similar to structure 2. Consequently, the N-terminal folded structure of the Arctic mutants closely resembles the N-terminal structure of Abeta42, suggesting that both Arctic Abeta peptides might assemble into structures similar to toxic Abeta42 oligomers.

Parallel folding pathways in the SH3 domain protein.

The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive molecular dynamics simulations of the Go model and computing the folding probability of a generated set of TSE candidate conformations. We found that the TSE possesses a well-defined hydrophobic core with variable enveloping structures resulting from the superposition of three parallel folding pathways. The most preferred pathway agrees with the experimentally determined TSE, while the two least preferred pathways differ significantly. The knowledge of the different pathways allows us to design the interactions between amino acids that guide the protein to fold through the least preferred pathway. This particular design is akin to a circular permutation of the protein. The finding motivates the hypothesis that the different experimentally observed TSEs in homologous proteins and circular permutants may represent potentially available pathways to the wild-type protein.

Automated identification of neurons and their locations.

Individual locations of many neuronal cell bodies (>10(4)) are needed to enable statistically significant measurements of spatial organization within the brain such as nearest-neighbour and microcolumnarity measurements. In this paper, we introduce an Automated Neuron Recognition Algorithm (ANRA) which obtains the (x, y) location of individual neurons within digitized images of Nissl-stained, 30 microm thick, frozen sections of the cerebral cortex of the Rhesus monkey. Identification of neurons within such Nissl-stained sections is inherently difficult due to the variability in neuron staining, the overlap of neurons, the presence of partial or damaged neurons at tissue surfaces, and the presence of non-neuron objects, such as glial cells, blood vessels, and random artefacts. To overcome these challenges and identify neurons, ANRA applies a combination of image segmentation and machine learning. The steps involve active contour segmentation to find outlines of potential neuron cell bodies followed by artificial neural network training using the segmentation properties (size, optical density, gyration, etc.) to distinguish between neuron and non-neuron segmentations. ANRA positively identifies 86 +/- 5% neurons with 15 +/- 8% error (mean +/- SD) on a wide range of Nissl-stained images, whereas semi-automatic methods obtain 80 +/- 7%/17 +/- 12%. A further advantage of ANRA is that it affords an unlimited increase in speed from semi-automatic methods, and is computationally efficient, with the ability to recognize approximately 100 neurons per minute using a standard personal computer. ANRA is amenable to analysis of huge photo-montages of Nissl-stained tissue, thereby opening the door to fast, efficient and quantitative analysis of vast stores of archival material that exist in laboratories and research collections around the world.

Cascading Failures in Interdependent Networks with Multiple Supply-Demand Links and Functionality Thresholds.

Various social, financial, biological and technological systems can be modeled by interdependent networks. It has been assumed that in order to remain functional, nodes in one network must receive the support from nodes belonging to different networks. So far these models have been limited to the case in which the failure propagates across networks only if the nodes lose all their supply nodes. In this paper we develop a more realistic model for two interdependent networks in which each node has its own supply threshold, i.e., they need the support of a minimum number of supply nodes to remain functional. In addition, we analyze different conditions of internal node failure due to disconnection from nodes within its own network. We show that several local internal failure conditions lead to similar nontrivial results. When there are no internal failures the model is equivalent to a bipartite system, which can be useful to model a financial market. We explore the rich behaviors of these models that include discontinuous and continuous phase transitions. Using the generating functions formalism, we analytically solve all the models in the limit of infinitely large networks and find an excellent agreement with the stochastic simulations.

Recovery of Interdependent Networks.

Recent network research has focused on the cascading failures in a system of interdependent networks and the necessary preconditions for system collapse. An important question that has not been addressed is how to repair a failing system before it suffers total breakdown. Here we introduce a recovery strategy for nodes and develop an analytic and numerical framework for studying the concurrent failure and recovery of a system of interdependent networks based on an efficient and practically reasonable strategy. Our strategy consists of repairing a fraction of failed nodes, with probability of recovery γ, that are neighbors of the largest connected component of each constituent network. We find that, for a given initial failure of a fraction 1 - p of nodes, there is a critical probability of recovery above which the cascade is halted and the system fully restores to its initial state and below which the system abruptly collapses. As a consequence we find in the plane γ - p of the phase diagram three distinct phases. A phase in which the system never collapses without being restored, another phase in which the recovery strategy avoids the breakdown, and a phase in which even the repairing process cannot prevent system collapse.

Cascading failures in interdependent networks with finite functional components.

We present a cascading failure model of two interdependent networks in which functional nodes belong to components of size greater than or equal to s. We find theoretically and via simulation that in complex networks with random dependency links the transition is first order for s≥3 and continuous for s=2. We also study interdependent lattices with a distance constraint r in the dependency links and find that increasing r moves the system from a regime without a phase transition to one with a second-order transition. As r continues to increase, the system collapses in a first-order transition. Each regime is associated with a different structure of domain formation of functional nodes.

Publisher's Note: Cascading failures in interdependent networks with finite functional components [Phys. Rev. E 94, 042304 (2016)].

This corrects the article DOI: 10.1103/PhysRevE.94.042304.