What is the dimension of citation space?

© 2016 Published by Elsevier B.V.Citation networks represent the flow of information between agents. They are constrained in time and so form directed acyclic graphs which have a causal structure. Here we provide novel quantitative methods to characterise that structure by adapting methods used in the causal set approach to quantum gravity by considering the networks to be embedded in a Minkowski spacetime and measuring its dimension using Myrheim-Meyer and Midpoint-scaling estimates. We illustrate these methods on citation networks from the arXiv, supreme court judgements from the USA, and patents and find that otherwise similar citation networks have measurably different dimensions. We suggest that these differences can be interpreted in terms of the level of diversity or narrowness in citation behaviour

Transitive reduction of citation networks

In many complex networks, the vertices are ordered in time, and edges represent causal connections. We propose methods of analysing such directed acyclic graphs taking into account the constraints of causality and highlighting the causal structure. We illustrate our approach using citation networks formed from academic papers, patents and US Supreme Court verdicts. We show how transitive reduction (TR) reveals fundamental differences in the citation practices of different areas, how it highlights particularly interesting work, and how it can correct for the effect that the age of a document has on its citation count. Finally, we transitively reduce null models of citation networks with similar degree distributions and show the difference in degree distributions after TR to illustrate the lack of causal structure in such models

Embedding graphs in Lorentzian spacetime

Geometric approaches to network analysis combine simply defined models with great descriptive power. In this work we provide a method for embedding directed acyclic graphs (DAG) into Minkowski spacetime using Multidimensional scaling (MDS). First we generalise the classical MDS algorithm, defined only for metrics with a Riemannian signature, to manifolds of any metric signature. We then use this general method to develop an algorithm which exploits the causal structure of a DAG to assign space and time coordinates in a Minkowski spacetime to each vertex. As in the causal set approach to quantum gravity, causal connections in the discrete graph correspond to timelike separation in the continuous spacetime. The method is demonstrated by calculating embeddings for simple models of causal sets and random DAGs, as well as real citation networks. We find that the citation networks we test yield significantly more accurate embeddings that random DAGs of the same size. Finally we suggest a number of applications in citation analysis such as paper recommendation, identifying missing citations and fitting citation models to data using this geometric approach

Rattus Model Utilizing Selective Pulmonary Ischemia Induces Bronchiolitis Obliterans Organizing Pneumonia

Bronchiolitis obliterans organizing pneumonia (BOOP), a morbid condition when associated with lung transplant and chronic lung disease, is believed to be a complication of ischemia. Our goal was to develop a simple and reliable model of lung ischemia in the Sprague-Dawley rat that would produce BOOP. Unilateral ischemia without airway occlusion was produced by an occlusive slipknot placed around the left main pulmonary artery. Studies were performed 7 days later. Relative pulmonary and systemic flow to each lung was measured by injection of technetium Tc 99m macroaggregated albumin. Histological sections were examined for structure and necrosis and scored for BOOP. Apoptosis was detected by immunohistochemistry with an antibody against cleaved caspase 3. Pulmonary artery blood flow to left lungs was less than 0.1% of the cardiac output, and bronchial artery circulation was ~2% of aortic artery flow. Histological sections from ischemic left lungs consistently showed Masson bodies, inflammation, and young fibroblasts filling the distal airways and alveoli, consistent with BOOP. In quantitative evaluation of BOOP using epithelial changes, inflammation and fibrosis were higher in ischemic left lungs than right or sham-operated left lungs. Apoptosis was increased in areas exhibiting histological BOOP, but there was no histological evidence of necrosis. Toll-like receptor 4 expression was increased in ischemic left lungs over right. An occlusive slipknot around the main left pulmonary artery in rats produces BOOP, providing direct evidence that ischemia without immunomodulation or coinfection is sufficient to initiate this injury. It also affords an excellent model to study signaling and genetic mechanisms underlying BOOP

Conforming finite element methods for the clamped plate problem

Finite element methods for solving biharmonic boundary value problems are considered. The particular problem discussed is that of a clamped thin plate. This problem is reformulated in a weak, form in the Sobolev space Techniques for setting up conforming trial Functions are utilized in a Galerkin technique to produce finite element solutions. The shortcomings of various trial function formulations are discussed, and a macro—element approach to local mesh refinement using rectangular elements is given

Rapid consumption of phytoplankton and ice algae by Arctic soft-sediment benthic communities: Evidence using natural and 13C-labeled food materials

Reduction of sea ice in the Arctic may significantly alter the relative fluxes of phytoplankton and ice algae to the seafloor. To examine the response of Arctic benthic communities to changing food supplies, we incubated sediment cores collected from two sites (Smeerenburg Fjord, northwest Svalbard in May 2003 and Storfjord Trench, Barents Sea in May 2004) with controlled additions of natural phytoplankton and ice algal assemblages, and laboratory-cultured 13C-labeled ice algae (Nitzschia frigida, in 2004 only). We measured sediment respiration, pigments, lipid biomarkers, and compound-specific δ13C signals over the course of incubations. Both communities responded rapidly to the addition of food materials: regardless of food type, concentrations of organic biomarkers (pigments and fatty acids) decreased to the levels of control cores within seven days. Although we found no evidence for selective ingestion of the different food types by macrofauna, fatty acids were differentially consumed. The enriched polyunsaturated fatty acids of the ice algae were preferentially utilized compared to saturated and monounsaturated fatty acids bound in ice algae. However, the saturated and monounsaturated fatty acids of phytoplankton (with depleted polyunsaturated fatty acids) are utilized more efficiently than those counterparts bound in ice algae. Bacterial activity was stimulated by food addition, indicated by the immediate increase of bacteria-specific fatty acids, but the direct assimilation of 13C-labeled carbon into bacterial biomass was limited. Our results imply that Arctic benthic communities can meet their energetic requirements by altering strategies to assimilate different components from variable food supplies

Distribution of Capillary Transit Times in Isolated Lungs of Oxygen-Tolerant Rats

Rats pre-exposed to 85% O2 for 5–7 days tolerate the otherwise lethal effects of 100% O2. The objective was to evaluate the effect of rat exposure to 85% O2 for 7 days on lung capillary mean transit time (t¯c) and distribution of capillary transit times (h c(t)). This information is important for subsequent evaluation of the effect of this hyperoxia model on the redox metabolic functions of the pulmonary capillary endothelium. The venous concentration vs. time outflow curves of fluorescein isothiocyanate labeled dextran (FITC-dex), an intravascular indicator, and coenzyme Q1 hydroquinone (CoQ1H2), a compound which rapidly equilibrates between blood and tissue on passage through the pulmonary circulation, were measured following their bolus injection into the pulmonary artery of isolated perfused lungs from rats exposed to room air (normoxic) or 85% O2 for 7 days (hyperoxic). The moments (mean transit time and variance) of the measured FITC-dex and CoQ1H2 outflow curves were determined for each lung, and were then used in a mathematical model [Audi et al. J. Appl. Physiol. 77: 332–351, 1994] to estimate t¯c and the relative dispersion (RDc) of h c(t). Data analysis reveals that exposure to hyperoxia decreases lung t¯c by 42% and increases RDc, a measure h c(t) heterogeneity, by 40%

A persistent homology-based topological loss function for multi-class CNN segmentation of cardiac MRI

With respect to spatial overlap, CNN-based segmentation of short axis cardiovascular magnetic resonance (CMR) images has achieved a level of performance consistent with inter observer variation. However, conventional training procedures frequently depend on pixel-wise loss functions, limiting optimisation with respect to extended or global features. As a result, inferred segmentations can lack spatial coherence, including spurious connected components or holes. Such results are implausible, violating the anticipated topology of image segments, which is frequently known a priori. Addressing this challenge, published work has employed persistent homology, constructing topological loss functions for the evaluation of image segments against an explicit prior. Building a richer description of segmentation topology by considering all possible labels and label pairs, we extend these losses to the task of multi-class segmentation. These topological priors allow us to resolve all topological errors in a subset of 150 examples from the ACDC short axis CMR training data set, without sacrificing overlap performance.Comment: To be presented at the STACOM workshop at MICCAI 202

Denitrification and nitrous oxide emissions from riparian forests soils exposed to prolonged nitrogen runoff

Compared to upland forests, riparian forest soils have greater potential to remove nitrate (NO3) from agricultural run-off through denitrification. It is unclear, however, whether prolonged exposure of riparian soils to nitrogen (N) loading will affect the rate of denitrification and its end products. This research assesses the rate of denitrification and nitrous oxide (N2O) emissions from riparian forest soils exposed to prolonged nutrient run-off from plant nurseries and compares these to similar forest soils not exposed to nutrient run-off. Nursery run-off also contains high levels of phosphate (PO4). Since there are conflicting reports on the impact of PO4 on the activity of denitrifying microbes, the impact of PO4 on such activity was also investigated. Bulk and intact soil cores were collected from N-exposed and non-exposed forests to determine denitrification and N2O emission rates, whereas denitrification potential was determined using soil slurries. Compared to the non-amended treatment, denitrification rate increased 2.7- and 3.4-fold when soil cores collected from both N-exposed and non-exposed sites were amended with 30 and 60 μg NO3-N g-1 soil, respectively. Net N2O emissions were 1.5 and 1.7 times higher from the N-exposed sites compared to the non-exposed sites at 30 and 60 μg NO3-N g-1 soil amendment rates, respectively. Similarly, denitrification potential increased 17 times in response to addition of 15 μg NO3-N g-1 in soil slurries. The addition of PO4 (5 μg PO4–P g-1) to soil slurries and intact cores did not affect denitrification rates. These observations suggest that prolonged N loading did not affect the denitrification potential of the riparian forest soils; however, it did result in higher N2O emissions compared to emission rates from non-exposed forests

Earthquake research in China

A visit to China of an American seismological delegation, which took place October 5 to November 5, 1974, is covered in this report. The Americans were sponsored by the Committee on Scholarly Communication with the People's Republic of China (CSCPRC), and the hosts in China were the Scientific and Technical Association and the State Seismological Bureau. The CSCPRC is sponsored jointly by the National Academy of Sciences, the Social Science Research Council, and the American Council of Learned Societies. The visit had its origins in an invitation extended in January 1973 by Carl Kisslinger, as President of the Seismological Society of America, to the Chinese Academy of Sciences to send representatives to a Symposium on Earthquake Prediction Research. Although the Chinese declined to participate, this invitation was one step towards a reciprocal exchange of seismologists between the United States and the People's Republic of China. Several months after Kisslinger's letter the CSCPRC visited Peking. Their purpose was to arrange an exchange program with the Chinese Scientific and Technical Association. Prompted by Kisslinger, the committee's proposals for American delegations included seismology. Not only was this particular exchange accepted, but the Chinese in turn suggested that a Chinese seismology group visit the United States