Element-centric clustering comparison unifies overlaps and hierarchy

Clustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster-centric philosophy. We demonstrate that, in contrast to standard clustering similarity measures, our framework does not suffer from critical biases and naturally provides unique insights into how the clusterings differ. We illustrate the strengths of our framework by revealing new insights into the organization of clusters in two applications: the improved classification of schizophrenia based on the overlapping and hierarchical community structure of fMRI brain networks, and the disentanglement of various social homophily factors in Facebook social networks. The universality of clustering suggests far-reaching impact of our framework throughout all areas of science

Human Sexual Cycles are Driven by Culture and Match Collective Moods

It is a long-standing question whether human sexual and reproductive cycles are affected predominantly by biology or culture. The literature is mixed with respect to whether biological or cultural factors best explain the reproduction cycle phenomenon, with biological explanations dominating the argument. The biological hypothesis proposes that human reproductive cycles are an adaptation to the seasonal cycles caused by hemisphere positioning, while the cultural hypothesis proposes that conception dates vary mostly due to cultural factors, such as vacation schedule or religious holidays. However, for many countries, common records used to investigate these hypotheses are incomplete or unavailable, biasing existing analysis towards primarily Christian countries in the Northern Hemisphere. Here we show that interest in sex peaks sharply online during major cultural and religious celebrations, regardless of hemisphere location. This online interest, when shifted by nine months, corresponds to documented human birth cycles, even after adjusting for numerous factors such as language, season, and amount of free time due to holidays. We further show that mood, measured independently on Twitter, contains distinct collective emotions associated with those cultural celebrations, and these collective moods correlate with sex search volume outside of these holidays as well. Our results provide converging evidence that the cyclic sexual and reproductive behavior of human populations is mostly driven by culture and that this interest in sex is associated with specific emotions, characteristic of, but not limited to, major cultural and religious celebrations.Comment: Main Paper: 21 pages, 4 figures Supplementary Material: 66 pages, 15 figures, 13 table

Conditions for the spectrum associated with a leaky wire to contain the interval [− α2/4, ∞)

The method of singular sequences is used to provide a simple and, in some respects, a more general proof of a known spectral result for leaky wires. The method introduces a new concept of asymptotic straightness

Boundary triplets and M-functions for non-selfadjoint operators, with applications to elliptic PDEs and block operator matrices

Starting with an adjoint pair of operators, under suitable abstract versions of standard PDE hypotheses, we consider the Weyl M-function of extensions of the operators. The extensions are determined by abstract boundary conditions and we establish results on the relationship between the M-function as an analytic function of a spectral parameter and the spectrum of the extension. We also give an example where the M-function does not contain the whole spectral information of the resolvent, and show that the results can be applied to elliptic PDEs where the M-function corresponds to the Dirichlet to Neumann map

Gap localization of multiple TE‐Modes by arbitrarily weak defects

This paper considers the propagation of TE‐modes in photonic crystal waveguides. The waveguide is created by introducing a linear defect into a periodic background medium. Both the periodic background problem and the perturbed problem are modelled by a divergence type equation. A feature of our analysis is that we allow discontinuities in the coefficients of the operator, which is required to model many photonic crystals. Using the Floquet–Bloch theory in negative‐order Sobolev spaces, we characterize the precise number of eigenvalues created by the line defect in terms of the band functions of the original periodic background medium for arbitrarily weak defects

Mining social media data for biomedical signals and health-related behavior

Social media data has been increasingly used to study biomedical and health-related phenomena. From cohort level discussions of a condition to planetary level analyses of sentiment, social media has provided scientists with unprecedented amounts of data to study human behavior and response associated with a variety of health conditions and medical treatments. Here we review recent work in mining social media for biomedical, epidemiological, and social phenomena information relevant to the multilevel complexity of human health. We pay particular attention to topics where social media data analysis has shown the most progress, including pharmacovigilance, sentiment analysis especially for mental health, and other areas. We also discuss a variety of innovative uses of social media data for health-related applications and important limitations in social media data access and use.Comment: To appear in the Annual Review of Biomedical Data Scienc

Plasma ATP concentration and venous oxygen content in the forearm during dynamic handgrip exercise

Background It has been proposed that adenosine triphosphate (ATP) released from red blood cells (RBCs) may contribute to the tight coupling between blood flow and oxygen demand in contracting skeletal muscle. To determine whether ATP may contribute to the vasodilatory response to exercise in the forearm, we measured arterialised and venous plasma ATP concentration and venous oxygen content in 10 healthy young males at rest, and at 30 and 180 seconds during dynamic handgrip exercise at 45% of maximum voluntary contraction (MVC). Results Venous plasma ATP concentration was elevated above rest after 30 seconds of exercise (P < 0.05), and remained at this higher level 180 seconds into exercise (P < 0.05 versus rest). The increase in ATP was mirrored by a decrease in venous oxygen content. While there was no significant relationship between ATP concentration and venous oxygen content at 30 seconds of exercise, they were moderately and inversely correlated at 180 seconds of exercise (r = -0.651, P = 0.021). Arterial ATP concentration remained unchanged throughout exercise, resulting in an increase in the venous-arterial ATP difference. Conclusions Collectively these results indicate that ATP in the plasma originated from the muscle microcirculation, and are consistent with the notion that deoxygenation of the blood perfusing the muscle acts as a stimulus for ATP release. That ATP concentration was elevated just 30 seconds after the onset of exercise also suggests that ATP may be a contributing factor to the blood flow response in the transition from rest to steady state exercise

Author Correction: Human Sexual Cycles are Driven by Culture and Match Collective Moods

This deposit is composed simultaneously by the original published article and also by the "correction" for the published article (erratum).This deposit is composed by the main article plus the supplementary materials of the publication.The link for the original article: https://www.nature.com/articles/s41598-017-18262-5A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.Human reproduction does not happen uniformly throughout the year and what drives human sexual cycles is a long-standing question. The literature is mixed with respect to whether biological or cultural factors best explain these cycles. The biological hypothesis proposes that human reproductive cycles are an adaptation to the seasonal (hemisphere-dependent) cycles, while the cultural hypothesis proposes that conception dates vary mostly due to cultural factors, such as holidays. However, for many countries, common records used to investigate these hypotheses are incomplete or unavailable, biasing existing analysis towards Northern Hemisphere Christian countries. Here we show that interest in sex peaks sharply online during major cultural and religious celebrations, regardless of hemisphere location. This online interest, when shifted by nine months, corresponds to documented human births, even after adjusting for numerous factors such as language and amount of free time due to holidays. We further show that mood, measured independently on Twitter, contains distinct collective emotions associated with those cultural celebrations. Our results provide converging evidence that the cyclic sexual and reproductive behavior of human populations is mostly driven by culture and that this interest in sex is associated with specific emotions, characteristic of major cultural and religious celebrations.National Institutes of Health grant: (01LM011945-01); Fundação para a Ciência e a Tecnologia grant: (PTDC IVC ESCT 5337 2012); Welcome DFRH WIIA 60 2011; Marie Curie Actions; Defense Advanced Research Projects Agency (DARPA) - NGS2 program grant: (#D17AC00005); Economic Development Agency grant: (ED17HDQ3120040); NSF Award grant: (IIS-0811994).info:eu-repo/semantics/publishedVersio

Proteome phenotypes discriminate the growing location and malting traits in field-grown barley

Barley is one of the key cereal grains for malting and brewing industries. However, climate variability and unprecedented weather events can impact barley yield and end-product quality. The genetic background and environmental conditions are key factors in defining the barley proteome content and malting characteristics. Here, we measure the barley proteome and malting characteristics of three barley lines grown in Western Australia, differing in genetic background and growing location, by applying liquid chromatography-mass spectrometry (LC-MS). Using data-dependent acquisition LC-MS, 1571 proteins were detected with high confidence. Quantitative data acquired using sequential window acquisition of all theoretical (SWATH) MS on barley samples resulted in quantitation of 920 proteins. Multivariate analyses revealed that the barley lines\u27 genetics and their growing locations are strongly correlated between proteins and desired traits such as the malt yield. Linking meteorological data with proteomic measurements revealed how high-temperature stress in northern regions affects seed temperature tolerance during malting, resulting in a higher malt yield. Our results show the impact of environmental conditions on the barley proteome and malt characteristics; these findings have the potential to expedite breeding programs and malt quality prediction

Apples and pears? A comparison of two sources of national lung cancer audit data in England

In 2014, the method of data collection from NHS trusts in England for the National Lung Cancer Audit (NLCA) was changed from a bespoke dataset called LUCADA (Lung Cancer Data). Under the new contract, data are submitted via the Cancer Outcome and Service Dataset (COSD) system and linked additional cancer registry datasets. In 2014, trusts were given opportunity to submit LUCADA data as well as registry data. 132 NHS trusts submitted LUCADA data, and all 151 trusts submitted COSD data. This transitional year therefore provided the opportunity to compare both datasets for data completeness and reliability. We linked the two datasets at the patient level to assess the completeness of key patient and treatment variables. We also assessed the interdata agreement of these variables using Cohen’s kappa statistic, κ. We identified 26 001 patients in both datasets. Overall, the recording of sex, age, performance status and stage had more than 90% agreement between datasets, but there were more patients with missing performance status in the registry dataset. Although levels of agreement for surgery, chemotherapy and external-beam radiotherapy were high between datasets, the new COSD system identified more instances of active treatment. There seems to be a high agreement of data between the datasets, and the findings suggest that the registry dataset coupled with COSD provides a richer dataset than LUCADA. However, it lagged behind LUCADA in performance status recording, which needs to improve over time