Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs

Cell signaling pathways, which are a series of reactions that start at receptors and end at transcription factors, are basic to systems biology. Properly modeling the reactions in such pathways requires directed hypergraphs, where an edge is now directed between two sets of vertices. Inferring a pathway by the most parsimonious series of reactions then corresponds to finding a shortest hyperpath in a directed hypergraph, which is NP-complete. The state of the art for shortest hyperpaths in cell-signaling hypergraphs solves a mixed-integer linear program to find an optimal hyperpath that is restricted to be acyclic, and offers no efficiency guarantees. We present for the first time a heuristic for general shortest hyperpaths that properly handles cycles, and is guaranteed to be efficient. Its accuracy is demonstrated through exhaustive experiments on all instances from the standard NCI-PID and Reactome pathway databases, which show the heuristic finds a hyperpath that matches the state-of-the-art mixed-integer linear program on over 99% of all instances that are acyclic. On instances where only cyclic hyperpaths exist, the heuristic surpasses the state-of-the-art, which finds no solution; on every such cyclic instance, enumerating all possible hyperpaths shows that the solution found by the heuristic is in fact optimal

Social-Media-Algorithmen als Gefahr für Öffentlichkeit und Demokratie: Anwendungen, Risikoassemblagen und Verantwortungszuschreibungen

Der Beitrag beschreibt die Einsatzbereiche von Algorithmen auf Social-Media-Plattformen sowie die Risiken für Öffentlichkeit und Demokratie. Dabei wird herausgearbeitet, dass Algorithmen aus unterschiedlichen Gründen zur Entstehung einzelner Risiken beitragen, z.B. durch Fehlerhaftigkeit, Verstärkungseffekte, Manipulation, als Opportunitätsstruktur für gefährliche Praktiken und als Faktor für die Etablierung von Machtasymmetrien. Meist lassen sich Risiken jedoch nicht ausschließlich auf den Einsatz von Algorithmen zurückführen, sondern auf ein Zu-sammenwirken verschiedener Einflussfaktoren wie regulatorische Rahmenbedingungen, Geschäftsinteressen der Plattformbetreiber, Plattformdesign und Nutzungsverhalten. Entsprechend lassen sich Risiken algorithmischer Selektion auf Internet-Plattformen am besten als „sozio-technische Assemblagen“ beschreiben, um involvierte Akteur*innen, Technologien und vielfältige Wirkungszusammenhänge angemessen zu erfassen. Eine solche Beschreibung wiederum eröffnet Perspektiven für Fragen nach der Verantwortlichkeit für Risiken, die im Zusammenspiel von Menschen und Technik entstehen und sie ermöglicht eine Differenzierung der Zurech-nungspunkte für Verantwortlichkeit (Plattformunternehmen, Entwickler*innen, Nut-zer*innen, Politik/Regulierung, etc.), die gemeinsam ein Verantwortungsnetzwerk bilden

Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020.

In this meeting overview, we summarise the scientific program and organisation of the 16th International Society for Computational Biology Student Council Symposium in 2020 (ISCB SCS2020). This symposium was the first virtual edition in an uninterrupted series of symposia that has been going on for 15 years, aiming to unite computational biology students and early career researchers across the globe. [Abstract copyright: Copyright: © 2021 Cuypers WL et al.

The Development Of Biomagnetic Systems : Planar Gradiometers And Software Tools

This thesis is concerned with two aspects of the design and construction of biomagnetic systems. Firstly, it considers the optimum design of planar gradiometers. The modelling of gradiometers is discussed and an algorithm for optimising the sensitivity of a specific type of gradiometer is presented. A test thin-film procedure for the manufacture of a planar gradiometer is outlined. The performance of three different types of gradiometer in recovering test current distributions, using a distributed current analysis technique, is assessed. Secondly, four major software tools that are essential in the analysis of data from large multi-channel biomagnetic systems are presented. These tools are then used to analyze data from a visual evoked response experiment. The system used to collect data was the Helsinki multi-channel system which consists of 24 planar gradiometers. The results confirm the retinotopic mapping of visual field information, and suggest that the time evolution of activity in different parts of the visual cortex is similar for early latencies

Public Benefits of Undeveloped Lands on Urban Outskirts: Non-Market Valuation Studies and their Role in Land Use Plans

Over the past three decades, the economics profession has developed methods for estimating the public benefits of green spaces, providing an opportunity to incorporate such information into land-use planning. While federal regulations routinely require such estimates for major regulations, the extent to which they are used in local land use plans is not clear. This paper reviews the literature on public values for lands on urban outskirts, not just to survey their methods or empirical findings, but to evaluate the role they have played--or have the potential to play-- in actual land use plans. Based on interviews with authors and representatives of funding agencies and local land trusts, it appears that academic work has had a mixed reception in the policy world. Reasons for this include a lack of interest in making academic work accessible to policy makers, emphasizing revealed preference methods which are inconsistent with policy priorities related to nonuse values, and emphasis on benefit-cost analyses. Nevertheless, there are examples of success stories that illustrate how such information can play a vital role in the design of conservation policies. Working Paper 07-2

Socioeconomic status and prostate cancer incidence and mortality rates among the diverse population of California

The racial/ethnic disparities in prostate cancer rates are well documented, with the highest incidence and mortality rates observed among African-Americans followed by non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders. Whether socioeconomic status (SES) can account for these differences in risk has been investigated in previous studies, but with conflicting results. Furthermore, previous studies have focused primarily on the differences between African-Americans and non-Hispanic Whites, and little is known for Hispanics and Asian/Pacific Islanders. To further investigate the relationship between SES and prostate cancer among African-Americans, non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders, we conducted a large population-based cross-sectional study of 98,484 incident prostate cancer cases and 8,997 prostate cancer deaths from California. Data were abstracted from the California Cancer Registry, a population-based surveillance, epidemiology, and end results (SEER) registry. Each prostate cancer case and death was assigned a multidimensional neighborhood-SES index using the 2000 US Census data. SES quintile-specific prostate cancer incidence and mortality rates and rate ratios were estimated using SEER*Stat for each race/ethnicity categorized into 10-year age groups. For prostate cancer incidence, we observed higher levels of SES to be significantly associated with increased risk of disease [SES Q1 vs. Q5: relative risk (RR) = 1.28; 95% confidence interval (CI): 1.25–1.30]. Among younger men (45–64 years), African-Americans had the highest incidence rates followed by non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders for all SES levels. Yet, among older men (75–84 years) Hispanics, following African-Americans, displayed the second highest incidence rates of prostate cancer. For prostate cancer deaths, higher levels of SES were associated with lower mortality rates of prostate cancer deaths (SES Q1 vs. Q5: RR = 0.88; 95% CI: 0.92–0.94). African-Americans had a twofold to fivefold increased risk of prostate cancer deaths in comparison to non-Hispanic Whites across all levels of SES. Our findings suggest that SES alone cannot account for the greater burden of prostate cancer among African-American men. In addition, incidence and mortality rates of prostate cancer display different age and racial/ethnic patterns across gradients of SES

Strandings of NE Atlantic gorgonians

Publisher policy: author can archive post-print on open access repository after an embargo period of 18 months. Publisher's version/PDF cannot be used. Must link to publisher version with DOI. Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License. publisher: Elsevier articletitle: Strandings of NE Atlantic gorgonians journaltitle: Biological Conservation articlelink: http://dx.doi.org/10.1016/j.biocon.2017.03.020 content_type: article copyright: © 2017 Elsevier Ltd. All rights reserved