Temporal Network Analysis of Email Communication Patterns in a Long Standing Hierarchy

An important concept in organisational behaviour is how hierarchy affects the voice of individuals, whereby members of a given organisation exhibit differing power relations based on their hierarchical position. Although there have been prior studies of the relationship between hierarchy and voice, they tend to focus on more qualitative small-scale methods and do not account for structural aspects of the organisation. This paper develops large-scale computational techniques utilising temporal network analysis to measure the effect that organisational hierarchy has on communication patterns within an organisation, focusing on the structure of pairwise interactions between individuals. We focus on one major organisation as a case study - the Internet Engineering Task Force (IETF) - a major technical standards development organisation for the Internet. A particularly useful feature of the IETF is a transparent hierarchy, where participants take on explicit roles (e.g. Area Directors, Working Group Chairs). Its processes are also open, so we have visibility into the communication of people at different hierarchy levels over a long time period. We utilise a temporal network dataset of 989,911 email interactions among 23,741 participants to study how hierarchy impacts communication patterns. We show that the middle levels of the IETF are growing in terms of their dominance in communications. Higher levels consistently experience a higher proportion of incoming communication than lower levels, with higher levels initiating more communications too. We find that communication tends to flow "up" the hierarchy more than "down". Finally, we find that communication with higher-levels is associated with future communication more than for lower-levels, which we interpret as "facilitation". We conclude by discussing the implications this has on patterns within the wider IETF and for other organisations

Interviewer-driven Variability in Social Network Reporting: Results from Health and Aging in Africa: a Longitudinal Study of an INDEPTH community (HAALSI) in South Africa

Social network analysis depends on how social ties to others are elicited during interviews, a process easily affected by respondent and interviewer behaviors. We investigate how the number of self-reported important social contacts varied within a single data collection round. Our data come from Health and Aging in Africa: a Longitudinal Study of an INDEPTH community (HAALSI), a comprehensive population-based survey of individuals aged 40 years and older conducted over 13 months at the Agincourt health and demographic surveillance site in rural South Africa. As part of HAALSI, interviewers elicited detailed egocentric network data. The average number of contacts reported by the 5,059 respondents both varied significantly across interviewers and fell over time as the data collection progressed, even after adjusting for respondent, interviewer, and respondent–interviewer dyad characteristics. Contact numbers rose substantially after a targeted interviewer intervention. We conclude that checking (and adjusting) for interviewer effects, even within one data collection round, is critical to valid and reliable social network analysis. Measurements of social networks depend on the number and type of social ties to others (Berkman et al. 2000; Smith and Christakis 2008). These ties are typically elicited through interviews, a process easily affected by respondent or interviewer characteristics and behaviors. Understanding social network structure and composition requires substantial amounts of information from respondents (“egos”) about the people (“alters”) they have relationships with (Marsden 1990). Notably, the survey burden associated with network data collection depends heavily on the number of alters elicited through “name generator” questions: Each alter named leads to the repetition of all follow-up questions characterizing the ego–alter relationship (“name interpreters”; Burt 1984). Interviewers have been identified as a key source of variation in survey responses, particularly for questions that are attitudinal, ambiguous, or have complex skip patterns (West and Blom 2016). Several studies have previously identified interviewer effects on network size (Brüderl et al. 2013; Josten and Trappmann 2016; Marsden 2003; Paik and Sanchagrin 2013; van Tilburg 1998). These interviewer effects may arise from differential understanding of survey questions, and therefore how questions are presented to respondents. Interviewers can also affect which alters are elicited due to their own characteristics (e.g., sex, race, age, or experience), or the nature of the interviewer–respondent dyad (e.g., gender, race, or age homophily), leading to different lines of enquiry, levels of probing, or expectations of social acceptability (Collins 1980; Hox 1994; Marsden 2003; Phung et al. 2015). Furthermore, if respondents or interviewers are aware that naming more alters substantially increases survey length, then either group may consciously or unconsciously seek to minimize the number of alters named (Eagle and Proeschold-Bell 2015; van der Zouwen and van Tilburg 2001). In cross-sectional surveys, the opportunities for respondents to learn are limited, but those for interviewers will increase as the survey period progresses. Interviewers may try to reduce survey burden, either for themselves or for respondents, by favoring language or probes that decrease the number of alters elicited. Indeed, past studies in Europe have found evidence of interviewers intentionally filtering out questions by entering fewer responses that would trigger more questions. Such filtering behavior has been seen in Europe for interviewers who are being compensated by the interview rather than by the hour (Josten and Trappmann 2016; Kosyakova et al. 2014), for interviewers with prior experience using the relevant screening tool (Matschinger et al. 2005), and where interviewers are under substantial pressure to complete more interviews (Schnell and Kreuter 2000). We aim to extend this literature by assessing how the number of alters elicited systematically changed over the course of a cross-sectional social network survey of older adults in rural South Africa. We show a substantial drop in alter numbers over time, and a swift reversal following retraining, providing substantial evidence for interviewer effects

A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become one of the most used tools in mass spectrometry based proteomics. Various algorithms have since been developed to automate the process for modern high-throughput LC-MS/MS experiments.</p> <p>Results</p> <p>A probability based statistical scoring model for assessing peptide and protein matches in tandem MS database search was derived. The statistical scores in the model represent the probability that a peptide match is a random occurrence based on the number or the total abundance of matched product ions in the experimental spectrum. The model also calculates probability based scores to assess protein matches. Thus the protein scores in the model reflect the significance of protein matches and can be used to differentiate true from random protein matches.</p> <p>Conclusion</p> <p>The model is sensitive to high mass accuracy and implicitly takes mass accuracy into account during scoring. High mass accuracy will not only reduce false positives, but also improves the scores of true positive matches. The algorithm is incorporated in an automated database search program MassMatrix.</p

Changes in microphytobenthos fluorescence over a tidal cycle: implications for sampling designs

Intertidal microphytobenthos (MPB) are important primary producers and provide food for herbivores in soft sediments and on rocky shores. Methods of measuring MPB biomass that do not depend on the time of collection relative to the time of day or tidal conditions are important in any studies that need to compare temporal or spatial variation, effects of abiotic factors or activity of grazers. Pulse amplitude modulated (PAM) fluorometry is often used to estimate biomass of MPB because it is a rapid, non-destructive method, but it is not known how measures of fluorescence are altered by changing conditions during a period of low tide. We investigated this experimentally using in situ changes in minimal fluorescence (F) on a rocky shore and on an estuarine mudflat around Sydney (Australia), during low tides. On rocky shores, the time when samples are taken during low tide had little direct influence on measures of fluorescence as long as the substratum is dry. Wetness from wave-splash, seepage from rock pools, run-off, rainfall, etc., had large consequences for any comparisons. On soft sediments, fluorescence was decreased if the sediment dried out, as happens during low-spring tides on particularly hot and dry days. Surface water affected the response of PAM and therefore measurements used to estimate MPB, emphasising the need for care to ensure that representative sampling is done during low tide

Hydroxymethylglutaryl-CoA reductase inhibition with simvastatin in acute lung injury to reduce pulmonary dysfunction (HARP-2) trial : study protocol for a randomized controlled trial

Acute lung injury (ALI) is a common devastating clinical syndrome characterized by life-threatening respiratory failure requiring mechanical ventilation and multiple organ failure. There are in vitro, animal studies and pre-clinical data suggesting that statins may be beneficial in ALI. The Hydroxymethylglutaryl-CoA reductase inhibition with simvastatin in Acute lung injury to Reduce Pulmonary dysfunction (HARP-2) trial is a multicenter, prospective, randomized, allocation concealed, double-blind, placebo-controlled clinical trial which aims to test the hypothesis that treatment with simvastatin will improve clinical outcomes in patients with ALI

Microspatial variability in community structure and photophysiology of calcified macroalgal microbiomes revealed by coupling of hyperspectral and high-resolution fluorescence imaging

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The attached file is the published version of the article

A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra

<p>Abstract</p> <p>Background</p> <p>High-throughput shotgun proteomics data contain a significant number of spectra from non-peptide ions or spectra of too poor quality to obtain highly confident peptide identifications. These spectra cannot be identified with any positive peptide matches in some database search programs or are identified with false positives in others. Removing these spectra can improve the database search results and lower computational expense.</p> <p>Results</p> <p>A new algorithm has been developed to filter tandem mass spectra of poor quality from shotgun proteomic experiments. The algorithm determines the noise level dynamically and independently for each spectrum in a tandem mass spectrometric data set. Spectra are filtered based on a minimum number of required signal peaks with a signal-to-noise ratio of 2. The algorithm was tested with 23 sample data sets containing 62,117 total spectra.</p> <p>Conclusions</p> <p>The spectral screening removed 89.0% of the tandem mass spectra that did not yield a peptide match when searched with the MassMatrix database search software. Only 6.0% of tandem mass spectra that yielded peptide matches considered to be true positive matches were lost after spectral screening. The algorithm was found to be very effective at removal of unidentified spectra in other database search programs including Mascot, OMSSA, and X!Tandem (75.93%-91.00%) with a small loss (3.59%-9.40%) of true positive matches.</p

The writing on the wall: the concealed communities of the East Yorkshire horselads

This paper examines the graffiti found within late nineteenth and early-twentieth century farm buildings in the Wolds of East Yorkshire. It suggests that the graffiti were created by a group of young men at the bottom of the social hierarchy - the horselads – and was one of the ways in which they constructed a distinctive sense of communal identity, at a particular stage in their lives. Whilst it tells us much about changing agricultural regimes and social structures, it also informs us about experiences and attitudes often hidden from official histories and biographies. In this way, the graffiti are argued to inform our understanding, not only of a concealed community, but also about their hidden histor

SAMPI: Protein Identification with Mass Spectra Alignments

BACKGROUND: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs often suffer from missing or heuristic analysis of the significance of search results and insufficient handling of missing and additional peaks. RESULTS: We present an unified framework for analyzing Peptide Mass Fingerprints that offers a number of advantages over existing methods: First, comparison of mass spectra is based on a scoring function that can be custom-designed for certain applications and explicitly takes missing and additional peaks into account. The method is able to simulate almost every additive scoring scheme. Second, we present an efficient deterministic method for assessing the significance of a protein hit, independent of the underlying scoring function and sequence database. We prove the applicability of our approach using biological mass spectrometry data and compare our results to the standard software Mascot. CONCLUSION: The proposed framework for analyzing Peptide Mass Fingerprints shows performance comparable to Mascot on small peak lists. Introducing more noise peaks, we are able to keep identification rates at a similar level by using the flexibility introduced by scoring schemes

Eurasian Tree Sparrows, Risk for H5N1 Virus Spread and Human Contamination through Buddhist Ritual: An Experimental Approach

Background: The Highly Pathogenic Avian Influenza H5N1 virus has dramatically spread throughout Southeast Asia since its first detection in 1997. Merit Release Birds, such as the Eurasian Tree Sparrow, are believed to increase one's positive karma when kissed and released during Buddhist rituals. Since these birds are often in close contact with both poultry and humans, we investigated their potential role in the spread of H5N1 virus. Methodology/Principal Findings: Seven series of experiments were conducted in order to investigate the possible interactions between inoculated and exposed birds, including sparrow/sparrow, sparrow/chicken, duck/sparrow. Daily and post-mortem samples collected were tested for H5N1 virus by real-time RT-PCR and egg inoculation. When directly inoculated, Eurasian Tree Sparrows were highly susceptible to the H5N1 virus, with a fatality rate approaching 100% within 5 days post-inoculation. Although transmission of fatal infection between sparrows did not occur, seroconversion of the exposed birds was observed. Up to 100% chickens exposed to inoculated sparrows died of H5N1 infection, depending on the caging conditions of the birds, while a fatality rate of 50% was observed on sparrows exposed to infected ducks. Large quantities of H5N1 virus were detected in the sparrows, particularly in their feathers, from which infectious particles were recovered. Conclusions/Significance: Our study indicates that under experimental conditions, Eurasian Tree Sparrows are susceptible to H5N1 infection, either by direct inoculation or by contact with infected poultry. Their ability to transmit H5N1 infection to other birds is also demonstrated, suggesting that the sparrows may play a role in the dissemination of the virus. Finally, the presence of significant quantities of H5N1 virus on sparrows' feathers, including infectious particles, would suggest that Merit Release Birds represent a risk for human contamination in countries where avian influenza virus is circulating and where this religious ritual is practiced. © 2011 Gutiérrez et al.published_or_final_versio