Thursday, June 27, 2013

Russian mortality for cohorts with 50+ registered age points

the first cohort, 1899 - has 50 points, the last - also 50, in between --- 51 points.
These are the longest available series for Russia, albeit at advanced ages not really reliable

Thursday, June 20, 2013

more linx2 PLOSEONE must read papers

In April 2009, the most recent pandemic of influenza A began. We present the first estimates of pandemic mortality based on the newly-released final data on deaths in 2009 and 2010 in the United States.

We obtained data on influenza and pneumonia deaths from the National Center for Health Statistics (NCHS). Age- and sex-specific death rates, and age-standardized death rates, were calculated. Using negative binomial Serfling-type methods, excess mortality was calculated separately by sex and age groups.

In many age groups, observed pneumonia and influenza cause-specific mortality rates in October and November 2009 broke month-specific records since 1959 when the current series of detailed US mortality data began. Compared to the typical pattern of seasonal flu deaths, the 2009 pandemic age-specific mortality, as well as influenza-attributable (excess) mortality, skewed much younger. We estimate 2,634 excess pneumonia and influenza deaths in 2009–10; the excess death rate in 2009 was 0.79 per 100,000.

Pandemic influenza mortality skews younger than seasonal influenza. This can be explained by a protective effect due to antigenic cycling. When older cohorts have been previously exposed to a similar antigen, immune memory results in lower death rates at older ages. Age-targeted vaccination of younger people should be considered in future pandemics.

Nguyen AM, Noymer A (2013)

Influenza Mortality in the United States, 2009 Pandemic: Burden, Timing and Age Distribution

PLoS ONE 8(5): e64198. doi:10.1371/journal.pone.0064198

We construct a stochastic SIR model for influenza spreading on a D-dimensional lattice, which represents the dynamic contact network of individuals. An age distributed population is placed on the lattice and moves on it. The displacement from a site to a nearest neighbor empty site, allows individuals to change the number and identities of their contacts. The dynamics on the lattice is governed by an attractive interaction between individuals belonging to the same age-class. The parameters, which regulate the pattern dynamics, are fixed fitting the data on the age-dependent daily contact numbers, furnished by the Polymod survey. A simple SIR transmission model with a nearest neighbors interaction and some very basic adaptive mobility restrictions complete the model. The model is validated against the age-distributed Italian epidemiological data for the influenza A(H1N1) during the  season, with sensible predictions for the epidemiological parameters. For an appropriate topology of the lattice, we find that, whenever the accordance between the contact patterns of the model and the Polymod data is satisfactory, there is a good agreement between the numerical and the experimental epidemiological data. This result shows how rich is the information encoded in the average contact patterns of individuals, with respect to the analysis of the epidemic spreading of an infectious disease.

Liccardo A, Fierro A (2013)

A Lattice Model for Influenza Spreading

PLoS ONE 8(5): e63935. doi:10.1371/journal.pone.0063935


Reducing health inequalities is a key objective for many governments and public health organizations. Whether inequalities are measured on the absolute (difference) or relative (ratio) scale can have a significant impact on judgments about whether health inequalities are increasing or decreasing, but both of these measures are not often presented in empirical studies. In this study we investigated the impact of selective presentation of health inequality measures on judgments of health inequality trends among 40 university undergraduates. We randomized participants to see either a difference or ratio measure of health inequality alongside raw mortality rates in 5 different scenarios. At baseline there were no differences between treatment groups in assessments of inequality trends, but selective exposure to the same raw data augmented with ratio versus difference inequality graphs altered participants’ assessments of inequality change. When absolute inequality decreased and relative inequality increased, exposure to ratio measures increased the probability of concluding that inequality had increased from 32.5% to 70%, but exposure to difference measures did not (35% vs. 25%). Selective exposure to ratio versus difference inequality graphs thus increased the difference between groups in concluding that inequality had increased from 2.5% (95% CI −9.5% to 14.5%) to 45% (95% CI 29.4 to 60.6). A similar pattern was evident for other scenarios where absolute and relative inequality trends gave conflicting results. In cases where measures of absolute and relative inequality both increased or both decreased, we did not find any evidence that assignment to ratio vs. difference graphs had an impact on assessments of inequality change. Selective reporting of measures of health inequality has the potential to create biased judgments of progress in ameliorating health inequalities.

Harper S, King NB, Young ME (2013)

Impact of Selective Evidence Presentation on Judgments of Health Inequality Trends: An Experimental Study

PLoS ONE 8(5): e63362. doi:10.1371/journal.pone.0063362


A criminal career can be either general, with the criminal committing different types of crimes, or specialized, with the criminal committing a specific type of crime. A central problem in the study of crime specialization is to determine, from the perspective of the criminal, which crimes should be considered similar and which crimes should be considered distinct. We study a large set of Swedish suspects to empirically investigate generalist and specialist behavior in crime. We show that there is a large group of suspects who can be described as generalists. At the same time, we observe a non-trivial pattern of specialization across age and gender of suspects. Women are less prone to commit crimes of certain types, and, for instance, are more prone to specialize in crimes related to fraud. We also find evidence of temporal specialization of suspects. Older persons are more specialized than younger ones, and some crime types are preferentially committed by suspects of different ages.

Tumminello M, Edling C, Liljeros F, Mantegna RN, Sarnecki J (2013)

The Phenomenology of Specialization of Criminal Suspects

PLoS ONE 8(5): e64703. doi:10.1371/journal.pone.0064703


The expanding global air network provides rapid and wide-reaching connections accelerating both domestic and international travel. To understand human movement patterns on the network and their socioeconomic, environmental and epidemiological implications, information on passenger flow is required. However, comprehensive data on global passenger flow remain difficult and expensive to obtain, prompting researchers to rely on scheduled flight seat capacity data or simple models of flow. This study describes the construction of an open-access modeled passenger flow matrix for all airports with a host city-population of more than 100,000 and within two transfers of air travel from various publicly available air travel datasets. Data on network characteristics, city population, and local area GDP amongst others are utilized as covariates in a spatial interaction framework to predict the air transportation flows between airports. Training datasets based on information from various transportation organizations in the United States, Canada and the European Union were assembled. A log-linear model controlling the random effects on origin, destination and the airport hierarchy was then built to predict passenger flows on the network, and compared to the results produced using previously published models. Validation analyses showed that the model presented here produced improved predictive power and accuracy compared to previously published models, yielding the highest successful prediction rate at the global scale. Based on this model, passenger flows between 1,491 airports on 644,406 unique routes were estimated in the prediction dataset. The airport node characteristics and estimated passenger flows are freely available as part of the Vector-Borne Disease Airline Importation Risk (VBD-Air).

Citation: Huang Z, Wu X, Garcia AJ, Fik TJ, Tatem AJ (2013)

An Open-Access Modeled Passenger Flow Matrix for the Global Air Network in 2010

PLoS ONE 8(5): e64317. doi:10.1371/journal.pone.0064317


There is believed to be a ‘beauty premium’ in key life outcomes: it is thought that people perceived to be more physically attractive have better educational outcomes, higher-status jobs, higher wages, and are more likely to marry. Evidence for these beliefs, however, is generally based on photographs in hypothetical experiments or studies of very specific population subgroups (such as college students). The extent to which physical attractiveness might have a lasting effect on such outcomes in ‘real life’ situations across the whole population is less well known. Using longitudinal data from a general population cohort of people in the West of Scotland, this paper investigated the association between physical attractiveness at age 15 and key socioeconomic outcomes approximately 20 years later. People assessed as more physically attractive at age 15 had higher socioeconomic positions at age 36– in terms of their employment status, housing tenure and income - and they were more likely to be married; even after adjusting for parental socioeconomic background, their own intelligence, health and self esteem, education and other adult socioeconomic outcomes. For education the association was significant for women but not for men. Understanding why attractiveness is strongly associated with long-term socioeconomic outcomes, after such extensive confounders have been considered, is important.

Benzeval M, Green MJ, Macintyre S (2013)

Does Perceived Physical Attractiveness in Adolescence Predict Better Socioeconomic Position in Adulthood? Evidence from 20 Years of Follow Up in a Population Cohort Study

PLoS ONE 8(5): e63975. doi:10.1371/journal.pone.0063975


Can online behaviour be used as a proxy for studying urban mobility? The increasing availability of digital mobility traces has provided new insights into collective human behaviour. Mobility datasets have been shown to be an accurate proxy for daily behaviour and social patterns, and behavioural data from Twitter has been used to predict real world phenomena such as cinema ticket sale volumes, stock prices, and disease outbreaks. In this paper we correlate city-scale urban traffic patterns with online search trends to uncover keywords describing the pedestrian traffic location. By analysing a 3-year mobility dataset we show that our approach, called Location Archetype Keyword Extraction (LAKE), is capable of uncovering semantically relevant keywords for describing a location. Our findings demonstrate an overarching relationship between online and offline collective behaviour, and allow for advancing analysis of community-level behaviour by using online search keywords as a practical behaviour proxy.

Kostakos V, Juntunen T, Goncalves J, Hosio S, Ojala T (2013)

Where Am I? Location Archetype Keyword Extraction from Urban Mobility Patterns

PLoS ONE 8(5): e63980. doi:10.1371/journal.pone.0063980

Monday, June 17, 2013

Do Altmetrics Work?

Altmetric measurements derived from the social web are increasingly advocated and used as early indicators of article impact and usefulness. Nevertheless, there is a lack of systematic scientific evidence that altmetrics are valid proxies of either impact or utility although a few case studies have reported medium correlations between specific altmetrics and citation rates for individual journals or fields. To fill this gap, this study compares 11 altmetrics with Web of Science citations for 76 to 208,739 PubMed articles with at least one altmetric mention in each case and up to 1,891 journals per metric. It also introduces a simple sign test to overcome biases caused by different citation and usage windows. Statistically significant associations were found between higher metric scores and higher citations for articles with positive altmetric scores in all cases with sufficient evidence (Twitter, Facebook wall posts, research highlights, blogs, mainstream media and forums) except perhaps for Google+ posts. Evidence was insufficient for LinkedIn, Pinterest, question and answer sites, and Reddit, and no conclusions should be drawn about articles with zero altmetric scores or the strength of any correlation between altmetrics and citations. Nevertheless, comparisons between citations and metric values for articles published at different times, even within the same year, can remove or reverse this association and so publishers and scientometricians should consider the effect of time when using altmetrics to rank articles. Finally, the coverage of all the altmetrics except for Twitter seems to be low and so it is not clear if they are prevalent enough to be useful in practice.

Thelwall M, Haustein S, Larivière V, Sugimoto CR (2013)

Do Altmetrics Work? Twitter and Ten Other Social Web Services 

PLoS ONE 8(5): e64841. doi:10.1371/journal.pone.0064841

Prevalence of TB/HIV Co-Infection

They searched PubMed, Embase, and Web of Science for studies of the prevalence of TB/HIV co-infection. We also searched bibliographic indices, scanned reference lists, and corresponded with authors. We summarized the estimates using meta-analysis and explored potential sources of heterogeneity in the estimates by metaregression analysis.

Our analyses suggest that it is necessary to attach importance to HIV/TB co-infection, especially screening of TB/HIV co-infection using methods with high sensitivity, specificity and predictive values in the countries with high HIV/AIDS prevalence in the general population.

Gao J, Zheng P, Fu H (2013)

Prevalence of TB/HIV Co-Infection in Countries Except China: A Systematic Review and Meta-Analysis

PLoS ONE 8(5): e64915. doi:10.1371/journal.pone.0064915

Efficient Control of Epidemics Spreading on Networks

The authors analyse two models describing disease transmission and control on regular and small-world networks. We use simulations to find a control strategy that minimizes the total cost of an outbreak, thus balancing the costs of disease against that of the preventive treatment. The models are similar in their epidemiological part, but differ in how the removed/recovered individuals are treated. The differences in models affect choice of the strategy only for very cheap treatment and slow spreading disease. However for the combinations of parameters that are important from the epidemiological perspective (high infectiousness and expensive treatment) the models give similar results. Moreover, even where the choice of the strategy is different, the total cost spent on controlling the epidemic is very similar for both models.

Oleś K, Gudowska-Nowak E, Kleczkowski A (2013)

Efficient Control of Epidemics Spreading on Networks: Balance between Treatment and Recovery 

PLoS ONE 8(6): e63813. doi:10.1371/journal.pone.0063813

Two Rusian males cohorts

They are 1931 (my father), and 1956 (my). For the span of ages with data from both cohorts we could see apparent deterioration in mortality. However, likely that younger cohort will do better at the advanced ages, and it probably was better at younger ages.

Saturday, June 15, 2013

Norway Cohort (1979) Mortality

Obviously, the numbers of events is too small to observe regularities. However, rising gender gap at age 21 is provoking ;)
Source: Human Mortality Data Base

Friday, June 14, 2013

how wrong I was

Trying yahoo search engine I found a year or two old paper By SOPHIA KISHKOVSKY / The New York Times "Russia Enacts Law Opposing Abortion", reprinted in and by awid.

What I had said to her:
 "Since obscurantists cannot turn history back, they limit themselves to small meanness like a week without abortion."
Two years ago I was unable to imagine obscurantism that developed ;(

RLMS data sets and dox

Correct reference = Source: “Russia Longitudinal Monitoring survey, RLMS-HSE”, conducted by the National Research University Higher School of Economics and ZAO “Demoscope” together with Carolina Population Center, University of North Carolina at Chapel Hill and the Institute of Sociology RAS.

see links to more various data, including UNICEF MICS
+ more from Stephania Lovo

Abstracts of the First International Russia Longitudinal Monitoring Survey of HSE User Conference

Abstracts of the First International Russia's Longitudinal Monitoring Survey of HSE User Conference are available in the HSE web site (in one pdfile), click here, the conference program is here (also pdf), and info with links here.
Some guys told that the conference was not the first one, however, it is its  formal title ;)
Likely, it is the first since it belongs to HSE.

Sunday, June 2, 2013

Which of vessels are communicating?

On May 28 and 29 I took part in two events:

  1. Partners' Forum on Russian Reproductive Health Survey (info about it lived short on Rosstat site, today it is already removed from news list) + I am going to write about partners separately, and
  2. Experts' round table at Gorbachov Fund “Demographic problems in the context of the modernization of Russian society”.

Many other people participated in the events, especially in Rosstat's one, probably more than one hundred, and only about twenty at Gorby fund. I talked on Current Russian Govt Approach to Reproductive Health. Certainly, I gave my own personal opinion and value judgments, and I am reproducing them below, presentation in Russian is here.

1. Complimentary part:
It was necessary to congratulate Rosstat for its 150th birthday (1863, Tsar-Liberator attempted to civilize Russia). Concerning the survey: Better late than never. The first RHS took place in El Salvador, 1975, Russia has experience of 1996 and 1999, when this methodology had been applied to estimate the efficiency of (breastfeeding promotion?) project. A unified program allows international comparisons of detailed indicators, which government statistics do not posses, albeit only 27 of about 80 sets of survey data are freely accessible from CDC site. However, most interesting for us data set (Ukraine, 1999 despite not very recent) is available. There is a large amount of new data that will give the opportunity to test some specific hypotheses (use of contraception+abortion culture).
Thanks for the survey, thank you for publishing the results, for the invitation to discuss.
Nikitina nodded, when I said about the possibility to work with data obtained in the Russian Federation. These data will also be available, thanks in advance.
Frankly speaking, I supposed, we are discussing a draft report, since there are a lot of stupid errors, mistypings, etc., but to our surprise the printed final version had been distributed. Thus the forum aim became unclear. I had supposed to speak about the text, since tables are not possible to comment. Results showed no significant discrepancies with what was previously known from other sources, and nothing counter-intuitive.

2. Scary reading:
Examples (section 11.3. Opinion about the risks ...)

  • Most of the women ... have no idea how dangerous are the use of injectable hormonal contraceptives or tubal ligation ...
  • Increasing knowledge about the dangers of abortion may contribute to the increased use of modern contraceptives.

It is a beloved horror story: Do not use these capitalist shit! From the same set of common arguments: pill use causes the mustache growth, breast cancer, and extra weight. As far as I understand, bureaucracy calls it: report agreed with the Ministry of Health. My suggestion was = remove it. And they did, removed by rephrasing, added a sheet of paper inside the book. They (organizers) also asked me to avoid speaking about it, they had removed the slide from my presentation sent beforehand. That made me redirect my speech from critics of MoH to critics of ideology of abortion perception (subj). inadequately considers fertility v abortion not abortion v contraception.

4. Abortion
It is likely the central theme of reproductive health domain in this country. Russia is remaining a leader, although births recently (five years ago) surpassed the number of abortions. It is interesting that the lag from two neighbor countries strangely coincides with changes in approach to reproductive health. The dynamics of reduction is not as favorable as it may seem, but the forum does not cover the issue with a particularly needed and inevitable section. However, the topic had been attached to the speech on fertility!!! made by Serbanescu. Despite I was invited to make a comment on contraception, this is not possible without concerning abortion. These are communicating vessels, not fertility and abortion.
Why we do not discuss abortion? The level of post-abortion complications in Russia is ten times higher than in the USA despite Russia has the longest history of legal abortion, 74 years. During this period MoH had been unable to train personnel to perform safe abortion. Why do we welcome them to a floor and reconcile anything with guys not knowing how to work properly.

5. More from the report:

  • section 7.3: This points to the need for education in this (family planning) regard.
  • section 9: This information can be used to effectively manage the system of family planning services, as well as monitoring and evaluating the effectiveness of the system.
  • section 9.3: We must carefully anticipate the needs for contraception in the future. This information will help policy makers and program planners to estimate the volume of the stocks to plan a budget.

Wow! Yyess. But what is it? My impression, – it is written about some other country, not about Russia. The authors probably borrowed the text from report on Kenya. Have we a system of family planning services? Or bodies responsible for this policy? Nobody have seen them.

Before moving on to the recommendations, I want to draw your attention to a couple of facts from the sources other than this report

6. Menarche and age at the first sex (data: RLMS-HSE, 19th round, 2010)
Median age at menarche is 13 years, i.e., a half of the girls starts to have a risk of pregnancy at about school's 7th degree, and by the end of the school a little less than half has already had a sexual experience (penetration).

7. The growth of HIV prevalence (data: Federal AIDS Center)
In 2012 Federal AIDS Center registered 62+ thousand new cases of HIV (in 2011 – 58+), about 20% of them was a result of heterosexual contact (since for about a half of new cases the transmission mode is unknown Federal AIDS Center prorates to 40%), thus one person a day in age group 15-20 is expected to be infected (my estimate;).
Condom prevents (hetero)sexual HIV-transmission, but MoH destroyed all HIV prevention programs.

8. Recommendations. Two parts: (1) concerning survey, (2) concerning policy.

  • open data for researchers +Another conference in a about a year after disclosure to discuss the results of independent researches
  • regular conduction of such a survey


  1. Introduction of sex education lessons in school, in particular, the use of contraception.
  2. Resumption of funding of the federal family planning program
  3. Renascence the full scale activities of Russian Association of Family Planning

Concerning policy recommendations can be combined into one: abandonment the obscurantist (Medvedev) modernization and return to the position that Russia held in the early wild 90's (before the Cairo conference)

I understand that the Ministry of Health does not need my nor any other recommendations, but I still hope the open data.

Next day after the partners forum in the news:
Measures that Ministry of Health is preparing to minimize fertility reduction are associated with a decrease in the number of abortions
Russian LJ about the event (and here)