Phylogenetic methods have revolutionised evolutionary biology and have recently been applied to studies of linguistic and cultural evolution. However, the basic comparative data on the languages of the world required for these analyses is often widely dispersed in hard to obtain sources. Here we outline how our Austronesian Basic Vocabulary Database (ABVD) helps remedy this situation by collating wordlists from over 500 languages into one web-accessible database. We describe the technology underlying the ABVD and discuss the benefits that an evolutionary bioinformatic approach can provide. These include facilitating computational comparative linguistic research, answering questions about human prehistory, enabling syntheses with genetic data, and safe-guarding fragile linguistic information. GenBank® (http://www.ncbi.nlm.nih.gov), contains over 80 million DNA sequences from over 260,000 organisms and doubles in size approximately every 18 months  is as important to scientific progress today as is access to a laboratory or library” , and New Zealand . This reIn previous studies we tested the “Out of Taiwan” scenario by conducting phylogenetic analyses of lexical data derived from Blust’s Austronesian Comparative Dictionary Project , which despite being an excellent linguistic resource, is primarily a worldwide Bible translation project , or contain no information about the provenance or quality of the linguistic information , or are private hobby databases with limited public accessibility , or are inextricably linked to dubious language subgrouping proposals . Finally, much of the basic information on the languages of the world is unfortunately quite fragile. Substantial amounts of comparative linguistic data can only be found in disintegrating field notes and recordings. Sometimes this information may be the only evidence that a language—and a culture—ever existed. The projects to properly store this information, like PARADISEC (http://paradisec.org.au/), are seriously under-funded. The fragility of current linguistic data storage is made all the more worrying by the fact that, on average, a language goes extinct every two weeks. At least a half of the world’s languages are expected to go extinct in the next century  approached Robert Blust at the University of Hawaii with the idea of producing an electronic database of Blust’s extensive collection of Austronesian wordlists. Blust had collected basic vocabulary wordlists from a total of 231 Austronesian languages in order to test variation in retention rates as part of a general critique of lexicostatistical methods of language subgrouping , 2000. TAustronesian Basic Vocabulary Database , where it has grown substantially. In the following sections we will describe the database structure, detail some of the features of the ABVD web application, and describe its usage. We finish by outlining how evolutionary bioinformatics ideas could be extended to create a new field of study—a field that could be dubbed, with a hint of a grin, “lexomics”.We took the 231 word-lists collected by Blust, expanded them from 200 to 210 items of basic vocabulary , and entMySQL as a series of database tables linked by standard foreign key architecture. Due to the extended and phonetic characters used for the lexical orthography, all information is encoded in the Unicode format UTF-8. The core database schema of the ABVD is shown in languages stores information about each language. This includes the name of language (“language”), the data source information (“author”), and the name of the person entering the data (“typedby”). The field “silcode” contains the ISO 639-3 language identification code. This identification code provides a way of linking each language to broader information about the language at other resources such as SIL International’s Ethnologue  for any extra information about the language. The languages table is linked to the locations table via a one-to-many foreign key. The locations table stores geographical information  about each language to enable plotting of the languages on a map. The resources table is also linked to the languages table via foreign key. This table contains links to other relevant websites about a language, such as Wikipedia entries, homepages of research groups investigating the language, or other online resources like dictionaries.The lexical and cognate data in the ABVD is stored in the open-source relational database The table “words” contains information about the word meaning categories in the database. Each word category  has an edata contains the lexical entries and is the main data store for the database. Each entry in this table is linked to a language in languages and to a word in words via foreign key. This allows each language to have multiple entries for each word. For example, Nukuoro has three entries in the word meaning category for “hair”: “ngangailu” (hair on head), “ngae” (a single hair on the head), and “hulu” (body hair). The field “item” contains the lexical entry itself. The “annotations” field contains any comments about this item, such as slightly different meanings, or information about irregular sound change. If the entry is known to be borrowed from another language, the field “loan” is used to flag this status. The “cognacy” field contains information about cognate set membership for this entry, that links words that have evolved from a common ancestor (see below).The table history table. The information logged for each change includes which language and word were modified . This is supplemented with a comment field (“comment”) for annotating the change, and a timestamp of when the change occurred (“changetime”). The field “person_id” denotes the editor who made the change, and is a foreign key onto the table people that stores user information, access credentials, etc.All changes to the data are tracked using the http://language.psy.auckland.ac.nz/austronesian/people.php#authors for a full contributor list). As the ABVD has grown, a number of languages from outside the family have been incorporated for comparative purposes. These languages include the Sino-Tibetan language Old Chinese and the Tai-Kadai language Buyang (both added by Laurent Sagart).The data in the ABVD comes from three primary sources. The first source of data are wordlists collected by linguists during fieldwork. The major providers have been Robert Blust, John Lynch, and Malcolm Ross. Many other linguists have graciously contributed word lists for languages they are familiar with. The second primary source of data has been published wordlists and dictionaries. The major publications mined for information were the Polynesian Lexicon project POLLEX , and a lJust as biologists are interested in homologous genes to trace ancestry, linguists are interested in homologous words. These homologous words—cognates—can be identified using systematic sound correspondences between words of similar meaning across languages. For example, Cognate judgements were done by or in consultation with a number of linguistic experts. Robert Blust provided cognate decisions for most areas within the Austronesian family. Jeff Marck assessed the languages of Polynesia, Micronesia and neighbouring regions for cognation. John Lynch assessed Vanuatu and New Caledonia languages, and Malcolm Ross assisted with the cognation judgements of languages in Near Oceania. Laurent Sagart provided cognation judgements for a number of Formosan languages. Graham Thurgood provided the judgements for the Chamic language subgroup. Russell Gray, Simon Greenhill and Cordelia Nickelsen assessed the remaining regions in consultation with Robert Blust. Since these cognate decisions generally require a high level of linguistic expertise, only the database administrators can edit the cognate coding.The ABVD web interface is implemented in the programming language PHP running on an Apache webserver. The interface has a number of core functions: displaying information about languages, displaying information about words, enabling new data to be entered, searching through the data, and allowing editors to maintain the database. These functions will be discussed in turn.languages page displays all the information about a given language . This is followed by links to external resources relevant to this language from the resources table . Finally, the wordlist for this language is displayed, showing the lexical entries, annotations and judgements of cognation. All changes to this language are also published via RSS 2.0 feeds, allowing users to subscribe and be notified of any changes. To enable the data to be used “offline”, users can download the information for a language in comma-separated or XML format.The language . First, words page . We see the ABVD as a first step towards a similar “Linguagraphic” Project that would aim to map humanity’s linguistic and cultural journey through the ages.The second planned enhancement is the continued growth of the ABVD. We have information from at least another 200 Austronesian languages to enter, and there is much more data in the primary literature available for mining. This will be further augmented with wordlists from languages neighbouring the Austronesian language family, including those from Mon-Khmer, Tai-Kadai, Hmong-Mien, and Sino-Tibetan languages. Ultimately, we would like to construct a global database of basic information about the world’s languages. Naturally, trying to understand the histories of languages and their speakers based on a short sample of vocabulary has its limitations. For more detailed inferences this global database would ideally be extended to include additional data on morphology, phonology, structure, grammar, and typology. There has been a recent push towards large-scale genetic database projects like National Geographic and IBM’s Genographic Project e.g.  that aimTo facilitate the creation of a global database we need to abstract out common components of the databases to enable the storage of lexical information from different language families. We currently have databases under development for languages of the Mayan, Uto-Aztecan and Bantu language families. Each of these families requires slightly different information to be stored, and manipulated in different ways. For example, the Bantu languages require the lexical item and the nominal prefix to be separated. By taking the knowledge and experience we have acquired through developing the ABVD, we hope to be able to make a fully extensible database for storing a wide range of global linguistic information in future. Ideally the data in this global database would be coded in a way that facilitates analyses using computational phylogenetic methods.The Austronesian Basic Vocabulary Database provides a comprehensive comparative source of lexical data for a large number of Pacific languages. This lexical information is not only of enormous value in its own right, it also has much to offer geneticists interested in elucidating human history. Linguistic analyses can assist genetic studies by improving sampling designs. It is not uncommon for genetic studies to sample DNA from culturally meaningless groups like “Melanesians” or “Australians” . UnfortuLanguages are, as the poet Ralph Waldo Emerson noted, the “archives of history” , p. 417.−8 substitutions per site per year across the ~16,000 base pairs  stored in DNA. Despite mitochondrial DNA having higher mutation rates than nuclear DNA, there is still only around 1.7 × 10se pairs . Many inse pairs . In contThe combination of large comparative linguistic databases and computational phylogenetic methods we have advocated in this paper is the direct extension of evolutionary bioinformatic thinking to historical linguistics. This relatively new area of study could be christened “lexomics”. This nascent approach could provide a very powerful way of “triangulating” sensu  the hist


Twin and family studies indicate that genetic influences play an important part in the aetiology of all of these disorders, yet progress in identifying genes has been slow. One way forward is to cut loose from conventional clinical criteria for diagnosing disorders and to focus instead on measures of underlying cognitive mechanisms. Psychology can inform genetics by clarifying what the key dimensions are for heritable phenotypes. However, it is not a one-way street. By using genetically informative designs, one can gain insights about causal relationships between different cognitive deficits. For instance, it has been suggested that low-level auditory deficits cause phonological problems in SLI. However, a twin study showed that, although both types of deficit occur in SLI, they have quite different origins, with environmental factors more important for auditory deficit, and genes more important for deficient phonological short-term memory. Another study found that morphosyntactic deficits in SLI are also highly heritable, but have different genetic origins from impairments of phonological short-term memory. A genetic perspective shows that a search for  Several developmental disorders are of particular theoretical interest to psychologists because they are characterized by fairly selective impairments in specific domains of functioning. In developmental dyslexia In this paper, I consider what we know about causes of such disorders at two levels of description. Part 1, “How psychology can inform genetics”, focuses on studies of aetiology: genetic and environmental factors that are associated with developmental disorders. In Part 2, “How genetics can inform psychology”, attention shifts to their underlying cognitive basis. I focus mainly on SLI, but also briefly allude to relevant work on dyslexia and autism.When neuro-imaging first became widely available, people were surprised to find remarkably little evidence of focal brain damage in children with specific developmental disorders. As As is discussed below, it is now widely accepted that inherited brain anomalies, rather than acquired brain damage, are a key factor in the aetiology of developmental dyslexia, SLI, and autistic disorder. We understand very little about how genetic variations can lead to abnormal brain development, but it is conceivable that, by affecting processes such as neuronal migration, neurotransmitter activity, programmed cell death, synaptic connectivity, or myelination, they result in a brain that functions in a nonoptimal fashion.The bulk of the evidence for genetic aetiology of developmental disorders comes from behavioural studies adopting a genetically informative design. Such studies consider how far observed similarities between individuals  are correlated with their genetic similarity (similarities in their genotypes). At the simplest level, one can do family studies to see whether a disorder is more common in first-degree relatives (parents and siblings) of an affected child than in first-degree relatives of unaffected children. Such studies are not watertight, however, because relatives typically share environments as well as genes. A more satisfactory design is the twin study, which capitalizes on the fact that there are two different processes that can lead to twinning: Splitting of a fertilized ovum will lead to genetically identical or monozygotic (MZ) twins, whereas fertilization of two ova around the same time will lead to fraternal or dizygotic (DZ) twins, whose genetic similarity is equivalent to that seen in other siblings. Although media attention focuses on studies of twins reared apart, one does not need to use such rare cases to gain useful information from a twin study. Twins growing up together will resemble one another, insofar as they are subject to many of the same environmental influences, including prenatal as well as postnatal factors. However, if similarity between two members of a twin pair is greater for MZ than for DZ twins, this points to a role of genes. When considering developmental disorders, we can assess the degree of concordance between twins  in both MZ and DZ twins, to get estimates of the relative roles of genetic and environmental factors in the aetiology. Studies adopting this approach have found high estimates of heritability for autism  and SLI the gene for any of these disorders: They are heterogeneous, and such genes as exist are likely to act in a probabilistic fashion, in interaction with other genetic and environmental factors.With the advent of fast-throughput genetic sequencers, a sense of optimism was generated that we would quickly move on to identify risk genes for developmental disorders. However, progress has been surprisingly slow. Identifying genes that are implicated in disorder is not a single-step procedure. Typically, one first uses a method known as linkage analysis to home in on a region that is likely to harbour relevant genes. Linkage analysis relies on the fact that the closer together two bits of DNA are, the greater the likelihood they will be inherited together. Some stretches of DNA do not contain genes and are highly variable from one individual to another. These can act as “markers”, allowing one to identify whether a portion of DNA has been inherited from the mother or the father. One starts with a set of siblings, both of whom have a disorder. Then for a pair of alleles at a given locus, one can work out whether zero, one, or two alleles in siblings are “identical by descent” (IBD)—that is, inherited from the same parent see . The obsOne reason why progress in the genetics of developmental disorders is slow may be because most genetic studies rely on textbook descriptions of disorders to define the phenotype. These typically specify in rather broad terms the impairments that have to be present to merit a diagnosis, together with exclusionary factors. So, for instance, SLI is diagnosed in a child whose language development lags significantly behind nonverbal development, and there is no obvious causal factor or other medical diagnosis such as hearing loss, neurological disease, or autistic disorder. This kind of diagnosis can be useful in identifying those who require special services, but it does not yield a homogenous group of children. On the one hand, it will include children with diverse difficulties in areas such as syntax, semantics, phonology, and pragmatics. On the other hand, it may exclude a child with significant language deficits because an arbitrary IQ cut-off is not met. Furthermore, although textbook definitions imply discrete disorders, the boundaries between conditions are often fuzzy—for example, SLI can be hard to distinguish from dyslexia  and fromIdentification of subtypes of disorder is one way forward, but it is not the complete solution. Rather than subdividing a disorder into ever more selective subgroups, we may sometimes need to do the opposite and consider adopting a broader conceptualization of the phenotype. The idea is not that we should simply lump together individuals with diverse clinical profiles, but rather that we should move away from a focus solely on clinical “disease” categories and develop instead more quantitative measures of underlying processes— so-called “endophenotypes” .The value of this approach was demonstrated to me when I conducted a twin study of SLI , in whic2g, will lead to twin dissimilarity. Nonshared environment includes measurement error as well as longer term idiosyncratic influences on the child . If performance on nonword repetition were determined solely by e2g then regardless of Twin A's score, we would predict that Twin B would score at the population mean. Now consider the hypothetical situation where performance on nonword repetition is determined solely by environmental factors shared by both twins—for example, the amount of language input they received from parents. Environmental factors that are common to both twins, or c2g, make twins similar to one another, so, if such factors exert a large effect, when Twin A has a low score, we predict that Twin B will also have a low score. The effect of c2g will be the same, regardless of whether twins are MZ or DZ. Finally, consider the situation where genes, or heritable factors (h2g), are the only important influence on poor nonword repetition performance. Because MZ twins are genetically identical, if MZ Twin A has a low score, we predict that MZ Twin B will have an equally low score. However, DZ twins have, on average, 50% of segregating genes in common.2g, c2g, and e2g, and our goal is to estimate the relative contribution of each of these in explaining the observed variance. 2g) was close to 1.0, suggesting that genes play a major role in causing deficient phonological short-term memory (STM). These striking results from behavioural analysis have led to the inclusion of nonword repetition as a phenotypic index in molecular genetic studies. Strong linkage has been found to a site on chromosome 16 . Estimates of genetic influence (h2g) were negligible. This was a surprising result, in the light of much higher heritability estimates for dyslexia obtained by other researchers  was smaller than that seen for CNRep (η2 = .289), and the pattern of ART errors suggested a general auditory problem, rather than a deficit specific to brief or rapid sounds. DeFries–Fulker analysis was used to analyse the heritability of deficits on both measures and yielded remarkably clear-cut results: As in the r = .603) and DZ (r = .493) twins. This pattern shows that the ART is adequately reliable  and is compatible with the test being affected by environmental influences common to both twins. In a subsequent analysis  on the ART, the CNRep, neither, or both. The main difference between the four groups on our other language measures was in severity of language impairment, rather than pattern of strengths and weaknesses see . The impr = .35 after adjusting for age, IQ, and sex) between ART and CNRep, if they are not part of the same causal pathway? One possibility is that this is due to ascertainment bias: If children with A + B are more likely to have a diagnosis than children with either A or B alone, then if we pick a sample that is overrepresentative of those with a diagnosis, we see more cases than usual who have the A + B profile. Another possibility is that individuals with a genetic liability to SLI gravitate toward environments that do not favour the development of auditory processing skills in their children. They may, for instance, have less money to spend on music lessons.Why, then, should we see a modest correlation . The twin sample was a subset of children from the Twins Early Development Study ; two thi2 = .10) but the data suggested that this might be because of articulatory difficulties. We derived a measure that was intended to act as a purer index of phonological STM by using a regression equation to compute the mismatch between the score obtained with three- to five-syllable nonwords and that predicted from the two-syllable score. This phonological STM score did a better job than the raw nonword repetition total at discriminating children in the “language risk” group from the “low risk” group (η2 = .15), and it was significantly heritable (h2g = .61) on DeFries–Fulker analysis.The CNRep was less good at discriminating children with language difficulties than it had been in older children .The Rice–Wexler subtests were combined to give a single index of verb inflections. This was highly skewed, consistent with the extended optional infinitive theory, which maintains that most children have mastered this aspect of grammar by 4 years of age. The skewing does not affect results from DeFries–Fulker analysis and may indeed be a useful indicator of a major gene effect . Heritabp < .01. The fact that both measures were significantly heritable suggests that this lack of agreement is not readily explained by poor test reliability, as an unreliable test would simply show up on DeFries–Fulker analysis as having a large e2g term. To investigate the extent of aetiological overlap between the measures, a bivariate extension of DeFries–Fulker analysis was used. This involves predicting the score of twin B on test Y from the score of twin A on text X, after scaling both measures appropriately  were significantly, albeit weakly, correlated, when the twin analysis suggested that they had different origins. As with the previous work, one interpretation is in terms of additive risk factors; children with a double deficit may be more likely to have clinically significant language problems and hence find their way into a study such as this. Given that both of the measures were heritable, another possibility is that there may be assortative mating for language disorder, so that parents with either kind of impairment tend to have children together. To test this idea we would need to assess parents directly.Overall, these two twin studies  demonstrdisproving causation. Quite simply, if one can find a child who has grammatical deficits in the absence of auditory impairment, then this is evidence that the grammatical deficits are not caused by auditory impairment , but a more interesting possibility is that probabilistic associations between deficits are telling us something about causality. Most readers will agree that smoking causes lung cancer. We are willing, when arguing about the aetiology of this physical disease, to think of smoking as a risk factor that increases the risk of lung cancer, while accepting that the association between cause and disease is probabilistic, rather than deterministic. It would be a serious mistake to dismiss any role for smoking in causing lung cancer, because Uncle Fred smoked all his life and lived to a ripe old age, or Auntie Susan never smoked but died from lung cancer.A recurring finding in developmental disorders is that underlying deficits can be dissociated, but when they co-occur the disorder is more severe and more likely to be detected. In the case of SLI we found that weak phonological STM and auditory impairment were aetiologically as well as phenotypically dissociable, but when both deficits occurred together, the child was particularly likely to receive a clinical diagnosis. In a similar vein, syntactic and phonological impairments were genetically distinct and were often dissociated, but it was the children with both problems who had the most severe language difficulties . Such results suggest that children's language development is generally resilient in the face of a specific cognitive deficit, but that where two or more such deficits occur together, their effect is additive, and the chances increase that language learning will break down.Similar arguments have been put forward in the domains of developmental dyslexia and autism. For dyslexia, Autistic disorder is diagnosed on the basis of there being a triad of impairments affecting socialization, communication, and restricted interests/behaviour, but there is growing awareness that these areas of impairment can be dissociated from one another in children who fall short of meeting diagnostic criteria e.g., , and thothe cause of dyslexia or SLI. As In sum, cognitive studies of developmental disorders have often embraced parsimony and have looked for a single necessary and sufficient “cause” of disorders such as dyslexia, SLI, and autism. I suggest that this approach has led to theoretical stagnation, with much pointless debate about whether, for instance, auditory perceptual deficits are


Beachgoers enjoying the last days of summer might wish to take note: epidemiologist Chris Heaney of the University of North Carolina at Chapel Hill and colleagues from the U.S. Environmental Protection Agency have found that digging in sand and, to a greater extent, being buried in sand are associated with an increased risk of diarrhea and gastrointestinal illness. “The overall incidence of these cases we’re observing is quite low—less than ten percent,” Heaney says. “But such large numbers of people in the country and the world engage in sand contact activities that, even with a very modest relative risk, you could see substantial disease burden.”American Journal of Epidemiology, Heaney and colleagues analyzed data gathered from 26,609 participants in 2003–2005 and 2007 as part of a joint effort of the Environmental Protection Agency and the Centers for Disease Control and Prevention. Visitors to 7 freshwater and marine beaches in Michigan, Indiana, Ohio, Mississippi, Alabama, and Rhode Island were interviewed at the beach about their activities there. Then, 10–12 days later, an adult from each family participated in a telephone interview about the incidence of sickness since leaving the beach, including diarrhea alone and a broader group of “gastrointestinal illness” symptoms including diarrhea, vomiting, and nausea.As they report in the 15 July 2009 Of the people who dug in the sand, 6% reported diarrhea, whereas among those who didn’t dig in sand, the incidence of diarrhea was 4%. After accounting for other factors that might cause illness, that amounted to a 20% increase in risk for those exposed, Heaney says. Among people who reported being buried in the sand, 9% reported gastrointestinal illness. Among those who weren’t buried, 7% had gastrointestinal illness. That amounted to a 23% risk increase after accounting for other factors.Escherichia coli and enterococci, are considered markers of sewage contamination and other non–point sources of fecal waste. If found at sufficient levels in water, their presence can result in waterway closures. But current practices don’t take into account their presence in sand.Heaney’s study comes even as amendments to the Federal Water Pollution Control Act to strengthen pathogen monitoring in beach water wind their way through Congress. More than a decade of research has shown that sand at marine and freshwater beaches throughout the United States contains high levels of so-called fecal indicator bacteria. These bacteria, which include Enterococcus or E. coli from beach sand. Then a paper like this comes along, and you have to pause and say, ‘Well, maybe there is a risk.’”“[The Heaney study] is the first step showing that we need to look more closely at the risks of exposure to sand at beaches,” says Alexandria Boehm, an environmental engineer at Stanford University. “A year ago, scientists may have thought there are no risks associated with exposure to Some studies have suggested that sources of fecal indicator bacteria in sand and water may have little to do with sewage pollution, says Richard Whitman, an ecologist and branch chief at the U.S. Geological Survey Great Lakes Science Center. These and other microbes can come from bird feces, and sand itself makes a good breeding ground for such organisms, studies have shown. “Heaney’s study helps demonstrate that [ensuring beach safety is] far more complex than ‘sewage outfall equals a beachfront closure.’ We need to look at the whole ‘beachshed’ to understand health and pathogen implications,” Whitman says.Journal of Water and Health that bacteria and viruses from sand transferred readily to hands but that rinsing hands with water removed a large percentage of them.Now scientists must explore the possible routes of exposure behind the association between sand and illness. For instance, Heaney is studying whether high levels of fecal indicator bacteria in sand correspond to high incidence of illness. And Whitman reported in volume 7, issue 4 (2009) of the In the meantime, Heaney’s advice: after playing on the beach, be sure to wash your hands. And don’t swallow the sand!


Sir,There are some basic queries related to the article ‘Prevalence of Goiter in Rural Area of Belgaum District, Karnataka’. In the


A must-read for those who think flu pandemic preparedness is much ado about nothing, this first novel by Reina James brings home the severity and plausibility of a flu disaster. And without data, statistics, or comment, it makes a compelling case for progress on the matter of influenza, to ease suffering, prevent spread, and possibly eliminate the scourge.A series of journal entries beginning October 14 and ending November 7, 1918, this story of humans under stress unfolds in London against the savage backdrop of World War I and amidst the oft-recorded pestilence of Spanish flu. Without speculation, the author constructs population drama, one patient and one family at a time. The reader is drawn into it instantly and stays absorbed ’til the end.Characters from all walks of life make up the cast of the unfolding tragedy. They chase about in their masks obsessing over work, social and self-imposed restrictions, unrelenting class barriers, and daily trivia until the schools close, the servants die or flee the ailing households, businesses fail, or until they succumb, filling the streets, mortuaries, graveyards, churches. We are allowed into their disinfected homes, to watch the banality, madness, or sheer horror of their lives. Some are stars. The heroic physician is back from the war with heightened awareness of the health emergency. “A plague is now among us which may well leave the earth to the animals,” he writes in a note intended to alert the health authorities. “You must stop the movement of troops, close our ports and warn others to follow suit.” He dies, “a blue man in the road,” before he can deliver the message. “His lips and ears were purple-blue, like a plum, and the skin on his face was mottled and pale but still tinged with blue, as if he’d been wiped with an inky rag.” The undertaker, who finds the warning note crumbled in the dead physician’s palm, is a man who plays the piano in between constructing coffins and practicing the family trade. He becomes increasingly unsettled by the note as the dead overwhelm his business, his city, his life. “The world’s body can hardly draw breath; it is sick and brought to its bed,” the physician had written. “Its wounds are open. The young spill out ... Death is crossing every sea.” He confirms that indeed the dying “were unusually young,” tries in vain to inform the authorities, and concludes with disbelief that “They had no plan.” The knowledge imparted by the note changes the undertaker’s life, which is already complicated by his universally disapproved affair with a woman “a little bit above his station.” His friend dismissed her, “She’s like a bloke.” Her friend, in a moment of weakness, thought her “a foolish ageing woman with a weak, offended face. Her lips merged unpleasantly into the skin surrounding them; her cheeks were dragged flat by failing muscle. There was too much eyelid and too little eyebrow. There was even a suggestion of fluff above the mouth, of the type that would inevitably grow into a moustache.” Their attraction, slowed by awkwardness and saved by spunk, adds an endearing almost hopeful quality to a tale rife with decomposing bodies. opinion ... I’m too busy.” Exasperated by people reporting “cyanosis,” he admitted that few things irritated him “more than patients using medical terminology.” In the absence of medical interventions, he suggested “fresh air in the bedroom, aspirin for headache, plenty of fluids and light food only, if tolerated.” His unloved wife and assistant by default props him up in bed to sign a few more death certificates before he collapses. Another physician, a retired practitioner, is exhausted by the torrent of patients and his inability to improve their situation. Asked his opinion about the epidemic, he retorted angrily, “I haven’t got an Dedicated by the author to her maternal grandparents who died of it, this account of Spanish flu in London rings true for its hold on human behavior and of course for the flu, whose specter looms on our horizon. Along with the science, along with the vaccine, a dose of past history in human terms warns against underestimating a new pandemic. As James put it, “if every one of the newly bereaved were to hold a lantern in the sky, the man in the moon would think the world to be on fire.”


Environmental Threats to Healthy Aging: With a Closer Look at Alzheimer’s & Parkinson’s Diseases, now describes in greater detail how a lifetime of environmental factors from conception onward shapes our health in our later years.Age-related chronic diseases will put unprecedented stress on U.S. society with a near-doubling of the number of people aged 65 years and older by 2030, according to the U.S. Administration on Aging. These diseases are also complex. An October 2008 report, environment, encompassing the physical, biological, social, and cultural contexts in which our lives are rooted. These contexts influence biological pathways that determine various outcomes, from good health in old age to chronic health issues including cardiovascular disease, diabetes, obesity, metabolic syndrome, and neurodegenerative disorders such as Alzheimer disease (AD) and Parkinson disease (PD). The authors suggest that environmental improvements, from our diet to our access to quality health care, could reduce, delay, or someday perhaps prevent diseases associated with aging.The report, published by the Greater Boston Physicians for Social Responsibility and the Science and Environmental Health Network, uses a broad definition of “I think this report is exceptionally well done and valuable,” says Peter J. Whitehouse, a professor of neurology at Case Western Reserve University. “It will contribute in a major way to the reframing of AD, which desperately needs it.”But the inclusion of neurodegenerative diseases among potentially preventable diseases gives pause to some researchers. “It’s tempting to believe what they’re saying with regard to AD and PD, but it has not been proven to be true,” says Robert Butler, president and CEO of the nonprofit International Longevity Center–USA in New York City. “I applaud the concept of what they’ve done but with the proviso that it has not yet been established.”The report authors are confident that the possibility for prevention exists, though. They began their analysis with an interest in neurodegenerative diseases, but they quickly realized that the underlying mechanisms mirrored those involved in a suite of other disorders, including diabetes, obesity, metabolic syndrome, and cardiovascular disease—the so-called Western disease cluster. Those disorders share common biological pathways such as up-regulation of inflammation and oxidative stress and disruption of insulin signaling.Citing numerous published studies, the authors describe multiple ways in which the environment feeds into these pathways and ultimately into the Western disease cluster. Likewise, environmental factors that act via these pathways could promote neurodegenerative diseases, says coauthor Ted Schettler, science director of the Science and Environmental Health Network, a consortium of U.S. environmental groups.For example, he says there is ample evidence that oxidative stress and inflammation contribute to dopaminergic neuron loss in the substantia nigra, a hallmark of PD. “And given the strong body of evidence finding pesticides to be a risk factor for PD, along with mechanistic data from animal [studies] showing the role of oxidative stress and inflammation, our conclusions are not mere speculation but are based on several lines of evidence,” he says. Additionally, conditions such as diabetes and obesity are associated with increased risk for dementia and cognitive decline.“We should begin to think of cognitive decline and AD as being related to the same causal pathways that are leading into obesity, diabetes, and cardiovascular disease, which are so prevalent in today’s society,” says Schettler. “Our conclusion is that we’re sitting at the cusp of an explosion of neurodegenerative and related diseases, not only because of an aging population but also because we have set the stage through all of the things that are contributing to diabetes, obesity, and cardiovascular disease.”To meet and perhaps prevent the anticipated surge in age-related disease incidence, the authors outline potential cross-cutting solutions. Communities need to bolster access to healthful foods, which encompasses everything from providing business opportunities for groceries and food co-ops to supporting nursing mothers. Communities also need to support planning and development that incorporate green spaces and parks, public transport, and pedestrian and bicyclist safety.Nationally, farm policies need to support sustainable production of healthful foods. Meaningful federal oversight is needed for phasing out known toxics, acting on early warnings of adverse effects, and keeping the public informed and protected. However, the authors emphasize, strategies cannot be adopted in isolation from one another with the expectation that they’ll be successful.Julie Andersen, a professor at the nonprofit Buck Institute for Age Research in Novato, California, notes that the report consolidates information in a way that’s accessible to an educated lay audience. “The authors present information that is probably unknown to researchers outside specific areas and that almost certainly has not reached health care providers,” she says.S. Jay Olshansky, a professor of epidemiology at the University of Illinois at Chicago School of Public Health, adds that the authors bring to the forefront the concept that we are capable of creating a better environment for healthy aging. “There’s a lot of low-hanging fruit,” he says. “We just need to pick it.”


Although the pharmaceutical industry's “neglect” of neglected tropical diseases (NTDs) has been investigated, no study evaluating media coverage of NTDs has been published. Poor media coverage exacerbates the neglect. This study aimed to investigate, describe, and analyse international media coverage of “neglected diseases” in general and three specific NTDs—African trypanosomiasis, leishmaniasis, and Chagas disease—from 1 January 2003 to 1 June 2007.Archives of 11 leading international, English-language media were searched. A content analysis was done, coding for media organisation, date, author, type of report, slant, themes, and “frames”. Semi-structured interviews with journalists and key informants were conducted for further insight.Financial Times and Agence France Presse. CNN had the least coverage with one result. The term “neglected diseases” had good media currency and “sleeping sickness” was far more widely used than trypanosomiasis. The disease most covered was leishmaniasis and the least covered was Chagas. Academic researchers were most commonly quoted as a main source, while the World Health Organization (WHO) and pharmaceutical industry were the least quoted. Journalists generally agreed NTDs had not been adequately covered, but said a lack of real news development and the need to cater to domestic audiences were major obstacles for NTD reporting. All journalists said health agencies, particularly WHO, were not communicating adequately about the burden of NTDs.Only 113 articles in a 53-month time period met the inclusion criteria, with no strong trends or increases in coverage. Overall, the BBC had the highest coverage with 20 results, followed by the Public health agencies need to raise priority for NTD advocacy. Innovative strategies, such as reporting grants or creating a network of voices, may be needed. In recent years, there has been a flurry of activity to reverse the neglect that has characterised NTDs, mostly focussed on drug development. The drug gap may be explained by market failure, yet other forces also conspire to cause the neglect of NTDs. One problem is the low visibility of these diseases. By comparison, the high-profile “big three” infectious diseases of AIDS, tuberculosis, and malaria have received increased donor attention and funding with greater visibility. Efforts to remove the “neglect” from NTDs must involve raising their profile. This study, focussing on three of the most neglected diseases, aims to provide a context of the current media situation—the what, where, and why of NTD coverage—to support future advocacy work. Roughly one in six people globally, mostly the very poor, suffer from one or more NTDs. In recent years, there has been a surge of activity around NTDs. The Drugs for Neglected Diseases Initiative (DNDi), kickstarted by Médecins Sans Frontières (MSF), and the Institute of OneWorld Health (IOWH), were both set up to help spur development of drugs. Through public-private partnerships, new drug projects have flourished, with 63 ongoing by the end of 2004. The drug gap from market failure has been studied. A 2006 study found that in the past 30 years, only10 drugs were marketed for “most neglected diseases”; . This study aims to investigate, describe and analyse international media coverage of “neglected diseases” in general and three specific NTDs – African trypanosomiasis, leishmaniasis and Chagas disease  – between 01 January 2003 and 01 June 2007. These parasitic diseases were chosen as they are some of the most neglected diseases, affecting people in three continents. The study period was timed around a key DNDi NTD advocacy campaign to ascertain whether the campaign had influenced media coverage. The study aims to provide a context of the current media situation facing NTDs and help future advocacy work.Electronic databases of selected media were searched for articles with the general term “neglected diseases” or the three NTDs selected from 01 January 2003 – 01 June 2007, a period that covered two years before and after the DNDi 2005 campaign. The quantitative component of the study measured the number and nature of news articles and noted any trends and patterns. A qualitative analysis reviewed the focus and perspectives of articles by identifying themes and “frames” – how issues are presented. The analysis was supplemented by interviewing nine journalists and four key informants on their perspectives of NTDs, news priorities and obstacles to coverage.The study was restricted to English language media in order to standardise the analysis and enable comprehensive coverage within time constraints. It was also restricted to print media, which is common in media coverage analyses, due to the difficulty of obtaining complete records of radio or television coverage. As print and television coverage is generally strongly correlated, this was not expected to strongly distort the findings. Agence France Presse (AFP), the American news magazine Time, the international news magazine The Economist, the international business paper Financial Times, two British newspapers – The Guardian and Daily Telegraph – and three American newspapers – The New York Times, Washington Post and Los Angeles Times. Their databases are available online, some with a fee for access.The media selected were BBC online, CNN.com, the international news wire This selection was made as they have:International coverage – with international print editions, broadcasts, wire services or audiences. The newspapers selected, for example, sell stories to newspapers all over the world. The Los Angeles Times-Washington Post news wire has been described as the “world's leading supplemental wire service” in an American Journalism Review survey. AFP publishes in both English and French and although it trails Reuters and AP in terms of income, it in fact covers the widest geographical area among the agencies, located in 165 countries, particularly in Asia and francophone Africa.Significant financial and political weight – which could help influence international health policy through reaching donors and policymakers.Articles were defined as focussing on NTDs in general or one of the three NTDs studied if they had:at least two mentions of any of the search keywords;more than one paragraph with one mention of the search terms.kala azar” and “black fever” , which has been used in the US media without mention of any other disease name. Articles with only one mention of the term “neglected diseases” (in one paragraph) were excluded from the analysis but recorded separately to note how many times this term was used.The search terms included the term “neglected diseases”, medical names of the three diseases plus the names “sleeping sickness”, “The coding system used was adapted from methodological frameworks used in other content analyses, particularly to track tobacco coverage. Financial Times (FT), the Boston Globe and Washington Post were also interviewed. One academic and three former journalists now working on advocacy for international health agencies (two formerly with WHO) were also interviewed.Semi-structured interviews were performed with nine leading health journalists to gain insight into the findings and investigate factors influencing reporting. Journalists were chosen from leading media organisations such as BBC, CNN, Reuters, AFP and Associated Press. Leading global health journalists from the (see ). A slight peak was noted in mid-2005 but there was no specific theme tied with this increase, although DNDi's research appeal campaign calling for greater attention to NTDs in May could have helped generate interest in this area.During the 53-month study period, 113 articles met the inclusion criteria. There were no strong trends or increases in coverage Reporting on NTDs appeared to be sporadic and random, but a few events did prompt clusters of stories:a May 2003 NTD conference in Nairobi, Kenya;scientists “cracking” the genetic code of the three diseases studied;an 8 million pound grant to a UK university for tropical disease research;development of paromomycin for leishmaniasis treatment.see Themes/Frames subsection).Most articles were hard news stories, with only one editorial and three letters (possibly indicating that NTDs do not evoke strong emotive responses). Reporting was generally sympathetic towards NTDs; a few articles were even critical of “Big Pharma” ((see ). CNN had the least coverage with one result, for a story originally from Reuters. There were a wide variety of articles in the BBC and a notable number on sleeping sickness, including, uniquely, some from the field featuring patients. The FT had the most in-depth and detailed articles, often with exclusive financial perspectives. The new business model offered by public-private partnerships was explored in detail, in view of their potential for underfunded areas. The FT actually had the largest number of articles but many discussed the issue generally, rather in specific diseases, so did not meet the inclusion criteria.The BBC had the highest coverage with 20 results, followed by the FT and AFP with 19 and 18 results respectively New York Times. The Economist offered long, in-depth analyses while none of the articles in Time or Daily Telegraph were “hard news” stories.Although AFP's articles covered a wide area, reflecting the agency's mission, with three articles on sleeping sickness in Africa, none focussed on Chagas disease. Many stories from other organisations had a strong domestic angle, such as interviews with British scientists working on NTDs. The work of the US-based organisation IOWH, “black fever” among US troops in Iraq and the presence of Chagas in the US blood supply were some topics in the The term “neglected diseases” was commonly used, which partly explained why many articles fell in the “general” category rather than a specific disease. The disease most covered was leishmaniasis, mainly because of the wide reach of those affected (which includes US troops in Iraq) and recent drug developments led by IOWH. African trypanosomiasis was the next most covered disease (as sleeping sickness), primarily by the BBC. Chagas had significantly less coverage with no articles in the British media other than one in the BBC. The main focus of Chagas by the American media was the parasite's threat to the American blood supply. No article actually focussed on the problem itself in South America.The most common group to be quoted were local university researchers, accounting for main quotes in a third of articles with quotes. Academics represent a local, accessible and relatively independent source. With the “medical researchers” group, they accounted for 41% of all main quotes. WHO was quoted as a main source in only 4% of articles, while the Bill and Melinda Gates Foundation and pharmaceutical industry had even poorer media visibility. DNDi and MSF accounted for 18% of all main quotes.It was difficult to identify clear “frames”, but some broad themes of focus did emerge. The general need for more attention on NTDs, including calls for more research, drugs and funding, was the most common theme of articles collectively, with 19 articles. Public-private partnerships – which included the work of IOWH, DNDi and other such institutions - were another common focus, with 15 articles. Frames depicting the horror or tragedy of NTDs, often describing the reality of these “forgotten” diseases in term of the epidemic, victims, drugs or situation were almost as common. Other focuses for articles included:“Big Pharma”, where the industry was on the defensive or under pressure;scientific developments from genetic research;blood safety amidst the threat from Chagas .Journalists generally agreed that NTD were an important story that had not been adequately covered, but with the caveat that news stories had to be “newsworthy”. Health coverage veered towards “breaking news” such as bird flu outbreaks –headline-hitting events that raised ratings. Journalists who did cover NTDs were often personally motivated. Andrew Jack of the FT, who had the largest number of bylines in the study, said his reporting was “100%” driven by his interest.A lack of real news development, the drive to cater to domestic audiences and competing health interests were cited as the main obstacles for NTD reporting. “Poor people dying from an illness is not news,” unless there is some change or development, one producer from an international broadcaster said. But HIV/AIDS was widely reported on “because it sells stories” and has the funding and attention of policymakers. Coverage of global health issues was particularly poor in the American media, where health and foreign budgets are facing cuts.All journalists said health agencies were not communicating adequately about the burden of NTDs. Some journalists were particularly critical of WHO and the Bill and Melinda Gates Foundation for the difficulty in reaching officials for comment. Bill Gates was, however, credited with raising the profile of NTDs. NGOs such as MSF were cited as good sources for stories.Journalists said stories needed to have a broad appeal which touched core readership to get covered. New developments or “breakthroughs” were easier to sell as stories. The “human element” was powerful, but few journalists were able to get such stories first-hand from the field. This represented a real constraint for coverage. One communications advisor (consulting for DNDi) said health agencies needed to present stories featuring “real people” rather than “experts in their ivory towers” and the “yuck” factor about these diseases needed to be played up to “grab the public imagination” rather than facts about the lifecycle of the parasite.This study shows the general lack of coverage of NTDs in the media, with an average of about 10 articles per media organisation in a period of more than four years. By comparison, an unfiltered search for HIV/AIDS on AFP's database found more than 1,000 articles for the same period. There was a wide disparity in coverage between various media, with results for BBC 20-fold higher than CNN. No events or developments seemed to capture media interest across the board. The “newsworthy” element of NTDs clearly varied between media, ranging from the financial angles used by the FT to the emotive human stories featured in BBC.Wall Street Journal) had to be excluded due to time constraints. Also, only English-language media were selected and the term “international” is somewhat debatable. It would be useful to repeat the study in other language and compare ND coverage; a brief survey of Le Monde found many NTD articles, particularly on DNDi. Also, although some media had more profound articles on NTDs, this was not analysed due to a lack of an objective coding variable. However, this investigation is the first study to systematically analyse NTD media coverage. Further, the media selected still represent a sample of key media and some patterns clearly emerged. For example, the penchant for a local angle was even parochial at times. Stories get written about leishmaniasis in pets before humans, as was seen in The Daily Telegraph.The results reflect select international media – other leading organisations , did not yet result in coverage by the mainstream media included in the study. However this may improve as celebrity activity and the networks pick up more media currency, especially with the impetus provided by President George Bush's 2008 NTD Initiative.The interviews provided much insight, particularly on the struggle to cover global health issues in the American media, where foreign news budgets have been slashed. It is under such a challenging context that journalists face the pressure of reporting on relatively unknown diseases with limited information. Added to this is the difficulty in getting information on NTDs. Providing ready access to information and experts when needed is critical to improve coverage. Forming coalitions or networks could also help strengthen voices in the media.In selling a story, terminology was enormously important. “Human African trypanosomiasis” was clearly off-putting for journalists, who overwhelmingly preferred the term “sleeping sickness”. Journalists also found “neglected diseases” more catchy and concise than “neglected tropical diseases”. Clearly, NTD advocates need to speak the same language as journalists to engage the media. The study also showed the lack of vivid and powerful “human” stories from the field (very few stories quoted patients) which generally have media appeal. One solution would be for NGOs to sponsor journalists to join them in the field, but this may raise the thorny issue of independent reporting.In the market-driven setting of today's media, more innovative strategies may be needed. The same commercial context that constrains drug development of NTDs also curbs global health reporting, particularly in the American media. Just as public-private partnerships have transformed the landscape of drug development, some public-private funding may be needed to bring insightful, in-depth reporting on NTDs from the field to the pages of Western newspapers. Many fellowships, grants and awards are already available to promote reporting in certain fields. The Kaiser Family Foundation supports HIV/AIDS reporting projects This study showed that even in a select group of media, there are clear patterns in what diseases get covered, what topics, terms and sources are preferred, and in which media. The disparity in coverage between media reflects different news priorities and interests, yet also opens a door to potentially increasing coverage, particularly amidst growing interest in global health. Public health agencies need to consider sustained and innovative advocacy on NTDs. A variety of strategies may be needed, including those to shift current “frames” – media portrayal and perception of NTDs.


During development vertebrate embryos pass through a stage where their morphology is most conserved between species, the phylotypic period (approximately the pharyngula). To explain the resistance to evolutionary changes of this period, one hypothesis suggests that it is characterized by a high level of interactions. Based on this hypothesis, we examined protein–protein interactions, signal transduction cascades and miRNAs over the course of zebrafish development, and the conservation of expression of these genes in mouse development. We also investigated the characteristics of genes highly expressed before or during the presumed phylotypic period. We show that while there is a high diversity of interactions during the phylotypic period , which is well conserved with mouse, there is no clear difference with later, more morphologically divergent, stages. We propose that the phylotypic period may rather be the expression at the morphological level of strong conservation of molecular processes earlier in development. During the metazoan embryonic development, the complexity of the organism increases from one cell to an integrated multicellular animal. This is accompanied not only by an increasing number of parts, but also by changes in the pattern of interactions among these parts . In veryIn practice, such interactions must involve molecular pathways of signaling and regulation. Morphological models do not specifically predict that molecular pathways themselves should vary. But if signaling is dramatically different between early, middle (“phylotypic”), and late development, we expect to see changes in the activity of signaling pathways during development. Moreover, if changes in signaling are causal to the phylotypic period, we expect the timing of some changes in signaling to correspond with the boundaries of this period. Characterizing such molecular variation might help to reconcile divergent observations of developmental variation at the morphological and the genomic level ;.In this study, we use expression information to relate zebrafish genes to developmental stages, and investigate the variation in protein–protein interactions (PPI), signal transduction cascades, and micro-RNA signaling. We also investigate whether the timing of gene expression is conserved in mouse. This allows us to distinguish signaling pathways which are most active in early, mid, or late development, and can be related to the different phases of morphological integration.Danio rerio) development were retrieved from ArrayExpress . Spearman correlation between gene expression and centrality measures was performed for each stage.Degree, betweenness, and closeness centrality measures  were calZebrafish genes and their associated GO IDs were retrieved with Biomart  and the r) between the linear and parabola models was significant. A Bonferroni correction was applied to correct for multiple testing, considering the seven regressions of A linear regression between developmental time and number of expressed genes was fit to the data. To test for an hourglass-like model, we adjusted a parabola , as in Over and under representation of GO terms for “early,”“organogenesis,” and “late” genes were tested with a Fisher exact test using the Bioconductor package topGO . The refZebrafish genotypes and phenotypes were recovered from the Zebrafish Information Network  for “early,”“organogenesis,” and “late” genes were tested with a Fisher exact test using a version of the Bioconductor package topGO  modifiedZebrafish miRNAs were downloaded from the miRBase database .A time series of miRNA microarray data during zebrafish development  was retrc-means soft clustering algorithm implemented in the Mfuzz package . Targets were mapped from RefSeq IDs to Ensembl zebrafish genes. Ensembl genes that corresponded to more than one RefSeq IDs were removed.EIMMo  target pn1=119, n2=253) and calculated the difference in median expression between the two random groups, with 10,000 repetitions.Among the genes for which we have expression data, 119 are targeted only by “early onset” miRNAs and 253 only by “late onset” miRNAs. To assess the significance of the difference between median expression across development of the “early onset” miRNAs targets and the “late onset” miRNAs targets, we used a randomization approach as in . We poolMus musculus; 17,192 genes) from Bgee, a database to compare expression data between species  during development was retrieved for zebrafish (6305 genes) and mouse . We plot the mean ratios of observed coexpression of PPI pairs to random pairs.Zebrafish and mouse genes and their associated GO IDs were retrieved with Biomart and the GO terms were downloaded from Gene Ontology . Genes annotated with GO terms that contained “signal” and “transduction,”“receptor,”“kinase,” or “transcription” were retrieved. We kept the mouse–zebrafish one-to-one orthologs with GO annotation and expression data in both species. This resulted in 98 pairs for signal transduction, 124 for receptor, 127 for kinase, and 307 for transcription. We calculated the total number of mouse and zebrafish genes of each gene category expressed at each metastage, as well as the number of ortholog pairs both expressed at each metastage. To assess the significance of the number of orthologs expressed, we randomly created pairs of mouse–zebrafish genes from the same gene category. Repeating this process 10,000 times, we could define 1% confidence intervals.We first examined position in the PPI network, according to timing of expression of the genes encoding the interacting proteins. Proteins at the center of the network are more connected than those at the network periphery. Consequently, determining the network centrality of a protein is equivalent to evaluating its level of connectivity. Of note, we transferred information on human interactions to the zebrafish; whereas this may affect the precision of our results, it is probable that trends are essentially correct .We used three different measures to quantify the centrality of proteins: degree, betweenness, and closeness centrality . Degree To verify the evolutionary relevance of these observations, we measured whether the orthologs of pairs of genes, which are both expressed in the same broad developmental stage in zebrafish, are also both expressed in the corresponding stage in mouse. Although genes encoding pairs of interacting proteins have more conservation of coexpression than other genes at all stages, conservation is strongest in early development . Transcription genes peak earlier (P=0.0011). But abundant expression remains during larval development. Genes which possess both transcription and receptor functions  show the same behavior as receptors (data not shown).The number of signal transduction, receptor, and kinase genes expressed increases progressively to reach a maximum at 4 days  and then decreases at later stages . Excludi earlier , at 32 h earlier . There aFor all components of signaling tested, the expression of orthologs is significantly conserved in mouse development at all late stages, from organogenesis to adulthood ; but notThus signal transduction appears important, and evolutionarily conserved, over a large period of development, which starts during the phylotypic period but lasts into postembryonic development.It has been proposed that the control of protein coding genes by miRNAs leads to a gain of developmental precision at the cost of a loss of evolutionary plasticity . This suThe expression of miRNAs during zebrafish development  suggestsExpression of targets of the “late onset” is stable across development, whereas “early onset” targets experience a small decrease during development , Fig. S3There is no comparable data on expression of miRNAs during development of other vertebrate species, so we cannot investigate evolutionary conservation of these patterns.As an alternative to studying the expression profile of groups of candidate genes, we used soft clustering of expression profiles to generate groups of genes, whose properties may be related to the patterns of evolution and development ; Fig. S1P=0.0078, Kruskal–Wallis test). Mutation of “early” genes results in the most abnormal phenotypes (average of 10.5 vs. 5.28 for “organogenesis” genes and 6.86 for “late” genes). There is also a significant difference between the three categories for the number of anatomical structures in which each gene is detected . This is mostly due to “late” genes being expressed in fewer structures (5.48 vs. 10.3 for “organogenesis” genes and 9.5 for “early” genes); in other words, “late” genes are more tissue-specific. As might be expected, expression of “early” genes is enriched in presumptive structures. Expression of “organogenesis” genes is enriched in numerous anatomical structures, most of them related to the nervous system, the visual system, the muscle, the heart, and the pancreas. And expression of “late” genes is enriched in the visual, intestinal, and nervous systems.The average number of abnormal phenotypes reported for mutation of genes from these groups differs significantly  and later development. Early expressed genes appear to be both more conserved between zebrafish and mouse, and regulated by different pathways, than other genes, with more PPI and little or no miRNA regulation. We propose that morphological conservation at the phylotypic period is a consequence of this early genetic conservation.


Objective To explore female and transvestite sex workers’ perceptions of risk in the sex work environment in Serbia.Design Qualitative interview study.Setting Street based locations for sex work in Belgrade and Pancevo, Serbia.Participants 31 female and transvestite sex workers.Results Violence, including police violence, was reported as a primary concern in relation to risk. Violence was linked to unprotected sex and the reduced capacity for avoiding sexual risk. Participants reported that coerced sex was routinely provided to the police in exchange for freedom from detainment, arrest, or fine, and was enforced by the perceived threat of violence, sometimes realised. Accounts contained multiple instances of physical and sexual assault, presented as abuses of police authority, and described policing as a form of moral punishment. This was largely through non-physical means but was also enforced through physical violence, especially towards transvestite and Roma sex workers, whose experience of police violence was reported as relentless and brutal and connected with broader social forces of discrimination in this setting, especially towards Roma.Conclusion Preventing violence towards sex workers, which can link with vulnerability to sexually transmitted infections, is a priority in Serbia. This requires monitoring perpetrators of violence, providing legal support to sex workers, and creating safer environments for sex work. Physical violence links with vulnerability to sexually transmitted infections through coerced unprotected sex and the reduced capacity to negotiate sexual risk.11Preventing violence is a global public health and human rights priority.14Serbia is characterised by social and economic uncertainty, which links to poverty, illegal economies (including sex work), corruption, and ethnic and gender inequalities.We undertook 31 qualitative semistructured interviews with sex workers in two street based locations for sex work in Serbia; Belgrade, the capital, and Pancevo, a nearby town in Vojvodina region. The study included female and transvestite sex workers living or working in Belgrade or Pancevo who had exchanged sex for money, drugs, or other goods in the past month. This non-probability purposive sample set minimum quotas of outdoor and indoor sex workers, those under and over 21 years, injecting drug users, and Roma. We selected these purposive sampling dimensions to ensure variation in relation to contextual factors theorised to determine sexual risk differentially.We generated data using an interview topic guide containing key questions with prompts for patterns and organisation of sex work, use of condoms, risk perception, and risk in the sex work environment. The piloted topic guide was generated through close consultation with local sexual health and HIV prevention services, including non-governmental organisations, and fostered participant led description of experience related to sex work. Interviews were done in Serbian (by MS and SB) in cafes and restaurants (n=14), at local projects (n=12), at participants’ homes (n=4), and in quiet outdoor spaces (n=1). Participants were reimbursed €10 . Interviews were tape recorded after informed consent, lasted 60-90 minutes, and were transcribed verbatim by locally trained staff and the research team. Translated transcription was done through close collaboration with a translator, with translated text checked by bilingual members of the research team.Coding of data was descriptive and thematic, with an emphasis on typological description.The sample comprised 24 female sex workers and seven transvestite sex workers of average age 28 years. Most (n=25) were street based sex workers—that is, soliciting and negotiating sex with clients in street locations . Street based sexual services were provided in nearby parking lots and woods, and in central Belgrade in street alleyways and rooms rented for 15 minutes. The remaining sex workers solicited sex through advertising their telephone numbers, and one was connected with a bar/club. Half were Roma (n=15), all of whom worked the streets, and among whom were all the transvestites. Two thirds of the women had children (n=15). Only five sex workers self reported sexually transmitted infections and eight reported injecting drugs, one of whom reported being HIV positive and another three hepatitis C positive. All street based sex workers reported having experienced some kind of violence linked to their work. Sex work is illegal in Serbia under article 14 of the Law of Peace and Order, and thus operates in a prohibitive environment.Violence, and police violence in particular, was identified as a primary concern of sex workers in their descriptions of the risks involved in street based sex work in Belgrade and Pancevo, Serbia.As found elsewhere,Accounts thus emphasised the role of situational factors, and especially the risk of violence, in undermining a norm for condom use. The risk of violence seemed to be ubiquitous to this street setting for sex work, and was reported as a primary concern: “No kind of money is worth it when he beats you, when you are scared to death” . Violence was reported as linked to incidents during condom use or breakages resulting from rough or coerced sex: “If they push it in violently, then it [condom] breaks” . Violence was also described as being linked directly to unprotected sex through coercion: “I had to accept everything he asked for . . . without the rubber” . The perceived threat of physical violence also had indirect effects on sex workers’ capacity for reducing risk by feeding a sense of pervasive insecurity and loss of control in sex work transactions: “I get scared every time I get in [a car] with someone I don’t know, so that I am consumed with fear” ; “I find it very difficult to get into someone’s car . . . because life is at stake” . Physical violence by clients was reported to be common, but it was violence by police that was perceived as the greater threat and as less open to risk management: “You can manage your clients somehow, but to be honest, the greatest threat to us is the police” .Although some participants had not experienced physical violence perpetrated by the police—“I perhaps got two slaps one time, that’s all, but other girls were hurt pretty bad” ; “The police don’t know me well here, so I can stand freely where they don’t know me” —the following forms of police violence seemed normative: deception and coercion (box 1), extortion (box 2), and discrimination (box 3).What do you do? Give the money back And at the end of the job he shows me his badge, and says like “Give me my money back now.” That’s what he does. And he’s not on duty. But he’s some cop. He says “let’s do it.” I say, “Well, pay me, give me the money.” And then he asks, “Have you ever been taken in to the police?” Like he’s a cop and all. And I say, “Yes, I have.” And he says “Do you want to go to the station, you and I?” You know, they try you out, ask for blowjobs, sex in return. It’s just their thing They want blowjobs, fucking, if you want them to let you go. You’ve got to. The police like fucking us more than anyone. They don’t pay. It’s like this: they fuck us, and so they let us go And he pulled out a police badge and said “C’mon, you want me to take you in or screw you?” I was scared, and allowed him to screw me They want for blowjobs, fucks. I work for free, just so they don’t take me in He wants me to blow him for free. I don’t want to. Later, when he gets me on my shift, he beats me silly. Beats me silly He beat me up with a baton. Up in this park. He beat me up with the baton. And several times I had to be [have sex] with him. I really had to. I was forced They are screwing around with us. Like we need fuel, we need money for this, we need it for that Yesterday, or the day before, the patrol, they wanted money from us. First he says, “C’mon, get in the car.” Nothing to it, I get in the car. Then he says, “Why don’t you treat us?” And he says, “C’mon, sort it out among yourselves,” how much money we are to give him It’s really pathetic taking money from us. I don’t know how they don’t understand I struggled for that. I sold my body. I worked. The man, for instance, pardon me, fucked me and everything, for the money. And they take the money. Why? I don’t know, but so they say it goes into some fund, what do I know? The first time they beat me because I didn’t want to admit who I worked for. They slapped me around. Like, “Gypsy, motherfucker, why don’t you start talking?” I was pregnant, and he started beating me. Like, “You ain’t going to say you’re pregnant any more, now you’re going to get beaten up at the station, and nobody’s going to believe you, and if you report me, I beat you up” From what? From doing this work. “Why don’t you find another job?” I say, “Come on, find me another job and I will do it” And he goes, “Why should I look for a job for you?” and so on. It’s like that They [police] take us into their office, and one starts kicking you in the legs, the other one into kidney. Without any reason. They want to accomplish something, to prevent us from doing something. He [policemen] is swearing at us, saying we’re sluts, whores . . . Pancevo is forbidden grounds to us. We can’t even move on the streets, nor in bars. If I had a boyfriend now, and went for a drink, and he came, he’d kick me out of the place A few times I went out with my boyfriend. I would sit down, drink coffee, and they [police] come in. “Hey, do you know . . .?,” I mean, it’s the first thing they say, “Do you know what she . . .?” And he [my boyfriend] goes, “Well, can I not have a drink with her?” “You know, well . . . Do you know what, do you know what she does?” Most of the women get arrested. The last time they arrested people it was on television. I saw it in person. Arrested, chased, and filmed on camera They [police] started going wild, only on us transvestites. They let the girls go. They just pick us up, and go to the woods, and go wild on us . . . First, they beat us in the woods, and then they take us to the station. And then they tell us at the station “Hey, freshen up,” and they beat us up in the bathroom They [police] kicked, kicked, kicked the hell out of us. Just transvestites. They took me to the woods, down by the bridge . . . They stripped everything off me . . . Flashlight in the eyes. I said a million times, “Take me away. Did you come to arrest me? Arrest me then, but, do not beat me up.” . . . That makes it worse. “Shut up, motherfucker, shut up!” What’s the reason for them [police] to beat me up? The fact I’m like this is my business. One squad came over, and they beat me senseless because of what I am. I came back all black and blue . . . I didn’t know where the blows were coming from . . . They just have this hate. Whether it’s towards prostitutes or specifically trannies. But it’s terrible Sexual services were described as being commonly provided to police without payment as well as secured by them through deception and coercion (box 1). Police reportedly presented sex workers with the option of providing services without payment as a means of avoiding possible arrest, detainment (varying from hours to one month), and a certain fine . Sex workers described how in cases of deception, presumed clients would usually reveal their identity as policemen once services had been negotiated and exchanged, demanding the return of their money . This was described as a no choice situation, which for some had become routine: “They’re in power, and we are not, what can I do?” . Although exceptions were reported  ,sex would normatively be provided in exchange for freedom from detainment or arrest .The risk of detainment, arrest, or fine or the threat of physical violence were given as the reasons whysex workers acquiesced to police demands for sex without payment. Attempts to resist such demands were said to incite violence . We were given multiple examples of coerced sex involving violence perpetrated by those presumed to be police , although condoms were reported to be used in most: “Leave off mate, not only am I doing you for free, but you’re not jacking me up without a rubber” . Accounts also indicated routine extortion of money from sex workers by police, as unofficial fines or as “negotiated” payments to secure freedom from detainment, arrest, or registration as a prostitute . Extortion of money or information (particularly about pimps and when giving “statements by dictation”) was also reported to be enforced by the threat of violence .A common theme therefore was a fatalist acceptance to the inevitability of everyday police violence (“I can’t fight destiny”), borne out of the internalisation of police “rights” to victimise (“They have a right to beat us because we do this prostitution thing”) and recognition that rights to police protection are unrealised and unrealistic .A striking feature of sex workers’ accounts was that police violence was presented as transgressing boundaries of legal acceptability or rationality, and thus was thought to be moral punishment . Enforced sex and coerced payments to police, although outside the law, were experienced as discipline as if for moral wrongdoing, to “bring sex workers to their senses,” and suggesting that they were matter out of place . Policing thus extended into private life. A common tactic reported to be deployed was humiliation in the face of “normal others.” This involved unwanted disclosure of a sex worker’s identity to friends and family, thus disrupting the preservation of a dignified private self away from work . A striking instance of public shaming included police collaborations with national media, whereby police crackdowns and arrests of sex workers would be televised .Moral punishments for selling sex overlapped with other forms of social discrimination, especially towards Roma and transvestites: “There is nothing [about me] that is normal for our people here, for our nation, here in Serbia” . Police violence was described as especially brutal towards transvestites, all of whom in this study were Roma, and most Kosovo refugees . Extreme violence reported towards transvestites and Roma was generally interpreted as driven by contempt for being of minority or deviant status .Taken together there was strong emphasis in sex workers’ accounts on the need for greater protection from police violence and corruption as well as for creating safer and regulated off-street environments for sex work, including through legislative change: “Legalise it. I’ll be the first to pay taxes” ; “Make it legal, so that we have some papers and do not get messed with by the police” ; “[Legalising] it would bring a proper solution. I could work freely. I would be up for HIV testing. I’m here to pay taxes. I’m here to fulfil my obligations to the state” ; “We need some building—I’m standing in the street—so that the police can’t touch us, some workplace” ; “If it was legal, we’d go to doctors, we’d have medical records, it’d be much better” .Violence was reported as a primary risk concern of street based sex workers in Serbia and linked to coerced unprotected sex, breakages of condoms, and reduced capacity to negotiate sexual safety. Moreover, sex workers described being coerced into providing sex to police in exchange for freedom from detainment, arrest, or fine, and this was reportedly enforced by perceived risks, sometimes realised, of physical violence by police. Reports of police violence, deception, coercion, and extortion towards street sex workers in Serbia seem to contravene the Serbian police ethics guidelines, ratified in 2003 and based on the European Union Code of Ethics for Police Forces (2001). This study has limitations. It is an exploratory study generating findings for testing in future research. Generalisability is inevitably limited to this specific sample and setting. The study is an interpretative analysis of participants’ accounts and reflects the themes of these. Counter narratives are possible, and the study did not investigate accounts by the police. Also, what distinguishes excessive force from legitimate force in policing can be a fraught debate.39Interviews contained multiple descriptions of physical and sexual assault, presented as abuses of police authority. Reported coerced sex by police usually involved condoms, but the pervasive risk of violence contributed to a reduced sense of control over the negotiation of sexual transactions. Sex workers largely adopted a fatalistic acceptance to reported police demands for money or sex without payment. This study extends concepts of sex in exchange for money or goods to include coerced sex in exchange for freedom from police detainment, arrest, or fine.This study also identified possible policing practices with little basis in legal rationality but which acted as forms of moral punishment. These practices discipline and stigmatise, positioning sex workers as having waived rights to respect or protection on account of having transgressed. Such practices usually comprised bullying of a non-physical nature, such as humiliation and shaming involving the unwanted disclosure of a sex worker’s identity to “normal others.” But discriminatory policing practices were also embedded in physical violence, and much of it brutal, as in the case of the relentless violence reported by transvestite sex workers, all of whom were Roma. Previous studies have noted excessive use of force when policing female or transvestite sex workers40Police violence may be disproportionately directed towards vulnerable groups.In conclusion, physical violence, enacted or threatened, links with unprotected sex and vulnerability to sexually transmitted infectionsViolence can link with coerced unprotected sex and risk of sexually transmitted infections, but little is known about police violence towards female and transvestite sex workersIn Serbia, coerced sex was reported to be routinely provided to police in exchange for freedom from detainment, arrest, or fine, and was enforced by the perceived threat of violence, sometimes realisedPolicing acted as moral punishment through non-physical means but was also reportedly enforced through physical violence, especially towards transvestite and Roma sex workers