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New and Exciting in PLoS this week [A Blog Around The Clock]

I'd like to start today with Big Congratulations to the amazing PLoS IT/Web team for finishing the complex and long task of migrating all seven PLoS Journals onto the TOPAZ/Ambra platform. This week, the last of the seven journals, PLoS Biology, was successfully moved. This means that you can now rate the articles, post notes and comments and send trackbacks to articles in PLoS Biology just like you could do it on the other six titles that were migrated over the last couple of years. While I don't know exactly what is in the planning, I am sure that the team will continue to make regular upgrades and improvements of the platform and the site and to work on integrating the seven journals with each other.

So, while the PLoS Biology crew took an understandable week off during the migration, let's see what's new in the other six journals this week: PLoS Medicine, PLoS Genetics, PLoS Computational Biology, PLoS Pathogens, PLoS Neglected Tropical Diseases and PLoS ONE. Here are my own picks for the week - you go and look for your own favourites:

No More Free Drug Samples?:

Everybody likes something free, and free prescription drug samples are no exception. Patients love to receive them, and doctors feel good about handing them out. The practice of providing free drug samples is based on the tacit assumption that "sampling" does much more good than harm. In two separate news releases within the past year by the Pharmaceutical Research and Manufacturers of America (PhRMA), the trade organization that represents the country's largest and leading drug companies, a senior vice president claimed that free samples improve patient care, foster appropriate medication use, and help millions of financially struggling patients. He averred further that samples benefit physicians by exposing them to new treatment options [1],[2]. In this essay, we question the assumption that good trumps harm when prescription drugs are provided free to practicing doctors. We argue that "sampling" is not effective in improving drug access for the indigent, does not promote rational drug use, and raises the cost of care.

Bumble Bees (Bombus spp) along a Gradient of Increasing Urbanization:

Bumble bees and other wild bees are important pollinators of wild flowers and several cultivated crop plants, and have declined in diversity and abundance during the last decades. The main cause of the decline is believed to be habitat destruction and fragmentation associated with urbanization and agricultural intensification. Urbanization is a process that involves dramatic and persistent changes of the landscape, increasing the amount of built-up areas while decreasing the amount of green areas. However, urban green areas can also provide suitable alternative habitats for wild bees. We studied bumble bees in allotment gardens, i.e. intensively managed flower rich green areas, along a gradient of urbanization from the inner city of Stockholm towards more rural (periurban) areas. Keeping habitat quality similar along the urbanization gradient allowed us to separate the effect of landscape change (e.g. proportion impervious surface) from variation in habitat quality. Bumble bee diversity (after rarefaction to 25 individuals) decreased with increasing urbanization, from around eight species on sites in more rural areas to between five and six species in urban allotment gardens. Bumble bee abundance and species composition were most affected by qualities related to the management of the allotment areas, such as local flower abundance. The variability in bumble bee visits between allotment gardens was higher in an urban than in a periurban context, particularly among small and long-tongued bumble bee species. Our results suggest that allotment gardens and other urban green areas can serve as important alternatives to natural habitats for many bumble bee species, but that the surrounding urban landscape influences how many species that will be present. The higher variability in abundance of certain species in the most urban areas may indicate a weaker reliability of the ecosystem service pollination in areas strongly influenced by human activity.

Avian Influenza Virus Glycoproteins Restrict Virus Replication and Spread through Human Airway Epithelium at Temperatures of the Proximal Airways:

Influenza type A viruses are endemic in aquatic birds but can cross the species barrier to infect the human respiratory tract. While transmission from birds to humans is rare, the introduction of novel avian influenza viruses into immunologically naïve human populations has significant pandemic potential. Avian influenza viruses are adapted for growth at 40°C, the temperature of the avian enteric tract. However, the human proximal airways, the likely site of initial inoculation by influenza viruses, are maintained at a cooler temperature (32°C), suggesting that zoonotic transmission may be limited by temperature differences between the two hosts. Using an in vitro model of human ciliated airway epithelium, we show that avian influenza viruses grow well at 37°C, a temperature reflective of distal airways, but are restricted for infection at 32°C. A panel of genetically manipulated human influenza viruses possessing avian or avian-like surface glycoproteins were also restricted at 32°C, but not 37°C, suggesting that avian virus glycoproteins are not adapted for efficient infection at the temperature of the proximal airways. Thus, avian influenza virus infection is restricted in the human proximal airways due to the cooler temperature of this region, thus limiting the likelihood of zoonotic and subsequent human-to-human transmission of these viruses.

Do Electronic Health Records Help or Hinder Medical Education?:

Background to the debate: Many countries worldwide are digitizing patients' medical records. In the United States, the recent economic stimulus package ("the American Recovery and Reinvestment Act of 2009"), signed into law by President Obama, includes $US17 billion in incentives for health providers to switch to electronic health records (EHRs). The package also includes $US2 billion for the development of EHR standards and best-practice guidelines. What impact will the rise of EHRs have upon medical education? This debate examines both the threats and opportunities.

A "Shallow Phylogeny" of Shallow Barnacles (Chthamalus):

We present a multi-locus phylogenetic analysis of the shallow water (high intertidal) barnacle genus Chthamalus, focusing on member species in the western hemisphere. Understanding the phylogeny of this group improves interpretation of classical ecological work on competition, distributional changes associated with climate change, and the morphological evolution of complex cirripede phenotypes. We use traditional and Bayesian phylogenetic and 'deep coalescent' approaches to identify a phylogeny that supports the monophyly of the mostly American 'fissus group' of Chthamalus, but that also supports a need for taxonomic revision of Chthamalus and Microeuraphia. Two deep phylogeographic breaks were also found within the range of two tropical American taxa (C. angustitergum and C. southwardorum) as well. Our data, which include two novel gene regions for phylogenetic analysis of cirripedes, suggest that much more evaluation of the morphological evolutionary history and taxonomy of Chthamalid barnacles is necessary. These data and associated analyses also indicate that the radiation of species in the late Pliocene and Pleistocene was very rapid, and may provide new insights toward speciation via transient allopatry or ecological barriers.

Reconstructing the History of Yeast Genomes:

Some 12 years ago, Wolfe and colleagues demonstrated that Saccharomyces cerevisiae is the descendant of an ancient whole-genome duplication event [1],[2], much to the consternation of many of those who had recently completed the sequencing of this yeast [3], the first eukaryotic nuclear genome to be sequenced. Despite persistent rejectionist argument [4], this breakthrough discovery has been amply confirmed [5],[6] and has been the starting point for scores of papers on yeast evolution and phylogeny, culminating in the Yeast Gene Order Browser [7] and the paper by Gordon et al. in this issue of PLoS Genetics [8].

Folic Acid Supplementation and Spontaneous Preterm Birth: Adding Grist to the Mill?:

Preterm birth is increasing, and complicates 12% of deliveries in the United States. It is the dominant cause of neonatal mortality. Preterm birth also accounts for one in three children with vision impairment, one in five with mental retardation, and almost half with cerebral palsy [1]. Babies born weighing under 2,500 g are at heightened risk in adulthood of diabetes and cardiovascular disease [1]. These short- and long-term sequelae make the prevention of preterm birth a public health priority.

Discovery of Mating in the Major African Livestock Pathogen Trypanosoma congolense:

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen.
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Swine influenza virus (referred to as SIV) refers to influenza cases that are caused by Orthomyxoviruses that are endemic to pig populations. SIV strains isolated to date have been classified either as Influenzavirus C or one of the various subtypes of the genus Influenzavirus A. The 2009 swine flu outbreak is the spread of a new strain of H1N1 influenza virus that was first detected by public health agencies in March 2009. Local outbreaks of influenza-like illness were detected in three areas in Mexico, but the presence of this new strain was not discovered for a full month.

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