New and Exciting in PLoS this week

Still getting all my Legos together after the trip, here are some of the highlight from various PLoS journals from last Friday and today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

You Say You Want a Revolution: An Interview with Pat Brown:

I have known Pat Brown for about two decades and he never ceases to amaze me. Over the years, I have heard him speak quite a few times, and on each occasion I can feel my jaw drop. What will he think up next?
Pat (Image 1) is most frequently associated with the invention of microarrays and their use in studying gene expression, and he should be familiar to the readers of PLoS as a driving force behind open-access journals. But these are only two examples of his many successes, which span the worlds of topoisomerase, HIV integration, protein microarrays, and post-transcriptional regulation. Pat seems to have a brain in overdrive and the energy to match it. I was eager to tap into some of that electricity during the interview….

Does Publication in Top-Tier Journals Affect Reviewer Behavior?:

We show that when ecologists act as reviewers their reported rejection rates recommended for manuscripts increases with their publication frequency in high impact factor journals. Rejection rate however does not relate to reviewer age. These results indicate that the likelihood of getting a paper accepted for publication may depend upon factors in addition to scientific merit. Multiple reviewer selection for a given manuscript therefore should consider not only appropriate expertise, but also reviewers that have variable publication experience with a range of different journals to ensure balanced treatment. Interestingly since age did not relate to rejection rates, more senior scientists are not necessarily more jaded in reviewing practices.

The Role of Anorexia in Resistance and Tolerance to Infections in Drosophila:

Two routes to decreasing susceptibility to infection are resistance (the ability to clear pathogens) and tolerance (the ability to limit damage in response to pathogens). Anorexia induced by sickness puts animals into a diet-restricted state, a state that is generally believed to extend lifespan. We asked whether anorexia induced by sickness would alter the immune response. We measured the effects of diet restriction on both resistance and tolerance to two different infections in the fruit fly, Drosophila melanogaster. In one case we found that infection induced anorexia and the resulting diet restriction increased tolerance to this infection, thereby increasing survival of flies infected with this pathogen; however, this is not a universal effect. In a second case we found another pathogen that induced anorexia but here diet restriction lead to a reduction in resistance that collapsed the immune response and caused the fly to die faster. The relationship between diet restriction and immunity is complicated and must be evaluated on a pathogen-by-pathogen basis.

Vowel Identity between Note Labels Confuses Pitch Identification in Non-Absolute Pitch Possessors:

The simplest and likeliest assumption concerning the cognitive bases of absolute pitch (AP) is that at its origin there is a particularly skilled function which matches the height of the perceived pitch to the verbal label of the musical tone. Since there is no difference in sound frequency resolution between AP and non-AP (NAP) musicians, the hypothesis of the present study is that the failure of NAP musicians in pitch identification relies mainly in an inability to retrieve the correct verbal label to be assigned to the perceived musical note. The primary hypothesis is that, when asked to identify tones, NAP musicians confuse the verbal labels to be attached to the stimulus on the basis of their phonetic content. Data from two AP tests are reported, in which subjects had to respond in the presence or in the absence of visually presented verbal note labels (fixed Do solmization). Results show that NAP musicians confuse more frequently notes having a similar vowel in the note label. They tend to confuse e.g. a 261 Hz tone (Do) more often with Sol than, e.g., with La. As a second goal, we wondered whether this effect is lateralized, i.e. whether one hemisphere is more responsible than the other in the confusion of notes with similar labels. This question was addressed by observing pitch identification during dichotic listening. Results showed that there is a right hemispheric disadvantage, in NAP but not AP musicians, in the retrieval of the verbal label to be assigned to the perceived pitch. The present results indicate that absolute pitch has strong verbal bases, at least from a cognitive point of view.

Can the Relationship between Doctors and Drug Companies Ever Be a Healthy One?:

The financial ties between doctors and drug companies have come under intense scrutiny in recent years. Some commentators–such as Marcia Angell, former editor-in-chief of the New England Journal of Medicine–argue that the mission of doctors is fundamentally different to the mission of drug companies and that the ties between them should be completely cut. “Drug companies are investor owned businesses with a responsibility to maximise profits for their shareholders,” says Angell [1]. “That is quite different from the mission of the medical profession, which is to provide the best care possible for patients.” Other commentators have argued that clinicians and drug companies do have some shared goals in aiming to maximize human health. In this debate, Emma D’Arcy, co-founder of a social networking site that facilitates interactions between doctors and drug companies, argues that it would be valuable to the public if we could establish “authentic alliances” between these professionals. But journalist Ray Moynihan argues that such alliances are prone to the corrupting influence of pharmaceutical industry money, and that disentanglement is a healthier alternative.

Barcoding Nemo: DNA-Based Identifications for the Ornamental Fish Trade:

Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America. Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19-6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting. Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.

Evolution and Survival on Eutherian Sex Chromosomes:

Using recently available marsupial and monotreme genomes, we investigated nascent sex chromosome evolution in mammals. We show that, in eutherian mammals, X and Y genes acquired distinct evolutionary rates and functional constraints immediately after recombination suppression; X-linked genes maintained lower, ancestral (autosomal), rates, whereas the evolutionary rates of Y-linked genes increased. Most X and, unexpectedly, Y genes evolved under stronger purifying selection than similarly aged autosomal paralogs. However, we also observed that the divergence of gametologs and paralogs shared similar features. In addition, many Y-linked copies evolved unique functions and expression patterns compared to their counterparts on the X chromosome. Therefore, our results suggest that to be retained on the Y chromosome, genes need to acquire separately valuable expression and/or functions to be safeguarded by purifying selection.

From Construction Workers to Architects: Developing Scientific Research Capacity in Low-Income Countries:

Just a dozen years ago, the largest problem in tackling diseases that disproportionately affect the global South was the lack of resources available to identify and combat them. Now, as a result of the extraordinary rise in philanthropy and public giving, more funds than ever before are being directed toward pressing health issues that ravage the world’s poor. However, several factors may prevent this “bubble” of generosity from realizing major improvements in global health. Not only are substantial amounts of aid being diverted from their ultimate goals by bureaucratic barriers and corruption [1], but most funds come with strings attached and must be spent according to donors’ priorities, politics, and values. Many projects are planned, managed, and implemented in large part from the “North” with cooperation of local personnel and agencies. Because these projects pursue largely donor-driven agendas, they tend to reflect the donors’ interests rather than those of the recipients, with two major consequences–investments in local health infrastructure and capacity building are not prioritized, and diseases and issues that are the focus of a temporary spotlight often garner the most attention and funds.

Practice Makes Perfect: Learning Mind Control of Prosthetics:

More than 5 million people in the United States are afflicted with some form of paralysis, leaving them with diminished physical capacity. Fortunately, the past few years have seen advancements in both stem-cell technologies, which promise to repair such injuries, and in the development of sophisticated prosthetic devices that offer patients a way to interact with their environment. For example, recent studies have demonstrated that monkeys and humans can control computer cursors or robotic limbs through electrode arrays implanted in their brains. However, the neuronal changes associated with long-term prosthetic skill acquisition remain unclear. A better understanding of this process is crucial for the reliable control of prosthetic devices in a manner that mimics our effortless control of limb movements. In this issue of PLoS Biology, Karunesh Ganguly and Jose Carmena describe experiments that specifically track the neural changes associated with the process of learning and reliably controlling such devices through an implanted electrode array. This work demonstrates that the brain can create a stable mental representation of the prosthetic device that eventually allows for precise control.

Emergence of a Stable Cortical Map for Neuroprosthetic Control:

Brain-machine interfaces (BMIs) have the potential to revolutionize the care of neurologically impaired patients. Numerous studies have now shown the feasibility of direct “brain control” of a neuroprosthetic device, yet it remains unclear whether the neural representation for prosthetic control can become consolidated and remain stable over time. This question is especially intriguing given the evidence demonstrating that the neural representation for natural movements can be unstable: BMIs provide a window into the plasticity of cortical circuits in awake-behaving subjects. Here, we show that long-term neuroprosthetic control leads to the formation of a remarkably stable cortical map. Interestingly, this map has the putative attributes of a memory trace, namely, it is stable across time, readily recalled, and resistant to the storage of a second map. The demonstration of such a cortical map for prosthetic control indicates that neuroprosthetic devices could eventually be controlled through the effortless recall of motor memory in a manner that mimics natural skill acquisition and motor control.

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