There are 62 articles published this week in PLoS ONE. There are also two Journal Clubs going on right now - here and here. Here are some of my picks for the week - go read, rate, comment and send trackbacks:
A Comparison of Wood Density between Classical Cremonese and Modern Violins:
Classical violins created by Cremonese masters, such as Antonio Stradivari and Giuseppe Guarneri Del Gesu, have become the benchmark to which the sound of all violins are compared in terms of their abilities of expressiveness and projection. By general consensus, no luthier since that time has been able to replicate the sound quality of these classical instruments. The vibration and sound radiation characteristics of a violin are determined by an instrument's geometry and the material properties of the wood. New test methods allow the non-destructive examination of one of the key material properties, the wood density, at the growth ring level of detail. The densities of five classical and eight modern violins were compared, using computed tomography and specially developed image-processing software. No significant differences were found between the median densities of the modern and the antique violins, however the density difference between wood grains of early and late growth was significantly smaller in the classical Cremonese violins compared with modern violins, in both the top (Spruce) and back (Maple) plates (p = 0.028 and 0.008, respectively). The mean density differential (SE) of the top plates of the modern and classical violins was 274 (26.6) and 183 (11.7) gram/liter. For the back plates, the values were 128 (2.6) and 115 (2.0) gram/liter. These differences in density differentials may reflect similar changes in stiffness distributions, which could directly impact vibrational efficacy or indirectly modify sound radiation via altered damping characteristics. Either of these mechanisms may help explain the acoustical differences between the classical and modern violins.
Globally, natural ecosystems are being lost to agricultural land at an unprecedented rate. This land-use often results in significant reductions in abundance and diversity of the flora and fauna as well as alterations in their composition. Despite this, there is little public perception of which taxa are most important in terms of their total biomass, biodiversity or the ecosystem services they perform. Such awareness is important for conservation, as without appreciation of their value and conservation status, species are unlikely to receive adequate conservation protection. We investigated children's perceptions of rainforest biodiversity by asking primary-age children, visiting the University Museum of Zoology, Cambridge to draw their ideal rainforest. By recording the frequency at which children drew different climatic, structural, vegetative and faunal components of the rainforest, we were able to quantify children's understanding of a rainforest environment. We investigated children's perceptions of rainforest biodiversity by comparing the relative numbers of the taxa drawn with the actual contributions made by these taxa to total rainforest biomass and global biodiversity. We found that children have a sophisticated view of the rainforest, incorporating many habitat features and a diverse range of animals. However, some taxa were over-represented (particularly mammals, birds and reptiles) and others under-represented (particularly insects and annelids) relative to their contribution to total biomass and species richness. Scientists and naturalists must continue to emphasise the diversity and functional importance of lesser-known taxa through public communication and outdoor events to aid invertebrate conservation and to ensure that future generations are inspired to become naturalists themselves.
The quality of biomedical reporting is guided by statements of several organizations. Although not all journals adhere to these guidelines, those that do demonstrate "editorial leadership" in their author community. To investigate a possible relationship between editorial leadership and journal quality, research journals from two European countries, one Anglophone and one non-Anglophone, were studied and compared. Quality was measured on a panel of bibliometric parameters while editorial leadership was evaluated from journals' instructions to authors. The study considered all 76 Italian journals indexed in Medline and 76 randomly chosen UK journals; only journals both edited and published in these countries were studied. Compared to UK journals, Italian journals published fewer papers (median, 60 vs. 93; p = 0.006), less often had online archives (43 vs. 74; p<0.001) and had lower median values of impact factor (1.2 vs. 2.7, p<0.001) and SCImago journal rank (0.09 vs. 0.25, p<0.001). Regarding editorial leadership, Italian journals less frequently required manuscripts to specify competing interests (p<0.001), authors' contributions (p = 0.005), funding (p<0.001), informed consent (p<0.001), ethics committee review (p<0.001). No Italian journal adhered to COPE or the CONSORT and QUOROM statements nor required clinical trial registration, while these characteristics were observed in 15%-43% of UK journals (p<0.001). At multiple regression, editorial leadership predicted 37.1%-49.9% of the variance in journal quality defined by citation statistics (p<0.0001); confounding variables inherent to a cross-cultural comparison had a relatively small contribution, explaining an additional 6.2%-13.8% of the variance. Journals from Italy scored worse for quality and editorial leadership than did their UK counterparts. Editorial leadership predicted quality for the entire set of journals. Greater appreciation of international initiatives to improve biomedical reporting may help low-quality journals achieve higher status.
An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) (Jonathan Eisen explains):
Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of data has opened many new windows into microbial diversity and evolution, and at the same time has created significant methodological challenges. Those processes which commonly require time-consuming human intervention, such as the preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though computationally costly or difficult, we consider to be important. In particular, we regard both the building of multiple sequence alignments and the performance of high quality phylogenetic analysis to be necessary. We describe here our fully-automated ss-rRNA taxonomy and alignment pipeline (STAP). It generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species diversity in environmental samples. The pipeline combines publicly-available packages (PHYML, BLASTN and CLUSTALW) with our automatic alignment, masking, and tree-parsing programs. Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts.
Tibeto-Burman populations of India provide an insight into the peopling of India and aid in understanding their genetic relationship with populations of East, South and Southeast Asia. The study investigates the genetic status of one such Tibeto-Burman group, Adi of Arunachal Pradesh based on 15 autosomal microsatellite markers. Further the study examines, based on 9 common microsatellite loci, the genetic relationship of Adi with 16 other Tibeto-Burman speakers of India and 28 neighboring populations of East and Southeast Asia. Overall, the results support the recent formation of the Adi sub-tribes from a putative ancestral group and reveal that geographic contiguity is a major influencing factor of the genetic affinity among the Tibeto-Burman populations of India.
Attitudes Toward Consumption and Conservation of Tigers in China:
A heated debate has recently emerged between tiger farmers and conservationists about the potential consequences of lifting the ban on trade in farmed tiger products in China. This debate has caused unfounded speculation about the extent of the potential market for tiger products. To fill this knowledge gap, we surveyed 1880 residents from a total of six Chinese cities to understand Urban Chinese tiger consumption behavior, knowledge of trade issues and attitudes towards tiger conservation. We found that 43% of respondents had consumed some product alleged to contain tiger parts. Within this user-group, 71% said that they preferred wild products over farmed ones. The two predominant products used were tiger bone plasters (38%) and tiger bone wine (6.4%). 88% of respondents knew that it was illegal to buy or sell tiger products, and 93% agreed that a ban in trade of tiger parts was necessary to conserve wild tigers. These results indicate that while Urban Chinese people are generally supportive of tiger conservation, there is a huge residual demand for tiger products that could resurge if the ban on trade in tiger parts is lifted in China. We suspect that the current supply of the market is predominantly met by fakes or substitutes branded as tiger medicines, but not listing tiger as an ingredient. We suggest that the Traditional Chinese Medicine community should consider re-branding these products as bone-healing medicines in order to reduce the residual demand for real tiger parts over the long-term. The lifting of the current ban on trade in farmed tiger parts may cause a surge in demand for wild tiger parts that consumers say are better. Because of the low input costs associated with poaching, wild-sourced parts would consistently undercut the prices of farmed tigers that could easily be laundered on a legal market. We therefore recommend that the Chinese authorities maintain the ban on trade in tiger parts, and work to improve the enforcement of the existing ban.
Trait-Like Brain Activity during Adolescence Predicts Anxious Temperament in Primates:
Early theorists (Freud and Darwin) speculated that extremely shy children, or those with anxious temperament, were likely to have anxiety problems as adults. More recent studies demonstrate that these children have heightened responses to potentially threatening situations reacting with intense defensive responses that are characterized by behavioral inhibition (BI) (inhibited motor behavior and decreased vocalizations) and physiological arousal. Confirming the earlier impressions, data now demonstrate that children with this disposition are at increased risk to develop anxiety, depression, and comorbid substance abuse. Additional key features of anxious temperament are that it appears at a young age, it is a stable characteristic of individuals, and even in non-threatening environments it is associated with increased psychic anxiety and somatic tension. To understand the neural underpinnings of anxious temperament, we performed imaging studies with 18-fluoro-deoxyglucose (FDG) high-resolution Positron Emission Tomography (PET) in young rhesus monkeys. Rhesus monkeys were used because they provide a well validated model of anxious temperament for studies that cannot be performed in human children. Imaging the same animal in stressful and secure contexts, we examined the relation between regional metabolic brain activity and a trait-like measure of anxious temperament that encompasses measures of BI and pituitary-adrenal reactivity. Regardless of context, results demonstrated a trait-like pattern of brain activity (amygdala, bed nucleus of stria terminalis, hippocampus, and periaqueductal gray) that is predictive of individual phenotypic differences. Importantly, individuals with extreme anxious temperament also displayed increased activity of this circuit when assessed in the security of their home environment. These findings suggest that increased activity of this circuit early in life mediates the childhood temperamental risk to develop anxiety and depression. In addition, the findings provide an explanation for why individuals with anxious temperament have difficulty relaxing in environments that others perceive as non-stressful.v
Maternal Feeding Controls Fetal Biological Clock:
It is widely accepted that circadian physiological rhythms of the fetus are affected by oscillators in the maternal brain that are coupled to the environmental light-dark (LD) cycle. To study the link between fetal and maternal biological clocks, we investigated the effects of cycles of maternal food availability on the rhythms of Per1 gene expression in the fetal suprachiasmatic nucleus (SCN) and liver using a transgenic rat model whose tissues express luciferase in vitro. Although the maternal SCN remained phase-locked to the LD cycle, maternal restricted feeding phase-advanced the fetal SCN and liver by 5 and 7 hours respectively within the 22-day pregnancy. Our results demonstrate that maternal feeding entrains the fetal SCN and liver independently of both the maternal SCN and the LD cycle. This indicates that maternal-feeding signals can be more influential for the fetal SCN and particular organ oscillators than hormonal signals controlled by the maternal SCN, suggesting the importance of a regular maternal feeding schedule for appropriate fetal molecular clockwork during pregnancy.
The typical mandate in conservation planning is to identify areas that represent biodiversity targets within the smallest possible area of land or sea, despite the fact that area may be a poor surrogate for the cost of many conservation actions. It is also common for priorities for conservation investment to be identified without regard to the particular conservation action that will be implemented. This demonstrates inadequate problem specification and may lead to inefficiency: the cost of alternative conservation actions can differ throughout a landscape, and may result in dissimilar conservation priorities. We investigate the importance of formulating conservation planning problems with objectives and cost data that relate to specific conservation actions. We identify priority areas in Australia for two alternative conservation actions: land acquisition and stewardship. Our analyses show that using the cost surrogate that most closely reflects the planned conservation action can cut the cost of achieving our biodiversity goals by half. We highlight spatial differences in relative priorities for land acquisition and stewardship in Australia, and provide a simple approach for determining which action should be undertaken where. Our study shows that a poorly posed conservation problem that fails to pre-specify the planned conservation action and incorporate cost a priori can lead to expensive mistakes. We can be more efficient in achieving conservation goals by clearly specifying our conservation objective and parameterising the problem with economic data that reflects this objective.
Mating with Stressed Males Increases the Fitness of Ant Queens:
According to sexual conflict theory, males can increase their own fitness by transferring substances during copulation that increase the short-term fecundity of their mating partners at the cost of the future life expectancy and re-mating capability of the latter. In contrast, sexual cooperation is expected in social insects. Mating indeed positively affects life span and fecundity of young queens of the male-polymorphic ant Cardiocondyla obscurior, even though males neither provide nuptial gifts nor any other care but leave their mates immediately after copulation and die shortly thereafter. Here, we show that mating with winged disperser males has a significantly stronger impact on life span and reproductive success of young queens of C. obscurior than mating with wingless fighter males. Winged males are reared mostly under stressful environmental conditions, which force young queens to disperse and found their own societies independently. In contrast, queens that mate with wingless males under favourable conditions usually start reproducing in the safety of the established maternal nest. Our study suggests that males of C. obscurior have evolved mechanisms to posthumously assist young queens during colony founding under adverse ecological conditions.
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