bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamics of RNA structures by Wang–Landau sampling
Authors: Lou Feng , Clote Peter
Published: June 2010

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures.

Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations.

Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/.

Contact:  clote@bc.edu
PathText: a text mining integrator for biological pathway visualizations
Authors: Kemper Brian , Matsuzaki Takuya , Matsuoka Yukiko , Tsuruoka Yoshimasa , Kitano Hiroaki , Ananiadou Sophia , Tsujii Jun'ichi
Published: June 2010

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations.

Contact:  brian@monrovian.com.
Galectin‐3, cardiac structure and function, and long‐term mortality in patients with acutely decompensated heart failure
Authors: Shah Ravi V. , Chen‐Tournoux Annabel A. , Picard Michael H. , van Kimmenade Roland R. J. , Januzzi James L.
Published: June 2010

Aims

To determine the relationship between galectin‐3 concentrations and cardiac structure in patients with acute dyspnoea, and to evaluate the impact of galectin‐3 independent of echocardiographic measurements on long‐term mortality.

Methods and results

One hundred and fifteen patients presenting to the emergency department with acute dyspnoea who had galectin‐3 levels and detailed echocardiographic studies on admission were studied. Galectin‐3 levels were associated with older age (r = 0.26, P = 0.006), lower creatinine clearance (r = −0.42, P < 0.001), and higher levels of N‐terminal‐proBNP (r = 0.39, P < 0.001). Higher galectin‐3 levels were associated with tissue Doppler E/Ea ratio (r = 0.35, P = 0.01), a lower right ventricular (RV) fractional area change (r = −0.19, P = 0.05), higher RV systolic pressure (r = 0.37, P < 0.001), and more severe mitral (r = 0.30, P = 0.001) or tricuspid regurgitation (r = 0.26, P = 0.005). In patients diagnosed with heart failure (HF), the association between galectin‐3 and valvular regurgitation and RV systolic pressure persisted. In a multivariate Cox regression model, galectin‐3 remained a significant predictor of 4‐year mortality independent of echocardiographic markers of risk. Dyspnoeic patients with HF and galectin‐3 levels above the median value had a 63% mortality; patients less than the median value had a 37% mortality (P = 0.003).

Conclusion

Among dyspnoeic patients with and without ADHF, galectin‐3 concentrations are associated with echocardiographic markers of ventricular function. In patients with ADHF, a single admission galectin‐3 level predicts mortality to 4 years, independent of echocardiographic markers of disease severity.
Impact of erythropoiesis‐stimulating agents on morbidity and mortality in patients with heart failure: an updated, post‐TREAT meta‐analysis
Authors: Desai Akshay , Lewis Eldrin , Solomon Scott , McMurray John J.V. , Pfeffer Marc
Published: June 2010

Aims

Randomized clinical trials have suggested that treatment of anaemia with erythropoiesis‐stimulating agents (ESAs) in patients with cancer or chronic kidney disease may increase cardiovascular risk. We therefore examined the effect of treating anaemia with an ESA in patients with heart failure in a meta‐analysis of randomized clinical trials, including the recently reported TREAT study.

Methods and results

We performed a systematic review and meta‐analysis of all prospective, randomized, controlled studies of ESAs enrolling patients with heart failure and reporting data on mortality or non‐fatal heart failure events. Of 10 trials initially identified by our search strategy, we pooled data from 9 placebo‐controlled studies enrolling a total of 2039 patients, of whom 1023 (50.2%) were allocated to ESA treatment. The pooled risk ratio for ESA treatment relative to placebo was 1.03 [95% confidence interval (CI): 0.89–1.21, P = 0.68] for overall mortality and 0.95 (95% CI: 0.82–1.10, P = 0.46) for worsening heart failure.

Conclusions

The use of ESAs to manage anaemia in patients with heart failure was associated with a neutral effect on both mortality and non‐fatal heart failure events. Definitive assessment of the balance of risk and benefit in this population awaits the completion of a randomized clinical trial adequately powered to assess clinical outcomes.
Impact of Brown Spot Caused by Septoria glycines on Soybean in Ohio
Authors: Cruz Christian D. , Mills Dennis , Paul Pierce A. , Dorrance Anne E.
Published: June 2010

Brown spot, caused by Septoria glycines, is the most common foliar disease of soybean in Ohio, but its economic impact has not been assessed on modern cultivars. Therefore, the objectives of this study were to (i) evaluate the effect of S. glycines on soybean yield and (ii) evaluate the efficacy of strobilurin- and triazole-based fungicides on the control of brown spot. Yield loss associated with S. glycines was determined using weekly applications of chlorothalonil. The efficacy of azoxystrobin, pyraclostrobin, tebuconazole, and flutriafol alone and in combinations were also assessed using applications at the R3 and R5 growth stages at two locations over 3 years. Significantly different levels of brown spot developed following applications of chlorothalonil, with mean yield differences between treated and nontreated plots ranging from 196 to 293 kg/ha. Pyraclostrobin and azoxystrobin applied at the R3 growth stage significantly reduced final levels of brown spot; however, significant increases in yield occurred in only three of the six location-years. Triazoles, flutriafol and tebuconazole, applied at R3 or R5 did not significantly decrease levels of brown spot or impact yield. More data on the accurate timing of fungicides are still required to establish a long-term management program for this disease, and resistance to brown spot should be monitored in soybean cultivar development to prevent future yield losses.
A PCR-Based Assay for Detection of Fusarium oxysporum f. sp. lactucae in Lettuce Seed
Authors: Mbofung Gladys Chia Y. , Pryor Barry M.
Published: June 2010

A nested polymerase chain reaction-based (nPCR) assay was developed and evaluated for the rapid detection of Fusarium oxysporum f. sp. lactucae in seed of lettuce. Three primers were designed from sequences of the intergenic spacer region of the rDNA and were used in the PCR amplifications. The first amplification employed the primer pair GYCF1 and GYCR4C and produced a product of 2,270 bp. The second amplification employed the forward primer GYCF1 and the nested primer R943 and produced a single 936-bp PCR product. The nPCR protocol developed successfully detected the target sequence in genomic DNA at 1 fg/μl. A seed assay was tested that included a 4-day incubation step in which seed were maintained under high humidity conditions to increase fungal biomass for DNA extraction. In seed lots prepared by mixing known amounts of F. oxysporum f. sp. lactucae–infested seed with noninfested seed, this assay permitted the detection of the pathogen from lots with infestation rates as low as 0.1%. Samples of lettuce seed obtained from 88 commercial lettuce seed lots were assayed for the pathogen by direct plating and by using the nPCR assay. The pathogen was not detected by either diagnostic method, suggesting the seed lots were pathogen free or the level was below detection limits.
Rhizoctonia Web Blight Development on Container-Grown Azalea in Relation to Time and Environmental Factors
Authors: Copes Warren E. , Scherm Harald
Published: June 2010

Rhizoctonia web blight, caused by binucleate Rhizoctonia spp., is an annual problem in the southern United States on container-grown azaleas (Rhododendron spp.) that receive daily irrigation. Disease progress was assessed weekly from mid-May to mid-September on nursery-grown plants at three locations in Mississippi and Alabama in 2006, 2007, and 2008. Disease onset, defined as the appearance of blighted leaves at the exterior canopy of at least one plant, occurred on average on 20 July, and calendar date was a more precise predictor of disease onset than several combined time–weather variables. Disease progress curves exhibited weekly fluctuations around a typically exponential increase in the mean number of symptomatic leaves per plant until early to mid-September, after which web blight severity leveled off or declined due to disease-induced leaf dehiscence and the appearance of new, asymptomatic leaves. Based on the relative increase in the log-transformed number of infected leaves per plant, weekly assessment periods were classified as having slow (≤0%), intermediate (>0 to <10%), or rapid (≥10% increase) disease progress. Three-day moving averages (MA) of various weather variables were calculated, and lagged values (by 5 days) of the MA were used in an attempt to predict disease progress as slow, intermediate, or rapid. Of the periods assessed as having slow disease progress in the 2006–2007 data set (model development data), 90.6% (29 of 32) met at least one of the following heuristically derived criteria for the lagged MA: min. temperature < 20.0°C, max. temperature > 35.0°C, avg. vapor pressure deficit < 2.50 hPa, or day of the year > 240 (28 August). One or more of these same criteria were met in 5 of 16 (31.2%) assessment periods with rapid disease progress, indicating that periods with slow versus rapid disease progression could be distinguished reasonably well based on weather. Results were similar for the 2008 validation data. However, weather variables were not useful in separating periods with either slow or rapid disease progress from those having intermediate progress. Instead, weather variables were most useful when used in a negative-prognosis approach to predict disease progression as being “not rapid” (which includes slow and intermediate periods) or “not slow” (including intermediate and rapid periods). The data set was further analyzed using Classification and Regression Tree (CART) analysis to relate weekly disease progress periods to weather variables. The resulting CART model agreed with the heuristic approach in that temperature variables were more prominent than moisture variables in classifying disease progress periods. With both approaches, satisfactory accuracy was accomplished only with negative-prognoses that classified disease progress periods as not rapid or not slow based on temperature and moisture limits.
First Report of Leaf Spot Caused by Bipolaris setariae on Cassava in China
Authors: Shi T. , Li C.-P. , Li J.-F. , Cai J.-M. , Huang G.-X.
Published: June 2010

Cassava (Manihot esculenta Crantz) is an important food crop in tropical regions of China. Seventy percent of the cassava output is used for starch and ethanol production and it has become the base of food and bioenergy industries. In July 2009, a new leaf spot disease was found on cv. HuaNan205 from a cassava plantation in Danzhou, Hainan Province. Disease occurred on 50% or less of the plants. Initial symptoms were elliptical, chlorotic, and water-immersion lesions of 2 to 4 mm in diameter. These lesions became dry and yellow due to the progress of the disease. A brown halo was around the lesions, and in wet conditions, a dark gray mildew often appeared in the middle of the lesion. Diseased leaves turned yellow and the plants eventually became defoliated. The pathogen was isolated and pathogenicity was established by following Koch's postulates. Young, healthy, and fully expanded green leaves of Cassava cv. HuaNan205 were surface sterilized and then inoculated by spraying them with a suspension of conidia (1 × 105 conidia per ml) of the isolate. Sterile water was used as a control. The leaves were kept in a humid chamber at 28°C for 4 days, at which time similar symptoms to those described above were observed on the leaves. The pathogen was reisolated from inoculated leaves. Microscopic examination showed the conidiophores were fasciculate and brown, septate and straight, and the basal cell was enlarged and hemispherical. Well-developed conidia were long-obclavate, obtuse at both ends, straight, brown, with five to eight transverse septa, and measured 49.7 to 117.1 × 13.3 to 17.2 μm. Genomic DNA of this isolate was extracted with a cetyltrimethylammoniumbromide protocol, and amplification and sequencing of the internal transcribed spacer (ITS) region of rDNA was performed with procedures outlined by Cooke et al. (2). The sequence of the region was deposited in GenBank (Accession No. GU290228). Comparison of the sequences available in the GenBank database revealed that the current ITS sequence differs by three base pairs from two Bipolaris setariae isolates (EF452444 and FJ606786). Morphological identification and sequence analysis of ITS rDNA showed that the pathogen was B. setariae. B. setariae is one of the most important pathogens of lawn grass, gramineous crops, and other plants (1,3). However, no leaf spot disease caused by B. setariae has been recorded previously on cassava in China or elsewhere.

References: (1) P. Busey. Crop Sci. 43:1899, 2003. (2) D. E. L. Cooke et al. Fungal Genet. Biol. 30:17, 2000. (3) H. D. Wells and W. W. Hanna. Phytopathology 78:1179, 1988.
First Report of Bursaphelenchus thailandae on Pinus densiflora in Korea
Authors: Han H. , Chung Y.-J. , Shin S.-C.
Published: June 2010

A survey of nematodes on Pinus densiflora in Namyangju City, Gyeonggi Province, Korea was conducted in 2008. Namyangju is located in an area with pine wilt caused by Bursaphelenchus xylophilus and monitoring of wilt has been conducted periodically. Nematodes were extracted from wood chips by the Baermann's funnel method and were cultured on a medium of Botrytis cinerea. During the survey, B. xylophilus and B. thailandae were detected. B. thailandae was found in 20% of the trees tested and usually was found alone without B. xylophilus. Population density of B. thailandae ranged from 8,000 to 15,000 nematodes per 100 g of wood chips. The species was identified by morphology and molecular characterization. B. thailandae was differentiated from B. xylophilus by slight swellings of the stylet knobs, protruding vulval flaps and pointed tail in females, and the male spicule with distinctive shading in the dorsal region. Morphometric data was obtained by measurements of 20 females and 10 males: female, body length = 951.3 ± 56.6 μm, a = 31.8 ± 1.9, b = 10.8 ± 0.9, c = 23.4. ± 0.8, V = 76.2 ± 0.8, stylet length = 14.5 ± 0.6 μm, length of postuterine sac = 90.3 ± 13.5 μm; male, body length = 838.0 ± 71.5 μm, a = 31.1 ± 2.1, b = 5.2 ± 0.5, c = 30.4 ± 2.7, stylet length = 13.5 ± 1.1 μm, spicules length = 16.5 ± 0.7 μm. Measurements were compared with the original description of B. thailandae reported by Braasch and Braasch-Bidasak (1), which showed that the Korean isolate was larger in most body sizes. For molecular diagnosis, the internal transcribed spacer (ITS) and D2-D3 rDNA were amplified by PCR (US/PTC-0220; Bio Rad, Hercules, CA). The sequences of ITS and D2-D3 rDNA of B. thailandae from P. densiflora showed 98 and 99% homology to those of B. thailandae from GenBank Accession Nos. AM157746 and DQ497184, respectively. B. thailandae was originally described on Pinus merkusi in Pai, North Thailand (1) while Ningbo Entry-Exit Inspection and Quarantine Bureau in China reported a detection of B. thailandae in the imported packaging wood from Hong Kong, Japan, Korea, Italy, and the United States (2). However, packaging wood is a circulating product and the establishment of B. thailandae in those countries is not confirmed. The pathogenicity of B. thailandae on coniferous trees remains to be determined. To our knowledge, this is the first report of B. thailandae on P. densiflora in a natural area in Korea.

References: (1) H. Braasch and R. Braasch-Bidasak. Nematology 4:853, 2002. (2) J. Gu et al. For. Pathol. 36:323, 2006.
Allozyme-Specific Modification of a Maize Seed Chitinase by a Protein Secreted by the Fungal Pathogen Stenocarpella maydis
Authors: Naumann Todd A. , Wicklow Donald T.
Published: June 2010

Stenocarpella maydis causes both dry-ear rot and stalk rot of maize. Maize inbred lines have varying levels of resistance to ear rot caused by S. maydis. The genetic basis of resistance appears to rely on multiple genetic factors, none of which are known. The commonly used stiff-stalk inbred line B73 has been shown to be strongly susceptible to ear rot caused by S. maydis. Here, we report that the ChitA protein alloform from B73, ChitA-F, encoded by a known allele of the chiA gene, is susceptible to modification by a protein (Stm-cmp) secreted by S. maydis. We also identify a new allele of chiA (from inbred line LH82) which encodes ChitA-S, an alloform of ChitA that is resistant to Stm-cmp modification. Chitinase zymogram analysis of seed from a commercial field showed the presence of both ChitA alloforms in healthy ears, and showed that ChitA-F but not ChitA-S was modified in ears rotted by S. maydis. The ChitA-F protein was purified from inbred line B73 and ChitA-S from LH82. ChitA-F was modified more efficiently than ChitA-S by S. maydis protein extracts in vitro. The chiA gene from LH82 was cloned and sequenced. It is a novel allele that encodes six polymorphisms relative to the known allele from B73. This is the first demonstration that the susceptibility to modification of a fungal targeted plant chitinase differs among inbred lines. These findings suggest that the LH82 chiA allele may be a specific genetic determinant that contributes to resistance to ear rot caused by S. maydis whereas the B73 allele may contribute to susceptibility.
Plump Kernels with High Deoxynivalenol Linked to Late Gibberella zeae Infection and Marginal Disease Conditions in Winter Wheat
Authors: Cowger Christina , Arrellano Consuelo
Published: June 2010

Deoxynivalenol (DON) concentrations in mature wheat grain are usually correlated with symptoms produced by Gibberella zeae infection. However, there have been numerous observations of unacceptably high DON in asymptomatic crops, which can lead to lower-than-expected milling reductions in DON. We conducted a field experiment with winter wheat to examine the effect of infection timing and postanthesis moisture on grain quality and DON accumulation. Seven to eight soft red winter wheat cultivars were grown in three successive years in a misted nursery in Kinston, NC. Spikes were randomly selected for individual spray inoculation at 0, 10, or 20 days after anthesis (daa). Starting at anthesis, plots were subjected to 0, 10, 20, or 30 days of mist. Inoculated spikes and noninoculated controls were collected at harvest-ripeness, and the threshed grain was assayed for Fusarium-damaged kernels (FDK) and DON. In 2 of 3 years, percentages of FDK were significantly lower from 10-daa infections than from those at 0 daa, although DON concentrations were the same at the two inoculation timings in 2 of the 3 years. Those results indicate that the period of maximum susceptibility to wheat spike infections by G. zeae is close to or slightly less than 10 daa in North Carolina. In 2 of 3 years, FDK–DON correlation was greater for 0- and 10-daa inoculations and for 0- to 20-daa misted treatments than for the later-inoculated or longer-misted treatments, respectively. The percentage of “low-FDK, high DON” (LFHD) observations (defined as FDK ≤ 4.0%, DON ≥ 2 μg g–1) was higher in 2007 than in 2005 or 2006 (41, 14, and 18%, respectively). In both 2006 and 2007, high percentages of LFHD observations (≥60%) occurred under marginal disease conditions involving late infection. We conclude that late infection is an important factor leading to LFHD grain. Periods of rain soon after anthesis likely favor the low-symptom, high-DON scenario, and conditions that create greater within-crop variability of anthesis timing may also be important.
Interspecific assistance: fiddler crabs help heterospecific neighbours in territory defence
Authors: Booksmythe Isobel , Jennions Michael D. , Backwell Patricia R. Y.
Published: June 2010

Theory predicts that territory owners will help established neighbours to repel intruders, when doing so is less costly than renegotiating boundaries with successful usurpers of neighbouring territories. Here, we show for the first time, to our knowledge, cooperative territory defence between heterospecific male neighbours in the fiddler crabs
Uca elegans
and
Uca mjoebergi
. We show experimentally that resident
U. elegans
were equally likely to help a smaller
U. mjoebergi
or
U. elegans
neighbour during simulated intrusions by intermediate sized
U. elegans
males (50% of cases for both). Helping was, however, significantly less likely to occur when the intruder was a
U. mjoebergi
male (only 15% of cases).
Reconstruction of potential energy profiles from multiple rupture time distributions
Authors: Fok Pak-Wing , Chou Tom
Published: June 2010

We explore the mathematical and numerical aspects of reconstructing a potential energy profile of a molecular bond from its rupture time distribution. While reliable reconstruction of gross attributes, such as the height and the width of an energy barrier, can be easily extracted from a single first passage time (FPT) distribution, the reconstruction of finer structure is ill-conditioned. More careful analysis shows the existence of optimal bond potential amplitudes (represented by an effective Peclet number) and initial bond configurations that yield the most efficient numerical reconstruction of simple potentials. Furthermore, we show that reconstruction of more complex potentials containing multiple minima can be achieved by simultaneously using two or more measured FPT distributions, obtained under different physical conditions. For example, by changing the effective potential energy surface by known amounts, additional measured FPT distributions improve the reconstruction. We demonstrate the possibility of reconstructing potentials with multiple minima, motivate heuristic rules-of-thumb for optimizing the reconstruction, and discuss further applications and extensions.
Projected range contractions of montane biodiversity under global warming
Authors: La Sorte Frank A. , Jetz Walter
Published: June 2010

Mountains, especially in the tropics, harbour a unique and large portion of the world's biodiversity. Their geographical isolation, limited range size and unique environmental adaptations make montane species potentially the most threatened under impeding climate change. Here, we provide a global baseline assessment of geographical range contractions and extinction risk of high-elevation specialists in a future warmer world. We consider three dispersal scenarios for simulated species and for the world's 1009 montane bird species. Under constrained vertical dispersal (VD), species with narrow vertical distributions are strongly impacted; at least a third of montane bird diversity is severely threatened. In a scenario of unconstrained VD, the location and structure of mountain systems emerge as a strong driver of extinction risk. Even unconstrained lateral movements offer little improvement to the fate of montane species in the Afrotropics, Australasia and Nearctic. Our results demonstrate the particular roles that the geography of species richness, the spatial structure of lateral and particularly vertical range extents and the specific geography of mountain systems have in determining the vulnerability of montane biodiversity to climate change. Our findings confirm the outstanding levels of biotic perturbation and extinction risk that mountain systems are likely to experience under global warming and highlight the need for additional knowledge on species' vertical distributions, dispersal and adaptive capacities.
Genetic variation in the cellular response ofDaphnia magna(Crustacea: Cladocera) to its bacterial parasite
Authors: Auld Stuart K. J. R. , Scholefield Jennifer A. , Little Tom J.
Published: June 2010

Linking measures of immune function with infection, and ultimately, host and parasite fitness is a major goal in the field of ecological immunology. In this study, we tested for the presence and timing of a cellular immune response in the crustaceanDaphnia magnafollowing exposure to its sterilizing endoparasitePasteuria ramosa. We found thatD. magnapossesses two cell types circulating in the haemolymph: a spherical one, which we call a granulocyte and an irregular-shaped amoeboid cell first described by Metchnikoff over 125 years ago.Daphnia magnamounts a strong cellular response (of the amoeboid cells) just a few hours after parasite exposure. We further tested for, and found, considerable genetic variation for the magnitude of this cellular response. These data fostered a heuristic model of resistance in this naturally coevolving host–parasite interaction. Specifically, the strongest cellular responses were found in the most susceptible hosts, indicating resistance is not always borne from a response that destroys invading parasites, but rather stems from mechanisms that prevent their initial entry. Thus,D. magnamay have a two-stage defence—a genetically determined barrier to parasite establishment and a cellular response once establishment has begun.
Bigger brains cycle faster before neurogenesis begins: a comparison of brain development between chickens and bobwhite quail
Authors: Charvet Christine J. , Striedter Georg F.
Published: June 2010

The chicken brain is more than twice as big as the bobwhite quail brain in adulthood. To determine how this species difference in brain size emerges during development, we examined whether differences in neurogenesis timing or cell cycle rates account for the disparity in brain size between chickens and quail. Specifically, we examined the timing of neural events (e.g. neurogenesis onset) from Nissl-stained sections of chicken and quail embryos. We estimated brain cell cycle rates using cumulative bromodeoxyuridine labelling in chickens and quail at embryonic day (ED) 2 and at ED5. We report that the timing of neural events is highly conserved between chickens and quail, once time is expressed as a percentage of overall incubation period. In absolute time, neurogenesis begins earlier in chickens than in quail. Therefore, neural event timing cannot account for the expansion of the chicken brain relative to the quail brain. Cell cycle rates are also similar between the two species at ED5. However, at ED2, before neurogenesis onset, brain cells cycle faster in chickens than in quail. These data indicate that chickens have a larger brain than bobwhite quail mainly because of species differences in cell cycle rates during early stages of embryonic development.
Evolutionary conservation advice for despotic populations: habitat heterogeneity favours conflict and reduces productivity in Seychelles magpie robins
Authors: López-Sepulcre Andrés , Kokko Hanna , Norris Ken
Published: June 2010

Individual preferences for good habitat are often thought to have a beneficial stabilizing effect for populations. However, if individuals preferentially compete for better-quality territories, these may become hotspots of conflict. We show that, in an endangered species, this process decreases the productivity of favoured territories to the extent that differences in productivity between territories disappear. Unlike predictions from current demographic theory on site-dependent population regulation (ideal despotic distribution), we show that population productivity is reduced if resources are distributed unevenly in space. Competition for high-quality habitat can thus have detrimental consequences for populations even though it benefits individuals. Manipulating conflict (e.g. by reducing variation in habitat quality) can therefore prove an effective conservation measure in species with strong social or territorial conflict.
Memory in the making: localized brain activation related to song learning in young songbirds
Authors: Gobes Sharon M. H. , Zandbergen Matthijs A. , Bolhuis Johan J.
Published: June 2010

Songbird males learn to sing their songs from an adult ‘tutor’ early in life, much like human infants learn to speak. Similar to humans, in the songbird brain there are separate neural substrates for vocal production and for auditory memory. In adult songbirds, the caudal pallium, the avian equivalent of the auditory association cortex, has been proposed to contain the neural substrate of tutor song memory, while the song system is involved in song production as well as sensorimotor learning. If this hypothesis is correct, there should be neuronal activation in the caudal pallium, and not in the song system, while the young bird is hearing the tutor song. We found increased song-induced molecular neuronal activation, measured as the expression of an immediate early gene, in the caudal pallium of juvenile zebra finch males that were in the process of learning to sing their songs. No such activation was found in the song system. Molecular neuronal activation was significantly greater in response to tutor song than to novel song or silence in the medial part of the caudomedial nidopallium (NCM). In the caudomedial mesopallium, there was significantly greater molecular neuronal activation in response to tutor song than to silence. In addition, in the NCM there was a significant positive correlation between spontaneous molecular neuronal activation and the strength of song learning during sleep. These results suggest that the caudal pallium contains the neural substrate for tutor song memory, which is activated during sleep when the young bird is in the process of learning its song. The findings provide insight into the formation of auditory memories that guide vocal production learning, a process fundamental for human speech acquisition.
Mineral–microbe interactions in deep-sea hydrothermal systems: a challenge for Raman spectroscopy
Authors: Breier J. A. , White S. N. , German C. R.
Published: June 2010

In deep-sea hydrothermal environments, steep chemical and thermal gradients, rapid and turbulent mixing and biologic processes produce a multitude of diverse mineral phases and foster the growth of a variety of chemosynthetic micro-organisms. Many of these microbial species are associated with specific mineral phases, and the interaction of mineral and microbial processes are of only recently recognized importance in several areas of hydrothermal research. Many submarine hydrothermal mineral phases form during kinetically limited reactions and are either metastable or are only thermodynamically stable under
in situ
conditions. Laser Raman spectroscopy is well suited to mineral speciation measurements in the deep sea in many ways, and sea-going Raman systems have been built and used to make a variety of
in situ
measurements. However, the full potential of this technique for hydrothermal science has yet to be realized. In this focused review, we summarize both the need for
in situ
mineral speciation measurements in hydrothermal research and the development of sea-going Raman systems to date; we describe the rationale for further development of a small, low-cost sea-going Raman system optimized for mineral identification that incorporates a fluorescence-minimizing design; and we present three experimental applications that such a tool would enable.
Time-resolved remote Raman study of minerals under supercritical CO
2
and high temperatures relevant to Venus exploration
Authors: Sharma Shiv K. , Misra Anupam K. , Clegg Samuel M. , Barefield James E. , Wiens Roger C. , Acosta Tayro
Published: June 2010

We report time-resolved (TR) remote Raman spectra of minerals under supercritical CO
2
(approx. 95 atm pressure and 423 K) and under atmospheric pressure and high temperature up to 1003 K at distances of 1.5 and 9 m, respectively. The TR Raman spectra of hydrous and anhydrous sulphates, carbonate and silicate minerals (e.g. talc, olivine, pyroxenes and feldspars) under supercritical CO
2
(approx. 95 atm pressure and 423 K) clearly show the well-defined Raman fingerprints of each mineral along with the Fermi resonance doublet of CO
2
. Besides the CO
2
doublet and the effect of the viewing window, the main differences in the Raman spectra under Venus conditions are the phase transitions, the dehydration and decarbonation of various minerals, along with a slight shift in the peak positions and an increase in line-widths. The dehydration of melanterite (FeSO
4
 · 7H
2
O) at 423 K under approximately 95 atm CO
2
is detected by the presence of the Raman fingerprints of rozenite (FeSO
4
 · 4H
2
O) in the spectrum. Similarly, the high-temperature Raman spectra under ambient pressure of gypsum (CaSO
4
 · 2H
2
O) and talc (Mg
3
Si
4
O
10
(OH)
2
) indicate that gypsum dehydrates at 518 K, but talc remains stable up to 1003 K. Partial dissociation of dolomite (CaMg(CO
3
)
2
) is observed at 973 K. The TR remote Raman spectra of olivine, α-spodumene (LiAlSi
2
O
6
) and clino-enstatite (MgSiO
3
) pyroxenes and of albite (NaAlSi
3
O
8
) and microcline (KAlSi
3
O
8
) feldspars at high temperatures also show that the Raman lines remain sharp and well defined in the high-temperature spectra. The results of this study show that TR remote Raman spectroscopy could be a potential tool for exploring the surface mineralogy of Venus during both daytime and nighttime at short and long distances.
Microbial colonization of halite from the hyper-arid Atacama Desert studied by Raman spectroscopy
Authors: Vítek P. , Edwards H. G. M. , Jehlička J. , Ascaso C. , De Los Ríos A. , Valea S. , Jorge-Villar S. E. , Davila A. F. , Wierzchos J.
Published: June 2010

The hyper-arid core of the Atacama Desert (Chile) is the driest place on Earth and is considered a close analogue to the extremely arid conditions on the surface of Mars. Microbial life is very rare in soils of this hyper-arid region, and autotrophic micro-organisms are virtually absent. Instead, photosynthetic micro-organisms have successfully colonized the interior of halite crusts, which are widespread in the Atacama Desert. These endoevaporitic colonies are an example of life that has adapted to the extreme dryness by colonizing the interior of rocks that provide enhanced moisture conditions. As such, these colonies represent a novel example of potential life on Mars. Here, we present non-destructive Raman spectroscopical identification of these colonies and their organic remnants. Spectral signatures revealed the presence of UV-protective biomolecules as well as light-harvesting pigments pointing to photosynthetic activity. Compounds of biogenic origin identified within these rocks differed depending on the origins of specimens from particular areas in the desert, with differing environmental conditions. Our results also demonstrate the capability of Raman spectroscopy to identify biomarkers within rocks that have a strong astrobiological potential.
The effect of stopping smoking on perceived stress levels
Authors: Hajek Peter , Taylor Tamara , McRobbie Hayden
Published: June 2010

Aims  Many smokers believe that smoking helps them to cope with stress, and that stopping smoking would deprive them of an effective stress management tool. Changes in stress levels following long‐term smoking cessation are not well mapped. This longitudinal project was designed to provide more robust data on post‐cessation changes in perceived stress levels by following a cohort of smokers admitted to hospital after myocardial infarction (MI) or for coronary artery bypass (CAB) surgery, as such patients typically achieve higher continuous abstinence rates than other comparable samples.

Design  A total of 469 smokers hospitalized after MI or CAB surgery and wanting to stop smoking were seen in the hospital and completed 1‐year follow‐ups. Ratings of helpfulness of smoking in managing stress at baseline, smoking status (validated by salivary cotinine concentration) and ratings of perceived stress at baseline and at 1‐year follow‐up were collected.

Findings  Of the patients, 41% (n = 194) maintained abstinence for 1 year. Future abstainers and future smokers did not differ in baseline stress levels or in their perception of coping properties of smoking. However, abstainers recorded a significantly larger decrease in perceived stress than continuing smokers, and the result held when possible confounding factors were controlled for (P < 0.001).

Conclusions  In highly dependent smokers who report that smoking helps them cope with stress, smoking cessation is associated with lowering of stress. Whatever immediate effects smoking may have on perceived stress, overall it may generate or aggravate negative emotional states. The results provide reassurance to smokers worried that stopping smoking may deprive them of a valuable coping resource.
Anti‐drink driving reform in Britain, c. 1920–80
Authors: Luckin Bill
Published: June 2010

Aim  The goal of this report is to provide a framework for understanding and interpreting political, scientific and cultural attitudes towards drink driving in 20th‐century Britain. Exploring the inherent conservatism of successive governments, Members of Parliament (MPs) and the public towards the issue during the interwar years, the contribution seeks to explain the shift from legislative paralysis to the introduction of the breathalyser in 1967.

Design  Based on governmental, parliamentary and administrative records, the report follows a mainly narrative route. It places particular emphasis on connections between post‐war extra‐parliamentary and parliamentary movements for reform.

Setting  The paper follows a linear path from the 1920s to the 1970s. Britain lies at the heart of the story but comparisons are made with nations—particularly the Scandinavian states—which took radical steps to prosecute drinking and dangerous drivers at an early date.

Findings  The report underlines the vital post‐war role played by Graham Page, leading parliamentary spokesman for the Pedestrians' Association; the centrality of the Drew Report (1959) into an ‘activity resembling driving’; the pioneering Conservative efforts of Ernest Marples; and Barbara Castle's consolidating rather than radically innovative activities between 1964 and 1967.

Conclusion  Both before and after the Second World War politicians from both major parties gave ground repeatedly to major motoring organizations. With the ever‐escalating growth of mass motorization in the 1950s, both Conservative and Labour governments agonized over gridlock and ‘murder on the roads’. Barbara Castle finally took decisive action against drink drivers, but the ground had been prepared by Graham Page and Ernest Marples.
Cellular and transcriptional responses of wheat during compatible and incompatible race‐specific interactions with Puccinia striiformis f. sp. tritici
Authors: BOZKURT TOLGA O. , MCGRANN GRAHAM R.D. , MACCORMACK RUTH , BOYD LESLEY A. , AKKAYA MAHINUR S.
Published: June 2010

The initial stages of Puccinia striiformis f. sp. tritici (the causal agent of yellow rust in wheat) infection triggered a hypersensitive cell death (HCD) response in both compatible and Yr1‐mediated incompatible interactions, although the response was earlier and more extensive in the incompatible interaction. Later stages of fungal development were only associated with an HCD response in the incompatible interaction, the HCD response being effectively suppressed in the compatible interaction. Cell autofluorescence was seen in mesophyll cells in direct contact with fungal infection hyphae (primary HCD) and in adjacent mesophyll cells (secondary HCD), indicating the activation of cell‐to‐cell signalling. Microarray analysis identified a number of defence‐related transcripts implicated in Yr1‐mediated resistance, including classical pathogenesis‐related (PR) transcripts and genes involved in plant cell defence responses, such as the oxidative burst and cell wall fortification. A quantitative reverse transcriptase‐polymerase chain reaction time course analysis identified a number of defence‐related genes, including PR2, PR4, PR9, PR10 and WIR1 transcripts, associated with the latter stages of Yr1‐mediated resistance. A meta‐analysis comparison of the Yr1‐regulated transcriptome with the resistance transcriptomes of the race‐specific resistance gene Yr5 and the race‐nonspecific adult plant resistance gene Yr39 indicated limited transcript commonality. Common transcripts were largely confined to classic PR and defence‐related genes.
Evaluation of the McGrath® Series 5 videolaryngoscope after failed direct laryngoscopy*
Authors: Noppens R. R. , Möbus S. , Heid F. , Schmidtmann I. , Werner C. , Piepho T.
Published: June 2010

Unanticipated difficulties during tracheal intubation and failure to intubate are among the leading causes of anaesthesia‐related morbidity and mortality. Using the technique of video laryngoscopy, the alignment of the oral and pharyngeal axes to facilitate tracheal intubation is unnecessary. In this study we evaluated the McGrath® Series 5 videolaryngoscope for tracheal intubation in 61 patients who exhibited Cormack and Lehane grade 3 or 4 laryngoscopies with a Macintosh laryngoscope. Using the McGrath resulted in an improved glottic view, compared to Macintosh laryngoscope. Laryngoscopy was improved by one grade in 10%, by two grades in 80% and by three grades in 10% of cases (p < 0.0001). The success rate for intubation was 95% with the McGrath. These results suggest that the McGrath videolaryngoscope can be used with a high success rate to facilitate tracheal intubation in difficult intubation situations.
The addition of cyclophosphamide to lenalidomide and dexamethasone in multiply relapsed/refractory myeloma patients; a phase I/II study
Authors: Schey Stephen A. , Morgan Gareth J. , Ramasamy Karthik , Hazel Beth , Ladon Dariusz , Corderoy Sophie , Jenner Matthew , Phekoo Karen , Boyd Kevin , Davies Faith E.
Published: June 2010

We report the results of a Phase I/II dose escalation study to determine the maximum tolerated dose (MTD) of cyclophosphamide when combined with lenalidomide and dexamethasone in relapsed/refractory myeloma. Thirty‐one patients were enrolled in cohorts of 3, at five dose levels of cyclophosphamide to a maximum of 700 mg on days 1 and 8 of a 28‐d cycle. Patients received lenalidomide 25 mg days 1–21 and dexamethasone 20 mg orally days 1–4 and 8–11. The MTD was 600 mg cyclophosphamide, days 1 and 8. Grade 3/4 haematological complications occurred in 26% of patients, grade 3/4 infection in 3% (both at 700 mg cyclophosphamide), with thromboembolic complications in 6% of patients. Overall complete response (CR) rate was 29%, very good partial response rate 7% and partial response rate 45% giving an overall response rate of 81%. After 21 months median follow‐up, projected 2‐year progression‐free survival was 56%, with 80% overall survival at 30 months. Ten further patients were treated at MTD with a 40% CR rate. No dose reductions for any study drugs or deaths occurred during cycles 1–9. Lenalidomide, cyclophosphamide and dexamethasone is a safe, effective combination in relapsed myeloma inducing a high response rate, warranting further investigation in phase III trials.
Cytotoxicity of the anti‐CD22 immunotoxin HA22 (CAT‐8015) against paediatric acute lymphoblastic leukaemia
Authors: Mussai Francis , Campana Dario , Bhojwani Deepa , Stetler‐Stevenson Maryalice , Steinberg Seth M. , Wayne Alan S. , Pastan Ira
Published: June 2010

Acute lymphoblastic leukaemia (ALL) remains the most frequent cause of cancer‐related mortality in paediatrics and outcome is poor for patients who have high‐risk ALL or relapse. HA22 (CAT‐8015) is an immunotoxin composed of an anti‐CD22 variable fragment linked to a 38 kDa truncated protein derived from Pseudomonas exotoxin A. Using a bone marrow mesenchymal cell culture assay to support ALL cell viability, we investigated the in vitro cytotoxicity of HA22 against ALL blasts from newly diagnosed (n = 13) and relapsed patients (n = 22). There was interpatient variability in sensitivity to HA22. Twenty‐four of 35 patient samples tested were sensitive (median 50% lethal concentration 3 ng/ml, range 1–80 ng/ml). Blasts from the other 11 patients were not killed by 500 ng/ml HA22. The median 50% lethal concentration was 20 ng/ml for all patients. There was no significant difference in HA22 sensitivity between diagnosis and relapse samples but peripheral blood ALL blasts were more sensitive to HA22 than those from bone marrow (P = 0·008). Thus, HA22, at concentrations achievable in patients, is highly cytotoxic to B‐lineage ALL cells. These results provide a strong rationale for clinical testing of this agent in children with drug‐resistant ALL and offers the potential to reduce morbidities of treatment while improving outcome.