bluuebunny/crossref_metadata_2025 huggingface dataset:
Gaze and Arrow Distractors Influence Saccade Trajectories Similarly
Authors: Hermens Frouke , Walker Robin
Published: May 2010

Perceiving someone's averted eye-gaze is thought to result in an automatic shift of attention and in the preparation of an oculomotor response in the direction of perceived gaze. Although gaze cues have been regarded as being special in this respect, recent studies have found evidence for automatic attention shifts with nonsocial stimuli, such as arrow cues. Here, we directly compared the effects of social and nonsocial cues on eye movement preparation by examining the modulation of saccade trajectories made in the presence of eye-gaze, arrows, or peripheral distractors. At a short stimulus onset asynchrony (SOA) between the distractor and the target, saccades deviated towards the direction of centrally presented arrow distractors, but away from the peripheral distractors. No significant trajectory deviations were found for gaze distractors. At the longer SOA, saccades deviated away from the direction of the distractor for all three distractor types, but deviations were smaller for the centrally presented gaze and arrow distractors. These effects were independent of whether line-drawings or photos of faces were used and could not be explained by differences in the spatial properties of the peripheral distractor. The results suggest that all three types of distractors (gaze, arrow, peripheral) can induce the automatic programming of an eye movement. Moreover, the findings suggest that gaze and arrow distractors affect oculomotor preparation similarly, whereas peripheral distractors, which are classically regarded as eliciting an automatic shift of attention and an oculomotor response, induce a stronger and faster acting influence on response preparation and the corresponding inhibition of that response.
SUNYAEV–ZEL’DOVICH CLUSTER PROFILES MEASURED WITH THE SOUTH POLE TELESCOPE
Authors: Plagge T. , Benson B. A. , Ade P. A. R. , Aird K. A. , Bleem L. E. , Carlstrom J. E. , Chang C. L. , Cho H.-M. , Crawford T. M. , Crites A. T. , de Haan T. , Dobbs M. A. , George E. M. , Hall N. R. , Halverson N. W. , Holder G. P. , Holzapfel W. L. , Hrubes J. D. , Joy M. , Keisler R. , Knox L. , Lee A. T. , Leitch E. M. , Lueker M. , Marrone D. , McMahon J. J. , Mehl J. , Meyer S. S. , Mohr J. J. , Montroy T. E. , Padin S. , Pryke C. , Reichardt C. L. , Ruhl J. E. , Schaffer K. K. , Shaw L. , Shirokoff E. , Spieler H. G. , Stalder B. , Staniszewski Z. , Stark A. A. , Vanderlinde K. , Vieira J. D. , Williamson R. , Zahn O.
Published: May 2010

We present Sunyaev–Zel'dovich (SZ) measurements of 15 massive X-ray-selected galaxy clusters obtained with the South Pole Telescope (SPT). The SZ cluster signals are measured at 150 GHz, and concurrent 220 GHz data are used to reduce astrophysical contamination. Radial profiles are computed using a technique that takes into account the effects of the beams and filtering. In several clusters, significant SZ decrements are detected out to a substantial fraction of the virial radius. The profiles are fit to the β-model and to a generalized Navarro–Frenk–White (NFW) pressure profile, and are scaled and stacked to probe their average behavior. We find model parameters that are consistent with previous studies: β = 0.86 and r
core/r
500 = 0.20 for the β-model, and (αn, βn, γn, c
500) = (1.0, 5.5, 0.5, 1.0) for the generalized NFW model. Both models fit the SPT data comparably well, and both are consistent with the average SZ profile out to beyond r
500. The integrated Compton-y parameter Y
SZ is computed for each cluster using both model-dependent and model-independent techniques, and the results are compared to X-ray estimates of cluster parameters. We find that Y
SZ scales with YX
and gas mass with low scatter. Since these observables have been found to scale with total mass, our results point to a tight mass–observable relation for the SPT cluster survey.
Fast integration of heterogeneous data sources for predicting gene function with limited annotation
Authors: Mostafavi Sara , Morris Quaid
Published: May 2010

Motivation: Many algorithms that integrate multiple functional association networks for predicting gene function construct a composite network as a weighted sum of the individual networks and then use the composite network to predict gene function. The weight assigned to an individual network represents the usefulness of that network in predicting a given gene function. However, because many categories of gene function have a small number of annotations, the process of assigning these network weights is prone to overfitting.

Results: Here, we address this problem by proposing a novel approach to combining multiple functional association networks. In particular, we present a method where network weights are simultaneously optimized on sets of related function categories. The method is simpler and faster than existing approaches. Further, we show that it produces composite networks with improved function prediction accuracy using five example species (yeast, mouse, fly, Esherichia coli and human).

Availability: Networks and code are available from: http://morrislab.med.utoronto.ca/˜sara/SW

Contact:  smostafavi@cs.toronto.edu; quaid.morris@utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evoker: a visualization tool for genotype intensity data
Authors: Morris James A. , Randall Joshua C. , Maller Julian B. , Barrett Jeffrey C.
Published: May 2010

Summary: Genome-wide association studies (GWAS), which produce huge volumes of data, are now being carried out by many groups around the world, creating a need for user-friendly tools for data quality control (QC) and analysis. One critical aspect of GWAS QC is evaluating genotype cluster plots to verify sensible genotype calling in putatively associated single nucleotide polymorphisms (SNPs). Evoker is a tool for visualizing genotype cluster plots, and provides a solution to the computational and storage problems related to working with such large datasets.

Availability:  http://www.sanger.ac.uk/resources/software/evoker/

Contact:  barrett@sanger.ac.uk
Serotype-specific invasive disease potential of Streptococcus pneumoniae in Czech children
Authors: Zemlickova Helena , Jakubu Vladislav , Urbaskova Pavla , Motlova Jitka , Musilek Martin , Adamkova Vaclava
Published: May 2010

To estimate the invasive disease potential of Streptococcus pneumoniae serotypes, invasive isolates (n=138) were compared with nasopharyngeal isolates (n=153) from children under 6 years of age in the Czech Republic. Odds ratios (ORs) based on a comparison of the distribution of S. pneumoniae serotypes amongst invasive and carriage isolates were calculated for individual serotypes and 172 strains were characterized using multilocus sequence typing. The ORs of serotypes 9V and 14 were significantly greater than 1, suggesting an association with invasive disease, while serotypes 6A and 23F were significantly associated with carriage (ORs less than 1). A single predominant clone with high invasive disease potential was found in each of the 9V, 7F, 14 and 1 serotypes while carriage-associated serotypes were highly heterogeneous.
Antibody responses to pertussis toxin display different kinetics after clinical Bordetella pertussis infection than after vaccination with an acellular pertussis vaccine
Authors: Dalby Tine , Petersen Jesper Westphal , Harboe Zitta B. , Krogfelt Karen Angeliki
Published: May 2010

The measurement of IgG anti-pertussis toxin (IgG anti-PT) antibodies by ELISA is a frequently used method for studying the antibody responses after pertussis vaccination and after Bordetella pertussis infection. Such responses vary according to the different vaccines used as well as to the immunization and infection history of the participants. In the present study, the decay kinetics of the IgG anti-PT antibody response was determined for 71 Danish children and adults with bacteriologically confirmed B. pertussis infection and for 20 Danish adults booster-vaccinated with an acellular pertussis vaccine. For both groups, biphasic decay was seen, but the individual antibody responses varied greatly. No differences related to age were seen. Within each group, individual decay profiles showed parallel log-linear decay for the late part of the response. Antibody half-life was calculated for the late, slower part of the biphasic response curves for both groups (>5 months after diagnosis for individuals with confirmed infection; >3 months for vaccinated individuals). The median half-life for post-infection antibodies was 221 days [interquartile range (IQR) 159–314 days, 36 individuals], and the median half-life for post-vaccination antibodies was 508 days (IQR 428–616 days, 14 individuals). This difference was statistically significant (P<0.0001). Thus, in this setting, we found that the IgG anti-PT antibody decay after an infection with B. pertussis is more than twice as fast as the decay after booster vaccination with an acellular pertussis vaccine. Such knowledge of the IgG anti-PT decay kinetics is crucial for interpretation of serological data that will be used either for diagnosis or for epidemiological studies and surveillance of B. pertussis infections.
Mutagenesis of the Rns regulator of enterotoxigenic Escherichia coli reveals roles for a linker sequence and two helix–turn–helix motifs
Authors: Mahon Vivienne , Smyth Cyril J. , Smith Stephen G. J.
Published: May 2010

The pathogenesis of diarrhoeal disease due to human enterotoxigenic Escherichia coli absolutely requires the expression of fimbriae. The expression of CS1 fimbriae is positively regulated by the AraC-like protein Rns. AraC-like proteins are DNA-binding proteins that typically contain two helix–turn–helix (HTH) motifs. A program of pentapeptide insertion mutagenesis of the Rns protein was performed, and this revealed that both HTH motifs are required by Rns to positively regulate CS1 fimbrial gene expression. Intriguingly, a pentapeptide insertion after amino acid C102 reduced the ability of Rns to transactivate CS1 fimbrial expression. The structure of Rns in this vicinity (NACRS) was predicted to be disordered and thus might act as a flexible linker. This hypothesis was confirmed by deletion of this amino acid sequence from the Rns protein; a truncated protein that lacked this sequence was no longer functional. Strikingly, this sequence could be functionally substituted in vivo and in vitro by a flexible seven amino acid sequence from another E. coli AraC-like protein RhaS. Our data indicate that HTH motifs and a flexible sequence are required by Rns for maximal activation of fimbrial gene expression.
Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
Authors: Cutter Asher D. , Choi Jae Young
Published: May 2010

The combined actions of natural selection, mutation, and recombination forge the landscape of genetic variation across genomes. One frequently observed manifestation of these processes is a positive association between neutral genetic variation and local recombination rates. Two selective mechanisms and/or recombination-associated mutation (RAM) could generate this pattern, and the relative importance of these alternative possibilities remains unresolved generally. Here we quantify nucleotide differences within populations, between populations, and between species to test for genome-wide effects of selection and RAM in the partially selfing nematode Caenorhabditis briggsae. We find that nearly half of genome-wide variation in nucleotide polymorphism is explained by differences in local recombination rates. By quantifying divergence between several reproductively isolated lineages, we demonstrate that ancestral polymorphism generates a spurious signal of RAM for closely related lineages, with implications for analyses of humans and primates; RAM is, at most, a minor factor in C. briggsae. We conclude that the positive relation between nucleotide polymorphism and the rate of crossover represents the footprint of natural selection across the C. briggsae genome and demonstrate that background selection against deleterious mutations is sufficient to explain this pattern. Hill-Robertson interference also leaves a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g., Drosophila) versus pervasive background selection effects on the genomes of organisms with self-fertilizing lifestyles and/or small population sizes (e.g., Caenorhabditis elegans, C. briggsae, Arabidopsis thaliana, Lycopersicon, human). These results illustrate how recombination, mutation, selection, and population history interact in important ways to shape molecular heterogeneity within and between genomes.
Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome
Authors: DeKelver Russell C. , Choi Vivian M. , Moehle Erica A. , Paschon David E. , Hockemeyer Dirk , Meijsing Sebastiaan H. , Sancak Yasemin , Cui Xiaoxia , Steine Eveline J. , Miller Jeffrey C. , Tam Phillip , Bartsevich Victor V. , Meng Xiangdong , Rupniewski Igor , Gopalan Sunita M. , Sun Helena C. , Pitz Kathleen J. , Rock Jeremy M. , Zhang Lei , Davis Gregory D. , Rebar Edward J. , Cheeseman Iain M. , Yamamoto Keith R. , Sabatini David M. , Jaenisch Rudolf , Gregory Philip D. , Urnov Fyodor D.
Published: May 2010

Isogenic settings are routine in model organisms, yet remain elusive for genetic experiments on human cells. We describe the use of designed zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into thePPP1R12Cgene, a “safe harbor” locus known asAAVS1. ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including fibroblasts and hES cells. When added to this locus, transgenes such as expression cassettes for shRNAs, small-molecule-responsive cDNA expression cassettes, and reporter constructs, exhibit consistent expression and sustained function over 50 cell generations. By avoiding random integration and drug selection, this method allows bona fide isogenic settings for high-throughput functional genomics, proteomics, and regulatory DNA analysis in essentially any transformed human cell type and in primary cells.
Engagement of the PFC in consolidation and recall of recent spatial memory
Authors: Leon Wanda C. , Bruno Martin A. , Allard Simon , Nader Karim , Cuello A. Claudio
Published: May 2010

The standard model of system consolidation proposes that memories are initially hippocampus dependent and become hippocampus independent over time. Previous studies have demonstrated the involvement of the medial prefrontal cortex (mPFC) in the retrieval of remote memories. The transformations required to make a memory undergo system's consolidation are thought to require synaptic plasticity. In this study, we investigated the participation of the mitogen-activated protein kinase (MAPK)/ERK pathway in acquisition, memory consolidation, and recent memory recall of the Morris water maze (MWM) task using a 1-d training protocol. To this end, bilateral injections of the MEK inhibitor U0126 into the rat mPFC were performed. The injection of the MEK inhibitor in the mPFC did not affect the acquisition of the MWM. However, MEK inhibitor resulted in impairments on recent memory retrieval either when applied at the end of the learning phase (memory consolidation) or prior to the retention test. The results strongly support the concept that recently acquired and consolidated spatial memories require the mPFC, and that local activation of the MAPK/ERK pathway in the mPFC is necessary for the consolidation and recall of recent memories.
Super-Resolution Imaging of Plasmodesmata Using Three-Dimensional Structured Illumination Microscopy
Authors: Fitzgibbon Jessica , Bell Karen , King Emma , Oparka Karl
Published: May 2010

We used three-dimensional structured illumination microscopy (3D-SIM) to obtain subdiffraction (“super-resolution”) images of plasmodesmata (PD) expressing a green fluorescent protein-tagged viral movement protein (MP) in tobacco (Nicotiana tabacum). In leaf parenchyma cells, we were able to resolve individual components of PD (neck and central cavities) at twice the resolution of a confocal microscope. Within the phloem, MP-green fluorescent protein filaments extended outward from the specialized pore-PD that connect sieve elements (SEs) with their companion cells (CCs) along the tubular sieve element reticulum (SER). The SER was shown to interconnect individual pore-PD at the SE-CC interface. 3D-SIM resolved fine (less than 100 nm) endoplasmic reticulum threads running into individual pore-PD as well as strands that crossed sieve plate pores, structurally linking SEs within a file. Our data reveal that MP entering the SE from the CC may remain associated with the SER. Fluorescence recovery after photobleaching experiments revealed that this MP pool is relatively immobile compared with the membrane probe 3,3’-dihexyloxacarbocyanine iodide, suggesting that MP may become sequestered by the SER once it has entered the SE. The advent of 3D-SIM offers considerable potential in the subdiffraction imaging of plant cells, bridging an important gap between confocal and electron microscopy.
Assessing association of common variation in the C1Q gene cluster with systemic lupus erythematosus
Authors: Rafiq S , Frayling T M , Vyse T J , Cunninghame Graham D S , Eggleton P
Published: May 2010

Recent studies have tested genetic variation at the C1QA, C1QB and C1QC (complement component 1, q subcomponent, A chain, complement component 1, q subcomponent, B chain and complement component 1, q subcomponent, c chain) loci in relation to systemic lupus erythematosus (SLE) risk. Evidence for a significant effect of C1Q locus gene polymorphisms on SLE predisposition remains unclear. We aimed to identify associations between common C1Q polymorphisms and SLE risk and serum C1q, C3 and C4 levels. We performed family-based association tests in 295 nuclear families with one affected proband. Tag-single nucleotide polymorphisms (SNPs) ranging from 35·4 kb upstream of the C1QA gene to 28 kb downstream of the C1QB gene were selected to represent the entire C1Q gene locus. We performed transmission disequilibrium tests for affectation status and continuous traits, including C1q, C3 and C4 levels using family-based association tests (FBAT). There was no evidence for a significant role of C1Q locus gene polymorphisms in SLE risk predisposition. The strongest association was observed with a variant in the 3′UTR region of the C1QB gene (rs294223, P = 0·06). We found nominally significant associations with a second variant (rs7549888) in the 3′UTR region of the C1QB gene and C1q (P = 0·01), C3 (P = 0·004) and C4 levels (P = 0·01). In a large family-based association study of C1Q gene cluster polymorphisms no evidence for a genetic role of C1Q locus SNP in SLE risk predisposition was obtained in patients of European ancestry. This is in contrast to other cohorts, in which single variants associated with C1Q, C3 and C4 levels and nephritis have been studied and shown associations.
Turbidite system architecture and sedimentary processes along topographically complex slopes: the Makran convergent margin
Authors: BOURGET JULIEN , ZARAGOSI SEBASTIEN , ELLOUZ‐ZIMMERMANN NADINE , MOUCHOT NICOLAS , GARLAN THIERRY , SCHNEIDER JEAN‐LUC , LANFUMEY VALENTINE , LALLEMANT SIGFRIED
Published: May 2010

This study investigates the morphology and Late Quaternary sediment distribution of the Makran turbidite system (Makran subduction zone, north‐west Indian Ocean) from a nearly complete subsurface mapping of the Oman basin, two‐dimensional seismic and a large set of coring data in order to characterize turbidite system architecture across an active (fold and thrust belt) margin. The Makran turbidite system is composed of a dense network of canyons, which cut into high relief accreted ridges and intra‐slope piggyback basins, forming at some locations connected and variably tortuous paths down complex slopes. Turbidite activity and trench filling rates are high even during the Holocene sea‐level highstand conditions. In particular, basin‐wide, sheet‐like thick mud turbidites, probably related to major mass wasting events of low recurrence time, drape the flat and unchannellized Oman abyssal plain. Longitudinal depth profiles show that the Makran canyons are highly disrupted by numerous thrust‐related large‐scale knickpoints (with gradients up to 20° and walls up to 500 m high). At the deformation front, the strong break of slope can lead to the formation of canyon‐mouth ‘plunge pools’ of variable shapes and sizes. The plunge pools observed in the western Makran are considerably larger than those previously described in sub‐surface successions; the first insights into their internal architecture and sedimentary processes are presented here. Large plunge pools in the western Makran are associated with large scoured areas at the slope break and enhanced sediment deposition downstream: high‐amplitude reflectors are observed inside the plunge pools, while their flanks are composed of thin‐bedded, fine‐grained turbidites deposited by the uppermost part of the turbidity flows. Thus, these architectural elements are associated with strong sediment segregation leading to specific trench‐fill mechanisms, as only the finer‐grained component of the flows is transferred to the abyssal plain. However, the Makran accretionary prism is characterized by strong along‐strike variability in tectonics and fluvial input distribution that might directly influence the turbidite system architecture (i.e. canyon entrenchment, plunge pool formation or channel development at canyon mouths), the sedimentary dynamics and the resulting sediment distribution. Channel formation in the abyssal plain and trench‐fill characteristics depend on the theoretical ‘equilibrium’ conditions of the feeder system, which is related closely to the balance between erosion rates and tectonic regime. Thus, the Makran turbidite system constitutes an excellent modern analogue for deep‐water sedimentary systems with structurally complex depocentres, in convergent margin settings.
Efficacy of a surgical scrub including 2% chlorhexidine acetate for canine superficial pyoderma
Authors: Murayama Nobuo , Nagata Masahiko , Terada Yuri , Shibata Sanae , Fukata Tsuneo
Published: May 2010

The clinical efficacy of a surgical scrub containing 2% chlorhexidine acetate (2CA; Nolvasan® Surgical Scrub; Fort Dodge Animal Health, USA) was evaluated for the topical management of canine superficial pyoderma. The first study was a randomized, double‐blind, controlled trial. The control was a shampoo containing 4% chlorhexidine gluconate (4CG; Skin Clinic Shampoo; CHD MEDICS, Goyang, Korea). Ten dogs with symmetrical lesions of canine superficial pyoderma were allocated to receive either 2CA or the control shampoo applied to either side of the body twice weekly for 1 week. Both the owners and the investigators subjectively scored skin lesions including pruritus, erythema, crusted papules and scales on a scale of 0–3. The 2CA and 4CG resulted in almost the same degree of improvement of skin lesions, and there were no significant differences between the two groups. The second study was an open trial of 2CA monotherapy in eight dogs with cefalexin‐resistant Staphylococcus intermedius group‐associated superficial pyoderma. The 2CA monotherapy was applied every 2 days for 2 weeks. Five dogs improved with 2CA monotherapy, one partially improved and two did not. No adverse reactions were seen in either trial. This suggests that a 2CA surgical scrub could be a useful and safe topical adjunct therapy for dogs with superficial pyoderma involving cefalexin‐resistant Staphylococcus intermedius group.
Short‐term dynamics in fish assemblage structure on a sheltered sandy beach in Guanabara Bay, Southeastern Brazil
Authors: Vasconcellos Ruan Managna , Araújo Francisco Gerson , De Sousa Santos Joaquim Neto , De Araújo Silva Márcio
Published: May 2010

Short‐term dynamics in juvenile fish assemblage structure were studied to test whether the most abundant species show temporal segregation, in order to assess whether selected environmental variables could predict species groupings, and to examine the stability of sunset–day–sunrise–night differences. Samplings were collected at 3‐h intervals over 48 h on a seasonal basis between spring 2005 and winter 2006. Fish species richness and abundance were higher in spring, and the lowest values occurred in winter. Harengula clupeola occurred mainly in spring, whereas Atherinella brasiliensis peaked in summer and autumn. On the other hand, Trachinotus carolinus, Umbrina coroides and Mugil liza were abundant in winter. Although temperature, salinity and dissolved oxygen were not found to have a strong effect on the abundance patterns of most species, they did appear to have a significant influence on assemblage groupings, according to canonical correspondence analysis and Spearman rank correlation. There is no consistency of diel usage patterns by a given species across seasons. The relative abundance differed between the time of day, which differed among the seasons; this further complicates an understanding of the dynamics of an assemblage. Studies of diel changes that pooled the sampling period as day or night can miss important changes that occur in a short time scale, such as a 3‐h period.
Interstitial Foxp3‐positive T cells may predict renal survival in patients with myeroperoxidase anti‐neutrophil cytoplasmic antibody‐associated glomerulonephritis
Authors: Yoshimura Junko , Fukami Kei , Koike Kiyomi , Nagano Makio , Matsumoto Takafumi , Iwatani Ryuji , Kusumoto Takuo , Hazama Takuma , Ueda Seiji , Adachi Hisashi , Hirai Yuji , Takasu Konomi , Ohshima Koichi , Yamagishi Sho‐ichi , Okuda Seiya
Published: May 2010

1. Regulatory T cells (Treg) and cytotoxic T cells (CTL) are involved in various immune diseases. However, the prognostic impact of Treg and CTL in patients with myeroperoxidase anti‐neutrophil cytoplasmic antibody‐associated glomerulonephritis (MPO‐ANCA‐GN) is not well known. Therefore, in the present study, we examined the relationship between expression of forkhead box P3 (Foxp3) and T cell intracytoplasmic antigen (TIA)‐1, Treg and CTL markers and renal survival in patients with MPO‐ANCA‐GN.

2. Forty patients with MPO‐ANCA‐GN and 10 patients with minimal change nephrotic syndrome (MCNS) underwent physical examination, determination of blood chemistry and renal biopsy. Immunohistochemical staining for Foxp3 and TIA‐1 was performed on paraffin‐embedded renal sections.

3. Although almost all patients received standard immunosuppressive treatment for 6 months, seven MPO‐ANCA‐GN patients needed maintenance haemodialysis (HD), whereas 33 patients did not (non‐HD). Both Foxp3‐ and TIA‐1‐positive cells were detected in the interstitium and glomeruli of MPO‐ANCA‐GN patients, whereas they were rarely detected in patients with MCNS. The total crescent rate was significantly higher in the HD group than in the non‐HD group (35.9 ± 3.5 vs 65.8 ± 7.4, respectively). In the interstitium, the age‐adjusted Foxp3/TIA‐1 ratio was significantly higher in the non‐HD group than in the HD group (0.016 ± 0.016 vs 0.004 ± 0.008, respectively; P < 0.05). The Foxp3/TIA‐1 ratio, but not the Foxp3/CD3 ratio, remained significantly higher in the non‐HD group than in the HD group even after adjustment for crescent rate. Age‐ and total crescent rate‐adjusted renal survival rates were higher in patients with a Foxp3/TIA‐1 ratio ≥ 0.06 than in patients with a Foxp3/TIA‐1 ratio < 0.06 (P = 0.02).

4. The results of the present study suggest that Treg could play a protective role against MPO‐ANCA‐GN and that a decreased Foxp3/TIA‐1 ratio in interstitial areas may predict future renal failure in patients with MPO‐ANCA‐GN.
Role of the medial amygdala in mediating responses to aversive stimuli leading to hypertension
Authors: Davern Pamela J , Head Geoffrey A
Published: May 2010

1. The amygdala is a part of the limbic system that is associated with mediating the emotional and hormonal response to stress and although studies have focused on the central amygdala, there is increasing evidence that the medial amygdala is a major region activated by stressful stimuli.

2. Neuroanatomical studies in rats have shown greater activation in the medial amygdala following aversive stresses compared with other brain regions, including the central amygdala. Inhibition of the medial, but not the central, amygdala attenuates the development of hypertension in spontaneously hypertensive rats.

3. Schlager (BPH/2J) mice have a neurogenic form of hypertension that is most evident during the night when the mice are most active and is closely correlated with the level of activation of neurons in the medial, but not the central, amygdala. Pressor responses to aversive stimuli, such as restraint and cage‐switch stress, are much greater in BPH/2J hypertensive than BPN/3J normotensive mice, but appetitive arousal produces normal increases in blood pressure. The degree of activation in the medial amygdala in BPH/2J hypertensive mice during aversive stress closely correlates with the increased blood pressure.

4. Thus, the inappropriate activation of the medial amygdala evoked by specific fear or aversive stimuli may be key to the neurogenic hypertension.
Partial nephrectomy for selected renal cortical tumours of ≥7 cm
Authors: Karellas Michael E. , O’Brien M. Frank , Jang Thomas L. , Bernstein Melanie , Russo Paul
Published: May 2010

Study Type – Therapy (case series) Level of Evidence 4

OBJECTIVE

To examine our institutional experience in patients treated with partial nephrectomy (PN) for renal cortical tumours (RCTs) of ≥7 cm, as PN is an accepted surgical approach for appropriate RCTs of <7 cm but there are limited data on the use of PN for larger tumours.

PATIENTS AND METHODS

After Institutional Review Board approval, we examined our prospectively collected surgical database for patients treated with PN for RCTs of ≥7 cm between 1989 and 2008. Pertinent demographic, clinical, surgical and pathological data were reviewed.

RESULTS

In all, 34 patients (37 renal units) were identified for analysis with a median (interquartile range, IQR) age of 63 (52–71) years, median (IQR) tumour size of 7.5 (7.2–9.0) cm with the largest tumour being 19 cm. In 31 renal units (28 patients, 84%) carcinoma was evident, with 16 renal units (43%) having conventional clear cell carcinoma, followed by papillary in eight renal units (21%). Currently, 20 of these 28 patients (71%) are disease free, three are alive with metastatic disease (two had known preoperative metastatic disease), three died from disease and two died from other causes. The median (IQR) preoperative estimated glomerular filtration rate was 65 (55–73) mL/min/1.73 m2, compared with 55 (47–74) mL/min/1.73 m2 after PN (P= 0.003, paired Student’s t‐test).

CONCLUSIONS

Our findings suggest that PN for RCTs of ≥7 cm can be safely performed and provide effective tumour control for selected patients. PN should be considered for patients with appropriate tumours, solitary kidneys or pre‐existing renal insufficiency.
Changing antibiotic prophylaxis for transrectal ultrasound‐guided prostate biopsies: are we putting our patients at risk?
Authors: Hori Satoshi , Sengupta Anup , Joannides Alexis , Balogun‐Ojuri Ben , Tilley Rebecca , McLoughlin John
Published: May 2010

Study Type – Harm/Safety (case series) Level of Evidence 4

OBJECTIVE

To evaluate whether changing antibiotic prophylaxis from quinolone to penicillin antibiotics has affected infectious complication rates in those men undergoing transrectal ultrasound‐guided prostate biopsy (TRUSgpb).

PATIENTS AND METHODS

This interventional study was designed to determine whether changing antibiotic prophylaxis had any bearing on developing serious infectious complications after taking TRUSgpb. As a secondary aim, we also investigated Clostridium difficile (C. difficile) rates in the same groups of men undergoing TRUSgpb. Men historically received ciprofloxacin 500 mg orally 1 h before their procedure followed by a 3‐day course of 500 mg given twice daily (group A). Due to increasing local patterns of antimicrobial resistance to quinolones and concerns regarding potential antibiotic induced C. difficile infection, antibiotic prophylaxis was changed to a penicillin‐based regimen comprising of co‐amoxiclav 625 mg given orally 1 h before TRUSgpb followed by a three times daily course for 3 days (group B). Excluded from the study were those men given an alternative antibiotic prophylaxis than those given within the two distinct groups due to reasons of previous hypersensitivity reactions and/or clinical decision by the attending Urologist. Comparisons were made between the groups using two‐tailed Fisher’s exact tests.

RESULTS

In all, 119 and 110 men were identified in groups A and B, respectively. Two men in group A (1.68%) developed sepsis after TRUSgpb requiring hospital admission and intravenous antibiotic treatment. The sepsis rate in group B was significantly higher than that of group A (eight of 110, 7.27%; P= 0.036). Escherichia coli was the only organism isolated from our cohort of patients. There were no incidences of C. difficile infections in either antibiotic prophylaxis groups.

CONCLUSION

Ciprofloxacin appears to provide superior prophylaxis than co‐amoxiclav in men undergoing TRUSgpb and was not associated with an increased risk of quinolone induced C. difficile infections. Changing antibiotic prophylaxis from a quinolone‐based regime may therefore be putting our patients at an increased risk of serious infectious complications after TRUSgpb.
670. ANACAMPTIS MORIO
Authors: Fay Michael F. , Rankou Hassan
Published: May 2010

Anacamptis morio (L.) R. M. Bateman, Pridgeon & M. W. Chase, the green‐winged orchid, is described and illustrated. Its distribution is given, its pollination is recorded and suggestions for its cultivation are provided.
671. STRUMARIA BARBARAE
Authors: Duncan Graham
Published: May 2010

Strumaria barbarae Oberm. is a rarely collected winter‐growing geophyte endemic to arid southwestern Namibia and the northeastern Richtersveld in South Africa. Details of its history, taxonomy, life cycle, distribution and cultivation are given, together with an illustration and distribution map.
Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the rat nervous system reveals temporo‐spatial gradients
Authors: Löhmann Christian , Schachmann Elena , Dandekar Thomas , Villmann Carmen , Becker Cord‐Michael
Published: May 2010

J. Neurochem. (2010) 114, 1119–1134.

Phospholipids are important components of the nervous system, in particular of neuronal and glial membranes. Ontogenesis of the nervous system is associated with fundamental alterations in lipid patterns. Here, matrix‐assisted‐laser‐desorption/ionization time‐of‐flight mass spectrometry and electro‐spray‐ionization mass spectrometry were combined to analyze phosphatidylcholines and sphingomyelins, allowing an assessment of individual molecular species. Analysis in eight different regions of the nervous system during development of the Wistar rat, from embryonic day 14 to adulthood, produced informative patterns of developmental and regional changes in lipid contents. Phospholipids containing long chain fatty acyl residues exhibited a characteristic patterning, with dramatic increases in the caudal parts of the nervous system 2 weeks after birth. In contrast, relative contents of short chain phosphatidylcholines were low in the perinatal CNS, decreasing even further during development. The relative amounts of sphingomyelins carrying the fatty acid residues 18:0, 22:0, 24:0, and 24:1 increased developmentally in the caudal nervous system. The rostro‐caudal gradient of long chain lipid accumulation is matched by expression gradients of myelin structural and regulatory genes, as evident from bioinformatic analysis. These observations characterize the accumulation of individual lipid classes in the nervous system as a highly regulated process, with structurally related lipids showing a similar temporo‐spatial distribution and developmental patterning.
Reduced inflammatory and neuropathic pain and decreased spinal microglial response in fractalkine receptor (CX3CR1) knockout mice
Authors: Staniland Amelia A. , Clark Anna K. , Wodarski Rachel , Sasso Oscar , Maione Francesco , D’Acquisto Fulvio , Malcangio Marzia
Published: May 2010

J. Neurochem.(2010)114, 1143–1157.

The chemokine fractalkine (FKN) is a critical mediator of spinal neuronal‐microglial communication in chronic pain. Mature FKN is enzymatically cleaved from neuronal membranes and activation of its receptor, CX3CR1, which is expressed by microglia, induces phosphorylation of p38 MAPK. We used CX3CR1 knockout (KO) mice to examine pain behaviour in the absence of FKN signalling. Naive CX3CR1 KO mice had normal responses to acute noxious stimuli. However, KO mice showed deficits in inflammatory and neuropathic nociceptive responses. After intraplantar zymosan, KO mice did not display thermal hyperalgesia, whereas mechanical allodynia developed fully. In the partial sciatic nerve ligation model of neuropathic pain, both mechanical allodynia and thermal hyperalgesia were less severe in KO mice than in wild‐types (WT). Dorsal horn Iba1 immunostaining and phosphorylation of p38 MAPK increased after injury in WT controls but not in KO animals. In WT mice, inflammation and nerve injury increased spinal cord CX3CR1 and FKN expression. FKN protein was also increased in KO mice following inflammation but not after neuropathy, suggesting the FKN/CX3CR1 system is differently affected in the two pain models. Loss of FKN/CX3CR1 neuroimmune communication attenuates hyperalgesia and allodynia in a modality‐dependent fashion highlighting the complex nature of microglial response in pathological pain models.
Effects of super‐absorbent polymers on the physical and chemical properties of soil following different wetting and drying cycles
Authors: Bai W. , Zhang H. , Liu B. , Wu Y. , Song J.
Published: May 2010

Super‐absorbent polymers (SAPs), a group of new water‐saving materials and soil conditioners, have been widely adopted in agriculture, but little is known about their effects on soil physical and chemical properties under alternating dry and wet conditions. This study assesses soil moisture, bulk density, pH, electrical conductivity (EC) and available P and K after different wetting and drying cycles. Four types of SAPs, labelled BF, JP, BJ and WT, with organic macromolecules were mixed with sandy soils to give concentrations of 0%, 0.05%, 0.1%, 0.2% and 0.3%, with the aim of determining water retention and soil properties after amendment with the SAPs. Soil moisture increased by 6.2–32.8% with SAP application, while soil bulk density was reduced by 5.5–9.4% relative to the control, especially with a moderate water deficit when the relative soil moisture contents were about 40–50%. The largest increase in soil moisture and the greatest reduction in bulk density resulted from the WT treatment. The effects of SAPs on soil pH and EC were contrary. Soil available P increased slightly while available K significantly decreased, except following the first wetting and drying cycle. Available K increased with drying, but the opposite effect was observed for available P. Particular SAPs (JP and WT) seem more suitable under alternating dry and wet conditions. The effects on soil‐water retention and other soil properties varied according to the structure of the SAP and soil moisture.
Potassium channel activity and glutamate uptake are impaired in astrocytes of seizure‐susceptible DBA/2 mice
Authors: Inyushin Mikhail , Kucheryavykh Lilia Y. , Kucheryavykh Yuriy V. , Nichols Colin G. , Buono Russell J. , Ferraro Thomas N. , Skatchkov Serguei N. , Eaton Misty J.
Published: May 2010

Purpose:  KCNJ10 encodes subunits of inward rectifying potassium (Kir) channel Kir4.1 found predominantly in glial cells within the brain. Genetic inactivation of these channels in glia impairs extracellular K+ and glutamate clearance and produces a seizure phenotype. In both mice and humans, polymorphisms and mutations in the KCNJ10 gene have been associated with seizure susceptibility. The purpose of the present study was to determine whether there are differences in Kir channel activity and potassium‐ and glutamate‐buffering capabilities between astrocytes from seizure resistant C57BL/6 (B6) and seizure susceptible DBA/2 (D2) mice that are consistent with an altered K+ channel activity as a result of genetic polymorphism of KCNJ10.

Methods:  Using cultured astrocytes and hippocampal brain slices together with whole‐cell patch‐clamp, we determined the electrophysiologic properties, particularly K+ conductances, of B6 and D2 mouse astrocytes. Using a colorimetric assay, we determined glutamate clearance capacity by B6 and D2 astrocytes.

Results:  Barium‐sensitive Kir currents elicited from B6 astrocytes are substantially larger than those elicited from D2 astrocytes. In addition, potassium and glutamate buffering by D2 cortical astrocytes is impaired, relative to buffering by B6 astrocytes.

Discussion:  In summary, the activity of Kir4.1 channels differs between seizure‐susceptible D2 and seizure‐resistant B6 mice. Reduced activity of Kir4.1 channels in astrocytes of D2 mice is associated with deficits in potassium and glutamate buffering. These deficits may, in part, explain the relatively low seizure threshold of D2 mice.
Panayiotopoulos syndrome: A clinical, EEG, and neuropsychological study of 93 consecutive patients
Authors: Specchio Nicola , Trivisano Marina , Di Ciommo Vincenzo , Cappelletti Simona , Masciarelli Giovanni , Volkov Josiv , Fusco Lucia , Vigevano Federico
Published: May 2010

Purpose: To explore the clinical, electroencephalography (EEG), neuropsychological features, and prognosis of Panayiotopoulos syndrome (PS).

Methods: Of 1,794 children aged between 1 and 14 years referred for the first afebrile focal seizure, between January 1992 and December 2004, 93 (5.2%) had PS according to clinical criteria.

Results: Age at onset ranged from 1.1 to 8.6 years, and was earlier in children with more than one seizure. Autonomic seizures followed a stereotypical onset and progression. Emesis, pallor, or flushing was almost always among the first symptoms that usually culminated in vomiting (77.4% of patients). More than half (55%) of seizures were longer than 30 min but these did not appear to affect remission and number of seizures. Interictal EEG showed great variability, with 79.5% of patients showing spikes of variable localizations and evolution over time; 16.1% had background abnormalities only, and 5.4% had consistently normal EEG studies. Onsets in five ictal EEGs were posterior or anterior—left or right. On neuropsychological testing, IQ and subtests of Wechsler Intelligence Scale for Children–Revised (WISC‐R) were within normal limits, although some minor statistically significant differences were found in arithmetic, comprehension, and picture arrangement in comparison with controls. Cumulative probability of recurrence was 57.6%, 45.6%, 35.1%, and 11.7% at 6, 12, 24, and 36 months, respectively, after the first seizure. Thirty‐four (58.6%) of 59 patients treated with antiepileptic drugs continued having seizures before ultimate remission.

Discussion: PS is a uniform childhood susceptibility to autonomic seizures that is related to early age of development and with excellent prognosis with regard to seizure remission and neuropsychological development.
Sodium channelSCN1Aand epilepsy: Mutations and mechanisms
Authors: Escayg Andrew , Goldin Alan L.
Published: May 2010

Mutations in a number of genes encoding voltage‐gated sodium channels cause a variety of epilepsy syndromes in humans, including genetic (generalized) epilepsy with febrile seizures plus (GEFS+) and Dravet syndrome (DS, severe myoclonic epilepsy of infancy). Most of these mutations are in theSCN1Agene, and all are dominantly inherited. Most of the mutations that cause DS result in loss of function, whereas all of the known mutations that cause GEFS+ are missense, presumably altering channel activity. Family members with the same GEFS+ mutation often display a wide range of seizure types and severities, and at least part of this variability likely results from variation in other genes. Many different biophysical effects ofSCN1A‐GEFS+ mutations have been observed in heterologous expression systems, consistent with both gain and loss of channel activity. However, results from mouse models suggest that the primary effect of both GEFS+ and DS mutations is to decrease the activity of GABAergic inhibitory neurons. Decreased activity of the inhibitory circuitry is thus likely to be a major factor contributing to seizure generation in patients with GEFS+ and DS, and may be a general consequence ofSCN1Amutations.
Alcohol Expectancies and Drinking Refusal Self‐Efficacy Mediate the Association of Impulsivity With Alcohol Misuse
Authors: Gullo Matthew J. , Dawe Sharon , Kambouropoulos Nicolas , Staiger Petra K. , Jackson Chris J.
Published: May 2010

Background:  Recent work suggests that 2 biologically based traits convey risk for alcohol misuse: reward sensitivity/drive and (rash) impulsiveness. However, the cognitive mechanisms through which these traits convey risk are unclear. This study tested a model predicting that the risk conveyed by reward sensitivity is mediated by a learning bias for the reinforcing outcomes of alcohol consumption (i.e., positive alcohol expectancy). The model also proposed that the risk conveyed by rash impulsiveness (RI) is mediated by drinkers’ perceived ability to resist alcohol (i.e., drinking refusal self‐efficacy).

Methods:  Study 1 tested the model in a sample of young adults (n = 342). Study 2 tested the model in a sample of treatment‐seeking substance abusers (n = 121). All participants completed a battery of personality, cognitive, and alcohol use questionnaires and models were tested using structural equation modeling.

Results:  In both studies, the hypothesized model was found to provide a good fit to the data, and a better fit than alternative models. In both young adults and treatment‐seeking individuals, positive alcohol expectancy fully mediated the association between reward sensitivity and hazardous alcohol use. For treatment seekers, drinking refusal self‐efficacy fully mediated the association between RI and hazardous drinking. However, there was partial mediation in the young adult sample. Furthermore, neither trait was directly associated with the other cognitive mediator.

Conclusions:  The hypothesized model was confirmed on a large sample of young adults and replicated on a sample of treatment‐seeking substance abusers. Taken together, these findings shed further light on the mechanisms through which an impulsive temperament may convey risk for alcohol misuse.