bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size dominance regulates tree spacing more than competition within height classes in tropical Cameroon
Authors: Getzin Stephan , Worbes Martin , Wiegand Thorsten , Wiegand Kerstin 
Published: January 2011

Abstract:Does competition prevail in large size classes of trees in tropical forests? This question is fundamental to our understanding of the demography and dynamics occurring in rain forests. We investigated this question based on an undisturbed late-secondary forest on a 1-ha plot in central Cameroon. Trees were stem-mapped and classified into three size classes: understorey, midstorey and overstorey. The diameter at breast height and yearly biomass increment were determined as measures of plant growth and performance. Spatial statistics such as pair- and mark-correlation functions were used to detect scale-dependent patterns that could be caused by competition within and between the three size classes. The results revealed a random pattern and spatially uncorrelated measures of plant growth of overstorey trees. This suggests that competitive effects are of minor importance in the large size class of overstorey trees. Likewise, only weak evidence for competition between trees was found within the two lower size classes. However, negative distance correlations were found between the different size classes. We suggest that competition within height classes was relatively low due to the diversity of species with their variable niche differentiations and phenotypic plasticity that may compensate for competitive effects.
Caterpillar abundance and parasitism in a seasonally dry versus wet tropical forest of Panama
Authors: Connahs Heidi , Aiello Annette , Van Bael Sunshine , Rodríguez-Castañeda Genoveva 
Published: January 2011

Abstract:Rainfall seasonality can strongly influence biotic interactions by affecting host plant quality, and thus potentially regulating herbivore exposure to natural enemies. Plant defences are predicted to increase from dry to wet forests, rendering wet-forest caterpillars more vulnerable to parasitoids due to the slow-growth-high-mortality hypothesis. We collected and reared caterpillars from the understorey and trail edges of a wet forest and a seasonally dry forest to determine whether wet-forest caterpillars suffered a higher prevalence of parasitism and were less abundant than dry-forest caterpillars. In the two forests, caterpillar abundances (on average 8 h−1) and prevalence of parasitism (18%) were very similar regardless of feeding niche for both parasitism (27% versus 29% in shelter builders, and 16% versus 11% in external feeders) and caterpillar abundances (shelter builders: 1.42 versus 2.39, and external feeders: 8.27 versus 5.49 caterpillars h−1) in the dry and wet forests, respectively. A similar comparative analysis conducted in the canopy and understorey of the dry forest revealed a higher prevalence of parasitism in the canopy (43%) despite caterpillar densities similar to those in the understorey. Overall, shelter builders suffered higher parasitism than external feeders (32% versus 14.9%), and were attacked primarily by flies, whereas external feeders were more vulnerable to attack by parasitoid wasps.
Forest structure and territory size relationship in the neotropical understorey insectivoreHenicorhina leucosticta
Authors: Vargas Luis Esteban , Sánchez Natalie Viviana , Avalos Gerardo 
Published: January 2011

Abstract:The neotropical terrestrial insectivoreHenicorhina leucosticta(Troglodytidae) maintains long-term territories through vocalizations and forages among leaf litter trapped in the understorey vegetation and ground litter. The relationship between forest structure andH. leucostictaterritory size was studied in La Selva Biological Station, Costa Rica, during the non-breeding season in 2009. Forest structure was measured by assessing canopy openness and leaf area index (LAI) using hemispherical photography, while territory size was estimated with the playback technique using local conspecific vocalizations. Mean territory area was 3.8 ± 2.8 ha (mean ± SD, n = 10). Territory radius length was similar in old-growth forest and abandoned agro-forest plantations. We found thatH. leucostictaterritory size decreased as median LAI increased. We propose that LAI is related to territory size through the amount of leaf fall and subsequent leaf litter accumulation over the understorey plants, which constitutes an important reservoir of arthropod prey and nest materials forH. leucosticta. The long-term supply of food resources is likely to affect territory size in this species, as well as other insectivorous birds with similar foraging behaviour. These results are congruent with the structural cues hypothesis.
Canopy assemblages of ants in a New Guinea rain forest
Authors: Janda Milan , Konečná Martina 
Published: January 2011

Abstract:The ant assemblages in two common tree species in primary lowland forest of New Guinea were explored using direct canopy access and tuna bait traps. The 19 trees investigated were occupied by 21 ant species of which 18 were canopy inhabitants. On average only 3.6 ant species per tree and 3 species per bait were found. Height of bait position was positively related to ant species richness, with the upper parts of the canopy being occupied by the highest number of species. On the other hand, tree species and study site did not have any effect on ant species richness nor on structure of the ant assemblages. Ant species appeared to be distributed randomly and we did not detect any effect of distance on similarity of ant assemblage occurring on the trees. The dominant species (Crematogaster polita) had certain negative effects on the presence of some species at food sources co-occurring at the same tree, but it did co-occur with the other ants to some extent as well. The majority of species found in the canopy were generalist omnivores (depending mainly on trophobionts or plant exudates).
12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era
Authors: Wóycicki Rafał , Witkowicz Justyna , Pawełkowicz Magdalena , Siedlecka Ewa , Gutman Wojciech , Pląder Wojciech , Seroczyńska Anna , Śmiech Mieczysław , Niemirowicz-Szczytt Katarzyna , Karpiński Stanisław , Malepszy Stefan , Przybecki Zbigniew 
Published: January 2011

AbstractNew sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length and N50 2’324 Kbp. In the Celera/Arachne method contigs after prior pyrosequencing reads assembly (in the form of ~ 800 nt reads) were used together with the STCs as the input to Arachne assembler. Number of contigs were 15’764 of the length 193 Mbp with N50 23’280 bp. Number of supercontigs were 12’438 with the coverage of 323 Mbp and N50 323’092 bp. Correctness of the assemblies were proven after mapping 95,56% of 63’035 cucumber unigenes with the average identity 97,81%. Additionally 6 BAC/Fosmid cucumber sequences (totally 372’277 bp) had identity of 97,61% to the assembled genome. Average reads coverage of the genome were 14,20x and 98% of the assembled genome had reads coverage higher than 3x.Taking into consideration coverage used in already reported cucumber assemblies (32x by Miller J. et al., 2009 and 72x by Huang S. et al., 2009), as well as no differences in the quality and the best overall quantity statistics of contigs/scaffold lengths, the Celera approach used in this project should be considered the most optimal one to get omics-ready quality draft sequence of highly repeated eukaryotic genome.
A Note On The Denisova Cave mtDNA Sequence
Authors: Caldararo Niccolo , Guthrie Michael 
Published: January 2011

AbstractThe recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
The power of “Green” Energy: plant trait influences on microbial competition and greenhouse gas production
Authors: Sutton-Grier Ariana , Megonigal J. Patrick 
Published: January 2011

Abstract
Background/Questions/Methods
Species vary in the eco-physiological traits they possess which means species may differentially influence ecosystem functions such as microbial activity. In wetland ecosystems it is important to understand how different plant species influence microbial competition for resources because competition affects microbial respiration and one of the products of anaerobic microbial respiration is methane, a potent greenhouse gas. Plants influence the availability of substrates for microbial respiration, both available carbon and terminal electron acceptors (such as Fe(III)). Because methanogenic microbes must compete with other microbes for respiration substrates and can be out-competed if conditions are more favorable for other microbes, plants can influence the outcome of microbial competition as well as overall rates of microbial activity by changing substrate availability. In this study, we examined how plant traits related to plant productivity and carbon inputs (belowground and total biomass, and photosynthesis) and plant traits related to oxygen inputs and terminal electron acceptor availability (root porosity and Fe(III) on roots) influence microbial competition and methane production from wetland soils.

Results/Conclusions
Overall microbial respiration rates were positively correlated with plant productivity, but methane production was negatively correlated with plant productivity, suggesting that carbon inputs were not stimulating methanogenesis. Evidence that alternative microbial respiratory pathways were stimulated with higher plant productivity included: (1) higher CO2:CH4 ratios from the microbial communities of plants with higher productivity and (2) greater oxidized iron (Fe(III)) on roots of plants with higher productivity. Both of these results indicate that as plant productivity and belowground biomass increased, microbes used alternative respiration pathways and produced less methane. These results indicate that plant community composition plays an important role in methane production in wetlands. Therefore, human disturbances, such as climate change, invasive species, and eutrophication, which result in shifts in plant community composition are likely to have profound effects on methane production in wetlands.
Pioneer Discovery of secondary gold deposits-unique bacterioforms andplacers in north Goa from deep coremetabiosphere
Authors: Kamat Nandkumar 
Published: January 2011

AbstractBacterioform secondary gold deposits were discovered in tilloid overlaying archaean base rock (metagraywacke) in Sanvordem rock formation, at the depth of 65 metres in north Goa , India and were confirmed optically as microbiogenic Gold. Multiple and unique forms were seen. This is claimed to be first report of bacterioform Gold in deep cores in Goa, India and Asia.
Nutrient regime shift in the western North Atlantic indicated by compound-specific
δ
15
N of deep-sea gorgonian corals
Authors: Sherwood Owen A. , Lehmann Moritz F. , Schubert Carsten J. , Scott David B. , McCarthy Matthew D. 
Published: January 2011

Despite the importance of the nitrogen (N) cycle on marine productivity, little is known about variability in N sources and cycling in the ocean in relation to natural and anthropogenic climate change. Beyond the last few decades of scientific observation, knowledge depends largely on proxy records derived from nitrogen stable isotopes (
δ
15
N) preserved in sediments and other bioarchives. Traditional bulk
δ
15
N measurements, however, represent the combined influence of N source and subsequent trophic transfers, often confounding environmental interpretation. Recently, compound-specific analysis of individual amino acids (
δ
15
N-AA) has been shown as a means to deconvolve trophic level versus N source effects on the
δ
15
N variability of bulk organic matter. Here, we demonstrate the first use of
δ
15
N-AA in a paleoceanographic study, through analysis of annually secreted growth rings preserved in the organic endoskeletons of deep-sea gorgonian corals. In the Northwest Atlantic off Nova Scotia, coral
δ
15
N is correlated with increasing presence of subtropical versus subpolar slope waters over the twentieth century. By using the new
δ
15
N-AA approach to control for variable trophic processing, we are able to interpret coral bulk
δ
15
N values as a proxy for nitrate source and, hence, slope water source partitioning. We conclude that the persistence of the warm, nutrient-rich regime since the early 1970s is largely unique in the context of the last approximately 1,800 yr. This evidence suggests that nutrient variability in this region is coordinated with recent changes in global climate and underscores the broad potential of
δ
15
N-AA for paleoceanographic studies of the marine N cycle.
Interdisciplinary Research—Difficulties and Benefits
Authors: Kurz Ingrid 
Published: January 2011

Abstract
Part One outlines the desirability and difficulties of an interdisciplinary approach to interpretation research and theory. Part Two describes the design, implementation and first results of a collaborative study: EEG recordings during mental simultaneous interpretation into L1 and L2 were compared with EEG recordings during other cognitive tasks (shadowing, mental arithmetic, listening to music) and with the EEG at rest to investigate the cortical processes during simultaneous interpretation. Both hemispheres are involved in simultaneous interpretation, most of all the temporal regions (left more than right), and there are EEG differences between tasks involving verbal thinking and non-verbal tasks and between simultaneous interpretation into L1 and L2.
Rectal Biopsies Obtained With Jumbo Biopsy Forceps in the Evaluation of Hirschsprung Disease
Authors: Hirsch Barry Z , Angelides Anastasios G , Goode Susan P , Garb Jane L 
Published: January 2011

ABSTRACTBackground and Aim:Refractory constipation is an extremely common problem in infants and children. The diagnostic suspicion of Hirschsprung disease often arises in this clinical setting. Diagnosing Hirschsprung disease can be difficult; however, excluding the diagnosis is much easier, only requiring the demonstration of ganglion cells in the distal rectum. The most common method for obtaining tissue from the rectum involves a blind suction biopsy. This technique has been complicated by serious adverse events, equipment malfunction, and inadequate specimens. Our goal was to evaluate the adequacy of specimens obtained with a flexible endoscope and jumbo biopsy forceps to rule out Hirschsprung disease in the child outside the newborn period.Patients and Methods:We retrospectively reviewed 668 rectal biopsies taken during 167 endoscopies on 156 patients being evaluated for Hirschsprung disease from 2001 to 2008 at the Baystate Medical Center Children's Hospital. Four biopsies were taken from each patient approximately 2.5 cm from the anal verge. Biopsies were obtained using a flexible endoscope and jumbo biopsy forceps. During the first 6 years the Olympus FB‐50U‐1 large cup fenestrated biopsy forceps was used. During the last 2 years the Boston Scientific Radial Jaw 4 Jumbo biopsy forceps was used instead.Results:The Boston Scientific Radial Jaw 4 Jumbo biopsy forceps yielded adequate specimens 93% of the time, which surpassed most published results of other techniques. There were no complications reported.Conclusions:Obtaining rectal biopsies with a flexible endoscope and jumbo biopsy forceps is a safe and effective means to rule out the diagnosis of Hirschsprung disease in children.
Functional Characterization of Mutations in the Myosin Vb Gene Associated With Microvillus Inclusion Disease
Authors: Szperl Agata M , Golachowska Magdalena R , Bruinenberg Marcel , Prekeris Rytis , Thunnissen Andy‐Mark WH , Karrenbeld Arend , Dijkstra Gerard , Hoekstra Dick , Mercer David , Ksiazyk Janusz , Wijmenga Cisca , Wapenaar Martin C , Rings Edmond HHM , van IJzendoorn Sven CD 
Published: January 2011

ABSTRACTObjectives:Microvillus inclusion disease (MVID) is a rare autosomal recessive enteropathy characterized by intractable diarrhea and malabsorption. Recently, various MYO5B gene mutations have been identified in patients with MVID. Interestingly, several patients with MVID showed only a MYO5B mutation in 1 allele (heterozygous) or no mutations in the MYO5B gene, illustrating the need to further functionally characterize the cell biological effects of the MYO5B mutations.Patients and Methods:The genomic DNA of 9 patients diagnosed as having MVID was screened for MYO5B mutations, and quantitative polymerase chain reaction and immunohistochemistry on the material of 2 patients was performed to investigate resultant cellular consequences.Results:We demonstrate for the first time that MYO5B mutations can be correlated with altered myosin Vb messenger RNA expression and with an aberrant subcellular distribution of the myosin Vb protein. Moreover, we demonstrate that the typical and myosin Vb–controlled accumulation of Rab11a‐ and FIP5‐positive recycling endosomes in the apical cytoplasm of the cells is abolished in MVID enterocytes, which is indicative of altered myosin Vb function. Moreover, we report 8 novel MYO5B mutations in 9 patients of various ethnic backgrounds with MVID, including compound heterozygous mutations.Conclusions:Our functional analysis indicates that MYO5B mutations can be correlated with an aberrant subcellular distribution of the myosin Vb protein, and apical recycling endosomes, which, together with the additional compound heterozygous mutations, significantly strengthen the link between MYO5B and MVID.
Esophageal Subepithelial Fibrosis and Hyalinization Are Features of Eosinophilic Esophagitis
Authors: Li‐Kim‐Moy Jean P , Tobias Vivienne , Day Andrew S , Leach Steven , Lemberg Daniel A 
Published: January 2011

ABSTRACTBackground and Objective:Eosinophilic esophagitis (EE) is characterized by marked esophageal mucosal eosinophilia on histological examination. Although the clinical and histological features of EE are increasingly recognized, the overlap of clinical symptoms and histological findings with gastroesophageal reflux disease (GERD) can lead to diagnostic difficulty. In children with EE we sought to define the frequency of subepithelial fibrosis and define the clinical correlates of this feature. The specificity of this finding in EE was obtained by comparison with a matched group of children with GERD, to ascertain its usefulness as a histological aid in differentiating between the 2 diagnoses.Patients and Methods:Comparison was made between 27 patients with EE and 24 patients with GERD, whose endoscopic biopsy specimens included subepithelial tissue. Demographic data, symptoms, endoscopic findings, and other histological findings were also compared.Results:In contrast to patients with GERD, those with EE more commonly reported longer periods of symptoms (especially dysphagia) and were more likely to have endoscopic abnormalities. Subepithelial fibrosis was present in 89% of patients with EE and 37.5% of patients with GERD (P < 0.0001). The features of fibrosis in EE included uniformity and hyalinization, whereas the fibrosis in GERD was predominantly associated with lymphoid tissue.Conclusions:Subepithelial fibrosis commonly occurs in children with EE and is associated with increased age and length of symptoms. We propose that along with mucosal eosinophilic infiltration the presence of subepithelial fibrosis is a feature of EE.
Association of Mycobacterium avium subspecies paratuberculosis With Crohn Disease in Pediatric Patients
Authors: Lee Adrienne , Griffiths Tanya A , Parab Rohan S , King Robin K , Dubinsky Marla C , Urbanski Stefan J , Wrobel Iwona , Rioux Kevin P 
Published: January 2011

ABSTRACTObjectives:The aim of the present study was to determine the prevalence of Mycobacterium avium subsp paratuberculosis (MAP) DNA in intestinal biopsies from pediatric patients with granulomatous Crohn disease (CD) or ulcerative colitis (UC), and matched control subjects without inflammatory bowel disease (IBD).Patients and Methods:DNA was extracted from formalin‐fixed paraffin‐embedded colonic and ileal biopsies from patients with CD (n = 22) or UC (n = 20), and from controls without IBD (n = 21). IS900 nested polymerase chain reaction was performed in triplicate to determine the presence of MAP‐specific DNA.Results:In mucosal biopsies from terminal ileum, IS900 amplicons were detected in 1 of 19 (5.2%) control subjects, 1 of 20 (5%) patients with UC, and 7 of 20 (35%) patients with CD (P < 0.05 vs controls, odds ratio 9.6). In colonic biopsies, IS900 amplicons were detected in 0 of 19 control subjects, 1 of 19 (5.2%) patients with UC, and 5 of 19 (26.3%) patients with CD (P < 0.05 vs controls, odds ratio 14.8). In patients with CD, there was no correlation between disease activity and the presence of IS900.Conclusions:Our technique enabled sensitive and specific detection of MAP DNA in archival endoscopic biopsy specimens. Although MAP‐specific DNA can be detected in about 5% of intestinal biopsies from children with UC or controls without IBD, its presence was significantly associated with pediatric granulomatous CD, being particularly prevalent in ileal tissue. This easily defined clinical subset of patients may be useful for additional studies to determine the role of MAP in CD.
Preparation of Extracts from Yeast
Authors: Simpson Richard J. 
Published: January 2011

INTRODUCTIONBecause yeast is exceptionally well suited to genetic analysis, both classical and molecular, it is an attractive system for expressing recombinant animal proteins for purification purposes. Methods available for lysing yeast cells include autolysis, pressure cells (e.g., French press), abrasives (glass bead vortexing), and enzymatic lysis (e.g., zymolase). One of the simplest methods, discussed in this protocol, involves the abrasive action of well-agitated glass beads. This is a very effective method for both low volumes (e.g., <1 mL using a microcentrifuge tube) and many liters using a specialized DynoMill apparatus. Cell breakage is typically >95%, as assessed by phase-contrast microscopy.
Multicolor Brainbow Imaging in Zebrafish
Authors: Pan Y. Albert , Livet Jean , Sanes Joshua R. , Lichtman Jeff W. , Schier Alexander F. 
Published: January 2011

INTRODUCTIONThis protocol describes how to use the Brainbow strategy to label neurons in many different hues. The Brainbow system uses a random Cre/lox recombination to create varied combinations of red, blue, and green fluorescent proteins in each cell. The differences in color allow users to follow multiple cells, regardless of how closely they are positioned. This protocol describes how to use Brainbow imaging in zebrafish and provides examples of how to use color as a guide to trace axonal processes. We use the zebrafish trigeminal sensory ganglion as an example and discuss potential modifications for the general use of this technique.