bluuebunny/crossref_metadata_2025_split huggingface dataset:
The plant-ant Camponotus schmitzi helps its carnivorous host-plant Nepenthes bicalcarata to catch its prey
Authors: Bonhomme Vincent , Gounand Isabelle , Alaux Christine , Jousselin Emmanuelle , Barthélémy Daniel , Gaume Laurence 
Published: January 2011

Abstract:The Bornean climber, Nepenthes bicalcarata, is unique among plants because it is both carnivorous and myrmecophytic, bearing pitcher-shaped leaves and the ant Camponotus schmitzi within tendrils. We explored, in the peat swamp forests of Brunei, the hypothesis that these ants contribute to plant nutrition by catching and digesting its prey. We first tested whether ants increased plant's capture rate. We found that unlike most plant-ants, C. schmitzi do not exhibit dissuasive leaf-patrolling behaviour (zero patrol on 67 pitchers of 10 plants) but lie concealed under pitcher rim (13 ± 6 ants per pitcher) allowing numerous insect visits. However, 47 out of 50 individuals of the largest visitor dropped into the pitchers of five plants were attacked by ants and the capture rate of the same pitchers deprived of their ambush hunting ants decreased three-fold. We then tested whether ants participated in plant's digestion. We showed in a 15-d long experiment that ants fed on prey and returned it in pieces in seven out of eight pitchers. The 40 prey deposited in ant-deprived pitchers remained intact indicating a weak digestive power of the fluid confirmed to be only weakly acidic (pH ~5, n = 67). The analysis of 10 pitcher contents revealed that prey, mainly ants and termites, was very numerous (~400 per pitcher per plant) and highly fragmented. Altogether, these data suggest a positive effect of C. schmitzi on both prey intake and breakdown. This ant–plant interaction could thus be a nutritional mutualism involving the unusual association of carnivory and myrmecotrophy.
Effects of forest fragmentation on assemblages of pollinators and floral visitors to male- and female-phase inflorescences of Astrocaryum mexicanum (Arecaceae) in a Mexican rain forest
Authors: Aguirre Armando , Guevara Roger , Dirzo Rodolfo 
Published: January 2011

Abstract:We examined the consequences of habitat fragmentation on the assemblage of floral visitors and pollinators to male- and female-phase inflorescences of the understorey dominant palm Astrocaryum mexicanum at the Los Tuxtlas tropical rain forest. In six forest fragments ranging from 2 to 700 ha, we collected all floral visitors, pollinators and non-pollinators, to male- and female-phase inflorescences at the time of their greatest activity. We used multivariate and mixed-effects models to explore differences in guild composition between sexual phases of inflorescences and the effects of forest fragment size on several metrics of the assemblages of floral visitors. We detected 228 786 floral visitors, grouped into 57 species, across the six forest fragments. On average, abundance and species richness of floral visitors to female-phase inflorescences were higher than to male-phase ones. Forest fragmentation had no effect on species richness but negatively affected Shannon's diversity index. Overall, the most abundant species of floral visitors were predominantly found in inflorescences of plants from the large fragments. In contrast, most of the less common species were more abundant in the smallest fragments. The abundance of pollinators (those found on inflorescences of both phases and dusted with pollen that was carried to flower stigmas), and the ratio of pollinators to other floral visitors, increased with fragment size in both sexual phases of the inflorescences but these effects were significantly stronger on male-phase inflorescences than on female-phase inflorescences. These results show that tropical forest fragmentation correlates with changes in the composition of flower visitors to a dominant palm, with a reduction in the abundance of pollinators, but that such changes co-vary with the sexual phase of the plants.
Fire favours expansion of bamboo-dominated forests in the south-west Amazon
Authors: Smith Maira , Nelson Bruce Walker 
Published: January 2011

Abstract:Forests dominated by semi-scandent woody bamboos of the genusGuaduacover about 165 000 km2of the south-west Amazon. Because many woody bamboo species are favoured by disturbance some authors have inferred this landscape to be a consequence of indigenous or natural disturbance. As seen in satellite images, the rounded edges of some bamboo-dominated forests indicate expansion into surrounding forest. These edges are unrelated to topography and resemble the borders of ground fires in unlogged Amazon forests, suggesting that bamboo may have been favoured by past fires. We studied the recovery ofGuadua sarcocarpaand its competitors in the face of simulated fire by cutting all plant stems at ground level in ten 100-m2plots, compared with ten control plots, and by burning a 2500-m2plot. In the clear-cuts, bamboos recovered more successfully than did palms and dicots, by two measures: biomass accumulated and per cent recovery of pre-disturbance biomass. Resprouted bamboo attained higher stem densities than in control sites at 11 mo. In the burn plot, bamboo basal area recovered to pre-burn levels after 2 y and approached that of an undisturbed control area after 3 y. Though other natural disturbances are relevant, we conclude that forest fires should favour the spread and dominance ofGuaduaspecies in the south-west Amazon.
Successional trends in soil seed banks of abandoned pastures of a Neotropical dry region
Authors: Maza-Villalobos Susana , Lemus-Herrera Celina , Martínez-Ramos Miguel 
Published: January 2011

Abstract:A chronosequence was used to study seed-bank communities during the first 12 y of tropical-dry-forest regeneration in abandoned pastures in Chamela, Mexico. Prediction that seeds of woody species replace those of herbaceous species during succession was tested and mechanisms of species replacement (facilitation, tolerance, inhibition) were assessed. Four successional categories (three sites each) were considered: pasture (0–1 y since abandonment), early (3–5 y), intermediate (10–12 y), and old-growth forest. At the end of the dry season, 20 cylindrical soil samples (10 cm diameter, 15 cm depth) were randomly obtained within a 20 × 50-m plot in each site. Seeds ≥1 mm were counted and identified. Overall, 2941 seeds and 102 morphospecies (52 taxonomically identified) were recorded. Seed bank density reduced, species diversity remained fairly constant and seeds of herbaceous species were replaced by those of woody species over the chronosequence. A clear species-by-species replacement pattern was detected, as expected under a mechanism of succession by facilitation. Twelve years after abandonment, a diverse seed bank of woody species did exist, indicating a fast recovery of the tropical-dry-forest regenerative potential; nonetheless, the structure and composition of the seed bank was still different from that in the old-growth forest.
Progress in research on dry afterripening
Authors: Iglesias-Fernández Raquel , del Carmen Rodríguez-Gacio María , Matilla Angel J. 
Published: January 2011

AbstractThe transition from the dormant to the non-dormant state of a viable and mature seed can take place at low hydration by exposure to air-dry storage conditions (dry afterripening; AR). The events occurring during this loss of dormancy are of considerable physiological, ecological and agricultural interest. AR may be attributable to increased sensitivity to germination-stimulating factors and a widening of the temperature window for germination. Genetic, –omics and physiological studies on this mode of dormancy breaking provide support for a key role of the balance between gibberellin (GA) and abscisic acid (ABA) metabolism and sensitivity. Recent evidence also supports a possible role for ethylene (ET) in this complex signalling network that is necessary for AR implementation. However, hormone-independent signals, such as reactive oxygen species (ROS), nitrate (NO _{3}^{ - }) or nicotinamide adenine dinucleotide (NAD+), also appear to be involved. The way in which hormone- and non-hormone-signalling pathways affects each other (cross-talk) is still under study. This review provides updated information on the programmes that overcome seed dormancy. Thus, we have reviewed: (1) the –omic status in dry seeds; (2) the relationship between temperature and nitrate signalling and AR; (3) alterations in ABA/GA synthesis and signalling; (4) the action of hormone molecules other than ABA and GA (i.e. ET, salicylic and jasmonic acids); and (5) participation of reactive oxygen species (ROS), NAD+and protein carbonylation. Taken together, the acquisition and implementation of dry AR involve a complex signalling network that is difficult to disentangle.
Executive Function Profiles of Pedophilic and Nonpedophilic Child Molesters
Authors: Eastvold Angela , Suchy Yana , Strassberg Donald 
Published: January 2011

AbstractThere is increasing evidence of neurocognitive dysfunction among child molesters, supporting the notion of brain anomalies among pedophiles. However, approximately half of child molesters are not pedophilic (i.e., are not primarily attracted to children), and neurocognitive differences between pedophilic (PED) and nonpedophilic (NPED) child molesters are not well understood. The purpose of this study was to assess neurocognition, specifically executive functioning (EF), among phallometrically defined PED and NPED child molesters, relative to nonsexual offenders (NSO). Participants (N = 89) were compared on seven EF domains. Results revealed that (a) child molesters exhibited an overall executive profile that was different from that of NSOs, with PEDs differing from NSOs but not from NPEDs; (b) child molesters on the whole performed better than NSOs on abstract reasoning and more poorly on inhibition; and (c) PEDs performed better than NPEDs on planning and exhibited better overall performance accuracy relative to NPEDs. These results suggest that PEDs exhibit a more deliberate, planful response style characterized by greater self-monitoring; whereas NPEDs appear to respond more impulsively. The current report further elucidates neurocognition among child molesters and highlights the need for future research examining subtypes of child molesters. (JINS, 2011, 17, 295–307)
Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes
Authors: Biddle Jennifer F , White James Robert , Teske Andreas P , House Christopher H 
Published: January 2011

Abstract
The Brazos-Trinity Basin on the slope of the Gulf of Mexico passive margin was drilled during Integrated Ocean Drilling Progam Expedition 308. The buried anaerobic sediments of this basin are largely organic-poor and have few microbial inhabitants compared with the organic-rich sediments with high cell counts from the Peru Margin that were drilled during Ocean Drilling Program Leg 201. Nucleic acids were extracted from Brazos-Trinity Basin sediments and were subjected to whole-genome amplification and pyrosequencing. A comparison of the Brazos-Trinity Basin metagenome, consisting of 105 Mbp, and the existing Peru Margin metagenome revealed trends linking gene content, phylogenetic content, geological location and geochemical regime. The major microbial groups (Proteobacteria, Firmicutes, Euryarchaeota and Chloroflexi) occur consistently throughout all samples, yet their shifting abundances allow for discrimination between samples. The cluster of orthologous groups category abundances for some classes of genes are correlated with geochemical factors, such as the level of ammonia. Here we describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 likely represents the subsurface microbial inhabitants of turbiditic slopes that lack substantial upwelling.
Continuous-time model of structural balance
Authors: Marvel Seth A. , Kleinberg Jon , Kleinberg Robert D. , Strogatz Steven H. 
Published: January 2011

It is not uncommon for certain social networks to divide into two opposing camps in response to stress. This happens, for example, in networks of political parties during winner-takes-all elections, in networks of companies competing to establish technical standards, and in networks of nations faced with mounting threats of war. A simple model for these two-sided separations is the dynamical system
dX
/
dt
=
X
2
, where
X
is a matrix of the friendliness or unfriendliness between pairs of nodes in the network. Previous simulations suggested that only two types of behavior were possible for this system: Either all relationships become friendly or two hostile factions emerge. Here we prove that for generic initial conditions, these are indeed the only possible outcomes. Our analysis yields a closed-form expression for faction membership as a function of the initial conditions and implies that the initial amount of friendliness in large social networks (started from random initial conditions) determines whether they will end up in intractable conflict or global harmony.
Interpretation Research in Japan
Authors: Kondo Masaomi , Mizuno Akira 
Published: January 2011

Abstract
The following is a personal account of how a small number of conference interpreters and others interested in the conference interpreting profession in Japan launched the Interpreting Research Assocation of Japan. The paper also reviews some of the pertinent writings, mainly in Japanese, which discuss various aspects of conference interpreting. It is hoped that this article will help shed some light on a number of issues we face in promoting interpretation research, as well as on the profession itself, in Japan.
Tabix: fast retrieval of sequence features from generic TAB-delimited files
Authors: Li Heng 
Published: January 2011

Abstract
Summary: Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. Tabix features include few seek function calls per query, data compression with gzip compatibility and direct FTP/HTTP access. Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl and Python. It is particularly useful for manually examining local genomic features on the command line and enables genome viewers to support huge data files and remote custom tracks over networks.
Availability and Implementation: http://samtools.sourceforge.net.
Contact: hengli@broadinstitute.org
Wave-spec: a preprocessing package for mass spectrometry data
Authors: Li Ming , Chen Shuo , Zhang Joan , Chen Heidi , Shyr Yu 
Published: January 2011

Abstract
Summary:Wave-spec is a pre-processing package for mass spectrometry (MS) data. The package includes several novel algorithms that overcome conventional difficulties with the pre-processing of such data. In this application note, we demonstrate step-by-step use of this package on a real-world MALDI dataset.
Availability: The package can be downloaded at http://www.vicc.org/biostatistics/supp.php. A shared mailbox (wave-spec@vanderbilt.edu) also is available for questions regarding application of the package.
Contact: yu.shyr@vanderbilt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Effect of Different pH Criteria on Dual‐sensor pH Monitoring in the Evaluation of Supraesophageal Gastric Reflux in Children
Authors: Chiou Eric , Rosen Rachel , Nurko Samuel 
Published: January 2011

ABSTRACTBackground and Aim:Existing tests for supraesophageal gastric reflux (SEGR) that focus on pH drops <4 in the proximal esophagus have had limited sensitivity and specificity. The aim of the present study was to evaluate the effect of newly proposed pH criteria on SEGR detection.Patients and Methods:Twenty‐four‐hour dual‐sensor pH tracings of 32 patients were reviewed. Proximal esophageal pH data were evaluated according to the conventional definition of pH drop <4 and 2 proposed definitions: pH drop <5.5 while upright and <5.0 while supine and pH drop of >10% from a running baseline. For each potential SEGR event, the preceding 1‐minute window was examined for corresponding distal acid reflux.Results:Of the 542 distal acid reflux events detected, 200 were associated with a proximal pH drop <4; this number increased to 295 using the definition of proximal pH drop <5.5 (upright)/<5.0 (supine) and 301 using the definition of proximal pH drop >10%. A proportion of proximal events, however, was not associated with distal acid reflux: 21 of 200 (10.5%) proximal pH <4 events, 119 of 414 (29%) proximal pH <5.5 (upright)/<5.0 (supine) events, and 272 of 573 (47%) proximal pH drop >10% events lacked a preceding or simultaneous drop in distal pH <4.Conclusions:Although the use of more liberal pH criteria increased the diagnostic yield for SEGR events with dual‐sensor monitoring, a significant proportion of proximal pH events did not correlate with distal acid reflux. These events could represent either false‐positive measurements or association with weakly acid reflux.
Early Increases in Concentrations of Total, LDL, and HDL Cholesterol in HIV‐infected Children Following New Exposure to Antiretroviral Therapy
Authors: Sztam Kevin A , Jiang Hongyu , Jurgrau Andrea , Deckelbaum Richard J , Foca Marc D 
Published: January 2011

ABSTRACTAntiretroviral therapy (ART) is associated with dyslipidemia and cardiovascular disease in adults infected with HIV. For children perinatally infected with HIV, ART exposure is lifelong and early‐onset dyslipidemia could have significant long‐term effects. We examined cholesterol levels in children during the first year after exposure to a new ART regimen (initiation or switch). In 52 children, total cholesterol increased by 30.5 and 43 mg/dL at 6 and 12 months, respectively (P < 0.001). Low‐density lipoprotein cholesterol made the largest contribution, but high‐density lipoprotein cholesterol also increased within months of therapy alteration. Early identification of these children and intervention could mediate potential increased risk for future cardiovascular disease.
Dot Blot Assay for Determining Fusion Protein Antiserum Quality
Authors: Rebay Ilaria , Fehon Richard G. 
Published: January 2011

INTRODUCTIONWhen testing antiserum quality, it is essential to determine first whether the antiserum recognizes the fusion protein against which it was raised. A dot blot will provide a qualitative estimate of antibody titer, as described in this protocol. The same test can be done quantitatively by enzyme-linked immunosorbent assay (ELISA), but the technically simpler dot blot gives adequate information, uses less protein, and does not require an ELISA plate reader. If the same protein has been expressed in two different fusion-protein vectors, the test should be performed with the protein not used for immunization. If there is only one fusion protein—e.g., a glutathione-S-transferase (GST)-fusion—a second dot blot can be done in parallel with GST alone to compare the titers. If the antiserum recognizes the protein, there should be a lower titer of antibodies against GST alone as compared to the entire fusion protein. A preimmune control is always advisable. If a positive result is not obtained against the fusion protein, it is futile to proceed to secondary tests. Continue boosting and retesting until a positive response is achieved, or try a different approach.
Determining Fusion Protein Antiserum Quality by Staining of Transfected Drosophila S2 Cultured Cells
Authors: Rebay Ilaria , Fehon Richard G. 
Published: January 2011

INTRODUCTIONOnce antibodies against a Drosophila protein have been produced and an antiserum is determined to have a high titer against the fusion protein used for immunization, the next step is to ask whether the antiserum recognizes the appropriate antigen in Drosophila tissues. This protocol describes staining of transfected S2 cells for testing antisera. There are several advantages to using transfected S2 cells as a first tissue test. First, the antibody only needs to penetrate a single cell. In addition, these cells are easy to fix and stain and require no dissection. Second, the overexpressed protein will be easier to detect than lower levels of endogenous protein. Third, background is generally less of a problem in S2 cells than in embryonic or imaginal tissues, allowing lower dilutions of the antiserum to be tested if the response is marginal. Finally, the untransfected cells form a useful built-in control. S2 cell stainings are also an easy way to determine the subcellular localization of a particular protein.
Preparing Thick Sections of Frozen Adult Drosophila Retinas for Microscopy
Authors: Wolff Tanya 
Published: January 2011

INTRODUCTIONThis protocol is used for light microscopic analysis of the adult Drosophila eye. It provides nice preservation of pigment granules and photoreceptor rhabdomeres. Therefore, it is used primarily for phenotypic and mosaic analysis of adult eyes. Because this fixation method does not preserve either cell membranes or subcellular structures, transmission electron microscopy (TEM) is recommended for visualizing these structures.
Electroretinogram Recordings of Drosophila: FIGURE 1.
Authors: Dolph Patrick , Nair Amit , Raghu Padinjat 
Published: January 2011

INTRODUCTIONAnalysis of visual physiology in Drosophila photoreceptors has been central to understanding a number of important areas of modern biology, including the G-protein-coupled receptor cycle, phosphoinositide signaling, and calcium signaling. Analysis of photoreceptor performance and synaptic transmission are areas of neurobiology that have been studied using Drosophila photoreceptors as a model system. Electrophysiological analysis of responses to light is a powerful tool for characterizing and understanding visual transduction in Drosophila photoreceptors, and electroretinograms (ERGs) have long been used as a physiological assay in the Drosophila visual system. In these recordings, a microelectrode is placed on the eye and a reference electrode is placed elsewhere on the animal (typically in the thorax). Upon light stimulation, the voltage difference between these two electrodes is measured and displayed in real time. Because recordings are performed in live animals, all photoreceptor cells are intact and therefore surrounded by fluid containing endogenous concentrations of ions. Moreover, synaptic transmission between the photoreceptor and downstream laminar neurons can be detected.
Labeling Membranes with Carbocyanine Dyes (DiIs) as Phospholipid Analogs: FIGURE 1.
Authors: Chazotte Brad 
Published: January 2011

INTRODUCTIONCell membranes can be labeled with cationic lipophilic fluorescent carbocyanine dyes that function as phospholipid analogs. These dyes, such as DiI-C16(3) (1,1′-dihexadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate), label the plasma membrane and (eventually) label all of the membranes within a living cell. The dyes can be also used with model membranes. Carbocyanine dyes are commercially available in different carbon chain lengths (e.g., C12, C14, C18, and C22). Depending on the fatty acid composition of the phospholipids in the membrane studied with respect to chain length and degree of saturation, DiIs with different chain lengths can provide optimal incorporation and accurate reporting of membrane motions. DiI-labeled cells can be studied using fluorescence microscopy or fluorescence recovery after photobleaching (FRAP), as well as other techniques.