bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human
Authors: Piasecka Barbara , Robinson-Rechavi Marc , Bergmann Sven 
Published: May 2012

Abstract
Motivation: Comparative analyses of gene expression data from different species have become an important component of the study of molecular evolution. Thus methods are needed to estimate evolutionary distances between expression profiles, as well as a neutral reference to estimate selective pressure. Divergence between expression profiles of homologous genes is often calculated with Pearson's or Euclidean distance. Neutral divergence is usually inferred from randomized data. Despite being widely used, neither of these two steps has been well studied. Here, we analyze these methods formally and on real data, highlight their limitations and propose improvements.
Results: It has been demonstrated that Pearson's distance, in contrast to Euclidean distance, leads to underestimation of the expression similarity between homologous genes with a conserved uniform pattern of expression. Here, we first extend this study to genes with conserved, but specific pattern of expression. Surprisingly, we find that both Pearson's and Euclidean distances used as a measure of expression similarity between genes depend on the expression specificity of those genes. We also show that the Euclidean distance depends strongly on data normalization. Next, we show that the randomization procedure that is widely used to estimate the rate of neutral evolution is biased when broadly expressed genes are abundant in the data. To overcome this problem, we propose a novel randomization procedure that is unbiased with respect to expression profiles present in the datasets. Applying our method to the mouse and human gene expression data suggests significant gene expression conservation between these species.
Contact: marc.robinson-rechavi@unil.ch; sven.bergmann@unil.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
MicrobeDB: a locally maintainable database of microbial genomic sequences
Authors: Langille Morgan G. I. , Laird Matthew R. , Hsiao William W. L. , Chiu Terry A. , Eisen Jonathan A. , Brinkman Fiona S. L. 
Published: May 2012

Abstract
Summary: Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design.
Availability: MicrobeDB is freely available under the GNU-GPL at: http://github.com/mlangill/microbedb/
Contact: morgan.g.i.langille@gmail.com
Exploring the relationship betweenNDVIand African elephant population density in protected areas
Authors: Duffy James P. , Pettorelli Nathalie 
Published: May 2012

AbstractAssessing the extent to which populations are limited by bottom‐up processes driven by food limitation is crucial to our understanding of how ecosystems should be managed. Using satellite‐derived Normalised Difference Vegetation Index (NDVI) as an index of resource availability, we investigated the relationships between greenness levels and African elephant (Loxodonta africana) population densities. Our results unveiled a positive relationship betweenNDVIand elephant densities in nonforest populations, but failed to capture any significant effects of survey area and type, number of years after the continental poaching ban and theIUCNcategory of the protected area in which the survey was undertaken. The number of forest elephant populations for which density estimates were available was very low, and no significant relationship betweenNDVIand forest elephant density could be established. Altogether, our study suggests thatNDVIcan successfully be linked to megaherbivore abundance across Africa and further highlights that a continental approach to energy–abundance relationships can be conducted in a relatively low‐cost manner and short timescale, supporting managers' efforts to identify future suitable areas for elephant populations.
Are responses of herbivores to environmental variability spatially consistent in alpine ecosystems?
Authors: Nielsen Anders , Yoccoz Nigel G. , Steinheim Geir , Storvik Geir O. , Rekdal Yngve , Angeloff Michael , Pettorelli Nathalie , Holand Øystein , Mysterud Atle 
Published: May 2012

AbstractAnimal responses to global climate variation might be spatially inconsistent. This may arise from spatial variation in factors limiting populations' growth or from differences in the links between global climate patterns and ecologically relevant local climate variation. For example, the North Atlantic Oscillation (NAO) has a spatially consistent relation to temperature, but inconsistent spatial relation to snow depth in Scandinavia. Furthermore, there are multiple mechanistic ways by which climate may limit animal populations, involving both direct effects through thermoregulation and indirect pathways through trophic interactions. It is conceptually appealing to directly model the predicted mechanistic links. This includes the use of climate variables mimicking such interactions, for example, to use growing degree days (GDD) as a proxy for plant growth rather than average monthly temperature. Using a unique database of autumn body mass of 83331 domestic lambs from the period 1992–2007 in four alpine ranges in Norway, we demonstrate the utility of hierarchical, mechanistic path models fitted using a Bayesian approach to analyse explicitly predicted relationships among environmental variables and between lamb body mass and the environmental variables. We found large spatial variation in strength of responses of autumn lamb body mass to the NAO, to a proxy for plant growth in spring (the Normalized Difference Vegetation Index, NDVI) and effects even differed in direction to local summer climate. Average local temperature outperformed GDD as a predictor of the NDVI, whereas the NAO index in two areas outperformed local weather variables as a predictor of lamb body mass, despite the weaker mechanistic link. Our study highlights that spatial variation in strength of herbivore responses may arise from several processes. Furthermore, mechanistically more appealing measures do not always increase predictive power due to scale of measurement and since global measures may provide more relevant “weather packages” for larger scales.
Feedback from plant species change amplifies CO2 enhancement of grassland productivity
Authors: Polley H. Wayne , Jin Virginia L. , Fay Philip A. 
Published: May 2012

AbstractDynamic global vegetation models simulate feedbacks of vegetation change on ecosystem processes, but direct, experimental evidence for feedbacks that result from atmospheric CO2 enrichment is rare. We hypothesized that feedbacks from species change would amplify the initial CO2 stimulation of aboveground net primary productivity (ANPP) of tallgrass prairie communities. Communities of perennial forb and C4 grass species were grown for 5 years along a field CO2 gradient (250–500 μL L−1) in central Texas USA on each of three soil types, including upland and lowland clay soils and a sandy soil. CO2 enrichment increased community ANPP by 0–117% among years and soils and increased the contribution of the tallgrass species Sorghastrum nutans (Indian grass) to community ANPP on each of the three soil types. CO2‐induced changes in ANPP and Sorghastrum abundance were linked. The slope of ANPP‐CO2 regressions increased between initial and final years on the two clay soils because of a positive feedback from the increase in Sorghastrum fraction. This feedback accounted for 30–60% of the CO2‐mediated increase in ANPP on the upland and lowland clay soils during the final 3 years and 1 year of the experiment, respectively. By contrast, species change had little influence on the ANPP‐CO2 response on the sandy soil, possibly because Sorghastrum increased largely at the expense of a functionally similar C4 grass species. By favoring a mesic C4 tall grass, CO2 enrichment approximately doubled the initial enhancement of community ANPP on two clay soils. The CO2‐stimulation of grassland productivity may be significantly underestimated if feedbacks from plant community change are not considered.
Different inter‐annual responses to availability and form of nitrogen explain species coexistence in an alpine meadow community after release from grazing
Authors: Song Ming‐Hua , Yu Fei‐Hai , Ouyang Hua , Cao Guang‐Min , Xu Xing‐Liang , Cornelissen Johannes H.C. 
Published: May 2012

AbstractPlant species and functional groups in nitrogen (N) limited communities may coexist through strong eco‐physiological niche differentiation, leading to idiosyncratic responses to multiple nutrition and disturbance regimes. Very little is known about how such responses depend on the availability of N in different chemical forms. Here we hypothesize that idiosyncratic year‐to‐year responses of plant functional groups to availability and form of nitrogen explain species coexistence in an alpine meadow community after release from grazing. We conducted a 6 year N addition experiment in an alpine meadow on the Tibetan Plateau released from grazing by livestock. The experimental design featured three N forms (ammonium, nitrate, and ammonium nitrate), crossed with three levels of N supply rates (0.375, 1.500 and 7.500 g N m−2 yr−1), with unfertilized treatments without and with light grazing as controls. All treatments showed increasing productivity and decreasing species richness after cessation of grazing and these responses were stronger at higher N rates. Although N forms did not affect aboveground biomass at community level, different functional groups did show different responses to N chemical form and supply rate and these responses varied from year to year. In support of our hypothesis, these idiosyncratic responses seemed to enable a substantial diversity and biomass of sedges, forbs, and legumes to still coexist with the increasingly productive grasses in the absence of grazing, at least at low and intermediate N availability regimes. This study provides direct field‐based evidence in support of the hypothesis that idiosyncratic and annually varying responses to both N quantity and quality may be a key driver of community structure and species coexistence. This finding has important implications for the diversity and functioning of other ecosystems with spatial and temporal variation in available N quantity and quality as related to changing atmospheric N deposition, land‐use, and climate‐induced soil warming.
The trouble with isolation by distance
Authors: MEIRMANS PATRICK G. 
Published: May 2012

AbstractThe genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non‐spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non‐spatial Island model.
Lack of genetic differentiation between monarch butterflies with divergent migration destinations
Authors: LYONS JUSTINE I. , PIERCE AMANDA A. , BARRIBEAU SETH M. , STERNBERG ELEANORE D. , MONGUE ANDREW J. , De ROODE JACOBUS C. 
Published: May 2012

AbstractMonarch butterflies are best known for their spectacular annual migration from eastern North America to Mexico. Monarchs also occur in the North American states west of the Rocky Mountains, from where they fly shorter distances to the California Coast. Whether eastern and western North American monarchs form one genetic population or are genetically differentiated remains hotly debated, and resolution of this debate is essential to understand monarch migration patterns and to protect this iconic insect species. We studied the genetic structure of North American migratory monarch populations, as well as nonmigratory populations in Hawaii and New Zealand. Our results show that eastern and western migratory monarchs form one admixed population and that monarchs from Hawaii and New Zealand have genetically diverged from North American butterflies. These findings suggest that eastern and western monarch butterflies maintain their divergent migrations despite genetic mixing. The finding that eastern and western monarchs form one genetic population also suggests that the conservation of overwintering sites in Mexico is crucial for the protection of monarchs in both eastern and western North America.
Mutation in Torenia fournieri Lind. UFO homolog confers loss of TfLFY interaction and results in a petal to sepal transformation
Authors: Sasaki Katsutomo , Yamaguchi Hiroyasu , Aida Ryutaro , Shikata Masahito , Abe Tomoko , Ohtsubo Norihiro 
Published: May 2012

SummaryWe identified a Torenia fournieri Lind. mutant (no. 252) that exhibited a sepaloid phenotype in which the second whorls were changed to sepal‐like organs. This mutant had no stamens, and the floral organs consisted of sepals and carpels. Although the expression of a torenia class B MADS‐box gene, GLOBOSA (TfGLO), was abolished in the 252 mutant, no mutation of TfGLO was found. Among torenia homologs such as APETALA1 (AP1), LEAFY (LFY), and UNUSUAL FLORAL ORGANS (UFO), which regulate expression of class B genes in Arabidopsis, only accumulation of the TfUFO transcript was diminished in the 252 mutant. Furthermore, a missense mutation was found in the coding region of the mutant TfUFO. Intact TfUFO complemented the mutant phenotype whereas mutated TfUFO did not; in addition, the transgenic phenotype of TfUFO‐knockdown torenias coincided with the mutant phenotype. Yeast two‐hybrid analysis revealed that the mutated TfUFO lost its ability to interact with TfLFY protein. In situ hybridization analysis indicated that the transcripts of TfUFO and TfLFY were partially accumulated in the same region. These results clearly demonstrate that the defect in TfUFO caused the sepaloid phenotype in the 252 mutant due to the loss of interaction with TfLFY.
RPN1a, a 26S proteasome subunit, is required for innate immunity in Arabidopsis
Authors: Yao Chunpeng , Wu Yingying , Nie Haozhen , Tang Dingzhong 
Published: May 2012

SummaryAccumulating evidence shows that proper degradation of proteins that affect defense responses in a positive or negative manner is critical in plant immunity. However, the role of plant degradation systems such as the 26S proteasome in plant immunity is not well understood. Loss‐of‐function mutations in EDR2 (ENHANCED DISEASE RESISTANCE 2) lead to increased resistance to the adapted biotrophic powdery mildew pathogen Golovinomyces cichoracearum. To study the molecular interactions between powdery mildew pathogen and Arabidopsis, we performed a screen for suppressors of edr2 and found that mutation in the gene that encodes RPN1a, a subunit of the 26S proteasome, suppressed edr2‐associated disease resistance phenotypes. In addition, RPN1a is required for edr1‐ and pmr4‐mediated powdery mildew resistance and mildew‐induced cell death. Furthermore, we show that rpn1a displayed enhanced susceptibility to the fungal pathogen G. cichoracearum and to virulent and avirulent bacterial Pto DC3000 strains, which indicated that rpn1a has defects in basal defense and resistance (R) protein‐mediated defense. RPN1a–GFP localizes to both the nucleus and cytoplasm. Accumulation of RPN1a is affected by salicylic acid (SA) and the rpn1a mutant has defects in SA accumulation upon Pto DC3000 infection. Further analysis revealed that two other subunits of the 26S proteasome, RPT2a and RPN8a are also involved in edr2‐mediated disease resistance. Based on these results, we conclude that RPN1a is required for basal defense and R protein‐mediated defense. Our data provide evidence that some subunits of the 26S proteasome are involved in innate immunity in Arabidopsis.
Characteristics of persons who complied with and failed to comply with annual ivermectin treatment
Authors: Brieger William R. , Okeibunor Joseph C. , Abiose Adenike O. , Ndyomugyenyi Richard , Wanji Samuel , Elhassan Elizabeth , Amazigo Uche V. 
Published: May 2012

AbstractObjective  To assess individual compliance with annual ivermectin treatment in onchocerciasis‐endemic villages.Methods  Multi‐site study in eight APOC‐sponsored projects in Cameroon, Nigeria and Uganda to identify the socio‐demographic correlates of compliance with ivermectin treatment. A structured questionnaire was administered on 2305 persons aged 10 years and above. Two categories of respondents were purposively selected to obtain both high and low compliers: people who took ivermectin 6–8 times and 0–2 times previously. Simple descriptive statistics were employed in characterizing the respondents into high and low compliers, while some socio‐demographic and key perceptual factors were employed in regression models constructed to explain levels of compliance among the respondents.Results  Some demographic and perceptual factors associated with compliance were identified. Compliance was more common among men (54.4%) (P < 0.001). Adults (54.6%) had greater rates of high compliance (P < 0.001. The mean age of high compliers (41.5 years) was significantly older (35.8 years) (t = 8.46, P < 0.001). Perception of onchocerciasis and effectiveness of ivermectin influenced compliance. 81.4% of respondents saw benefits in annual ivermectin treatment, high compliance among those who saw benefits was 59.3% compared to 13.3% of those who did not (P < 0.001).Conclusion  Efforts to increase compliance with ivermectin treatment should focus on providing health education to youth and women. Health education should also highlight the benefits of taking ivermectin.
Owner assessment of therapeutic interventions for canine atopic dermatitis: a long‐term retrospective analysis
Authors: Dell Darin L. , Griffin Craig E. , Thompson Lori A. , Griffies Joel D. 
Published: May 2012

Background –  Canine atopic dermatitis is a frequent diagnosis in veterinary medicine; however, the long‐term prognosis for canine atopic dermatitis has not been evaluated in a systematic fashion.Hypothesis/Objectives –  To compare the relative efficacy of commonly used therapies for canine atopic dermatitis in two groups of dogs over 5 and 10 year time periods.Animals –  Dogs were identified from the medical record database of a privately owned veterinary dermatology practice in the USA.Methods –  Clients completed a four‐part, 28‐question, Internet‐based survey. Surveys were included in the analysis if one entire section was completed. Each question was completed independently of the answers to other questions.Results –  Several respondents failed to complete all questions. Some respondents answered similar questions with contradictory answers. Each question was analysed individually. A total of 136 owner surveys were completed, 39 from the 10 year and 97 from the 5 year study dogs. Eighty‐five of 135 respondents indicated that their pet was receiving some form of medical therapy for atopic dermatitis at the time of the survey. Thirty of 90 respondents (33.3%) indicated that their dog improved during a dietary trial. Five dogs met the study’s definition for clinical cure. All five of these dogs had been treated with allergen‐specific immunotherapy.Conclusions and clinical importance –  This study revealed that clients believe antihistamines can be a useful part of multimodal therapy for canine atopic dermatitis. The results also demonstrated that a significant number of canines benefited from dietary modification. In addition, allergen‐specific immunotherapy was the only treatment to induce true clinical remission of atopic dermatitis.
Cues that Spiders (Araneae: Araneidae, Tetragnathidae) Use to Build Orbs: Lapses in Attention to One Set of Cues because of Dissonance with Others?
Authors: Eberhard William G. , Hesselberg Thomas 
Published: May 2012

AbstractEven for small animals such as spiders, behavioral decisions are sometimes influenced by multiple cues. Orb webs constitute exquisitely precise records of the stimuli the spider experienced and the decisions that it made while building its web. In addition, because spiders appear to sense their webs largely by touch, direct behavioral observations can determine which stimuli they probably sense. Previous studies have shown that when an orb‐weaving spider decides how far apart to space successive sticky lines during orb construction, it responds to at least five different kinds of stimuli, all of which apparently use a cue from the web, the location of the previous, inner loop of sticky spiral (IL location), as a point of reference. Here we show that two additional cues from the web, which are related to the position of the temporary spiral (TS), also influence sticky spiral spacing. A combination of direct observations of spider movements, analyses of complete and partially complete webs, and responses to experimental modifications of the web of two species in different families, Micrathena duodecimspinosa (Araneidae) and Leucauge mariana (Tetragnathidae), indicate that both the TS‐IL distance itself and the short‐term memory of the change in TS‐IL distance compared with that on other recently encountered radii correlate with sticky spiral spacing. When the TS‐IL distance was large, the spiders apparently ceased to attend to other cues. Thus, even the relatively stereotyped behavior of orb construction includes variation that stems from attention‐like mental processes.