bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptochrome-dependent magnetic field effect on seizure response in Drosophila larvae
Authors: Marley Richard , Giachello Carlo N. G. , Scrutton Nigel S. , Baines Richard A. , Jones Alex R. 
Published: July 2014

AbstractThe mechanisms that facilitate animal magnetoreception have both fascinated and confounded scientists for decades and its precise biophysical origin remains unclear. Among the proposed primary magnetic sensors is the flavoprotein, cryptochrome, which is thought to provide geomagnetic information via a quantum effect in a light-initiated radical pair reaction. Despite recent advances in the radical pair model of magnetoreception from theoretical, molecular and animal behaviour studies, very little is known of a possible signal transduction mechanism. We report a substantial effect of magnetic field exposure on seizure response in Drosophila larvae. The effect is dependent on cryptochrome, the presence and wavelength of light and is blocked by prior ingestion of typical antiepileptic drugs. These data are consistent with a magnetically-sensitive, photochemical radical pair reaction in cryptochrome that alters levels of neuronal excitation and represent a vital step forward in our understanding of the signal transduction mechanism involved in animal magnetoreception.
Toll-like receptor 9 signaling acts on multiple elements of the germinal center to enhance antibody responses
Authors: Rookhuizen Derek C. , DeFranco Anthony L. 
Published: July 2014

Significance
The antibody response of B lymphocytes proceeds in two phases, a rapid low-affinity response and a slower germinal center (GC) response that is responsible for high-affinity antibody, long-lived antibody-secreting cells, and high-affinity memory B cells. We have examined how immune cell recognition of foreign nucleic acid by Toll-like receptors enhances the GC response and found that it does so by multiple complementary mechanisms. Recognition of foreign nucleic acid by dendritic cells led to increased numbers of helper T cells and GC B cells. In contrast, recognition by the antigen-specific B cells promoted the selection of high-affinity B cells and their differentiation into memory B cells, both of which are central goals for vaccination.
Stationary nanoliter droplet array with a substrate of choice for single adherent/nonadherent cell incubation and analysis
Authors: Shemesh Jonathan , Ben Arye Tom , Avesar Jonathan , Kang Joo H. , Fine Amir , Super Michael , Meller Amit , Ingber Donald E. , Levenberg Shulamit 
Published: July 2014

Significance
There is a substantial need for single-cell platforms in which each cell is chemically isolated in its own microenvironment and a lack of such platforms that support adherent cells. We present here a method that generates stationary nanoliter droplet arrays on a substrate of choice and supports long-term incubation and interrogation of single cells. We demonstrate the encapsulation of single human dermal fibroblast cells and their substrate attachment, viability, and proliferation, and show they can be retrieved and interfaced to standard cell culturing techniques. We also demonstrate a single-cell metabolic assay and track it over selected groups of indexed traps. The device does not require external equipment or machinery, making it available for point-of-care applications.
Genomics and host specialization of honey bee and bumble bee gut symbionts
Authors: Kwong Waldan K. , Engel Philipp , Koch Hauke , Moran Nancy A. 
Published: July 2014

Significance
Gut microbes are increasingly recognized as influential components of animal biology. Genomic, mechanistic, and evolutionary aspects of gut symbiont specialization remain understudied, however, largely due to the complexity of gut communities, especially in vertebrate systems. We show that the simple microbiota of eusocial bees exhibits host specificity and that coresident species in the bee gut possess complementary capabilities for energy metabolism, implying their occupancy in distinct ecological niches. In addition, coresidence in the gut of a host species results in horizontal exchange of genes between unrelated symbionts. Strains in different hosts have diverged, and honey bee symbionts are evolutionarily and functionally distinct from their bumble bee counterparts, indicating that gut symbionts may be critical elements in biological differences among bee species.
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments
Authors: Wen Bo , Xu Shaohang , Sheynkman Gloria M. , Feng Qiang , Lin Liang , Wang Quanhui , Xu Xun , Wang Jun , Liu Siqi 
Published: July 2014

Abstract
Summary: Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface.
Availability and implementation: sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license.
Contact: siqiliu@genomics.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Marine ecosystem acoustics (MEA): quantifying processes in the sea at the spatio-temporal scales on which they occur
Authors: Godø Olav Rune , Handegard Nils Olav , Browman Howard I. , Macaulay Gavin J. , Kaartvedt Stein , Giske Jarl , Ona Egil , Huse Geir , Johnsen Espen 
Published: July 2014

Abstract
Sustainable management of fisheries resources requires quantitative knowledge and understanding of species distribution, abundance, and productivity-determining processes. Conventional sampling by physical capture is inconsistent with the spatial and temporal scales on which many of these processes occur. In contrast, acoustic observations can be obtained on spatial scales from centimetres to ocean basins, and temporal scales from seconds to seasons. The concept of marine ecosystem acoustics (MEA) is founded on the basic capability of acoustics to detect, classify, and quantify organisms and biological and physical heterogeneities in the water column. Acoustics observations integrate operational technologies, platforms, and models and can generate information by taxon at the relevant scales. The gaps between single-species assessment and ecosystem-based management, as well as between fisheries oceanography and ecology, are thereby bridged. The MEA concept combines state-of-the-art acoustic technology with advanced operational capabilities and tailored modelling integrated into a flexible tool for ecosystem research and monitoring. Case studies are presented to illustrate application of the MEA concept in quantification of biophysical coupling, patchiness of organisms, predator–prey interactions, and fish stock recruitment processes. Widespread implementation of MEA will have a large impact on marine monitoring and assessment practices and it is to be hoped that they also promote and facilitate interaction among disciplines within the marine sciences.
First Report of a Leaf Spot of Radermachera sinica in China Caused by Bacillus megaterium
Authors: Li Y. L. , Zhou Z. , Yuan Y. C. , Ye J. R. 
Published: July 2014

Radermachera sinica is widely planted as an ornamental plant in homes, offices, and malls in China. A leaf spot of R. sinica occurred in Luoyang, China, from 2013 to 2014. Lesions mostly occurred in wounds and were irregular with light brown centers and purple borders. One or more lesions on a leaf sometimes covered the entire blade. Eighty plants were surveyed in Luoyang, with disease incidence of 17%. Five millimeter pieces from the borders of lesions were surface-disinfected with 75% ethanol for 30 s, 1% sodium hypochlorite for 5 min, washed three times in sterilized distilled water, placed on nutrient agar (NA) medium at 25°C in darkness, and incubated for 24 to 48 h. Four white, round, smooth, and shiny colonies were selected for further identification. All strains were gram-positive, aerobic rods with many peritrichous flagella, and could grow in medium containing 5% NaCl. The strains were positive for catalase, starch hydrolysis, liquefaction of gelatin, reduction of nitrate, acid production from glucose, mannitol, maltose, lactose, xylose, and pectinose. The strains were positive for phenylalanine deaminase, decomposition of tyrosine, and utilization of citrate. The strains were identified by biochemical tests as Bacillus megaterium (1). To confirm pathogenicity, the strains were grown on NA for 48 h and suspended in sterile distilled water to produce a suspension with a final concentration of 108 CFU/ml. Healthy leaves of biennial R. sinica plants were sterilized with 75% ethanol and washed three times with sterilized distilled water. Fresh wounds were made with a sterile needle on the healthy leaves. Each of four strains was tested by spray inoculation with a bacterial suspension on three leaves. Sterile distilled water was used as negative control. Plants were enclosed in plastic bags and placed in a growth chamber at 28°C with 80% relative humidity. After 5 days, water-soaked lesions were observed. Two weeks later, lesions 4 mm in diameter turned light brown with purple borders, and most of lesions occurred in puncture wounds. Symptoms similar to those observed on field plants developed on all inoculated leaves, while no symptoms appeared on the control leaves. B. megaterium was re-isolated from the lesions of inoculated leaves, but not from the control leaves. To confirm the bacterial identification, PCR was performed on the 16S rDNA gene with P1/P2 (P1: CAGAGTTTGATCCTGGCT, P2: AGGAGGTGATCCAGCCGCA) (2) and 1,463 bp of the 16S rDNA gene (GenBank Accession No. KJ789369) showed 100% sequence identity to B. megaterium DSM 319 (NC_014103.1). To our knowledge, this is the first report of a leaf spot of R. sinica caused by B. megaterium in China as well as anywhere in the world. References: (1) P. Vos et al. Bergey's Manual of Systematic Bacteriology. Vol 3: The Firmicutes. Springer, 2009. (2) W. G. Weisbury et al. J. Bacteriol. 173:697, 1991.
TAA1-Regulated Local Auxin Biosynthesis in the Root-Apex Transition Zone Mediates the Aluminum-Induced Inhibition of Root Growth inArabidopsis
Authors: Yang Zhong-Bao , Geng Xiaoyu , He Chunmei , Zhang Feng , Wang Rong , Horst Walter J. , Ding Zhaojun 
Published: July 2014

AbstractThe transition zone (TZ) of the root apex is the perception site of Al toxicity. Here, we show that exposure of Arabidopsis thaliana roots to Al induces a localized enhancement of auxin signaling in the root-apex TZ that is dependent on TAA1, which encodes a Trp aminotransferase and regulates auxin biosynthesis. TAA1 is specifically upregulated in the root-apex TZ in response to Al treatment, thus mediating local auxin biosynthesis and inhibition of root growth. The TAA1-regulated local auxin biosynthesis in the root-apex TZ in response to Al stress is dependent on ethylene, as revealed by manipulating ethylene homeostasis via the precursor of ethylene biosynthesis 1-aminocyclopropane-1-carboxylic acid, the inhibitor of ethylene biosynthesis aminoethoxyvinylglycine, or mutant analysis. In response to Al stress, ethylene signaling locally upregulates TAA1 expression and thus auxin responses in the TZ and results in auxin-regulated root growth inhibition through a number of auxin response factors (ARFs). In particular, ARF10 and ARF16 are important in the regulation of cell wall modification–related genes. Our study suggests a mechanism underlying how environmental cues affect root growth plasticity through influencing local auxin biosynthesis and signaling.
How detectable is predation in stage‐structured populations? Insights from a simulation‐testing analysis
Authors: Oken Kiva L. , Essington Timothy E. 
Published: July 2014

SummaryThe potential of predation to structure marine food webs is widely acknowledged. However, available tools to detect the regulation of prey population dynamics by predation are limited, partly because available population data often aggregate a population's age structure into a single biomass or abundance metric. Additionally, many food webs are relatively complex, with prey species subject to different assemblages of predators throughout their ontogeny.The goal of this study was to evaluate the extent to which stage‐structured predation could be reliably detected from time series of total biomass of predators and prey.We simulated age‐structured populations of four mid‐trophic‐level fish species with distinct life‐history traits, exposed them to variable predation at different life stages and fit production models to resulting population biomass to determine how reliably the effects of predators could be detected.Predation targeting early life history and juvenile life stages generally led to larger fluctuations in annual production and was therefore more detectable. However, ecologically realistic levels of observation error and environmental stochasticity masked most predator signals. The addition of predation at a second life stage sharply decreased the ability to detect the effect of each predator.We conclude that the absence of detectable species interactions from biomass time series may be partly due to the interactive effects of environmental variability and complex food web linkages and life histories. We also note that predation signals are most robust for predator–prey systems where predators primarily act on mortality of submature life‐history stages. Simulation testing can be applied widely to evaluate the statistical power of analyses to detect predation effects.
A host as an ecosystem:Wolbachiacoping with environmental constraints
Authors: Sicard Mathieu , Dittmer Jessica , Grève Pierre , Bouchon Didier , Braquart‐Varnier Christine 
Published: July 2014

SummaryTheWolbachiaare intracellular endosymbionts widely distributed among invertebrates. These primarily vertically transmittedα‐proteobacteriahave been intensively studied during the last decades because of their intriguing interactions with hosts, ranging from reproductive manipulations to mutualism. To optimize their vertical transmission from mother to offspring, theWolbachiahave developed fine‐tuned strategies. However, theWolbachiaare not restricted to the female gonads and frequently exhibit wide intra‐host distributions. This extensive colonization of somatic organs might be necessary forWolbachiato develop their diverse extended phenotypes. From an endosymbiont's perspective, the within‐host environment potentially presents different environmental constraints. Hence, theWolbachiahave to face different intracellular habitats, their host's immune system as well as other microorganisms co‐occurring in the same host individual and sometimes even in the same cell. A means for theWolbachiato protect themselves from these environmental constraints may be to live ‘hidden’ in vacuoles within host cells. In this review, we summarize the current knowledge regarding the extent of theWolbachiapandemic and discuss the various environmental constraints these bacteria may have to face within their ‘host ecosystem’. Finally, we identify new avenues for future research to better understand the complexity ofWolbachia's interactions with their intracellular environment.
The Prevalence of Encoded Digital Trace Evidence in the Nonfile Space of Computer Media,,
Authors: Garfinkel Simson L. 
Published: July 2014

AbstractForensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP.
Bushfires, Human Health Economics, and Pyrogeography
Authors: BOWMAN DAVID , JOHNSTON FAY 
Published: July 2014

AbstractBushfires (landscape fires) are a key Earth system process that affects humans and our societies and economies. In a recent article, we explored the coupling of humans to landscape fire through the lens of human health impacts of bushfire smoke. We noted that such an approach demands recognition of the indirect impacts and costs of bushfires that cannot be captured by simplistic proxies such as deaths directly attributable to a fire front. Evaluation of direct and indirect economic costs of bushfire disasters, and bushfire fire management remains a poorly developed research frontier that demands collaboration of expertise from a broad cross‐section of fields that often have limited experience of collaborating together. The need for such synthetic thinking about fire's place on Earth has spawned the discipline of pyrogeography.
Organisational Capacity for Engaging with Indigenous Australians
Authors: HOWITT RICHARD , COLYER CLAIRE , HAMMER MITCHELL R. , HAVNEN OLGA , HUCHENDORF KAREN , HUBERT CAROL 
Published: July 2014

AbstractCommunity capacity building is a common goal for programmes and policies involving Indigenous peoples, but it relies heavily on organisational capacity to work effectively in intercultural settings. This paper reviews the organisational capacity of the senior leaders of Australian Red Cross and institutional efforts to build a culturally appropriate and respectful organisation. It reports results from a survey of the organisation's leadership team and follow‐up interviews undertaken in 2010, reviews the challenges facing the organisation in working with Aboriginal and Torres Strait Islander Australians, and considers institutional progress in building internal capacity to lead change in working with Aboriginal and Torres Strait Islander Australians. The paper concludes with discussion of wider implications of this research.
Meteorological Sub‐divisional Scale Rainfall Monitoring Using Kalpana‐1 VHRR Measurements
Authors: MAHESH C. , PRAKASH S. , GAIROLA R.M. , SHAH S. , PAL P.K. 
Published: July 2014

AbstractGeostationary satellites provide measurements over a wider geographical area with high temporal sampling, while microwave measurements are more accurate but sparse. For continuous monitoring of the Indian monsoon, geostationary platform would be ideal. In this study, INSAT (Indian National Satellite) Multi‐spectral Rainfall Algorithm (IMSRA) has been used for the estimation of rainfall from Kalpana‐1 very high resolution radiometer (VHRR) measurements. IMSRA benefits from the relative advantages of infrared and microwave sensors and is operational at the India Meteorological Department (IMD). In this paper, rainfall is estimated over India at meteorological sub‐divisional scale during the south‐west monsoon season of 2009 using Kalpana‐1 satellite measurements. This is the first experimental attempt to generate meteorological sub‐divisional scale rainfall maps using Kalpana‐1 satellite measurements. The rainfall maps for the south‐west monsoon season over the Indian land region are successfully utilised as a space input for the drought monitoring of the year 2009. The results have been compared with the IMD gauge‐based accumulated rainfall maps at monthly and seasonal time scales. The qualitative comparison suggests that rainfall maps generated using the present methodology is in good agreement with the IMD rainfall maps. The quantitative comparison of the sub‐divisional monthly accumulated rainfall shows a correlation of 0.77 and standard error of 71 mm over the non‐orographic regions, whereas a correlation of 0.60 and standard error of 117 mm is observed over the orographic regions. The present study shows that Kalpana‐1 satellite‐based rainfall estimates (IMSRA technique) can act as a complementary tool for the monsoon monitoring over the Indian meteorological sub‐divisions and can be used for various meteorological and hydrological applications.
Mapping 100 Years of Thornthwaite Moisture Index: Impact of Climate Change in Victoria, Australia
Authors: LEAO SIMONE 
Published: July 2014

AbstractGeographer C. W. Thornthwaite proposed in 1948 a moisture index called Thornthwaite Moisture Index (TMI) as part of a water balance model for a new classification system for climate. The importance of TMI climatic classification has been recognised in many areas of knowledge and practice worldwide over the last 60 years. However, although past climate research was focused on developing adequate methods for climate classification, current research is more concerned with understanding the patterns of climate change. The use of TMI as an indicator for climate change is still an incipient area of research. The contributions of this paper are twofold. First, it is to fully document a methodology based on geostatistics adopted to produce a time series of TMI maps that are accurate and have high spatial resolution. The state of Victoria, in Australia, over the last century, is used as the case study. Second, by analysing these maps, the paper presents a general evaluation of the spatial patterns found in Victoria related to moisture variability across space and over time. Some potential implications of the verified moisture changes are discussed, and a number of ideas for further development are suggested.
Flavobacterium psychrophilum vaccine development: a difficult task
Authors: Gómez Esther , Méndez Jessica , Cascales Desirée , Guijarro José A. 
Published: July 2014

SummaryBacterial cold water disease (BCWD) is a globally distributed freshwater fish disease caused by the Gram‐negative bacterium Flavobacterium psychrophilum. It is a particularly devastating infection in fry salmonids and may lead to high levels of mortality. In spite of its economic impact on fish farms, neither the biology of the bacterium nor the bacterium–host interactions are well understood. This review provides a synopsis of the major problems related to critical remaining questions about research into the use of vaccines against F. psychrophilum and the development of a commercial vaccine against this disease. Studies using sera from convalescent rainbow trout have shown the antigenic properties of different proteins such as OmpH, OmpA and FspA, as well as low and high molecular mass lipopolysaccharide of F. psychrophilum, which are potential candidates for subunit vaccines. Inactivated F. psychrophilum bacterins have been successfully tested as vaccines under laboratory conditions by both immersion and intraperitoneal routes. However, the efficacy and the practical usefulness of these preparations still have to be proved. The use of attenuated and wild‐type strains to immunize fish showed that these systems offer high levels of protection. Nevertheless, their application clashes with the regulations for environmental protection in many countries. In conclusion, protective vaccines against BCWD are theoretically possible, but substantial efforts still have to be made in order to permit the development of a commercial vaccine.