bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Bursaphelenchus yongensis on Pinus rigida in Korea
Authors: Han H. 
Published: September 2014

During a pinewood nematode survey in 2011, a dead pitch pine (Pinus rigida) was found in Daejeon city, Korea. Samples were taken from several regions of the trunk and nematodes were extracted from the wood samples by a modified Baermann funnel method (1). Recovered nematodes were then cultured on Botrytis cinerea grown in potato dextrose agar (PDA) medium. Males and females (n = 10) were examined under an inverted light microscope. Morphologically, these nematodes were identified as Bursaphelenchus yongensis sharing the characters of the genus Bursaphelenchus including a large median bulb, offset cephalic region, a well-developed stylet with small basal knobs, female with vulva at 70% of body length, and males with terminal bursa. Females of B. yongensis were similar to B. muconatus and B. fraudulentus by presence of tail mucron, but they were differentiated by a smaller vulval flap. Males had spicules with small cucullus, pointed rostrum, and with strongly dorsally bent condylus. The identity of the nematode was confirmed through molecular diagnosis. DNA was extracted from each of 10 nematodes using commercial DNeasy kits (Qiagen, Valencia, CA) and the ITS regions were amplified with a primer set by PCR (Bio Rad, US/PTC-0220) (3,5). Amplified ITS DNA was cloned and sequenced, and the sequence data was deposited to GenBank (Accession No. KJ857070). The ITS sequence of Korean isolate (KJ857070) showed 99% similarity to that from Chinese isolate in GenBank (AM180513). ITS-RFLP patterns using five different restriction enzymes, RsaI, HaeIII, MspI, HinfI, and AluI, matched 100% with those previously reported for B. yongensis (2,4). Host pathogenicity tests were conducted from June to August on saplings of five native and introduced conifer species found in Korea (Abies sp., Larix leptolepsis, P. koraiensis, P. strobus, and P. thunbergii). All saplings were 5 to 6 years old and 15 saplings were inoculated for each species. B. yongensis was cultures on B. cinerea for 10 days at 25°C and the inoculum concentration was calibrated at 5,000 nematodes/50 μl sterile water. Nematodes were artificially inoculated by making a 1-cm-long incision into the stem using a sterile razor blade. B. yongensis was pathogenic on L. leptolepsis, causing wilt and death in all inoculated saplings; however, the nematode had no effect on P. thunbergii, P. koraiensis, Abies sp., or P. strobus. To our knowledge, this is the first report of B. yongensis in Korea. This nematode is a potential threat to L. leptolepsis; however, the role of B. yongensis in the mortality of P. rigida is uncertain at this time. References: (1) S. M. Ayoub. Plant Nematology in Agricultural Training Aid. Department of Food and Agriculture, Division of Plant Industry, Sacramento, CA, 1977. (2) W. Burgermeister et al. Nematology 11:649, 2009. (3) V. R. Ferris et al. Fund. Appl. Nematol. 16:177, 1993. (4) J. Gu et al. Russian J. Nematol. 14:91, 2006. (5) T. C. Vrain. J. Nematol. 25:361, 1993.
First Report of Leaf Spot Disease in Coconut Seedling Caused by Bipolaris setariae in China
Authors: Niu X.-Q. , Yu F.-Y. , Zhu H. , Qin W.-Q. 
Published: September 2014

Coconut (Cocos nucifera L.), an important oilseed as well as a multipurpose perennial plantation crop, is distributed and planted in humid tropical areas. In October 2012, a new leaf spot disease was observed on 3-year-old coconut seedlings in Wenchang, Hainan Province, China. The symptom first appeared as spindly or elliptical and brown flecks with water-soaked lesions that became yellow with the progress of the disease. In the later stage of the disease, the lesions merged together, gradually expanding to the leaf apex. In recent years, the disease has been prevalent in all the nursery gardens surveyed. Once young leaves got infected and nearly all the leaves of the tree showed diseased symptoms, the coconut eventually became defoliated. The pathogen was isolated from the lesion margin, surface sterilized with 75% ethanol and 0.1% mercury bichloride, washed by sterile distilled water, and then placed excising pieces of leaves from the leision margin onto potato dextrose agar (PDA). Plates were incubated at 25°C for 4 days. After 7 days, the colony was grayish black and produced black pigment in the medium. Aerial mycelium was fluffy, septate, and branched, the conidiophores were slightly flexuous or straight, 5 to 11 μm thick, and produced curved, spindle-shaped, or fusiform, septate conidia with 4 to 10 septa, measuring 39 to 86 × 9 to 16 μm, with a slightly protuberant hilum, truncated. Based on the symptoms and mycelial and conidial characters above, the fungus was identified as Bipolaris setariae (1). The pathogenicity was established and repeated for six times by following Koch's postulates. Two 1-year-old coconut seedlings were washed with sterilized water and six leaves were wounded with a sterile needle and then inoculated by spraying them with a suspension of conidia of the isolate. The seedlings were kept in two incubators at 25°C for 12 days. Inoculated leaves showed typical symptoms similar to those described above. The pathogen was re-isolated from inoculated leaves. Morphological characteristics were identical to the original isolated fungus. In contrast, the control leaves did not show any symptoms. The genomic DNA of this fungus was extracted, amplification of the internal transcribed spacer (ITS) region was performed with primer ITS1 and ITS4, and the purified PCR product was sequenced (GenBank Accession No. KJ605157). BLASTn analysis revealed 99% sequence similarity with four B. setariae isolates (HE792936.1, JX462256, GU073108.1, and FJ606786.1). Morphologic characters and sequence analysis of the ITS rDNA confirmed that the pathogen was B. setariae. Bipolaris incurvata has been reported causing disease on coconut (2), but B. setariae was not previously reported on coconut. So far, this is the first report of B. setariae caused coconut seedling leaf spot disease in Hainan, China. References: (1) K. C. da Cunha et al. J. Clin. Microbiol. 50:4061, 2012. (2) A. Kamalakannan et al. New Dis. Rep. 12:18, 2005.
Some new addition formulae for Weierstrass elliptic functions
Authors: Eilbeck J. Chris , England Matthew , Ônishi Yoshihiro 
Published: September 2014

We present new addition formulae for the Weierstrass functions associated with a general elliptic curve. We prove the structure of the formulae in
n
-variables and give the explicit addition formulae for the 2- and 3-variable cases. These new results were inspired by new addition formulae found in the case of an equianharmonic curve, which we can now observe as a specialization of the results here. The new formulae, and the techniques used to find them, also follow the recent work for the generalization of Weierstrass functions to curves of higher genus.
BoCluSt: bootstrap clustering stability algorithm for community detection in networks
Authors: Garcia Carlos 
Published: September 2014

AbstractBackgroundThe identification of modules or communities of related variables is a key step in the analysis and modelling of biological systems. Many module identification procedures are available, but few of these can determine the module partitions best fitting a given dataset in the absence of previous information, in an unsupervised way, and when the links between variables have different weights. Here I propose such a procedure, which uses the stability under bootstrap resampling of different alternative module structures as a criterion to identify the structure best fitting to a set of variables. In its present implementation, the procedure uses linear correlations as link weights.ResultsComputer simulations show that the procedure is useful for problems involving moderate numbers of variables, such as those commonly found in gene regulation cascades or metabolic pathways, and also that it can detect hierarchical network structures, in which modules are composed of smaller sub modules. The procedure becomes less practical as the number of variables increases, due to increases in processing time.ConclusionsThe proposed procedure may be a valuable and robust network analysis tool. Because it is based on comparing the amount of evidence for different module partitions structures, this procedure may detect the existence of hierarchical network structures.
ProbAlign: a re-alignment method for long sequencing reads
Authors: Zeng Feng , Jiang Rui , Ji Guoli , Chen Ting 
Published: September 2014

AbstractThe incorrect alignments are a severe problem in variant calling, and remain as a challenge computational issue in Bioinformatics field. Although there have been some methods utilizing the re-alignment approach to tackle the misalignments, a standalone re-alignment tool for long sequencing reads is lacking. Hence, we present a standalone tool to correct the misalignments, called ProbAlign. It can be integrated into the pipelines of not only variant calling but also other genomic applications. We demonstrate the use of re-alignment in two diverse and important genomics fields: variant calling and viral quasispecies reconstruction. First, variant calling results in the Pacific Biosciences SMRT re-sequencing data of NA12878 show that false positives can be reduced by 43.5%, and true positives can be increased by 24.8% averagely, after re-alignment. Second, results in reconstructing a 5-virus-mix show that the viral population can be completely unraveled, and also the estimation of quasispecies frequencies has been improved, after re-alignment. ProbAlign is freely available in the PyroTools toolkit (https://github.com/homopolymer/PyroTools).
Scleroderma renal crisis following pericardial effusion in a Japanese female
Authors: Shu En , Kanoh Hiroyuki , Seishima Mariko 
Published: September 2014

AbstractScleroderma renal crisis (SRC) occurs in 4–5% of Japanese patients with systemic sclerosis (SSc) and is one of the most severe complications, along with interstitial pneumonia and pulmonary hypertension, which lead to a poor outcome. The factors predicting SRC include diffuse progressive skin thickening, a duration of SSc of 4 years or less, having autoantibodies against RNA polymerase III, systemic corticosteroid (CS) administration and recent cardiac events, including pericarditis. We herein report a female case of SRC preceded by pericardial effusion during the treatment with CS for rapidly progressive skin thickening. She had none of the known autoantibodies and was successfully treated with an angiotensin II receptor blocker.
The Effect of Light Exposure on the Degradation of Latent Fingerprints on Brass Surfaces: The Use of Silver Electroless Deposition as a Visualization Technique
Authors: Payne Imogen C. , McCarthy Imogen , Almond Matthew J. , Baum John V. , Bond John W. 
Published: September 2014

AbstractWe have studied the degradation of sebaceous fingerprints on brass surfaces using silver electroless deposition (SED) as a visualization technique. We have stored fingerprints on brass squares either (i) in a locked dark cupboard or (ii) in glass‐filtered natural daylight for periods of 3 h, 24 h, 1 week, 3 weeks, and 6 weeks. We find that fingerprints on brass surfaces degrade much more rapidly when kept in the light than they do under dark conditions with a much higher proportion of high‐quality prints found after 3 or 6 weeks of aging when stored in the dark. This process is more marked than for similar fingerprints on black PVC surfaces. Identifiable prints can be achieved on brass surfaces using both SED and cyanoacrylate fuming (CFM). SED is quick and straightforward to perform. CFM is more time‐consuming but is versatile and can be applied to a wider range of metal surfaces than SED, for example brass surfaces which have been coated by a lacquer.
Soybean aphid intrabiotype variability based on colonization of specific soybean genotypes
Authors: Pawlowski Michelle , Hill Curtis B. , Voegtlin David J. , Hartman Glen L. 
Published: September 2014

AbstractThe soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is one of the most destructive insect pests on soybeans in the United States. One method for managing this pest is through host plant resistance. Since its arrival in 2000, 4 aphid biotypes have been identified that are able to overcome soybean aphid resistance (Rag) genes. A soybean aphid isolate collected from Moline, Illinois readily colonized soybean plants with the soybean aphid resistance gene Rag2, unlike biotypes 1 and 2, but similar to soybean aphid biotype 3. Two no‐choice experiments compared the virulence of the Moline isolate with biotype 3. In both experiments, differences in aphid population counts were not significant (P > 0.05) on soybean genotypes LD08–12957a (Rag2) and LD11–5413a (Rag2), but the aphid counts for the Moline isolate were significantly (P < 0.05) lower than the aphid counts for the biotype 3 isolate on the soybean genotypes Dowling (Rag1), LD05–16611 (Rag1), LD11–4576a (Rag1), and PI 567598B (rag1b and rag3). The Moline isolate was a variant of aphid biotype 3, which is the first report showing that soybean aphid isolates classified as the same biotype, based on virulence against specific Rag genes, can differ in aggressiveness or ability to colonize specific host genotypes.
Fly‐In/Fly‐Out, Flexibility and the Future: Does Becoming a Regional FIFO Source Community Present Opportunity or Burden?
Authors: MCKENZIE FIONA , HASLAM MCKENZIE FIONA , HOATH AILEEN 
Published: September 2014

AbstractThe resources boom in Australia has resulted in considerable competition for labour, particularly in remote mining areas. Shortage of skilled labour has led mining companies to source workers from far afield, while the high incomes created by a tight labour market draw labour from across the country through long‐distance commuting arrangements such as fly‐in/fly‐out (FIFO). While much recent literature has focused on the impacts on receiving communities of these long‐distance commuters, less attention has been given to the experience of source communities. This paper compares the situation between two regional towns in which long‐distance commuters reside. The first, Busselton in Western Australia, is among several chosen by Rio Tinto to be labour source communities. The second, Stawell in Victoria, is looking to long‐distance commuting as a response to the impending closure of their existing gold mine. Hence the case studies offer not only insights into source communities' experience of long‐distance commuting, but also a comparison between the bottom‐up approach of Stawell in trying to establish FIFO with the experience of Busselton as an example of top‐down labour sourcing. This paper seeks to highlight some of the development challenges encountered by communities and offer solutions as to how these might be addressed for the future.
Large‐scale spatial analysis of ringing and re‐encounter data to infer movement patterns: A review including methodological perspectives
Authors: Thorup Kasper , Korner‐Nievergelt Fränzi , Cohen Emily B. , Baillie Stephen R. 
Published: September 2014

SummaryA major aim of bird ringing is to provide information about the migration and movements of bird populations. However, in comparison with demographic studies, little research has been devoted to improving quantitative inferences through large‐scale spatial analyses. This represents a serious knowledge gap because robust information on geographical linkages of migratory populations throughout the annual cycle is necessary to understand the ecology and evolution of migrants and for the conservation and management of populations.Here, we review recent developments and emerging opportunities for the quantitative study of movements of bird populations based on marked birds. Large‐scale spatial analyses of ringing data need to account for spatiotemporal variation in re‐encounter probability and the complexity of movement processes, including variability among individuals and populations in migration direction and distance.We identify seven recent studies that used quantitative methods for large‐scale spatial analyses of ringing and re‐encounter data gathered by national ringing centres. In most cases, numbers ringed and recovered in a series of source and destination areas were used to derive estimates of the proportion of each source population travelling to each destination area. Where recovery data were sparse, precision was improved by incorporating information on re‐encounter probabilities of similar species. When numbers ringed were not available, inferences could sometimes be drawn based on local recapture data from the source areas.Studies to date illustrate that analyses of these large‐scale ringing data sets can provide robust quantitative inferences. Further work is needed to develop these modelling approaches and to test their sensitivity to key assumptions using both real and simulated data. Data for all birds that were marked, not only those re‐encountered, are often inaccessible and should be computerised in parallel with analytical developments. Further, there is great potential for the formal combination of re‐encounter data with information from additional data sources such as counts and detailed movement data from radiotracking or data loggers. Because data from bird ringing operations cover long periods of time and exist in large quantities, they hold great promise for inferring spatiotemporal migration patterns, including changes in relation to climate, land use change and other environmental drivers.
Damage functions and thermal requirements of Meloidogyne javanica and Meloidogyne incognita on watermelon
Authors: López‐Gómez M. , Gine A. , Vela M.D. , Ornat C. , Sorribas F.J. , Talavera M. , Verdejo‐Lucas S. 
Published: September 2014

ABSTRACTThe relationship between the initial (Pi) and final (Pf) population densities of Meloidogyne javanica and yield of watermelon, Citrullus lanatus, cv. Sugar Baby were determined in pot and field experiments. In the pots, the maximum reproduction rate of the nematode was 14, and the equilibrium density was 49 400 eggs/100 cm3 of soil. Yield data represented as fresh top weight fitted the Seinhorst damage function (P < 0.001, R2 = 0.7), and the minimum relative yield (m) was 0.65 at Pi ≥ 3200 eggs/100 cm3 of soil and the tolerance limit (T) 74 eggs/100 cm3. In the field experiments (2011 and 2012), the maximum reproduction rate was 73 and 70, and the equilibrium density 32 and 35 second‐stage juveniles (J2)/100 cm3 soil. Yield data represented as fruit weight fitted the Seinhorst damage function in 2011 (P < 0.001, R2 = 0.92) and the m‐ and T‐values were 0.63 and 20 J2/100 cm3 of soil, respectively. Meloidogyne incognita and M. javanica needed similar length of time for development to egg‐laying females and life cycle completion at 24.4°C.
Molecular basis of reduced birth weight in smoking pregnant women: mitochondrial dysfunction and apoptosis
Authors: Garrabou Glòria , Hernàndez Ana‐Sandra , Catalán García Marc , Morén Constanza , Tobías Ester , Córdoba Sarai , López Marta , Figueras Francesc , Grau Josep M. , Cardellach Francesc 
Published: September 2014

AbstractIn utero exposure of fetuses to tobacco is associated with reduced birth weight. We hypothesized that this may be due to the toxic effect of carbon monoxide (CO) from tobacco, which has previously been described to damage mitochondria in non‐pregnant adult smokers. Maternal peripheral blood mononuclear cells (PBMCs), newborn cord blood mononuclear cells (CBMCs) and placenta were collected from 30 smoking pregnant women and their newborns and classified as moderate and severe smoking groups, and compared to a cohort of 21 non‐smoking controls. A biomarker for tobacco consumption (cotinine) was assessed by ELISA (enzyme‐linked immunosorbent assay). The following parameters were measured in all tissues: mitochondrial chain complex IV [cytochrome c oxidase (COX)] activity by spectrophotometry, mitochondrial DNA levels by reverse transcription polymerase chain reaction, oxidative stress by spectrophotometric lipid peroxide quantification, mitochondrial mass through citrate synthase spectrophotometric activity and apoptosis by Western blot parallelly confirmed by TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labelling) assay in placenta. Newborns from smoking pregnant women presented reduced birth weight by 10.75 percent. Materno‐fetal mitochondrial and apoptotic PBMC and CBMC parameters showed altered and correlated values regarding COX activity, mitochondrial DNA, oxidative stress and apoptosis. Placenta partially compensated this dysfunction by increasing mitochondrial number; even so ratios of oxidative stress and apoptosis were increased. A CO‐induced mitotoxic and apoptotic fingerprint is present in smoking pregnant women and their newborn, with a lack of filtering effect from the placenta. Tobacco consumption correlated with a reduction in birth weight and mitochondrial and apoptotic impairment, suggesting that both could be the cause of the reduced birth weight in smoking pregnant women.
Decomposition and nutrient release patterns of mistletoe litters in a semi‐arid savanna, southwest Zimbabwe
Authors: Ndagurwa Hilton G. T. , Dube John S. , Mlambo Donald 
Published: September 2014

AbstractNutrient loss from litter plays an essential role in carbon and nutrient cycling in nutrient‐constrained environments. However, the decomposition and nutrient dynamics of nutrient‐rich mistletoe litter remains unknown in semi‐arid savanna where productivity is nutrient limited. We studied the decomposition and nutrient dynamics (nitrogen: N, phosphorous; P, carbon: C) of litter of three mistletoe species, Erianthemum ngamicum, Plicosepalus kalachariensis, and Viscum verrucosum and N‐fixing Acacia karroo using the litter‐bag method in a semi‐arid savanna, southwest Zimbabwe. The temporal dynamics of the soil moisture content, microbial populations, and termite activity during decomposition were also assessed. Decay rates were slower for A. karroo litter (k = 0.63), but faster for the high quality mistletoe litters (mean k‐value = 0.79), which supports the premise that mistletoes can substantially influence nutrient availability to other plants. Nitrogen loss was between 1.3 and 3 times greater in E. ngamicum litter than in the other species. The litter of the mistletoes also lost C and P faster than A. karroo litter. However, soil moisture content and bacterial and fungal colony numbers changed in an opposite direction to changes in the decomposition rate. Additionally, there was little evidence of termite activity during the decay of all the species litters. This suggests that other factors such as photodegradation could be important in litter decomposition in semi‐arid savanna. In conclusion, the higher rate of decay and nutrient release of mistletoe than A. karroo litter indicate that mistletoes play an important role in carbon and nutrient fluxes in semi‐arid savanna.