bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable effects of termite mounds on African savanna grass communities across a rainfall gradient
Authors: Davies Andrew B. , Robertson Mark P. , Levick Shaun R. , Asner Gregory P. , van Rensburg Berndt J. , Parr Catherine L. 
Published: May 2014

AbstractQuestionsTermite mounds of the genus Macrotermes are prominent features in African savannas, forming nutrient hotspots that support greater plant diversity, which is of higher nutritional value than the surrounding savanna matrix. However, little is known about grass communities on and around mounds or how the functional importance of mounds varies across sites. As mean annual rainfall increases, savannas in southern Africa become increasingly dystrophic through increased denitrification (including pyrodenitrification) and the leaching of soil nutrients. The functional importance of mounds is concomitantly expected to increase as the difference in foliar nutrient levels between mounds and the savanna matrix increases. We tested this prediction on grass communities across a rainfall gradient to: (i) determine the degree to which grass assemblages differ between termite mounds and the savanna matrix; (ii) determine the spatial extent to which mounds influence grass communities; and (iii) investigate whether these patterns differ across savanna types.LocationKruger National Park, South Africa.MethodsGrass communities were surveyed at three savanna sites differing in mean annual rainfall (550–750 mm·yr−1). Grass diversity and tissue nitrogen concentrations were measured on and off termite mounds and along transects away from mounds in order to calculate the spatial influence of termite mounds on savanna grass communities. Using termite mound densities estimated from airborne LiDAR, we up‐scaled field‐based results to determine the percentage of the landscape influenced by Macrotermes termite activity.ResultsAlthough species richness of grasses was lower on mounds than in the savanna matrix, the assemblage composition varied significantly, with higher nutrient concentrations in grasses located on mounds. This pattern became more distinct with increasing rainfall. The spatial extent of these nutrient‐rich grasses also differed across the rainfall gradient, with a larger sphere of influence around mounds in wetter areas. Mounds distinctly altered grass communities over ca. 2% of the entire landscape.ConclusionsOur results show that Macrotermes mounds are important components of savanna heterogeneity, and reveal that the functional importance of mounds increases with increasing rainfall.
Growth and population dynamics of the non‐indigenous species Branchiomma luctuosum Grube (Annelida, Sabellidae) in the Ionian Sea (Mediterranean Sea)
Authors: Mastrototaro Francesco , Chimienti Giovanni , Matarrese Alfonso , Gambi Maria Cristina , Giangrande Adriana 
Published: May 2014

AbstractThe population dynamics and gametogenesis of the non‐indigenous polychaete species Branchiomma luctuosum Grube, 1869 (Annelida, Sabellidae) has been investigated at three sites in the Taranto Seas (Ionian Sea, Mediterranean Sea). The species, probably introduced from the Red Sea, has been reported in the Mediterranean Sea since 1983. The species is hermaphrodite, and the reproductive season is between June and October when the largest mean size of oocytes was recorded together with the presence of mature spermatozoa. Small oocytes are present in specimens reaching about 20–25 mm in length. Therefore oogenesis seems to begin early during the first year of life, but the first reproduction can occur when the worms attain a larger size and are at least 6 months of age. Although most of the individuals reproduce seasonally within a discrete period, some individuals can reproduce in different periods during the year, the oogenesis of individuals not being synchronous. A life span of at least 2 years is highlighted, with a faster growth rate during the first months (about 20 mm per month) decreasing to about 10 mm from the 3rd to the 8th months and slowing down again after the worm reaches 100 mm in size. Some differences in growth performance are discussed, enhanced by comparing the sites located at greater depth (5–7 m) and those located at 0.5 m depth, together with the possible interactions of this alien species with the autochthonous sabellid Sabella spallanzanii.
Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations
Authors: Bosse Mirte , Megens Hendrik‐Jan , Madsen Ole , Frantz Laurent A. F. , Paudel Yogesh , Crooijmans Richard P. M. A. , Groenen Martien A. M. 
Published: May 2014

AbstractThe merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine‐scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.
A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
Authors: Kawakami Takeshi , Smeds Linnéa , Backström Niclas , Husby Arild , Qvarnström Anna , Mugal Carina F. , Olason Pall , Ellegren Hans 
Published: May 2014

AbstractDetailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high‐density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best‐order map contained 4215 markers, with a total distance of 3132 cM and a mean genetic distance between markers of 0.12 cM. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second‐generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super‐scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cM/Mb and correlated closely with chromosome size, from 2 cM/Mb for chromosomes >100 Mb to >10 cM/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cM was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
Authors: De Kort Hanne , Vandepitte Katrien , Bruun Hans Henrik , Closset‐Kopp Déborah , Honnay Olivier , Mergeay Joachim 
Published: May 2014

AbstractThe adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought‐sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping‐by‐sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation by distance, the very low genetic differentiation among populations and the high intrapopulation genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.
Comparative analysis of Gram's stain, PNA‐FISH and Sepsityper with MALDI‐TOF MS for the identification of yeast direct from positive blood cultures
Authors: Gorton Rebecca L. , Ramnarain P. , Barker K. , Stone N. , Rattenbury S. , McHugh T. D. , Kibbler C. C. 
Published: May 2014

SummaryFungaemia diagnosis could be improved by reducing the time to identification of yeast from blood cultures. This study aimed to evaluate three rapid methods for the identification of yeast direct from blood cultures; Gram's stain analysis, the AdvanDX Peptide Nucleic Acid in Situ Hybridisation Yeast Traffic Light system (PNA‐FISH YTL) and Bruker Sepsityper alongside matrix‐assisted laser desorption ionisation time of flight mass spectrometry (MALDI‐TOF MS). Fifty blood cultures spiked with a known single yeast strain were analysed by blinded operators experienced in each method. Identifications were compared with MALDI‐TOF MS CHROMagar Candida culture and ITS rRNA sequence‐based identifications. On first attempt, success rates of 96% (48/50) and 76% (36/50) were achieved using PNA‐FISH YTL and Gram's stain respectively. MALDI‐TOF MS demonstrated a success rate of 56% (28/50) when applying manufacturer's species log score thresholds and 76% (38/50) using in‐house parameters, including lowering the species log score threshold to >1.5. In conclusion, PNA‐FISH YTL demonstrated a high success rate successfully identifying yeast commonly encountered in fungaemia. Sepsityper™ with MALDI‐TOF MS was accurate but increased sensitivity is required. Due to the misidentification of commonly encountered yeast Gram's stain analysis demonstrated limited utility in this setting.
Legal Reform, Contract Enforcement and Firm Size in Mexico
Authors: Dougherty Sean M. 
Published: May 2014

AbstractThe variation in legal system quality across states in Mexico is used to examine the relationship between judicial quality and firm size over the course of the 2000s, when systemic changes were taking place. Using economic census microdata and survey‐based measures of legal institutions, a robust effect of judicial quality is observed on the firm size distribution and efficiency, instrumenting for underlying historical determinants of institutions. Indicative evidence is found that the effect is strongest in more capital‐intensive industries. Market size and distance‐to‐market are also found to matter for firm size outcomes, consistent with the new trade literature.
Mapping Large Spatial Flow Data with Hierarchical Clustering
Authors: Zhu Xi , Guo Diansheng 
Published: May 2014

AbstractIt is challenging to map large spatial flow data due to the problem of occlusion and cluttered display, where hundreds of thousands of flows overlap and intersect each other. Existing flow mapping approaches often aggregate flows using predetermined high‐level geographic units (e.g. states) or bundling partial flow lines that are close in space, both of which cause a significant loss or distortion of information and may miss major patterns. In this research, we developed a flow clustering method that extracts clusters of similar flows to avoid the cluttering problem, reveal abstracted flow patterns, and meanwhile preserves data resolution as much as possible. Specifically, our method extends the traditional hierarchical clustering method to aggregate and map large flow data. The new method considers both origins and destinations in determining the similarity of two flows, which ensures that a flow cluster represents flows from similar origins to similar destinations and thus minimizes information loss during aggregation. With the spatial index and search algorithm, the new method is scalable to large flow data sets. As a hierarchical method, it generalizes flows to different hierarchical levels and has the potential to support multi‐resolution flow mapping. Different distance definitions can be incorporated to adapt to uneven spatial distribution of flows and detect flow clusters of different densities. To assess the quality and fidelity of flow clusters and flow maps, we carry out a case study to analyze a data set of 243,850 taxi trips within an urban area.
Peritonitis caused by Blastomyces dermatitidis in a kidney transplant recipient: case report and literature review
Authors: Barocas J.A. , Gauthier G.M. 
Published: May 2014

AbstractBlastomyces dermatitidis is a dimorphic fungus endemic to the midwestern, south‐central, and southeastern United States known to cause disseminated infection in immunocompromised individuals. We report a case of B. dermatitidis peritonitis in a renal allograft recipient with new‐onset ascites and cytomegalovirus encephalitis. Peritoneal blastomycosis is a rare clinical entity and, to our knowledge, this patient represents the first known case of peritoneal blastomycosis in a solid organ transplant recipient. We review the clinical characteristics of B. dermatitidis peritonitis as well as the literature on fungal peritonitis with emphasis on dimorphic fungal pathogens. Clinical features suggestive of fungal peritonitis include new‐onset ascites, abdominal pain, and fevers, especially with antecedent or concomitant pneumonia. A high index of clinical suspicion, along with the use of culture and non‐culture diagnostics, is needed for early diagnosis and prompt initiation of therapy.
Control of clonorchiasis in Korea: effectiveness of health education for community leaders and individuals in an endemic area
Authors: Oh Jin‐Kyoung , Lim Min Kyung , Yun E. Hwa , Cho Heeyoun , Park Eun Young , Choi Min‐Ho , Shin Hai‐Rim , Hong Sung‐Tae 
Published: May 2014

AbstractObjectivesTo develop effective intervention programmes to control Clonorchis sinensis infection, three interventions were evaluated in a clonorchiasis‐endemic area of Korea.MethodsFour thousand two hundred and sixty‐seven voluntary participants in Sancheong county were tested at baseline and two follow‐up surveys after 1 and 3 years. Faecal samples were examined for C. sinensis eggs using the Kato‐Katz method. Participants were divided into three intervention groups by areas and year recruited: national prevention programme only (mass health campaign and praziquantel treatment) for Group A; health education for community leaders added for Group B; and individual health education added for Group C.ResultsThe prevalence of C. sinensis infection fell substantially in all three intervention groups between baseline and 3‐year follow‐up: from 31.1% to 14.9% in Group A, from 29.6% to 6.8% in Group B and from 21.9% to 8.6% in Group C. The control effectiveness was highest in Group B with 76.8%. The new infection rate was 16.3%, 12.8% and 7.6% in Group A, B and C, respectively. The reinfection rate was lower in Group B (3.8%) than Group C (12.2%).ConclusionsTo control C. sinensis infection in endemic areas of Korea, health education for community leaders or individuals on prevention of C. sinensis infection should be added to national control programmes.
RNA‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA
Authors: Böhmdorfer Gudrun , Rowley M. Jordan , Kuciński Jan , Zhu Yongyou , Amies Ivan , Wierzbicki Andrzej T. 
Published: May 2014

SummaryRibonucleic acid‐mediated transcriptional gene silencing (known as RNA‐directed DNA methylation, or RdDM, in Arabidopsis thaliana) is important for influencing gene expression and the inhibition of transposons by the deposition of repressive chromatin marks such as histone modifications and DNA methylation. A key event in de novo methylation of DNA by RdDM is the production of long non‐coding RNA (lncRNA) by RNA polymerase V (Pol V). Little is known about the events that connect Pol V transcription to the establishment of repressive chromatin modifications. Using RNA immunoprecipitation, we elucidated the order of events downstream of lncRNA production and discovered interdependency between lncRNA‐associated proteins. We found that the effector protein ARGONAUTE4 (AGO4) binds lncRNA independent of the RNA‐binding protein INVOLVED IN DE NOVO2 (IDN2). In contrast, IDN2 binds lncRNA in an AGO4‐dependent manner. We further found that the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) also associates with lncRNA produced by Pol V and that this event depends on AGO4 and IDN2. We propose a model where the silencing proteins AGO4, IDN2 and DRM2 bind to lncRNA in a stepwise manner, resulting in DNA methylation of RdDM target loci.
Gross, histologic, and micro‐computed tomographic anatomy of the lacrimal system of snakes
Authors: Souza Nicole M. , Maggs David J. , Park Shin Ae , Puchalski Sarah M. , Reilly Christopher M. , Paul‐Murphy Joanne , Murphy Christopher J. 
Published: May 2014

AbstractObjectiveTo describe the lacrimal system of snakes using contrast micro‐computed tomography (micro‐CT) with 3‐dimensional reconstruction, fluorescein passage (‘Jones’) testing, histology, and gross dissection.Animals studiedOne royal python and 19 snake cadavers representing 10 species.ProceduresDirect observation following injection of fluorescein into the subspectacular space, micro‐CT following injection of three contrast agents into the subspectacular space, gross dissection following injection of latex into the subspectacular space, and histopathology.ResultsInjection of fluorescein confirmed patency, but not course of the lacrimal duct. Barium enabled clear visualization of the lacrimal duct, whereas two iodinated contrast agents proved inadequate. Collectively, micro‐CT, anatomic dissections, and histology suggest tears are produced by a single, large, serous, retrobulbar gland, released into the subspectacular space via several ductules, and drained through a single punctum originating in the ventronasal subspectacular space, and the lacrimal duct, which takes one of three routes of variable tortuosity before opening into the oral cavity in close association with the opening of the duct of the vomeronasal organ.ConclusionsThe ophidian lacrimal duct has a generally tortuous course, and the details of its anatomy are species‐variable. The tortuous course of the duct likely predisposes snakes to duct occlusion and must be considered when planning medical and surgical interventions in snakes with pseudobuphthalmos and subspectacular abscessation.
Penetrating sclerokeratoplasty and autologous pinnal cartilage and conjunctival grafting to treat a large limbal melanoma in a dog
Authors: Mathes Rachel L. , Moore Philip A. , Ellis Angela E. 
Published: May 2014

AbstractA four‐year‐old neutered male Labrador retriever presented to Portland Veterinary Specialists Ophthalmology Service for evaluation of a pigmented mass oculus sinister (OS) of approximately 4‐month duration. Complete ophthalmic examination revealed a large, pigmented, raised, well‐demarcated, epibulbar mass appearing to originate from the nasodorsal limbal region. The mass was smooth and roughly circular, extending approximately 4 mm into the sclera and 14 mm into the nasodorsal cornea. Gonioscopy directly under the mass was not possible due to mass size. The visible iridocorneal angle was normal. High‐resolution B‐scan ultrasound showed mass extension to Descemet's membrane and deep sclera, but no intraocular invasion. Penetrating sclerokeratoplasty was performed followed by autologous pinnal cartilage and conjunctival grafting to repair the corneoscleral defect (20 mm x 19 mm) and to restore globe integrity and function. Histopathology confirmed the mass to be a benign limbal melanoma with complete excision. The surgery site healed without complication, and the pinnal cartilage became fully incorporated into the globe. Twelve months postoperatively, the patient remains visual with a normal intraocular and fundic examination. The pinnal harvest site on the right ear healed without complication. To the authors’ knowledge, this is the first reported case of corneoscleral grafting using autologous pinnal cartilage. This may represent a viable alternative to other corneoscleral grafting procedures for large defects and is an attractive treatment option due to lack of host rejection, readily available source of donor cartilage, and provision of tectonic support to the globe.
The Potential of Mesenchymal Stem Cell in Prion Research
Authors: Mediano D. R. , Sanz‐Rubio D. , Ranera B. , Bolea R. , Martín‐Burriel I. 
Published: May 2014

SummaryScrapie and bovine spongiform encephalopathy are fatal neurodegenerative diseases caused by the accumulation of a misfolded protein (PrPres), the pathological form of the cellular prion protein (PrPC). For the last decades, prion research has greatly progressed, but many questions need to be solved about prion replication mechanisms, cell toxicity, differences in genetic susceptibility, species barrier or the nature of prion strains. These studies can be developed in murine models of transmissible spongiform encephalopathies, although development of cell models for prion replication and sample titration could reduce economic and timing costs and also serve for basic research and treatment testing. Some murine cell lines can replicate scrapie strains previously adapted in mice and very few show the toxic effects of prion accumulation. Brain cell primary cultures can be more accurate models but are difficult to develop in naturally susceptible species like humans or domestic ruminants. Stem cells can be differentiated into neuron‐like cells and be infected by prions. However, the use of embryo stem cells causes ethical problems in humans. Mesenchymal stem cells (MSCs) can be isolated from many adult tissues, including bone marrow, adipose tissue or even peripheral blood. These cells differentiate into neuronal cells, express PrPC and can be infected by prions in vitro. In addition, in the last years, these cells are being used to develop therapies for many diseases, including neurodegenerative diseases. We review here the use of cell models in prion research with a special interest in the potential use of MSCs.