bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations
Authors: Chen Alan A. , García Angel E. 
Published: May 2012

An RNA kissing loop from the Moloney murine leukemia virus (MMLV) exhibits unusual mechanical stability despite having only two intermolecular base pairs. Mutations at this junction have been shown to destabilize genome dimerization, with concomitant reductions in viral packaging efficiency and infectivity. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an 11-bp RNA hairpin [Li PTX, Bustamante C, Tinoco I (2006)
Proc Natl Acad Sci USA
103:15847–15852]. Using nonequilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV dimerization initiation site kissing loop. Two hundred and eight dissociation events were simulated (approximately 16 μs total simulation time) under conditions of constant applied external force, which we use to construct a Markov state model for kissing-loop dissociation. We find that the complex undergoes a conformational rearrangement, which allows for equal distribution of the applied force among all of the intermolecular hydrogen bonds, which is intrinsically more stable than the sequential unzipping of an ordinary hairpin. Stacking interactions with adjacent, unpaired loop adenines further stabilize the complex by increasing the repair rate of partially broken H-bonds. These stacking interactions are prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site.
Ferruccio Busoni and the Absolute in Music: Form, Nature and Idee
Authors: Knyt Erinn E. 
Published: May 2012

ABSTRACTFerruccio Busoni could be called an advocate of absolute music because of his frequent description of music as ‘absolute’ and his discussion of music as consisting of pure tones and rhythms found in the vibrating universe. However, he developed idiosyncratic theories about the term, its usage and its ideal manifestation in Tonkunst that remain largely unexamined in scholarly literature. True, Carl Dahlhaus noted Busoni's use of the concept to refer to music unconstrained by traditional forms, but this is merely one aspect of Busoni's views, which also, paradoxically, allowed for and included the visual and explicit connections to culture. The hybridity of Busoni's notion, which this article explores through an examination of writings and representative compositions, is especially relevant for current musicological discourse about absolute music. Sitting uneasily with Dahlhaus's more consistent view of absolute music as music apart from text or programme as well as with new musicological approaches that seek to refute the notion of music's autonomy, Busoni's view of absolute music offers a fascinating middle ground between compositions as discrete artistic artefacts on the one hand and as representations of their immediate culture on the other.
Multiplicity – Fragmentation – Simultaneity: Sound-Space as a Conveyor of Meaning, and Theatrical Roots in Luigi Nono's Early Spatial Practice
Authors: Santini Andrea 
Published: May 2012

ABSTRACTLuigi Nono's early spatial works with tape are characterized by strong political commitment as well as by compositional devices and performance solutions that reflect the composer's involvement with technology and theatrical practices after his detachment from Darmstadt in the late 1950s. Looking at the tape works composed between 1961 and 1969, the article outlines the development of Luigi Nono's unique spatial practice, its theatrical influences and the dramaturgical implications. The analysis is centred on the composer's use of acoustic space as a conveyor of meaning designed to stimulate active and critical audience engagement. Particular emphasis is thus placed on the use of tape and amplification in performance, introducing notions such as ‘doubling’, ‘con-fusion’, fragmentation, non-linearity, simultaneity and multiplicity, which inform Nono's vision of space and are essential for a serious understanding of the composer's engaged spatial aesthetic.
Spring partitioning of Disko Bay, West Greenland, by Arctic and Subarctic baleen whales
Authors: Laidre Kristin L. , Heide-Jørgensen Mads Peter 
Published: May 2012

Abstract
Laidre, K. L., and Heide-Jørgensen, M. P. 2012. Spring partitioning of Disko Bay, West Greenland, by Arctic and Subarctic baleen whales. – ICES Journal of Marine Science, 69: . Movements of co-occurring bowhead (Balaena mysticetus) and humpback (Megaptera novaeangliae) whales in Disko Bay, West Greenland, were examined using satellite telemetry. Data on movements, habitat use, and phenology were collected from tagged 49 bowheads and 44 humpbacks during the transition from sea-ice breakup to open water between 2008 and 2010. Bowhead whales began their northward spring migration around 27 May (median day-of-the-year departure date = 147, interquartile range 141–153) and were distributed broadly in northern and central Disko Bay in water depths between 100 and 400 m. Humpback whales arrived in Disko Bay no later than 2 June and were located in shallow water (<100 m) along the coasts of the mainland or Disko Island. Trends in departure date from Disko Bay were significant for bowhead whales (∼15 d later, p < 0.001) between two periods: 2001–2006 and 2008–2010. Many species are predicted to arrive earlier in the Arctic and to expand their range northwards with reduced sea ice and increasing temperatures under climate change. Quantifying the spatial and temporal relationships between co-occurring Arctic and Subarctic top predators allows for baseline insight to be gained on how climate change might alter interspecies interactions.
First Ocurrence of a Rhabdovirus Infecting Maize in Argentina
Authors: Maurino M. F. , Laguna G. , Giolitti F. , Nome C. , Pecci M. P. Giménez 
Published: May 2012

Maize (Zea mays) plants showing symptoms of shortened internodes, dwarfism, panicle sterility, and a mosaic of coarse and fine yellow stripes on leaf blades and sheaths, were found from December to March in experimental maize plantings in every crop year since 2000-01. Although the disease appeared at a very low incidence (estimates less than 1%), it was found in several locations such as Santa Isabel and Venado Tuerto, Santa Fe Province; Río Cuarto, Colonia Caroya, Río Segundo, and Sampacho, Córdoba Province; and Pedro Luro, Buenos Aires Province. Leaf tissue from eight symptomatic plants collected in Colonia Caroya in December 2011 was used to perform “leaf dips” and ultrathin sections. Electron microscopy of these preparations revealed membrane-bound bullet-shaped particles characteristic of the Rhabdoviridae family in mesophyll cytoplasm and vascular bundle parenchyma. The virus was experimentally transmitted to healthy 9-day-old corn plants, with Peregrinus maidis (order Hemiptera, family Delphacidae) raised under laboratory conditions using acquisition, latency, and inoculation vector periods of 7, 21, and 7 days, respectively. The field observed symptoms were replicated in the transmitted plants. Total RNA was extracted from symptomatic and asymptomatic plants with the RNeasy Plant Mini Kit (Qiagen, Germany), and one step RT-PCR (Access RT-PCR Kit, Promega, Madison, WI) was performed, using two sets of degenerate primers targeting conserved regions of rhabdovirus L polymerase gene, primers PVO (1) and Rhab (2). The agarose gel bands shown only in symptomatic samples were 450 bp (1) and 1,000 bp (2), as expected. The approximately 1 kb amplicon, which includes that of 450 bp, was cloned into pGEM-T Easy Vector System (Promega). Five independent clones were sequenced in both directions with M13 F/R universal primers to generate a consensus sequence (GenBank Accession No. JQ715419), which was compared to similar plant rhabdovirus sequences available on GenBank. The partial L polymerase gene sequence of the corn rhabdovirus, Maize yellow striate virus had 73% and 71% sequence identity with the members of the Cytorhabdovirus genus Barley yellow striate mosaic virus isolate Zanjan-1 (BYSMV; GenBank Accession No. FJ665628) and Northern cereal mosaic virus (NCMV; GenBank Accession No. NC002251), respectively. A phylogenetic tree from the partial nucleotide L polymerase sequence indicates that the rhabdovirus infecting maize in Argentina is closely related to the cytorhabdovirus members and is separated from the nucleorhabdovirus group. To our knowledge, this is the first mention of a Rhabdoviridae family virus infecting maize detected in Argentina. References: (1) H. Bourhy et al. J. Gen. Virol. 86:2849, 2005. (2) R. L. Lamprecht et al. Eur. J. Plant Pathol. 123:105, 2009.
First Report of Subanguina moxae Infecting Mugwort in Yunnan, China
Authors: Yao R. Y. , Hu X. Q. , Xue J. P. 
Published: May 2012

Mugwort is a perennial in the Compositae family distributed throughout Asia and Europe. The leaves are reported to have various pharmaceutical properties, e.g., antibacterial, antiviral, antitussive, and hemostatic properties, and have been used in traditional Chinese medicine for more than 2,000 years. In August 2011, a field of mugwort in Kunming, Yunnan Province, China, exhibited more than 90% incidence of whitish and rounded galls on the leaves. There were approximately 10 galls on each leaf, impacting the quality of the leaves for medicinal use. Parasitic nematodes were found upon dissection of the galls, then eggs, second-stage juveniles (J2), and mature males and females were observed. Through the morphologic observation of juveniles and female and male adults, the parasitic nematode was identified as Subanguina moxae (Yokoo and Choi, 1968) Brzeski, 1981 (3). Key morphological features are as follows: eggs (n = 20) measured 54.0 to 71.4 × 24.1 to 30.0 μm; J2 (n = 20) had the following characteristics: body length 689.3 to 873.2 μm (x = 775.5 μm); stylet length 8.2 to 9.8 μm (x = 8.8 μm); tail length 49.5 to 74.5 μm (x = 60.1 μm); a (total body length/maximum body width) ranged from 28.6 to 38.6 μm (x = 34.1 μm); and c (total body length/the length of the tail) ranged from 11.2 to 16.0 μm (x = 13.0 μm). Females (n = 20) had the following characteristics: body length 1,252.8 to 1,665.2 μm (x = 1,475.7 μm); stylet length 7.2 to 9.2 μm (x = 8.2 μm); V of 88.0 to 92.3 μm (x = 89.6 μm); a ranged from 17.6 to 24.5 μm (x = 21.3 μm); and c ranged from 20.2 to 28.9 μm (x = 22.8 μm). Males (n = 20) had the following characteristics: body length 994.2 to 1,453.6 μm (x = 1,253.2 μm); stylet length 7.5 to 9.9 μm (x= 9.1 μm); tail length 69.2 to 88.1 μm (x = 78.0 μm); spicule length 22.2 to 33.4 μm (x = 29.4 μm); gubernaculum length 10.4 to 14.2 μm (x = 12.2 μm); a ranged from 23.1 to 37.2 μm (x = 29.9 μm); and c ranged from 13.9 to 18.7 μm (x = 16.1 μm). Amplification of the rDNA-internal transcribed spacer (ITS) region and the D2/D3 (1) fragments of the 28S RNA with universal primers rDNA1/rDNA2 and D2A/D3B yielded PCR fragments of 934 bp and 754 bp, respectively. The ITS sequence (JN865234) and D2D3 sequence (JN885540) were submitted to GenBank. The ITS sequence (JN865234) exhibited 99.4% similarity with Mesoanguina moxae (AF396314) (synonym of S. moxae) (4). S. moxae has been identified from the common mugwort in Japan (2) and in China, was reported to infect wheat in Guizhou Province, but to our knowledge, this is the first report of this nematode affecting mugwort in Yunnan, China. References: (1) S. Amiri et al. Eur. J. Plant Pathol. 108:497, 2002. (2) K. Daigo et al. Bull. School Agric. Meiji University. 56:237, 2007. (3) M. R. Siddiqi. Tylenchida: Parasites of Plants and Insects. CABI Publishing, New York, 2000. (4) S. A. Subbotin et al. Mol. Phylogenet. Evol. 30:226, 2004.
Spatial and temporal variation in butterfly biodiversity in a West African forest: lessons for establishing efficient rapid monitoring programmes
Authors: Aduse‐Poku Kwaku , William Oduro , Oppong Samuel K. , Larsen Torben , Ofori‐Boateng Caleb , Molleman Freerk 
Published: May 2012

AbstractBecause tropical forests face serious threats and are usually situated in developing countries, cheap and easy Rapid Biodiversity Assessment (RBA) seems an ideal strategy for documenting changes in habitat quality and setting conservation priorities. Fruit‐feeding butterflies are often used as focal taxa to document biodiversity trends in tropical forests. However, the choice of inappropriate sampling strategies may nullify its value. More extensive data sets that sample multiple months and seasons and incorporate the vertical dimension are needed as a baseline for designing reliable sampling regimes. Therefore, we performed a butterfly trapping study in Ghana, using both understorey and canopy traps, and sampling seven periods covering dry and wet seasons. Both individual numbers and species richness were on average three to four times higher in the understorey than in the canopy traps with strikingly different species composition (only 11% overlap in species). The number of species and individual abundance recorded in a month varied extensively. This study underlined the importance of taking into account temporal variation and vertical stratification when designing RBAs of fruit‐feeding butterflies in West African forests. We recommend the use of both understorey and canopy traps and inclusion of both ‘wet’ and ‘dry’ seasons into RBA sampling regimes.
Animal models of anti-neutrophil cytoplasmic antibody-associated vasculitis
Authors: Coughlan A M , Freeley S J , Robson M G 
Published: May 2012

SummaryOTHER ARTICLES PUBLISHED ON ANCA IN THIS ISSUEHow anti-neutrophil cytoplasmic autoantibodies activate neutrophils. Clinical and Experimental Immunology 2012, 169: 220–8.Antibodies against neutrophil proteins myeloperoxidase (MPO) and proteinase 3 are thought to cause disease in anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. There have been a number of recent developments in the animal models of ANCA vasculitis in both mice and rats. These include models based on an immune response to MPO generated in MPO-deficient mice, with other models using MPO-sufficient mice and rats. In addition, there is a report of the use of humanized mice where immunodeficient mice have been engrafted with human haematopoietic stem cells and injected with patient ANCA. Antibodies to another protein lysosomal-associated protein-2 have been found in patients with ANCA vasculitis, and evidence from a rat model suggests that they are also pathogenic. These models all have advantages and disadvantages, which are discussed. We also consider what these models have taught us about the pathogenesis of ANCA vasculitis. Experiments using genetically modified mice and pharmacological inhibition have given insights into disease mechanisms and have identified potential therapeutic targets. Toll-like receptor stimulation modifies disease by acting both at the level of tissue injury and in the generation of the autoimmune response. Complement is also potentially important with data to support the role of the alternative pathway and C5a in particular. Intracellular pathways have been examined, with a role showing p38 mitogen-activated protein kinase and phosphatidylinositol 3-kinase γ. Serine proteases are now known to contribute to disease by release of interleukin-1β in ANCA-activated neutrophils and monocytes. Other potential therapies studied in these models include the use of bortezemib and strategies to modify antibody glycosylation.
Amelioration of renal damage by administration of anti-thymocyte globulin to potential donors in a brain death rat model
Authors: Cicora F , Stringa P , Guerrieri D , Roberti J , Ambrosi N , Toniolo F , Cicora P , Palti G , Vásquez D , Raimondi C 
Published: May 2012

SummaryBrain death (BD), a non-immunological factor of renal injury, triggers an inflammatory process causing pathological signs of cell death in the kidney, such as necrosis and apoptosis. Kidneys from brain dead donors show lower success rates than kidneys from living donors and one strategy to improve transplantation outcome is to precondition the donors. For the first time, anti-rat thymoglobulin (rATG) was administered in an experimental brain death animal model to evaluate if it could ameliorate histopathological damage and improve organ function. Animals were divided into three groups: V (n = 5) ventilated for 2 h; BD (n = 5) brain death and ventilated for 2 h; and BD+rATG (n = 5) brain death, ventilated for 2 h, rATG was administered during brain death (10 mg/kg). We observed lower creatinine levels in treatment groups (means): V, 0·88 ± 0·22 mg/dl; BD, 1·37 ± 0·07 mg/dl; and BD+rATG, 0·64 ± 0·02 mg/dl (BD versus BD+rATG, P &lt; 0·001). In the BD group there appeared to be a marked increase of ATN, whereas ATN was decreased significantly in the rATG group (V, 2·25 ± 0·5 versus BD, 4·75 ± 0·5, P &lt; 0·01; BD+rATG, 2·75 ± 0·5 versus BD 4·75 ± 0·5 P &lt; 0·01). Gene expression was evaluated with reverse transcription–polymerase chain reaction; tumour necrosis factor (TNF)-α, interleukin (IL)-6, C3, CD86 showed no significant difference between groups. Increased IL-10 and decreased CCL2 in BD+rATG compared to BD (both cases P &lt; 0·01). Myeloperoxidase was increased significantly after the brain death setting (V: 32 ± 7·5 versus BD: 129 ± 18). Findings suggest that rATG administered to potential donors may ameliorate renal damage caused by BD. These findings could contribute in the search for specific cytoprotective interventions to improve the quality and viability of transplanted organs.
The immunobiology of apotransferrin in type 1 diabetes
Authors: Mangano K , Fagone P , Di Mauro M , Ascione E , Maiello V , Milicic T , Jotic A , Lalic N M , Saksida T , Stojanovic I , Selmi C , Farina C , Stosic-Grujicic S , Meroni P , Nicoletti F 
Published: May 2012

Summary
The transferrin (Tf) family of iron binding proteins includes important endogenous modulators of the immune function that may modulate autoimmune diseases. To define more clearly the role of apotransferrin (apoTf) in type 1 diabetes we determined the impact of this protein on type 1 diabetes as investigated in islet cells, animal models and patient sera. First, we demonstrated that recombinant apoTf counteracts the cytokine-induced death of murine pancreatic islet cells. Secondly, human apoTf administration favourably influences the course of type 1 diabetes in animal models, resulting in protection against disease development that was associated with reduction of insulitis and reduced levels of proinflammatory cytokines. Finally, we confirmed that patients with newly diagnosed type 1 diabetes manifest significantly lower apoTf serum levels compared to healthy controls and patients with long-lasting disease. In conclusion, our data suggest the apoTf pivotal role in the perpetuation of type 1 diabetes pathology.
Experimental litterfall manipulation drives large and rapid changes in soil carbon cycling in a wet tropical forest
Authors: Leff Jonathan W. , Wieder William R. , Taylor Philip G. , Townsend Alan R. , Nemergut Diana R. , Grandy A. Stuart , Cleveland Cory C. 
Published: May 2012

AbstractGlobal changes such as variations in plant net primary production are likely to drive shifts in leaf litterfall inputs to forest soils, but the effects of such changes on soil carbon (C) cycling and storage remain largely unknown, especially in C‐rich tropical forest ecosystems. We initiated a leaf litterfall manipulation experiment in a tropical rain forest in Costa Rica to test the sensitivity of surface soil C pools and fluxes to different litter inputs. After only 2 years of treatment, doubling litterfall inputs increased surface soil C concentrations by 31%, removing litter from the forest floor drove a 26% reduction over the same time period, and these changes in soil C concentrations were associated with variations in dissolved organic matter fluxes, fine root biomass, microbial biomass, soil moisture, and nutrient fluxes. However, the litter manipulations had only small effects on soil organic C (SOC) chemistry, suggesting that changes in C cycling, nutrient cycling, and microbial processes in response to litter manipulation reflect shifts in the quantity rather than quality of SOC. The manipulation also affected soil CO
2 fluxes; the relative decline in CO
2 production was greater in the litter removal plots (−22%) than the increase in the litter addition plots (+15%). Our analysis showed that variations in CO
2 fluxes were strongly correlated with microbial biomass pools, soil C and nitrogen (N) pools, soil inorganic P fluxes, dissolved organic C fluxes, and fine root biomass. Together, our data suggest that shifts in leaf litter inputs in response to localized human disturbances and global environmental change could have rapid and important consequences for belowground C storage and fluxes in tropical rain forests, and highlight differences between tropical and temperate ecosystems, where belowground C cycling responses to changes in litterfall are generally slower and more subtle.
Preparation and analysis of hydrolysates from whey protein concentrate using the proteases from Bacillus licheniformis and Aspergillus oryzae
Authors: Silvestre Marialice Pinto Coelho , Morais Harriman Aley , Silva Mauro Ramalho , de Souza Mariana Wanessa Santana , Silva Viviane Dias Medeiros 
Published: May 2012

SummaryThe action of proteases from Bacillus licheniformis and Aspergillus oryzae was studied with the aim of preparing hydrolysates from whey protein concentrate with nutritionally appropriate peptide profile. Various enzyme/substrate ratios were used, and the peptides were fractionated by size‐exclusion HPLC followed by their quantification using the rapid method of correct fraction area (CFA). The protease from B. licheniformis (E:S of 8:100) produced the best peptide with a much lower amount of large peptides (44.61%), greater of di‐ and tripeptides (8.79%) and higher sum of the di‐ and tripeptides with free amino acids (9.99%) than the other hydrolysates. The advantage of using a lower E:S ratio to obtain a nutritionally adequate peptide profile was observed for the protease of A. oryzae when it passed from 3:100 to 2:100.