bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution structure of the E3 ligase HOIL‐1 Ubl domain
Authors: Beasley Steven A. , Safadi Susan S. , Barber Kathryn R. , Shaw Gary S. 
Published: April 2012

AbstractThe E3 ligases HOIL‐1 and parkin are each comprised of an N‐terminal ubiquitin‐like (Ubl) domain followed by a zinc‐binding region and C‐terminal RING–In‐between‐RING–RING domains. These two proteins, involved in the ubiquitin‐mediated degradation pathway, are the only two known E3 ligases to share this type of multidomain architecture. Further, the Ubl domain of both HOIL‐1 and parkin has been shown to interact with the S5a subunit of the 26S proteasome. The solution structure of the HOIL‐1 Ubl domain was solved using NMR spectroscopy to compare it with that of parkin to determine the structural elements responsible for S5a intermolecular interactions. The final ensemble of 20 structures had a β‐grasp Ubl‐fold with an overall backbone RMSD of 0.59 ± 0.10 Å in the structured regions between I55 and L131. HOIL‐1 had a unique extension of both β1 and β2 sheets compared to parkin and other Ubl domains, a result of a four‐residue insertion in this region. A similar 15‐residue hydrophobic core in the HOIL‐1 Ubl domain resulted in a comparable stability to the parkin Ubl, but significantly lower than that observed for ubiquitin. A comparison with parkin and other Ubl domains indicates that HOIL‐1 likely uses a conserved hydrophobic patch (W58, V102, Y127, Y129) found on the β1 face, the β3–β4 loop and β5, as well as a C‐terminal basic residue (R134) to recruit the S5a subunit as part of the ubiquitin‐mediated proteolysis pathway.
Biochemical and molecular characterisation of acetylcholinesterase in four field populations of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)
Authors: Shen Guang‐Mao , Wang Xiao‐Na , Dou Wei , Wang Jin‐Jun 
Published: April 2012

AbstractBACKGROUND: The oriental fruit fly, Bactrocera dorsalis, is a major pest that infects fruits and agricultural products worldwide. The latest resistance monitoring of B. dorsalis from mainland China has identified high levels of resistance to insecticides. In this study, the biochemical and molecular characteristics of acetylcholinesterase (AChE) in four field populations of B. dorsalis are investigated.RESULTS: Among the four populations, the DG population and its purified AChE were found to be the least susceptible to malathion and five inhibitors, whereas the KM population and its purified AChE were the most susceptible. The highest catalytic activity of purified AChE was found for the KM population, and the catalytic activity of the DG population was the lowest. Among developmental stages, the AChE purified from larvae was found to be the most insusceptible to inhibitors, but its catalytic activity was the highest. Sequence analysis of the cDNA encoding AChE showed that some residue differences existed. However, no significant differences in expression levels of the AChE gene among populations and developmental stages were detected.CONCLUSION: The results suggest that the decrease in susceptibility of B. dorsalis was mainly caused by decrease in AChE activity, and they provide a broad view on the relation between AChE and resistance. Copyright © 2012 Society of Chemical Industry
EPSPS gene amplification in glyphosate‐resistant Italian ryegrass (Lolium perenne ssp. multiflorum) from Arkansas
Authors: Salas Reiofeli A , Dayan Franck E , Pan Zhiqiang , Watson Susan B , Dickson James W , Scott Robert C , Burgos Nilda R 
Published: April 2012

AbstractBACKGROUND: Resistance to glyphosate in weed species is a major challenge for the sustainability of glyphosate use in crop and non‐crop systems. A glyphosate‐resistant Italian ryegrass population has been identified in Arkansas. This research was conducted to elucidate its resistance mechanism.RESULTS: The investigation was conducted on resistant and susceptible plants from a population in Desha County, Arkansas (Des03). The amounts of glyphosate that caused 50% overall visual injury were 7 to 13 times greater than those for susceptible plants from the same population. The EPSPS gene did not contain any point mutation that has previously been associated with resistance to glyphosate, nor were there any other mutations on the EPSPS gene unique to the Des03 resistant plants. The resistant plants had 6‐fold higher basal EPSPS enzyme activities than the susceptible plants, but their I50 values in response to glyphosate were similar. The resistant plants contained up to 25 more copies of EPSPS gene than the susceptible plants. The level of resistance to glyphosate correlated with increases in EPSPS enzyme activity and EPSPS copy number.CONCLUSION: Increased EPSPS gene amplification and EPSPS enzyme activity confer resistance to glyphosate in the Des03 population. This is the first report of EPSPS gene amplification in glyphosate‐resistant Italian ryegrass. Other resistance mechanism(s) may also be involved. Copyright © 2012 Society of Chemical Industry
Local structures and roles of Fe3+ and Cr3+ in p‐type semiconductor CuAlO2
Authors: Huang Dan , Lin Jinru , Nilges Mark J. , Pan Yuanming 
Published: April 2012

AbstractSingle crystals of the p‐type semiconductor CuAlO2, synthesized from the CuO flux method, have been investigated by electron paramagnetic resonance (EPR) spectroscopy at temperatures from 3.5 to 294 K. EPR spectra reveal an axial Cr3+ center and an axial Fe3+ center, presumably arising from impurities in the starting materials. The Cr3+ center at 294 K is characterized by g = 1.979(1) and D = − 7803(3) × 10−4 cm−1. The Fe3+ center at 294 K has g// = 1.9942(1), g⟂ = 1.9964(1), D = 261.9(3) × 10−4 cm−1, $B_{4}^{0} = 4.533(3) \times 10^{- 4} \,{\rm cm}^{- 1} $, and $B_{4}^{3} = 104.23(3) \times 10^{- 4} \,{\rm cm}^{- 1} $. These spin‐Hamiltonian parameters, evaluated by superposition model analyses and periodic density functional theory (DFT) calculations, suggest that both Cr3+ and Fe3+ occupy the Al3+ site but the latter involves distortion related to perturbation from a substitutional Cu+ ion at the nearest Al site. This difference in the local structure between Fe3+ and Cr3+ explains their contrasting effects on the p‐type conductivity in CuAlO2.
Solid‐state formation of ferromagnetic δ‐Mn0.6Ga0.4 thin films with high rotatable uniaxial anisotropy
Authors: Myagkov V. G. , Zhigalov V. S. , Bykova L. E. , Bondarenko G. N. , Mikhlin Yu. L. , Patrin G. S. , Velikanov D. A. 
Published: April 2012

AbstractSolid‐state reactions in Ga/Mn polycrystalline films of the composition 1 Ga:3 Mn were experimentally investigated. Our X‐ray study showed that the formation of the Ga/Mn → (250 °C) ϕ‐Ga7.7Mn2.3 → (350 °C) δ‐Mn0.6Ga0.4 phase sequence occurs when the annealing temperature is increased to 400 °C. δ‐Mn0.6Ga0.4 samples were found to have high rotatable uniaxial anisotropy. We also showed that magnetic fields with coercivities above H > HC = 8.3 kOe can be used to orient the easy anisotropy axis in any spatial direction while taking the angle of the lag into account.
An Overview of the Applications of Graphene‐Based Materials in Supercapacitors
Authors: Huang Yi , Liang Jiajie , Chen Yongsheng 
Published: April 2012

AbstractDue to their unique 2D structure and outstanding intrinsic physical properties, such as extraordinarily high electrical conductivity and large surface area, graphene‐based materials exhibit great potential for application in supercapacitors. In this review, the progress made so far for their applications in supercapacitors is reviewed, including electrochemical double‐layer capacitors, pseudo‐capacitors, and asymmetric supercapacitors. Compared with traditional electrode materials, graphene‐based materials show some novel characteristics and mechanisms in the process of energy storage and release. Several key issues for improving the structure of graphene‐based materials and for achieving better capacitor performance, along with the current outlook for the field, are also discussed.
Acculock: accurate and efficient detection of data races
Authors: Xie Xinwei , Xue Jingling , Zhang Jie 
Published: April 2012

SUMMARYThis paper introduces a new dynamic data race detector, ACCULOCK, to detect data races in Java programs. ACCULOCK is the first hybrid detector that combines lockset and epoch‐based happens‐before for race detection. ACCULOCK analyzes a program execution by reasoning about the subset of the happens‐before relation observed with lock acquires and releases excluded, thereby making it less sensitive to thread interleaving than pure happens‐before detectors. When this relaxed happens‐before relation is violated, ACCULOCK applies a new lockset algorithm to verify the locking discipline by distinguishing reads and writes, thereby making it more immune to false positives than pure lockset detectors. In addition, ACCULOCK is designed to achieve these design objectives by maintaining comparable instrumentation overheads (in both time and space) to that of FASTTRACK, the fastest happens‐before detector available (at least for Java programs). All these properties of ACCULOCK have been validated and confirmed by comparing it against FASTTRACK and five other (pure happens‐before, pure lockset, or hybrid) detectors, which are implemented in the Jikes Research Virtual Machine using a collection of large benchmark programs from a variety of applications. Furthermore, porting ACCULOCK and FASTTRACK to a different platform, RoadRunner, and repeating our experiments yield similar observations in terms of their effectiveness in race detection and instrumentation overheads. Copyright © 2012 John Wiley & Sons, Ltd.
Maxillary brown tumor as initial presentation of parathyroid adenoma: A case report
Authors: Sia Hon‐Ke , Hsieh Ming‐Chia , Yang Li‐Heng , Tu Shih‐Te 
Published: April 2012

AbstractBrown tumor is a rare late‐stage skeletal change caused by long‐term stimulation of excess parathyroid hormone. It is not neoplastic, but a reparative cellular process. Common sites of brown tumor are the ribs, clavicle, long bones and pelvic girdle. Solitary maxillary brown tumor as initial presentation of primary hyperparathyroidism is rare; it is often accompanied by brown tumors of the other facial bones. Here, we present the first case of solitary maxillary brown tumor in a 29‐year‐old ethnic Chinese woman with initial presentation of a large tumor filling the left maxillary sinus. Underlying long‐standing primary hyperparathyroidism caused by a large parathyroid adenoma was finally diagnosed. Brown tumor tends to be misdiagnosed as malignancy, and delayed diagnosis of the underlying hyperparathyroidism is common. Our case validates the suggestion that young women have a higher probability of brown tumor. Biopsy of the suspicious bone tumor and blood tests for calcium and parathyroid hormone level are crucial and essential to reach the correct diagnosis. Most brown tumors show spontaneous regression after parathyroidectomy. However, direct excision of the brown tumor may be indicated to avoid the risk of facial deformity and orbital compression at a special anatomical site, as in our case.
Morphological aspects of the biological function of the osteocytic lacunar canalicular system and of osteocyte‐derived factors
Authors: Sasakia Muneteru , Hongo Hiromi , Hasegawa Tomoka , Suzuki Reiko , Zhusheng Liu , Luiz de Freitas Paulo Henrique , Yamada Tamaki , Oda Kimimitsu , Yamamoto Tsuneyuki , Li Minqi , Totsuka Yasunori , Amizuka Norio 
Published: April 2012

AbstractOsteocytes are organized in functional syncytia collectively referred to as the osteocytic lacunar‐canalicular system (OLCS). The osteocytes are interconnected through gap junctions between their cytoplasmic processes, which pass through narrow passageways referred to as osteocytic canaliculi. There are two possible ways molecules can be transported throughout the OLCS: via the cytoplasmic processes and their gap junctions, and via the pericellular space in the osteocytic canaliculi. Transport of minerals and small molecules through a spatially well‐organized OLCS is vital for bone mineral homeostasis, mechanosensing, and bone remodeling control. Recently, osteocyte‐derived molecules – sclerostin, dentin matrix protein‐1, fibroblast growth factor 23 (FGF23) – have been put in evidence as they may be related to osteocytic functions such as mechanosensing, regulation of bone remodeling, and so forth. FGF23 regulates serum phosphate concentration by affecting renal function, while sclerostin can inhibit osteoblastic activities. In our observations, FGF23 and sclerostin synthesis seemed to be associated with the spatial regularity of the OLCS. This review will introduce our recent morphological studies on the regularity of OLCS and the synthesis of osteocyte‐derived FGF23 and sclerostin.
Hydrodynamics of self-propulsion near a boundary: predictions and accuracy of far-field approximations
Authors: Spagnolie Saverio E. , Lauga Eric 
Published: April 2012

AbstractThe swimming trajectories of self-propelled organisms or synthetic devices in a viscous fluid can be altered by hydrodynamic interactions with nearby boundaries. We explore a multipole description of swimming bodies and provide a general framework for studying the fluid-mediated modifications to swimming trajectories. A general axisymmetric swimmer is described as a linear combination of fundamental solutions to the Stokes equations: a Stokeslet dipole, a source dipole, a Stokeslet quadrupole, and a rotlet dipole. The effects of nearby walls or stress-free surfaces on swimming trajectories are described through the contribution of each singularity, and we address the question of how accurately this multipole approach captures the wall effects observed in full numerical solutions of the Stokes equations. The reduced model is used to provide simple but accurate predictions of the wall-induced attraction and pitching dynamics for model Janus particles, ciliated organisms, and bacteria-like polar swimmers. Transitions in attraction and pitching behaviour as functions of body geometry and propulsive mechanism are described. The reduced model may help to explain a number of recent experimental results.
SET IN STONE: HOMELESS CORPSES AND DESECRATED GRAVES IN MODERN IRAN
Authors: Amanat Mehrdad 
Published: April 2012

AbstractViolence toward corpses and graves, especially the unusual practice of exhuming and burning remains, persisted sporadically through the 20th century in Iran but found new dimensions in the form of mass graves and a systematic desecration of cemeteries in the period following the 1979 Islamic Revolution. This paper seeks to explore the roots of cemetery violence by examining the dynamics of apostasy and the experiences and challenges Babi and Bahaʾi converts faced in their interment practices in the late 19th and early 20th centuries. This period witnessed a significant change in communal identities. Unconventional self-definitions expressed in religious conversions and in fluid or multiple communal affiliations and religious convictions defied traditional boundaries and led to tension between nonconformists and religious authorities. One way for Shiʿi ʿulamaʾ and Jewish rabbis to reassert a conventional center was through the control of cemeteries, including by not allowing converts to be buried in these semisacred spaces.
Childhood trauma and auditory verbal hallucinations
Authors: Daalman K. , Diederen K. M. J. , Derks E. M. , van Lutterveld R. , Kahn R. S. , Sommer Iris E. C. 
Published: April 2012

BackgroundHallucinations have consistently been associated with traumatic experiences during childhood. This association appears strongest between physical and sexual abuse and auditory verbal hallucinations (AVH). It remains unclear whether traumatic experiences mainly colour the content of AVH or whether childhood trauma triggers the vulnerability to experience hallucinations in general. In order to investigate the association between hallucinations, childhood trauma and the emotional content of hallucinations, experienced trauma and phenomenology of AVH were investigated in non-psychotic individuals and in patients with a psychotic disorder who hear voices.MethodA total of 127 non-psychotic individuals with frequent AVH, 124 healthy controls and 100 psychotic patients with AVH were assessed for childhood trauma. Prevalence of childhood trauma was compared between groups and the relation between characteristics of voices, especially emotional valence of content, and childhood trauma was investigated.ResultsBoth non-psychotic individuals with AVH and patients with a psychotic disorder and AVH experienced more sexual and emotional abuse compared with the healthy controls. No difference in the prevalence of traumatic experiences could be observed between the two groups experiencing AVH. In addition, no type of childhood trauma could distinguish between positive or negative emotional valence of the voices and associated distress. No correlations were found between sexual abuse and emotional abuse and other AVH characteristics.ConclusionsThese results suggest that sexual and emotional trauma during childhood render a person more vulnerable to experience AVH in general, which can be either positive voices without associated distress or negative voices as part of a psychotic disorder.
Maintenance of permeable habitable subsurface environments by earthquakes and tidal stresses
Authors: Sleep Norman H. 
Published: April 2012

AbstractLife inhabits the subsurface of the Earth down to depths where temperature precludes it. Similar conditions are likely to exist within the traditional habitable zone for objects between 0.1 Earth mass (Mars) and 10 Earth masses (superearth). Long-term cooling and internal radioactivity maintain surface heat flow on the Earth. These heat sources are comparable and likely to be comparable in general within old rocky planets. Surface heat flow scales with mass divided by surface area and hence with surface gravity. The average absolute habitable subsurface thickness scales inversely with heat flow and gravity. Surface gravity varies by only 0.4 g for Mars to 3.15 g for a superearth. This range is less than the regional variation of heat flow on the Earth. Still ocean-boiling asteroid impacts (if they occur) are more likely to sterilize the thin habitable subsurface of large objects than thick habitable subsurface of small ones. Tectonics self-organizes to maintain subsurface permeability and habitability within both stable and active regions on the Earth. Small earthquakes within stable regions allow sudden mixing of water masses. Large earthquakes at plate boundaries allow surface water to descend to great habitable depths. Seismic shaking near major faults cracks shallow rock forming permeable regolith. Strong tidal strains form a similar porous regolith on small bodies such as Enceladus with weak stellar heating. This regolith may be water-saturated within rocky bodies and thus habitable.
Epithelial–mesenchymal interaction during UVB-induced up-regulation of neutral endopeptidase
Authors: Nakajima Hiroaki , Ezaki Yoshiyuki , Nagai Tomoyashu , Yoshioka Ryosuke , Imokawa Genji 
Published: April 2012

We recently reported that overexpression of the elastase NEP (neutral endopeptidase) by fibroblasts plays a pivotal role in the mechanism of UVB-induced skin wrinkling by degrading dermal elastic fibres. Since UVB does not penetrate to the dermis, we hypothesized that factors secreted by UVB-exposed keratinocytes in the epidermis trigger fibroblasts in the dermis to increase their expression of NEP which then degrades the elastic fibres. In the present study, we characterized the epithelial–mesenchymal interaction between keratinocytes and fibroblasts which leads to increased expression of NEP. Human fibroblasts co-cultured with UVB-exposed human keratinocytes in cell inserts significantly increased their expression of NEP at the transcriptional, translational and enzymatic levels. Neutralizing antibodies to IL (interleukin)-1α or GM-CSF (granulocyte/macrophage colony-stimulating factor) significantly abolished the increased expression of NEP at the enzymatic levels in human fibroblasts co-cultured with UVB-exposed human keratinocytes, whereas neutralizing antibodies to IL-6, IL-8 or TNFα (tumour necrosis factor α) had no such effect. The addition of IL-1α or GM-CSF, but not TNFα, IL-6 or IL-8, at concentrations ranging from 1 to 10 nM, significantly stimulated the expression of NEP in human fibroblasts at the transcriptional and translational levels. These findings suggest that IL-1α and GM-CSF are intrinsic cytokines secreted by UVB-exposed keratinocytes that stimulate expression of NEP by fibroblasts.
Understanding the survival strategies of nematodes.
Authors: Perry R. N. 
Published: April 2012

Abstract
Nematodes are a remarkable group of invertebrates with enormous economic and social importance. Free-living nematodes are found in a wide variety of habitats, from the Antarctic to the hot springs in New Zealand. Parasitic species of nematodes parasitize almost every species of plants and animals, including humans. The success of nematodes depends partly on sophisticated adaptations to withstand environmental extremes and, for parasitic forms, to overcome the switch between the external environment and the internal environment of the host, and the ensuing antagonistic response of the host. This review briefly outlines the astonishing abilities of some species of nematodes to survive environmental extremes, including desiccation, and to withstand host responses. Understanding the mechanisms for survival has relevance to many other biological fields and the importance of molecular approaches to unravel the mechanisms is discussed.
TSSi—an R package for transcription start site identification from 5′ mRNA tag data
Authors: Kreutz C. , Gehring J. S. , Lang D. , Reski R. , Timmer J. , Rensing S. A. 
Published: April 2012

AbstractSummary: High-throughput sequencing has become an essential experimental approach for the investigation of transcriptional mechanisms. For some applications like ChIP-seq, several approaches for the prediction of peak locations exist. However, these methods are not designed for the identification of transcription start sites (TSSs) because such datasets contain qualitatively different noise.In this application note, the R package TSSi is presented which provides a heuristic framework for the identification of TSSs based on 5′ mRNA tag data. Probabilistic assumptions for the distribution of the data, i.e. for the observed positions of the mapped reads, as well as for systematic errors, i.e. for reads which map closely but not exactly to a real TSS, are made and can be adapted by the user. The framework also comprises a regularization procedure which can be applied as a preprocessing step to decrease the noise and thereby reduce the number of false predictions.Availability: The R package TSSi is available from the Bioconductor web site: www.bioconductor.org/packages/release/bioc/html/TSSi.html.Contact: ckreutz@fdm.uni-freiburg.deSupplementary information: Supplementary data are available at Bioinformatics online.