bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outer Shock Interaction in Young Core-Collapse SNRs
Authors: Lee Jae-Joon 
Published: January 2014

AbstractStudying the environments in which core-collapse supernovae (SNe) explode and then subsequently evolve is essential to establish the nature of the mass loss and the explosion of the progenitor star. The spatial structure of the outer shock in young core-collapse SNRs provides an opportunity to study the nature of the medium into which the remnant has been expanding. We present our X-ray study of the outer shocks in young core-collapse SNRs in our Galaxy. For Cas A and G292.0+1.8, we find that both remnants have been likely interacting with dense red supergiant winds. For other remnants with bright thermal X-ray emission from the shell, we suggest that they are interacting with pre-existing circumstellar structure. We discuss the nature of the winds and the progenitor stars.
Radio studies of relativistic SN 2009bb
Authors: Ray Alak , Yadav Naveen , Chakraborti Sayan , Soderberg Alicia , Chandra Poonam 
Published: January 2014

AbstractA local sub-population of type Ib/c supernovae (stripped envelope SNe) with mildly relativistic outflows have been detected as sub-energetic Gamma Ray Bursts (GRBs) or X-ray Flashes (XRFs) and as radio afterglows without detected GRB counterpart. SN 2009bb belongs to the last class of objects. The long term radio observations with (J)VLA and GMRT of this SN map the dynamics of the relativistic ejecta characteristic of Central Engines associated with GRBs. We present here GMRT observations of this SN from October 2009 onwards.
Clumping of ejecta and accelerated cosmic rays in the evolution of type Ia SNRs
Authors: Orlando S. , Bocchino F. , Miceli M. , Petruk O. , Pumo M. L. 
Published: January 2014

AbstractWe investigate the role played by initial clumping of ejecta and by efficient acceleration of cosmic rays (CRs) in determining the density structure of the post-shock region of a Type Ia supernova remnant (SNR) through detailed 3D MHD modeling. Our model describes the expansion of a SNR through a magnetized interstellar medium (ISM), including the initial clumping of ejecta and the effects on shock dynamics due to back-reaction of accelerated CRs. The model predictions are compared to the observations of SN 1006. We found that the back-reaction of accelerated CRs alone cannot reproduce the observed separation between the forward shock (FS) and the contact discontinuity (CD) unless the energy losses through CR acceleration and escape are very large and independent of the obliquity angle. On the contrary, the clumping of ejecta can naturally reproduce the observed small separation and the occurrence of protrusions observed in SN 1006, even without the need of accelerated CRs. We conclude that FS-CD separation is a probe of the ejecta structure at the time of explosion rather than a probe of the efficiency of CR acceleration in young SNRs.
Incorporating Target Shedding Into a Minimal PBPK–TMDD Model for Monoclonal Antibodies
Authors: Li L , Gardner I , Rose R , Jamei M 
Published: January 2014

Shedding of a pharmacological target from cells, giving rise to a soluble target that can also bind therapeutic proteins, is a common phenomenon. In this study, a minimal physiologically based pharmacokinetic model was used to simulate the pharmacokinetics of trastuzumab and the simultaneous binding of the compound to soluble (in blood and tissue interstitial space) and membrane‐bound (in the tissue interstitial space) forms of human epidermal growth factor receptor 2 (HER2). The parameter values describing binding of trastuzumab to HER2 were largely derived from in vitro data, and the effects of varying HER2 levels, the affinity difference between membrane‐bound HER2 and shed antigen, and slow binding kinetics were investigated. The model simulates a sharp decrease in trough drug concentrations at concentrations of soluble target between 500 and 1,000 ng/ml in plasma. This corresponds with the clinical concentration range of soluble target wherein changes in half‐life of trastuzumab have been observed.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e96; doi:10.1038/psp.2013.73; published online 29 January 2014
Design of fast low‐power floating high‐voltage level‐shifters
Authors: Lehmann T. 
Published: January 2014

What limits performance in some recently published digital floating level‐shifters are identified and a new level‐shifter is proposed to address these limitations. An order‐of‐magnitude reduction in power dissipation compared with the recently published fast high‐voltage level‐shifters is obtained; simulations in a high‐voltage 0.35 μm process show the proposed design is capable of shifting a 2.5 V logic signal up by 17.5 V with a propagation delay of 3 ns and a transition energy of 6 pJ.
4 × 2 Tbit/s superchannel self‐coherent transmission based on carrier tracking and expanding
Authors: Xiao Xiao , Yang Qi , Yi Xingwen , Yang Chao , Li Zhaohui , He Zhixue , Luo Ming , Gui Tao , Li Chao , Zhang Xu , Xue Daojun , Hu Rong , Yu Shaohua 
Published: January 2014

A novel superchannel transmission scheme is proposed where an optical comb source is used to carry the multiband signal and one subcarrier is reserved for regeneration as a local oscillator at the receiver end. By combining carrier tracking and carrier expanding, a 4 × 2 Tbit/s superchannel wavelength division multiplexed self‐coherent transmission over a 320 km standard single mode fibre has been successfully demonstrated.
Feasibility test of deformable BAN electrodes in ear canal
Authors: Arman Woo S.H. 
Published: January 2014

Implantable and portable medical devices have attracted much interest in recent years and the interconnections of these devices have become an important issue. One interconnection method is the use of the body access network (BAN) that does not need high power consumption as conventional radio frequency communication methods. Previous studies of the BAN have focused on measuring between the chest, wrist and other surface parts of the skin which are easily accessible with conventional electrodes. Deformable BAN electrodes are implemented to study the effectiveness of BAN communications in the ear canal. Conventional earphones and Bluetooth devices can easily access the ear canal and could be used for the BAN communication channel. The experimental results show various transmission loss among the ear canal, the wrist and the chest. The lowest attenuation showed as 23 dB at 34 MHz.
Compact square spiral printed antenna
Authors: Wei Heng , Lin Min , Xiang Yang 
Published: January 2014

A novel compact printed antenna with a spiral winding and a loop feed is proposed. After optimising the design parameters, the prototype of the antenna with a small electrical size of 0.043λc × 0.043λc × 0.001λc is fabricated. It is shown that a central frequency as low as 425.9 MHz can be achieved without any additional matching networks, and a good omnidirectional radiation pattern similar to the dipole antenna is obtained.
S/MAR sequence confers long-term mitotic stability on non-integrating lentiviral vector episomes without selection
Authors: Verghese Santhosh Chakkaramakkil , Goloviznina Natalya A. , Skinner Amy M. , Lipps Hans J. , Kurre Peter 
Published: January 2014

Abstract
Insertional oncogene activation and aberrant splicing have proved to be major setbacks for retroviral stem cell gene therapy. Integrase-deficient human immunodeficiency virus-1-derived vectors provide a potentially safer approach, but their circular genomes are rapidly lost during cell division. Here we describe a novel lentiviral vector (LV) that incorporates human ß-interferon scaffold/matrix-associated region sequences to provide an origin of replication for long-term mitotic maintenance of the episomal LTR circles. The resulting ‘anchoring’ non-integrating lentiviral vector (aniLV) achieved initial transduction rates comparable with integrating vector followed by progressive establishment of long-term episomal expression in a subset of cells. Analysis of aniLV-transduced single cell-derived clones maintained without selective pressure for &gt;100 rounds of cell division showed sustained transgene expression from episomes and provided molecular evidence for long-term episome maintenance. To evaluate aniLV performance in primary cells, we transduced lineage-depleted murine hematopoietic progenitor cells, observing GFP expression in clonogenic progenitor colonies and peripheral blood leukocyte chimerism following transplantation into conditioned hosts. In aggregate, our studies suggest that scaffold/matrix-associated region elements can serve as molecular anchors for non-integrating lentivector episomes, providing sustained gene expression through successive rounds of cell division and progenitor differentiation in vitro and in vivo.
First Report of a New Subgroup 16Sr II-M ‘Candidatus Phytoplasma aurantifolia’ Associated with Witches'-Broom Disease of Tephrosia purpurea in India
Authors: Yadav A. , Bhale U. , Thorat V. , Shouche Y. 
Published: January 2014

Wild indigo (Tephrosia purpurea (L.) Pers.) grows as a common weed throughout the Indian subcontinent. The plant has pinnate leaves, white or purplish flowers, and flat hairy pods, and is cultivated as a green manure crop. The plant extracts contain compounds such as tephrosin, an aromatic ester, prenylated flavonoid, and sesquiterpene (2) that have medicinal properties. The newly recognized disease, Tephrosia purpurea witches' broom (TPWB), was characterized by chlorosis, stunting, and proliferative branching, which were suggestive of phytoplasma infection during a field survey conducted in November 2013. To determine the presence of phytoplasma, 2 g of compound leaves from three symptomatic and asymptomatic plants were used for total DNA extraction using the CTAB method. The phytoplasma 16S rRNA gene was detected in all three symptomatic plants using nested PCR with universal phytoplasma primer pairs, P1/P7 followed by R16F2n/R16R2 (4). No amplification was observed in DNA isolated from asymptomatic plants. PCR fragments (1,246 bp in length) generated from symptomatic T. purpurea plants were sequenced directly using five different primers viz. 343R, 536F, 704F, 907R, and 1103F. TPWB phytoplasma 16S rRNA gene sequence (GenBank Accession No. HG792252) showed 99.12% homology with a ‘Candidatus Phytoplasma aurantifolia’ strain WBDL (U15442) when compared using the EzTaxon 16S rRNA database (3). Virtual restriction fragment length polymorphism (RFLP) analysis was carried out on the obtained sequence using iPhyClassifier (5). The virtual RFLP pattern derived from the HG792252 sequence was different to the reference patterns of previously established 16Sr groups and subgroups. The reference pattern of the 16Sr group II, subgroup C (AJ293216) was most similar with a similarity coefficient of 0.92, which placed it in a new subgroup, 16Sr II-M (1). Furthermore, virtual RFLP results were confirmed by digesting R16F2n/R16R2 amplicon with BstUI, DraI, HinfI, HpaI, and MseI restriction enzymes according to manufacturer's instructions. To our knowledge, this is the first report of a ‘Ca. P. aurantifolia’-related strain associated with witches'-broom disease of T. purpurea in India. References: (1) H. Cai et al. Int. J. Syst. Evol. Microbiol. 58:1448, 2008. (2) A. K. Khalafalah et al. Pharmacognosy Res. 2:72, 2010. (3) O.-S. Kim et al. Int. J. Syst. Evol. Microbiol. 62:716, 2012. (4) C. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (5) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Cytoplasmic nanojunctions between lysosomes and sarcoplasmic reticulum are required for specific calcium signaling
Authors: Fameli Nicola , Ogunbayo Oluseye A. , van Breemen Cornelis , Evans A. Mark 
Published: January 2014

AbstractHerein we demonstrate how nanojunctions between lysosomes and sarcoplasmic reticulum (L-SR junctions) serve to couple lysosomal activation to regenerative, ryanodine receptor-mediated cellular Ca2+waves. In pulmonary artery smooth muscle cells (PASMCs) it has been proposed that nicotinic acid adenine dinucleotide phosphate (NAADP) triggers increases in cytoplasmic Ca2+via L-SR junctions, in a manner that requires initial Ca2+release from lysosomes and subsequent Ca2+-induced Ca2+release (CICR) via ryanodine receptor (RyR) subtype 3 on the SR membrane proximal to lysosomes. L-SR junction membrane separation has been estimated to be<400 nm and thus beyond the resolution of light microscopy, which has restricted detailed investigations of the junctional coupling process. The present study utilizes standard and tomographic transmission electron microscopy to provide a thorough ultrastructural characterization of the L-SR junctions in PASMCs. We show that L-SR nanojunctions are prominent features within these cells and estimate that the junctional membrane separation and extension are about 15 nm and 300 nm, respectively. Furthermore, we develop a quantitative model of the L-SR junction using these measurements, prior kinetic and specific Ca2+signal information as input data. Simulations of NAADP-dependent junctional Ca2+transients demonstrate that the magnitude of these signals can breach the threshold for CICR via RyR3. By correlation analysis of live cell Ca2+signals and simulated Ca2+transients within L-SR junctions, we estimate that “trigger zones” with a 60–100 junctions are required to confer a signal of similar magnitude. This is compatible with the 130 lysosomes/cell estimated from our ultrastructural observations. Most importantly, our model shows that increasing the L-SR junctional width above 50 nm lowers the magnitude of junctional [Ca2+] such that there is a failure to breach the threshold for CICR via RyR3. L-SR junctions are therefore a pre-requisite for efficient Ca2+signal coupling and may contribute to cellular function in health and disease.
Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer
Authors: Li Yongsheng , Zhang Yunpeng , Li Shengli , Lu Jianping , Chen Juan , Zhao Zheng , Bai Jing , Xu Juan , Li Xia 
Published: January 2014

ABSTRACTThe development of human breast cancer is driven by changes in the genetic and epigenetic landscape of the cell. Despite growing appreciation of the importance of epigenetics in breast cancers, our knowledge of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancers remains limited. Here, we explored the epigenetic patterns of ncRNAs in breast cancers via a sequencing-based comparative methylome analysis, mainly focusing on two most popular ncRNA biotypes, long non-coding RNAs (lncRNAs) and miRNAs. Besides global hypomethylation and extensive CpG islands (CGIs) hypermethylation, we observed widely aberrant methylation in the promoters of ncRNAs, which was higher than that of protein-coding genes. Specifically, intergenic ncRNAs were observed to contribute a large slice of the aberrantly methylated ncRNA promoters. Moreover, we summarized five patterns of ncRNA promoter aberrant methylation in the context of genomic CGIs, where aberrant methylation occurred not only on the CGIs, but also flanking regions and CGI sparse promoters. Integration with transcriptional datasets, we found that the ncRNA promoter methylation events were associated with transcriptional changes. Furthermore, a panel of ncRNAs were identified as biomarkers that were able to discriminate between disease phenotypes (AUCs>0.90). Finally, the potential functions for aberrantly methylated ncRNAs were predicted based on similar patterns, adjacency and/or target genes, highlighting that ncRNAs and coding genes coordinately mediated pathways dysregulation in the development and progression of breast cancers. This study presents the aberrant methylation patterns of ncRNAs, which will be a highly valuable resource for investigations at understanding epigenetic regulation of breast cancers.[Supplemental material is available online atwww.genome.org.]
Remarkable Reproducibility of Enzyme Activity Profiles in Tomato Fruits Grown under Contrasting Environments Provides a Roadmap for Studies of Fruit Metabolism
Authors: Biais Benoît , Bénard Camille , Beauvoit Bertrand , Colombié Sophie , Prodhomme Duyên , Ménard Guillaume , Bernillon Stéphane , Gehl Bernadette , Gautier Hélène , Ballias Patricia , Mazat Jean-Pierre , Sweetlove Lee , Génard Michel , Gibon Yves 
Published: January 2014

Abstract
To assess the influence of the environment on fruit metabolism, tomato (Solanum lycopersicum ‘Moneymaker’) plants were grown under contrasting conditions (optimal for commercial, water limited, or shaded production) and locations. Samples were harvested at nine stages of development, and 36 enzyme activities of central metabolism were measured as well as protein, starch, and major metabolites, such as hexoses, sucrose, organic acids, and amino acids. The most remarkable result was the high reproducibility of enzyme activities throughout development, irrespective of conditions or location. Hierarchical clustering of enzyme activities also revealed tight relationships between metabolic pathways and phases of development. Thus, cell division was characterized by high activities of fructokinase, glucokinase, pyruvate kinase, and tricarboxylic acid cycle enzymes, indicating ATP production as a priority, whereas cell expansion was characterized by enzymes involved in the lower part of glycolysis, suggesting a metabolic reprogramming to anaplerosis. As expected, enzymes involved in the accumulation of sugars, citrate, and glutamate were strongly increased during ripening. However, a group of enzymes involved in ATP production, which is probably fueled by starch degradation, was also increased. Metabolites levels seemed more sensitive than enzymes to the environment, although such differences tended to decrease at ripening. The integration of enzyme and metabolite data obtained under contrasting growth conditions using principal component analysis suggests that, with the exceptions of alanine amino transferase and glutamate and malate dehydrogenase and malate, there are no links between single enzyme activities and metabolite time courses or levels.
Defective barrier function accompanied by structural changes of psoriatic stratum corneum
Authors: Takahashi Hidetoshi , Tsuji Hitomi , Minami‐Hori Masako , Miyauchi Yuki , Iizuka Hajime 
Published: January 2014

AbstractAlthough barrier function of psoriatic skin is shown to be decreased by measuring transepidermal water loss (TEWL), few reports exist examining other physical skin properties and components including stratum corneum hydration, natural moisturizing factor (NMF), free fatty acids (FFA), β‐sheet and α‐helix ratio of structural protein(s), and sebum content. We compared the skin properties and components of normal, involved and uninvolved skin of psoriasis. Using a corneometer and attenuated total reflection‐infrared spectrometer, we measured TEWL, stratum corneum hydration, NMF, FFA, β/α ratio and sebum in psoriasis vulgaris patients and healthy controls. TEWL and β/α ratio of involved psoriatic skin were significantly increased compared with uninvolved skin and normal control skin. In contrast, stratum corneum hydration, NMF and FFA, but not sebum, are significantly decreased in the involved skin compared with uninvolved skin and normal skin. TEWL and stratum corneum hydration returned to the normal levels following clinical improvement of the lesion. Barrier function and hydration of psoriatic skin are defective and secondary structure in stratum corneum protein is altered in the involved psoriatic skin.
Raptors as surrogates of biodiversity along a landscape gradient
Authors: Burgas Daniel , Byholm Patrik , Parkkima Tiina 
Published: January 2014

Summary

With biodiversity facing threats, there is a need to improve reserve selection procedures. However, detailed information about different biodiversity measures (e.g. species richness) at potential sites is often lacking, and selecting areas that protect most biodiversity is difficult. To simplify matters, biodiversity surrogate species, that is, species associated with higher biodiversity than average, have been used for area selection. However, consensus about the performance of the surrogate species concept is lacking, and there are few studies investigating potential differences in the effectiveness of multiple predators as surrogates for biodiversity over large spatial scales.

We evaluated two avian predators, the northern goshawk Accipiter gentilis and the Ural owl Strix uralensis, as surrogates for biodiversity in the boreal forest biome in Western Finland. We used a study design including nest sites and two reference sites for each nest, the diversity of birds and wood‐decaying fungi (polypores). We assessed simultaneously whether surrogacy persisted at the landscape level while moving from one vegetation zone to another.

We generally found more birds and polypores around the nest sites for both goshawks and Ural owls than at their respective reference sites. However, the goshawk outperformed the Ural owl.

Additionally, although biodiversity was found to decrease at the landscape scale as a result of a decrease in vegetation complexity with increasing longitude, the surrogacy efficiency of the raptors remained unchanged.

Synthesis and applications. These findings suggest that the surrogate species concept applied to raptors may be an efficient addition to methods for identifying areas of conservation priority, even across vegetation zones. We conclude that protecting areas around raptor nests is a method to consider in order to halt forest biodiversity loss. Finally, sampling biodiversity along diversity and landscape gradients can improve the necessary assessment of surrogate species.
Antibiotic treatments and microbes in the gut
Authors: Macfarlane Sandra 
Published: January 2014

SummaryAntibiotic therapies are important in combating disease‐causing microorganisms and maintaining host health. It is widely accepted that exposure of the gut microbiota to antibiotics can lead to decreased susceptibility and the development of multi‐drug‐resistant disease‐causing organisms, which can be a major clinical problem. It is also important to consider that antibiotics not only target pathogenic bacteria in the gut, but also can have damaging effects on the ecology of commensal species. This can reduce intrinsic colonization resistance and contribute to problems with antibiotic resistance, including lateral transfer of resistance genes. Our knowledge of the impact of antibiotic treatment on the ecology of the normal microbiota has been increased by recent advances in molecular methods and use of in vitro model systems to investigate the impact of antibiotics on the biodiversity of gut populations and the spread of antibiotic resistance. These highlight the need for more detailed structural and functional information on the long‐term antibiotic‐associated alterations in the gut microbiome, and spread of antibiotic resistance genes. This will be crucial for the development of strategies, such as targeted therapeutics, probiotics, prebiotics and synbiotics, to prevent perturbations in the gut microbiota, the restoration of beneficial species and improvements in host health.