bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong anisotropic lifetime orientation distributions of a two-level quantum emitter around a plasmonic nanorod
Authors: Liu Jia-Ming , Liu Jing-Feng , Yu Yi-Cong , Zeng Ling-Yu , Wang Xue-Hua 
Published: April 2014

Abstract
Spontaneous emission lifetime orientation distributions of a two-level quantum emitter in metallic nanorod structures are theoretically investigated by the rigorous electromagnetic Green function method. It was found that spontaneous emission lifetime strongly depended on the transition dipole orientation and the position of the emitter. The anisotropic factor defined as the ratio between the maximum and minimum values of the lifetimes along different dipole orientations can reach up to 103. It is much larger than those in dielectric structures which are only several times usually. Our results show that the localized plasmonic resonance effect provides a new degree of freedom to effectively control spontaneous emission by the dipole orientation of the quantum emitters.

PACS: 78.67.Qa; 73.20.Mf; 42.50.-p
Morphological effect of oscillating magnetic nanoparticles in killing tumor cells
Authors: Cheng Dengfeng , Li Xiao , Zhang Guoxin , Shi Hongcheng 
Published: April 2014

Abstract
Forced oscillation of spherical and rod-shaped iron oxide magnetic nanoparticles (MNPs) via low-power and low-frequency alternating magnetic field (AMF) was firstly used to kill cancer cells in vitro. After being loaded by human cervical cancer cells line (HeLa) and then exposed to a 35-kHz AMF, MNPs mechanically damaged cell membranes and cytoplasm, decreasing the cell viability. It was found that the concentration and morphology of the MNPs significantly influenced the cell-killing efficiency of oscillating MNPs. In this preliminary study, when HeLa cells were pre-incubated with 100 μg/mL rod-shaped MNPs (rMNP, length of 200 ± 50 nm and diameter of 50 to 120 nm) for 20 h, MTT assay proved that the cell viability decreased by 30.9% after being exposed to AMF for 2 h, while the cell viability decreased by 11.7% if spherical MNPs (sMNP, diameter of 200 ± 50 nm) were used for investigation. Furthermore, the morphological effect of MNPs on cell viability was confirmed by trypan blue assay: 39.5% rMNP-loaded cells and 15.1% sMNP-loaded cells were stained after being exposed to AMF for 2 h. It was also interesting to find that killing tumor cells at either higher (500 μg/mL) or lower (20 μg/mL) concentration of MNPs was less efficient than that achieved at 100 μg/mL concentration. In conclusion, the relatively asymmetric morphological rod-shaped MNPs can kill cancer cells more effectively than spherical MNPs when being exposed to AMF by virtue of their mechanical oscillations.
Ultrasonography of the distal limbs in Nellore and Girolando calves 8 to 12 months of age
Authors: Gonçalves Pryscilla VR , Silva Luiz AF , Silva Luiz H , Costa Ana Paula A , Bragato Nathalia , Cardoso Julio R , Kofler Johann , Borges Naida C 
Published: April 2014

AbstractBackgroundUltrasonography can be used anywhere and allows rapid, noninvasive differentiation of soft tissue structures of the musculoskeletal system. The objectives of this study were to describe the ultrasonographic appearance of the structures of the metacarpo-/metatarsophalangeal and the interphalangeal joints, the appearance of the growth plates of the distal metacarpus/metatarsus and of the proximal phalanx and to measure the cross-sectional dimensions of the DDFT and SDFT in Nellore and Girolando calves eight to 12 months of age.ResultsIn the longitudinal dorsal view the common digital extensor tendon and the digital extensor tendon were depicted as echogenic parallel fiber bundles located directly under the skin. The joint spaces appeared as anechoic interruptions of the hyperechogenic bone surfaces. The normal amount of synovial fluid could not be depicted. The growth plates were seen as anechoic interruptions of the bone surface proximal and distal to the fetlock joint space. In transverse sonograms of the distal palmar/plantar regions, the flexor tendons and branchs of the suspensory ligament were imaged as echogenic structures. The lumen of the digital flexor tendon sheath could not be imaged in these normal cattle. The thin digital distal annular ligament and the reversal of positions of the DDFT and SDFT could be appreciated. No significant differences were found between the cross-sectional measurements of the DDFT and the SDFT from Nellore and Girolando in any age, thoracic/pelvic limbs, right/left sides and lateral/medial digits.ConclusionsThe results of this study establish important ultrasonographic reference data of the normal structures of the distal limbs and the normal dimensions of the flexor tendons in Nellore and Girolando calves for use in clinical practice.
Mind the gap: rigour and relevance in collaborative heritage science research
Authors: Dillon Catherine , Bell Nancy , Fouseki Kalliopi , Laurenson Pip , Thompson Andrew , Strlič Matija 
Published: April 2014

Abstract

Background
This paper examines if there is a ‘rigour-relevance gap’ in collaborative heritage science research and what enables and impedes effective collaboration between academic researchers and users of research evidence in practice. A quantitative attitudes questionnaire was distributed amongst the heritage science community: 210 responses were received. Respondents answered in relation to one project they had worked on in the UK in the previous five years. They were asked about their personal goals in relation to the project and whether these were achieved, satisfaction levels in relation to project outcomes and impact, level of agreement with a series of attitude statements to ascertain what helped and hindered projects, personal characteristics and project characteristics. The questionnaire was analysed using a factor analytic, segmentation and profiling approach.

Results
Most respondents sought both rigour and relevance in collaborative research, were generally satisfied with the outcomes of projects and reported positive experiences of collaboration. However, respondents were less satisfied that the impact of projects would be realised. Practice-focussed goals were associated with lower levels of self-rated achievement than academic goals and a sizeable minority reported challenges in collaborative research. Furthermore, researchers and users differed in terms of their goals, experiences and level of satisfaction. Users had high expectations that research would translate into practice, but did not always feel this was realised.

Conclusion
Results from this project will inform how to improve heritage science research collaborations.
Pretreatment of garden biomass by alkali-assisted ultrasonication: effects on enzymatic hydrolysis and ultrastructural changes
Authors: Gabhane Jagdish , William SPM Prince , Vaidya Atul Narayan , Anand Duraisamy , Wate Satish 
Published: April 2014

Abstract
The present investigation aims at studying the effectiveness of alkali-assisted ultrasonication on pretreatment of garden biomass (GB). Dry and powdered GB suspended in 1% NaOH was ultrasonicated for 15, 30 and 60 minutes at a frequency of 25 KHZ. The mode of action and effectiveness of alkali-assisted ultrasonication on GB was established through microscopic, scanning electron microscopic and X-ray diffraction studies. A perusal of results showed that alkali-assisted ultrasonication led to fibrillation of GB which ultimately facilitated enzymatic hydrolysis. The results also indicated that alkali-assisted ultrasonication is an efficient means of pretreatment of GB at moderate (45-50°C) working temperature and low (1%) concentration of alkali. The yield of reducing sugar after enzymatic hydrolysis increased almost six times as compared to control due to alkali-assisted ultrasonication.
Expression of endogenous Mkp1 in 6-OHDA rat models of Parkinson’s disease
Authors: Collins Louise M , Gavin Aisling M , Walsh Sinead , Sullivan Aideen M , Wyatt Sean L , O’Keeffe Gerard W , Nolan Yvonne M , Toulouse André 
Published: April 2014

Abstract
We have previously demonstrated that mitogen-activated protein kinase phosphatase 1, Mkp1, is expressed in the developing and rat adult substantia nigra and striatum, where it promotes the growth of nigral dopaminergic neurons. Mkp1 may therefore have therapeutic potential for Parkinson’s disease. In the present study, we have assessed the expression of Mkp1 and TH in the substantia nigra and striatum of parkinsonian rat models. Expression was measured at 4 and 10 days post-lesion in the 6-hydroxydopamine (6-OHDA) medial forebrain bundle lesion model and after 4, 10 and 28 days in the 6-OHDA striatal lesion model. Our results show that Mkp1 expression was transiently up-regulated in the substantia nigra at 4 days post-6-OHDA administration in the two models while TH expression was decreased at the later time-points examined. These data suggest that Mkp1 may play a role in counteracting the neurotoxic effects of 6-OHDA in nigral dopaminergic neurons.
Association of inflammatory and endothelial cell activation biomarkers with acute kidney injury after sepsis
Authors: Powell T Clark , Powell Stephen L , Allen Bryant K , Griffin Russell L , Warnock David G , Wang Henry E 
Published: April 2014

Abstract

Objective
Acute kidney injury (AKI) is a sequela of sepsis associated with increased morbidity and mortality. We sought to determine if individuals with elevated baseline levels of inflammation and endothelial cell activation are at increased risk for future AKI after sepsis.

Methods
We conducted an analysis of individuals developing sepsis in the national 30,239 subject REGARDS cohort. Biomarkers measured at the beginning of an 8-year observation period included high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), tumor necrosis factor (TNF-α), E-selectin, inter-cellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), and urinary Albumin-to-creatinine ratio (ACR). We defined subsequent sepsis as hospitalization for a serious infection with ≥2 Systemic Inflammatory Response Syndrome (SIRS) criteria. We excluded patients with prior dialysis or kidney transplantation, or those receiving less than two serum creatinine (sCr) measurements during hospitalization. We defined AKI as an increase in sCr ≥0.3 mg/dL from the initial sCr measurement, or the initiation of hemodialysis. Using logistic regression, we evaluated the associations between AKI and biomarker quartiles, adjusting for comorbidities.

Results
We identified 212 sepsis cases encompassing 41 (19.3%) AKI. Elapsed time from biomarker measurement to sepsis episode was 3.1 years (IQR 1.6-4.5). Compared with non-AKI, AKI individuals exhibited higher TNF-α (9.4 vs. 6.2 pg/mL, p = 0.003) and ACR (504.82 vs 61.81 mg/g, p < 0.001). hsCRP, IL-6, E-selectin, ICAM-1 and VCAM-1 were similar between AKI and non-AKI. After adjustment for confounders, AKI after sepsis was more likely in those with higher E-selectin (adjusted ORs 2.91 (0.95-8.93), 1.99 (0.61-6.47), 4.01 (1.30-12.35), test of linear trend p = 0.04), and higher ACR (adjusted ORs 2.29 (0.99-5.30), 10.67 (3.46-32.90), test of linear trend p < 0.001). Baseline hsCRP, TNF-α, IL-6, VCAM-1 and ICAM-1 were not associated with AKI after sepsis.

Conclusion
Elevated baseline levels of E-selectin and ACR are associated with future AKI in the setting of sepsis. Baseline inflammatory and endothelial activation biomarkers may be useful for predicting future risk of AKI in sepsis.
Effects of pine invasion on land planarian communities in an area covered by Araucaria moist forest
Authors: de Oliveira Simone Machado , Boll Piter Kehoma , dos Anjos Baptista Vanessa , Leal-Zanchet Ana Maria 
Published: April 2014

AbstractBackgroundCultivation of exotic pine species has increased in areas ofAraucariamoist forest, which is an ecosystem with high biological diversity. Land planarians are generally susceptible to replacement of natural habitat by exotic tree species plantations. However, how planarian communities respond to the invasion of exotic species in natural habitats is unknown: (1) Are there differences in richness and abundance of land planarians between sites ofAraucariamoist forest with (AMF-P) and without (AMF) pine trees and between these areas and pine plantations (P)? (2) Does the species composition of land planarians vary among AMF, AMF-P, and P?ResultsThis study shows that mean richness and abundance of land planarians per sample unit are higher in AMF sites than AMF-P sites. In addition, AMF sites have a higher estimated richness per sample unit than pine plantations and AMF-P sites. In AMF-P sites, mean richness and abundance are higher in sample units not influenced by pine trees than in those with pine needles. An ordination analysis indicated that the communities of each site are distinct, especially the communities of the AMF and P sites.ConclusionsThe present work demonstrated negative impacts from a recent invasion of an exotic species of pine on the richness and abundance of land planarians in a site ofAraucariamoist forest and significant variation in the planarian community composition between sites ofAraucariamoist forest and pine plantation.
Gene markers of cellular aging in human multipotent stromal cells in culture
Authors: Bellayr Ian H , Catalano Jennifer G , Lababidi Samir , Yang Amy X , Lo Surdo Jessica L , Bauer Steven R , Puri Raj K 
Published: April 2014

Abstract
Introduction
Human multipotent stromal cells (MSCs) isolated from bone marrow or other tissue sources have great potential to treat a wide range of injuries and disorders in the field of regenerative medicine and tissue engineering. In particular, MSCs have inherent characteristics to suppress the immune system and are being studied in clinical studies to prevent graft-versus-host disease. MSCs can be expanded in vitro and have potential for differentiation into multiple cell lineages. However, the impact of cell passaging on gene expression and function of the cells has not been determined.

Methods
Commercially available human MSCs derived from bone marrow from six different donors, grown under identical culture conditions and harvested at cell passages 3, 5, and 7, were analyzed with gene-expression profiling by using microarray technology.

Results
The phenotype of these cells did not change as reported previously; however, a statistical analysis revealed a set of 78 significant genes that were distinguishable in expression between passages 3 and 7. None of these significant genes corresponded to the markers established by the International Society for Cellular Therapy (ISCT) for MSC identification. When the significant gene lists were analyzed through pathway analysis, these genes were involved in the top-scoring networks of cellular growth and proliferation and cellular development. A meta-analysis of the literature for significant genes revealed that the MSCs seem to be undergoing differentiation into a senescent cell type when cultured extensively. Consistent with the differences in gene expression at passage 3 and 7, MSCs exhibited a significantly greater potential for cell division at passage 3 in comparison to passage 7.

Conclusions
Our results identified specific gene markers that distinguish aging MSCs grown in cell culture. Confirmatory studies are needed to correlate these molecular markers with biologic attributes that may facilitate the development of assays to test the quality of MSCs before clinical use.
The effect of Rho kinase inhibition on long-term keratinocyte proliferation is rapid and conditional
Authors: Chapman Sandra , McDermott David H , Shen Kui , Jang Moon Kyoo , McBride Alison A 
Published: April 2014

Abstract
Introduction
We previously demonstrated that the lifespan of primary human keratinocytes could be extended indefinitely by culture in the presence of the Rho kinase (ROCK) inhibitor Y-27632. This technique has proven to be very useful in diverse areas of basic and clinical research.

Methods
In this follow-up study we determine whether the continual presence of Y-27632 is required for sustained proliferation. We also test whether different ROCK inhibitors can be used for this technique and whether it can also promote indefinite proliferation of animal keratinocytes. We measure keratinocyte gene expression, proliferation, behaviour and lifespan in the presence and absence of Y-27632.

Results
We demonstrate that the extension of lifespan observed by culture of keratinocytes in the presence of fibroblast feeders and a ROCK inhibitor is reversible and that cells senesce gradually when the inhibitor is removed from the medium. Conversely, keratinocytes that are close to the end of their replicative life span can be revived by ROCK inhibition. We demonstrate that different inhibitors of ROCK can also efficiently extend the lifespan of human keratinocytes and that ROCK inhibition extends the lifespan of animal keratinocytes derived from mouse and bovine epithelia. Gene expression analysis of human epidermal keratinocytes cells grown in the presence of Y-27632 demonstrates that ROCK inhibition primarily inhibits keratinocyte differentiation. Live-imaging of keratinocytes cultured with ROCK inhibitors show that the effect of ROCK inhibition on cellular proliferation is immediate and ROCK inhibited cells proliferate rapidly without differentiation or stratification.

Conclusions
ROCK inhibition rapidly and conditionally induces indefinite proliferation of keratinocytes. This method has far-reaching applications for basic research, as well as for regenerative and personalized medicine.
Detailed mark‐up of semi‐monographic legacy taxonomic works using FlorML
Authors: Hamann Thomas D. , Müller Andreas , Roos Marinus C. , Sosef Marc , Smets Erik 
Published: April 2014

AbstractWe present FlorML, an XML schema, specifically designed for the detailed mark‐up of highly complicated semi‐monographic legacy taxonomic works, such as large Floras and Faunas. We discuss the prerequisites for developing a suitable XML schema, and the limitations presented by the legacy taxonomic works, requirements by stakeholders and the desired output format. Furthermore, we explain how FlorML was deployed to mark up two legacy taxonomic works, Flora Malesiana and Flore du Gabon, how that deployment was improved by the use of the scripting language Perl to automate major parts of the process, and discuss the issues commonly encountered during the mark‐up process. Examples and figures are provided for clarification. Finally, we make suggestions for future research and further developments in the field of biodiversity informatics.
Genetic identity of putative Linnaean plants: Successful DNA amplification of Linnaeus's crab apple Malus baccata
Authors: Andreasen Katarina , Manktelow Mariette , Sehic Jasna , Garkava-Gustavsson Larisa 
Published: April 2014

AbstractAdvancements in molecular techniques enable us to extract DNA from historic herbarium specimens and facilitate genetic comparisons between herbarium material and living plant collections. These recent advances offer an exciting opportunity for identifying extant Linnaean plants by genetic comparisons of Linnaeus's own herbarium specimens with potentially remnant plants from his cultivations. DNA from the lectotype of Malus baccata (L.) Borkh. in the Linnaean Herbarium was successfully extracted and amplified for five of twelve loci of microsatellites. Results of genetic comparisons with M. baccata trees from Linnaeus's Hammarby, Sweden, show that the trees at Hammarby are closely related to each other, but not to the lectotype, which is closer to material from Russia. This suggests that Linnaeus received M. baccata from more than one source. Although not close to the lectotype and not represented by a specimen in the Linnaean Herbarium, the extant M. baccata at Hammarby may still represent Linnaean plants, that were grown by Linnaeus himself, or the descendants to such plants. Future studies on the almost 50 living, potential Linnaean plants may reveal an invaluable biological, scientific and cultural heritage from the era that saw the rise of systematic biology.
Testing the boundaries of closely related daisy taxa using metabolomic profiling
Authors: Messina Andre , Callahan Damien L. , Walsh Neville G. , Hoebee Susan E. , Green Peter T. 
Published: April 2014

AbstractAdvances in high‐throughput, comprehensive small molecule analytical techniques have seen the development of the field of metabolomics. The coupling of mass spectrometry with high‐resolution chromatography provides extensive chemical profiles from complex biological extracts. These profiles include thousands of compounds linked to gene expression, and can be used as taxonomic characters. Studies have shown metabolite profiles to be taxon specific in a range of organisms, but few have investigated taxonomically problematic plant taxa. This study used a phenetic analysis of metabolite profiles to test taxonomic boundaries in the Olearia phlogopappa (Asteraceae) complex as delimited by morphological data. Metabolite profiles were generated from both field‐ and shade hous‐egrown material, using liquid chromatography‐mass spectrometry (LC‐MS). Aligned profiles of 51 samples from 12 taxa gave a final dataset of over 10,000 features. Multivariate analyses of field and shade house material gave congruent results, both confirming the distinctiveness of the morphologically defined species and subspecies in this complex. Metabolomics has great potential in alpha taxonomy, especially for testing the boundaries of closely related taxa where DNA sequence data has been uninformative.
Resolved phylogeny of Cleomaceae based on all three genomes
Authors: Patchell Melanie J. , Roalson Eric H. , Hall Jocelyn C. 
Published: April 2014

AbstractCleomaceae is a small pantropical family that is emerging as a promising system to investigate C4 photosynthesis, floral evolution, and comparative genomics. However, our understanding of these phenomena is hindered by a lack of a strong phylogenetic hypothesis, despite a number of previous studies. We reconstructed the phylogeny of the family using data from all three genomes, including three cpDNA (ndhF, matK, ycf1), one mtDNA (rps3), and one nrDNA (ITS) regions. Analyses strongly supported 15 clades: (1) Clade 1, which includes two Old World species, Cleome khorassanica and C. turkmena; (2) Cleome s.str., which includes the type C. ornithopodioides and Old World species; (3) Droserifolia, corresponding to three Old World species, C. droserifolia, C. fimbriata, C. quinquenervia; (4) Polanisia, equivalent to this New World genus; (5) Angustifolia, which includes four Old World species; (6) North American cleomoids, which includes four genera, Cleomella, Peritoma, Oxystylis, and Wislizenia; (7) Australian, which includes Old world species and worldwide weed Arivela viscosa; (8) Gynandropsis, equivalent to this monotypic genus; (9) Clade 6, which includes Old World species of Cleome and Dipterygium; (10) Dactylaena, corresponding to this genus and Physostemon; (11) African, which includes species distributed in Old World; (12) Andean, which includes Podandrogyne and tropical New World species of Cleome; (13) Melidiscus, which includes New World tropical species; (14) Cleoserrata, which includes New World tropical species; and (15) Tarenaya, a large New World clade. Major relationships amongst the clades are strongly supported for the first time, including North American cleomoids sister to all remaining Cleomaceae. While five genera are confirmed or newly identified here to be non‐monophyletic (Cleome, Cleomella, Hemiscola, Peritoma, Tarenaya), six are supported (Cleoserrata, Dactylaena, Melidiscus, Physostemon, Podandrogyne, Polanisia). Thus, there are many taxonomic and evolutionary implications to our revised phylogenetic hypothesis.