bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges in Implementing the European Convention against Trafficking in Human Organs
Authors: PIETROBON ALESSANDRA 
Published: April 2016

AbstractThe newest convention of the Council of Europe requires states parties to criminalize all activities related to the trafficking in human organs. It is the first international agreement specifically aimed at addressing this form or criminal trade. Trafficking in human organs is mostly a transnational criminal enterprise: the article highlights how contracting states will have to face specific problems in prosecuting offences committed in foreign countries. The effectiveness of the convention depends on the parties’ determination in solving such problems and in avoiding taking advantage from some reservations that – though admitted by the convention – could undermine its possible value as a means of combating transnational crime.
Post-Mongol States and Early Modern Chronology in Iran and China
Authors: CROSSLEY PAMELA KYLE , GARTHWAITE GENE R. 
Published: April 2016

AbstractIn the aftermath of the Mongol occupations of the largest and most populous societies of Eurasia, greater visibility of popular religion, more widespread vernacular language use, rising literacy, and fundamental shifts in the structure of rulership and the relationship of state and society could all be observed. Many historians have related these changes to a broader chronology of early modernity. This has been problematic in the case of Iran, whose eighteenth-century passage has not been adequately explored in recent scholarship. Our comparative review of ‘post-Mongol’ Iran and China suggests that this period marks as meaningful a break between a schematic medieval and schematic early modern history in Iran as it does in China. Here, we first consider both societies in the post-Mongol period as empires with secular rulerships and increasingly popular cultural trends, and look at the role of what Crossley has called “simultaneous rulership”—rulership in which the codes of legitimacy of civilisations recognised by the conquest authority are given distinct representation in the rulership — in marking the transition away from religious-endorsed rule to self-legitimating rule as a mark of comparative early modernity.
Scripting Mamlūk Cities: Insider's Look. Explorations into Landscape Narratives
Authors: LUZ NIMROD 
Published: April 2016

AbstractIn a memorial lecture for Charles Beckingham, David Morgan1evoked one of this prolific travel literature scholar's astute observations: “[T]he study of travel narratives, especially travel narratives about a culture quite different from the traveller's own, can be very revealing, not only about the culture he observed, but about the culture to which he belonged”.2This insight indeed undergirds my own approach to the descriptions of cities by both insiders and outsiders. Narratives of cities, indeed of any landscape, are but interpretative and hermeneutics texts which can be surely used to narrate the very landscape, but also as texts which may be used to understand the culture and perceptions of the narrator. Over the course of this paper, I examine two accounts (texts) of residents of Mamlūk provincial cities inal-Shām. These texts will be placed under the scrutiny of the data and the existing literature of those cities. In other words, the ‘conceptualised city’ as narrated by the sources will be compared with the ‘tangible city’. The latter we may unearth from various other sources (mostly texts) as well as the city's built environment. Thus, this chapter examines the ways in which Mamlūk cities ofal-Shāmwere scripted and narrated by two local ‘storytellers’ and ‘image-makers’ of the city.3In this context, ‘storyteller’ is an umbrella term for those who left us with a narrated legacy of their city. I decided to call them storytellers for the purpose of accentuating their inherent subjectivity. Informed and accurate as some of these narrators may have been, all of their experiences with and accounts of the urban landscape were guided by a personal understanding and their own cultural background. Since each of these texts is about spatial practices and spatial arrangement (landscape) of the city, the argument can be made that they all fall under the heading of travel writing.4What is more, any narrative with a spatial dimension (Michel de Certeau would argue that there is no such thing as a narrative without one) is a story that organises space. Against this backdrop, the objective of this chapter, above and beyond presenting ‘spatial stories’ of cities of Syria, is to demonstrate the complexity of the reading landscape and particularly the ways landscape descriptions need always be taken as subjective, culture-based, culturally constructed, and a constant negotiation between the traveller/story-teller/source narration, the ‘actual’ built environment and the political context.
Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics
Authors: Mosbæk Freya , Kjeldal Henrik , Mulat Daniel G , Albertsen Mads , Ward Alastair J , Feilberg Anders , Nielsen Jeppe L 
Published: April 2016

Abstract
Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of 13C-labeled CO2 and CH4 were detected immediately following incubation with [U-13C]acetate, indicating high turnover rate of acetate. The identified 13C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.
The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)
Authors: Gao Feng , Warren Alan , Zhang Qianqian , Gong Jun , Miao Miao , Sun Ping , Xu Dapeng , Huang Jie , Yi Zhenzhen , Song Weibo 
Published: April 2016

AbstractThe phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous generaAskenasia,CyclotrichiumParaspathidiumandPlagiocampashow close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded asincertae sediswithin Spirotrichea.
High activity of the stress promoter contributes to susceptibility to stress in the tree shrew
Authors: Fang Hui , Sun Yun-Jun , Lv Yan-Hong , Ni Rong-Jun , Shu Yu-Mian , Feng Xiu-Yu , Wang Yu , Shan Qing-Hong , Zu Ya-Nan , Zhou Jiang-Ning 
Published: April 2016

AbstractStress is increasingly present in everyday life in our fast-paced society and involved in the pathogenesis of many psychiatric diseases. Corticotrophin-releasing-hormone (CRH) plays a pivotal role in regulating the stress responses. The tree shrews are highly vulnerable to stress which makes them the promising animal models for studying stress responses. However, the mechanisms underlying their high stress-susceptibility remained unknown. Here we confirmed that cortisol was the dominate corticosteroid in tree shrew and was significantly increased after acute stress. Our study showed that the function of tree shrew CRH - hypothalamic-pituitary-adrenal (HPA) axis was nearly identical to human that contributed little to their hyper-responsiveness to stress. Using CRH transcriptional regulation analysis we discovered a peculiar active glucocorticoid receptor response element (aGRE) site within the tree shrew CRH promoter, which continued to recruit co-activators including SRC-1 (steroid receptor co-activator-1) to promote CRH transcription under basal or forskolin/dexamethasone treatment conditions. Basal CRH mRNA increased when the aGRE was knocked into the CRH promoter in human HeLa cells using CAS9/CRISPR. The aGRE functioned critically to form the “Stress promoter” that contributed to the higher CRH expression and susceptibility to stress. These findings implicated novel molecular bases of the stress-related diseases in specific populations.
Ecological restoration alters microbial communities in mine tailings profiles
Authors: Li Yang , Jia Zhongjun , Sun Qingye , Zhan Jing , Yang Yang , Wang Dan 
Published: April 2016

AbstractEcological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.
Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes
Authors: Kooi Irsan E. , Mol Berber M. , Massink Maarten P. G. , Ameziane Najim , Meijers-Heijboer Hanne , Dommering Charlotte J. , van Mil Saskia E. , de Vries Yne , van der Hout Annemarie H. , Kaspers Gertjan J. L. , Moll Annette C. , te Riele Hein , Cloos Jacqueline , Dorsman Josephine C. 
Published: April 2016

AbstractRetinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited. To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses. Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors. Targeted therapy based on these subclonal events might be insufficient for complete tumor control.
Single-wall carbon nanotubes and graphene oxide-based saturable absorbers for low phase noise mode-locked fiber lasers
Authors: Li Xiaohui , Wu Kan , Sun Zhipei , Meng Bo , Wang Yonggang , Wang Yishan , Yu Xuechao , Yu Xia , Zhang Ying , Shum Perry Ping , Wang Qi Jie 
Published: April 2016

AbstractLow phase noise mode-locked fiber laser finds important applications in telecommunication, ultrafast sciences, material science, and biology, etc. In this paper, two types of carbon nano-materials, i.e. single-wall carbon nanotube (SWNT) and graphene oxide (GO), are investigated as efficient saturable absorbers (SAs) to achieve low phase noise mode-locked fiber lasers. Various properties of these wall-paper SAs, such as saturable intensity, optical absorption and degree of purity, are found to be key factors determining the performance of the ultrafast pulses. Reduced-noise femtosecond fiber lasers based on such carbon-based SAs are experimentally demonstrated, for which the phase noise has been reduced by more than 10 dB for SWNT SAs and 8 dB for GO SAs at 10 kHz. To the best of our knowledge, this is the first investigation on the relationship between different carbon material based SAs and the phase noise of mode-locked lasers. This work paves the way to generate high-quality low phase noise ultrashort pulses in passively mode-locked fiber lasers.
A study of organic acid production in contrasts between two phosphate solubilizing fungi: Penicillium oxalicum and Aspergillus niger
Authors: Li Zhen , Bai Tongshuo , Dai Letian , Wang Fuwei , Tao Jinjin , Meng Shiting , Hu Yunxiao , Wang Shimei , Hu Shuijin 
Published: April 2016

AbstractPhosphate solubilizing fungi (PSF) have huge potentials in enhancing release of phosphorus from fertilizer. Two PSF (NJDL-03 and NJDL-12) were isolated and identified asPenicillium oxalicumandAspergillus nigerrespectively in this study. The quantification and identification of organic acids were performed by HPLC. Total concentrations of organic acids secreted by NJDL-03 and NJDL-12 are ~4000 and ~10,000 mg/L with pH values of 3.6 and 2.4 respectively after five-days culture. Oxalic acid dominates acidity in the medium due to its high concentration and high acidity constant. The two fungi were also cultured for five days with the initial pH values of the medium varied from 6.5 to 1.5. The biomass reached the maximum when the initial pH values are 4.5 for NJDL-03 and 2.5 for NJDL-12. The organic acids for NJDL-12 reach the maximum at the initial pH = 5.5. However, the acids by NJDL-03 continue to decrease and proliferation of the fungus terminates at pH = 2.5. The citric acid production increases significantly for NJDL-12 at acidic environment, whereas formic and oxalic acids decrease sharply for both two fungi. This study shows that NJDL-12 has higher ability in acid production and has stronger adaptability to acidic environment than NJDL-03.
High voltage and high current density vertical GaN power diodes
Authors: Armstrong A.M. , Allerman A.A. , Fischer A.J. , King M.P. , van Heukelom M.S. , Moseley M.W. , Kaplar R.J. , Wierer J.J. , Crawford M.H. , Dickerson J.R. 
Published: April 2016

The realisation of a GaN high voltage vertical p–n diode operating at >3.9 kV breakdown with a specific on‐resistance <0.9 mΩ cm2 is reported. Diodes achieved a forward current of 1 A for on‐wafer, DC measurements, corresponding to a current density >1.4 kA/cm2. An effective critical electric field of 3.9 MV/cm was estimated for the devices from analysis of the forward and reverse current–voltage characteristics. This suggests that the fundamental limit to the GaN critical electric field is significantly greater than previously believed.
The role of ions in the self-healing behavior of soft particle suspensions
Authors: Scotti Andrea , Gasser Urs , Herman Emily S. , Pelaez-Fernandez Miguel , Han Jun , Menzel Andreas , Lyon L. Andrew , Fernández-Nieves Alberto 
Published: April 2016

Significance
Understanding when a material crystallizes is of fundamental importance in condensed matter. In many materials, the presence of point defects suppresses crystallization. Surprisingly, colloidal hydrogels can overcome this limitation: A small number of large microgels can spontaneously deswell to fit in the crystal lattice of smaller microgels, thus avoiding the occurrence of point defects. We find that this unique particle deswelling is due to an osmotic pressure difference between the inside and the outside of the microgels resulting from the overlap of counterion clouds of neighboring particles. When this pressure difference exceeds the bulk modulus of the large microgels, these shrink, enabling crystallization without point defects.
In vivo metabolic labeling of sialoglycans in the mouse brain by using a liposome-assisted bioorthogonal reporter strategy
Authors: Xie Ran , Dong Lu , Du Yifei , Zhu Yuntao , Hua Rui , Zhang Chen , Chen Xing 
Published: April 2016

Significance
In mammals, the brain is the organ with the highest level of sialic acids, a family of negatively charged monosaccharides that are commonly expressed as outer terminal residues of cell-surface glycans. Brain sialoglycans play essential roles in brain development, cognition, and disease progression; however, in vivo visualization of the sialoglycan biosynthesis in the mouse brain has been impossible. Here, we introduce a liposome-assisted bioorthogonal reporter (LABOR) strategy for metabolic labeling and visualization of brain sialoglycans in living mice. Applying LABOR, we visualized the biosynthesis of brain sialoglycans by in vivo fluorescence imaging and histological analysis, and identified important sialylated glycoproteins in the brain by glycoproteomics. We discovered that the turnover of sialoglycans is spatially regulated in distinct brain regions.
Informed kmer selection for de novo transcriptome assembly
Authors: Durai Dilip A. , Schulz Marcel H. 
Published: April 2016

Abstract
Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice.
Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies.
Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use.
Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: mschulz@mmci.uni-saarland.de
The effect of baryons on redshift space distortions and cosmic density and velocity fields in the EAGLE simulation
Authors: Hellwing Wojciech A. , Schaller Matthieu , Frenk Carlos S. , Theuns Tom , Schaye Joop , Bower Richard G. , Crain Robert A. 
Published: April 2016

Abstract
We use the Evolution and Assembly of GaLaxies and their Environments (EAGLE) galaxy formation simulation to study the effects of baryons on the power spectrum of the total matter and dark matter distributions and on the velocity fields of dark matter and galaxies. On scales k ≳ 4 h Mpc−1 the effect of baryons on the amplitude of the total matter power spectrum is greater than 1 per cent. The back-reaction of baryons affects the density field of the dark matter at the level of ∼3 per cent on scales of 1 ≤ k/( h Mpc−1) ≤ 5. The dark matter velocity divergence power spectrum at k ≲ 0.5 h Mpc−1 is changed by less than 1 per cent. The 2D redshift space power spectrum is affected at the level of ∼6 per cent at $|\boldsymbol {k}|\gtrsim 1\,h\,{\rm Mpc}^{-1}$ (for μ &gt; 0.5), but for $|\boldsymbol {k}|\le 0.4\,h\,{\rm Mpc}^{-1}$ it differs by less than 1 per cent. We report vanishingly small baryonic velocity bias for haloes: the peculiar velocities of haloes with M200 &gt; 3 × 1011 M⊙ (hosting galaxies with M* &gt; 109 M⊙) are affected at the level of at most 1 km s−1, which is negligible for 1 per cent-precision cosmology. We caution that since EAGLE overestimates cluster gas fractions it may also underestimate the impact of baryons, particularly for the total matter power spectrum. Nevertheless, our findings suggest that for theoretical modelling of redshift space distortions and galaxy velocity-based statistics, baryons and their back-reaction can be safely ignored at the current level of observational accuracy. However, we confirm that the modelling of the total matter power spectrum in weak lensing studies needs to include realistic galaxy formation physics in order to achieve the accuracy required in the precision cosmology era.