bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new high‐quality set of singly (2H) and doubly (2H and 18O) stable isotope labeled reference waters for biomedical and other isotope‐labeled research
Authors: Faghihi V. , Verstappen‐Dumoulin B. M. A. A. , Jansen H. G. , van Dijk G. , Aerts‐Bijma A. T. , Kerstel E. R. T. , Gröning M. , Meijer H. A. J. 
Published: January 2015

RATIONALEResearch using water with enriched levels of the rare stable isotopes of hydrogen and/or oxygen requires well‐characterized enriched reference waters. The International Atomic Energy Agency (IAEA) did have such reference waters available, but these are now exhausted. New reference waters thus had to be produced in sufficient quantity, and higher characterization quality was desired.METHODSThe reference waters have been prepared gravimetrically from three parent waters: natural water, pure 2H water and highly 18O‐enriched water. These parent waters have been thoroughly assessed for their full isotopic compositions. To ensure the integrity and correctness of the gravimetric procedure, validation measurements have been carried out on the isotopic composition of the produced reference waters by two of our laboratories. These measurements corroborate the values obtained on the basis of gravimetric data.RESULTSTwo new sets of three reference waters enriched in the stable isotopes have been produced and certified: one set of singly labeled waters, only enriched in 2H, and another set of Doubly Labeled Waters, enriched in both 2H and 18O. They cover δ2H and δ18O values in the range of 800–16000 ‰ and 100–2000 ‰, respectively. The process has led to highly accurate isotopic values for these waters.CONCLUSIONSThese reference waters are now available (called IAEA‐604 to IAEA‐609). They will be valuable as reference materials for all fields using isotope labeling of water, most prominently, but not exclusively, biomedical research (body composition analyses, metabolic rate measurements). The two waters with the lowest enrichments will also be useful as anchor values for isotope measurements around the natural range. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.
Identification of effective substrates for the direct analysis of lipids from cell lines using desorption electrospray ionization mass spectrometry
Authors: Srimany Amitava , Jayashree Balasubramanyam , Krishnakumar Subramanian , Elchuri Sailaja , Pradeep Thalappil 
Published: January 2015

RationaleVarious disease conditions, particularly tumours, can be understood easily by studying changes in the lipid profile of cells. While lipid profiles of tissues have been recorded by desorption electrospray ionization mass spectrometric (DESI‐MS) imaging, there is paucity in standardized protocols for sample preparation involving cell cultures to generate reliable results. In this study, we report a method for the direct analysis of lipids from cultured cells by incorporating them onto Whatman 42 filter paper as a substrate for reliable DESI‐MS analysis.MethodsThe WERI‐RB1 cell line was spotted on commonly used substrates for DESI‐MS analysis, such as glass slides, Teflon coated glass slides, thin layer chromatography (TLC) plates, and Whatman 42 filter paper. A comparison of mass spectrometric images with two different lipids was made to understand the behaviour of different surfaces when the same sample was spotted on them. Relative intensities of different lipid peaks in the WERI‐RB1 cell line were compared and relative lipid abundances were also compared across two different human retinoblastoma cell lines; WERI‐RB1 and Y79.ResultsThe study demonstrates that good lipid signals can be obtained by DESI‐MS when the cells are spotted on Whatman 42 filter paper. Tandem mass spectrometry was performed to identify the lipids as glycerophosphocholines (PC). Better lipid images from assembly of cells were obtained with distinct boundary when they were spotted on Whatman 42 filter paper than other surfaces.ConclusionsWe demonstrate the use of a simple substrate for reliable DESI‐MS analysis of cultured cells. This method has the potential to understand various interactions of cells with other external agents. The current method would help in the application of DESI‐MS for biology in general and medical sciences in particular. Copyright © 2015 John Wiley & Sons, Ltd.
Simultaneous analysis of 210 prohibited substances in human urine by ultrafast liquid chromatography/tandem mass spectrometry in doping control
Authors: Jeong Eun Sook , Kim So‐Hee , Cha Eun‐Ju , Lee Kang Mi , Kim Ho Jun , Lee Sang‐Won , Kwon Oh‐Seung , Lee Jaeick 
Published: January 2015

RATIONALEDoping analysis is a two‐step process consisting of a screening step for prohibited substances and a confirmation step to verify the presence of specific substances found during the screening. The entire process must be performed within a limited time period, but traditional screening procedures commonly employ separate analytical methods for each class of prohibited substances being screened and thus require a great deal of human resources and instrumentation. A single simple and rapid multiresidue analytical method that could accommodate multiple classes of prohibited substances would be extraordinarily useful in doping analyses.METHODSUrine samples were extracted via two consecutive liquid–liquid extractions at different pH values following enzymatic hydrolysis. Analyses were performed by ultrafast liquid chromatography/triple‐quadrupole mass spectrometry with polarity switching and time‐dependent selected reaction monitoring.RESULTSWe developed a rapid multiresidue screening and confirmation method for efficient high‐throughput doping analyses. The present method was validated with regard to the limits of detection (0.01–100.0 ng/mL for screening analyses and 0.2–500.0 ng/mL for confirmation assays), matrix effects (48.9–118.9%), recovery (20.6–119.7%) and intra‐ (0.6–17.6%) and inter‐day (4.0–20.0%) precision.CONCLUSIONSA multiresidue analytical method was developed and validated for screening and confirming the presence of performance‐enhancing drugs. A total of 210 substances from diverse classes of prohibited substances were successfully identified with an analytical run time of 10 min. Copyright © 2015 John Wiley & Sons, Ltd.
Membrane funnel‐based spray ionization for protein/peptide analysis by Fourier transform ion cyclotron resonance mass spectrometry
Authors: Yeung Hoi Sze , Li Wan , Wang Ze , Wong Y. L. Elaine , Chen Xiangfeng , Chan T.‐W. Dominic 
Published: January 2015

RATIONALESamples analyzed in proteomic studies by nanoelectrospray ionization (nanoESI) are extremely limited in quantity requiring careful sample handling to prevent loss upon transfer and to maintain sample concentration. To alleviate the operational process and reduce the cost of nanoESI, it is essential to develop more robust, simple and sensitive analytical variants of the process. Membrane funnel‐based spray was developed for analysis of proteins/peptides in this study.METHODSThe membrane funnel was fabricated from thin flexible membrane by a punching method using a homemade device. The performance of the membrane funnel‐based spray was demonstrated by analyzing peptides, proteins and trypsin‐digested samples in comparison of nanoESI and the Teflon sheet based microfunnel.RESULTSCompared with the microfunnel, the membrane funnel can be fabricated easily by punching a thin flexible membrane using a sharp needle. Only 50 nL of sample was required for an analysis. The membrane funnel enhanced the spray sensitivity 100‐fold. A total of 5 amol of on‐spot sample loading was sufficient to provide a measurable signal on a 9.4 Tesla Fourier transform ion cyclotron resonance mass spectrometry system. High‐mass proteins (up to 66 kDa) could be analyzed using this funnel‐based spray system. Good sequence coverage was obtained for tryptic digested samples.CONCLUSIONSA rapid, simple and cheap membrane funnel‐based sample plate fabrication method was developed. The membrane funnel‐based spray is a promising new variant of nanoESI capable of fast and sensitive analysis of peptides/proteins with great potential that could be extended to other applications, including quantitative analysis at high throughput and imaging mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd.
Putative identification of new p‐coumaroyl glycoside flavonoids in grape by ultra‐high performance liquid chromatography/high‐resolution mass spectrometry
Authors: Panighel Annarita , De Rosso Mirko , Dalla Vedova Antonio , Flamini Riccardo 
Published: January 2015

RATIONALEGrape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p‐coumaric acid. Until now, only p‐coumaroyl anthocyanins have been found in grape.METHODSA method of 'suspect screening analysis' by ultra‐high‐performance liquid chromatography/high‐resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures.RESULTSThree putative p‐coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide‐3‐O‐p‐coumaroylhexoside‐like flavanone, isorhamnetin‐3‐O‐p‐coumaroylglucoside, and a chrysoeriol‐p‐coumaroylhexoside‐like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound.CONCLUSIONSCompounds were identified by overlapping various analytical methods according to recommendations in the MS‐based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties. Copyright © 2015 John Wiley & Sons, Ltd.
Reintegration of the regenerated and the remaining tissues during joint regeneration in the newt Cynops pyrrhogaster
Authors: Tsutsumi Rio , Inoue Takeshi , Yamada Shigehito , Agata Kiyokazu 
Published: January 2015

AbstractUrodele amphibians, such as newts, can regenerate a functional limb, including joints, after amputation at any level along the proximal−distal axis of the limb. The blastema can regenerate the limb morphology largely independently of the stump after proximal−distal identity has been established, but the remaining and regenerated tissues must be structurally reintegrated (matched in size and shape). Here we used newt joint regeneration as a model to investigate reintegration, because a functionally interlocking joint requires structural integration between its opposing skeletal elements. After forelimbs were amputated at the elbow joint, the joint was regenerated between the remaining and regenerated skeletal elements. The regenerated cartilage was thick around the amputated joint to make a reciprocally interlocking joint structure with the remaining bone. Furthermore, during regeneration, the extracellular matrix of the remaining tissues was lost, suggesting that the remaining tissues might contribute to the morphogenesis of regenerating cartilage. Our results showed that the area of the regenerated cartilage matched the area of the apposed remaining cartilage, thus contributing to formation of a functional structure.
Anticipatory Management for Instream Habitat: Application to Carneros Creek, California
Authors: Beagle J. R. , Kondolf G. M. , Adams R. M. , Marcus L. 
Published: January 2015

AbstractEcological research increasingly demonstrates that the best fish habitat is associated with complex, dynamically migrating channels. Active erosion and deposition create pools, side channels, and surfaces for recruitment of riparian vegetation, resulting in hydraulic complexity. As such, the most effective and sustainable restoration strategies restore natural processes, and in turn, create biological habitat. Nevertheless, there exists a social–cultural preference for stable channels. Landowners are often unhappy with eroding banks and, more broadly, are uncomfortable with ‘messy’ ecosystems and the erosion, deposition, and channel migration that are essential components of the dynamic channels that provide the greatest floodplain biodiversity. Episodic bank erosion and failure are often treated with emergency response measures, such as riprap and bank hardening. This often results in simplified channels with minimized instream habitat. Here, we propose an alternative management approach for streams with cohesive banks, and where active erosion is concentrated in ‘hot spots’ that are roughly predictable based on geomorphic analysis. We term the approach anticipatory management and present an application of the approach to Carneros Creek, an incised tributary to the Napa River. We contrast the likely habitat values and agricultural land loss of the anticipatory management approach to: (i) a conventional bank stabilization project proposed for the creek, and (ii) a series of uniform setbacks. Copyright © 2015 John Wiley & Sons, Ltd.
The Paved and the Unpaved: Toward a Political Economy of Infrastructure, Mobility, and Urbanization in Haiti
Authors: Yarrington Landon 
Published: January 2015

AbstractThis article argues that an ideological struggle organized around competing Haitian cultural definitions of liberté conditioned the development of Haiti's transport infrastructure from independence in 1804 to the U.S. Occupation of 1915–1934. This definition of liberté was linked to the ideological reproduction of state power by maintaining cultural constructions of people as urban or rural. Using historical sources, an analysis of the institutions, policies, and practices of infrastructure use and development shows that movement itself serves as cultural symbol and site of ideological struggle, as differential access to freedom of movement influences the maintenance of urban and rural classifications. During the colonial period and immediately after independence, the plantation economy neglected transport infrastructure, which helped keep cities small and laborers on plantations. By the mid‐19th century, the plantation economy collapsed, and landowners moved to port cities to enter commerce or politics. Smallholding peasantries emerged in rural areas, but continued lack of transport investment kept them there. Only in the late 19th century did Haitian elites invest in transport infrastructure; this was enhanced by the early‐20th‐century American occupation. Only then did cities begin to grow substantially.
Political Economy of Control: Urban Refugees and the Regulation of Space in Lusaka, Zambia
Authors: Frischkorn Rebecca 
Published: January 2015

AbstractAlthough Zambia is routinely praised by the international community for accepting the overwhelming majority of asylum seekers, it attempts to control refugee movement and residency by keeping the majority in refugee camps and settlements and limiting the number allowed in urban areas. However, many refugees continue to live in cities without the required urban residency permits and despite risks of arrest and exploitation. This article examines the efforts of the Zambian government to limit and control its urban refugee population in Lusaka, linking the structure of the global political economy to treatment of refugees. As the Ministry of Home Affairs implements its urban residency policy and registration systems and immigration officers often arbitrarily enforce it through raids on markets and neighborhoods, refugees negotiate the spaces of the city, discovering where to live and move; find work and housing; seek assistance and social services; and become detained, imprisoned, deported, or released. This article further considers not only how power is exercised in this context but also how and why systems of control fail to work effectively or efficiently.
Heterochromatin Protein 1 Alpha (HP1α: CBX5) is a Key Regulator in Differentiation of Endothelial Progenitor Cells to Endothelial Cells
Authors: Maeng Yong-Sun , Kwon Ja Young , Kim Eung Kweon , Kwon Young-Guen 
Published: January 2015

Abstract
As the ability to control the differentiation of endothelial stem/progenitor cells (EPCs) into vascular endothelial cell lineages could be useful for promoting neovascularization, it is important to obtain a deeper understanding of the epigenetic mechanisms that regulate EPC differentiation and neovascularization. Heterochromatin protein 1α (HP1α) is known to be involved in the epigenetic regulation of gene silencing. However, recent reports demonstrate that HP1α can also activate gene expression during cell differentiation. In this study, microarray analysis revealed that HP1α expression was induced during EPC differentiation and is associated with the expression of outgrowing endothelial cell (OEC)-specific protein markers. To explore the role of HP1α in the differentiation of EPCs to OECs, its expression was knocked-down or over-expressed in differentiating EPCs. Overexpression of HP1α promoted the differentiation and angiogenic activity of EPCs in vitro and in vivo, whereas knockdown of HP1α led to a defect in OEC migration, tube formation, and angiogenic sprouting activity. Gene expression profiling showed increased expression of angiogenic genes, including NOTCH1, cadherin-5, and angiopoietin-like-2, and decreased expression of progenitor cell marker genes, including CD133, CXCR4, and C-KIT, in HP1α-overexpressing EPCs. Also, increased HP1α at an early stage of EPC differentiation may regulate angiogenic gene transcription by interacting with chromatin that modifies epigenetic factors such as the methyl-CpG binding domain, Polycomb group ring finger 2, and DNA methyltransferases. Our findings demonstrate, for the first time, that HP1α plays an important role in the differentiation and angiogenic function of EPCs by regulating endothelial gene expression. Stem Cells 2015;33:1512–1522
Twist1 and Snail Link Hedgehog Signaling to Tumor-Initiating Cell-Like Properties and Acquired Chemoresistance Independently of ABC Transporters
Authors: Kong Ying , Peng Yuanqiu , Liu Yuan , Xin Hong , Zhan Xia , Tan Wenfu 
Published: January 2015

Abstract
The Hedgehog (Hh) signaling pathway has been implicated in acquired chemoresistance. However, it remains unclear whether and how the Hh pathway may maintain the chemoresistant phenotype by controlling the tumor-initiating cell-like properties of acquired chemoresistant cancer cells. In this study, using well-established acquired chemoresistant cancer cells and chemosensitive KB cancer cells with artificially elevated Hh pathway activity, we found that Hh pathway activity may transcriptionally control the expression of twist1 and snail, thereby maintaining the tumor-initiating cell-like properties and consequently the chemoresistant phenotype. Meanwhile, we obtained direct evidence that twist1, which may amplify Hh signaling activity and plays an essential role in limb development, is a direct transcriptional target of Gli, similar to snail. We further observed that the expression of ATP-binding cassette (ABC) transporters was dispensable for the chemoresistance mediated by twist1 and snail. Collectively, these findings demonstrate that twist1, together with snail, links the Hh pathway to the tumor-initiating cell-like properties of chemoresistant cells. This consequently promotes chemoresistance independently of ABC transporters, thereby contributing to future development of strategies for combating chemoresistance through Hh pathway interference. Furthermore, our finding that twist1 is a direct target of the transcription factor Gli improves the interpretation of the association between twist1 and the Hh pathway and the nature of the signaling transduction of the Hh pathway. Stem Cells 2015;33:1063–1074
The impact of atmospheric stability on the near‐surface wind over sea in storm conditions
Authors: Baas P. , Bosveld F. C. , Burgers G. 
Published: January 2015

AbstractWe study the influence of boundary layer stability on the near‐surface wind speed, especially for high‐wind conditions. An analysis of the wind speed ratio between two vertical levels observed at tall masts in the North Sea and The Netherlands demonstrates that over sea non‐neutral conditions commonly occur, even when the 10 m wind speed is 7 Bft or higher (at least 13.9 ms−1). Over land, stability conditions are always close to neutral for these strong wind conditions. This is because over land, large vertical temperature differences are rare in these conditions. An analysis of 30 years of station data shows that even in storm conditions the ratio of the 10 m wind speed between sea and land depends systematically on the difference between the air temperature and the sea surface temperature. The observational results are reproduced by HARMONIE, a state‐of‐the‐art Numerical Weather Prediction model, although the impact of stability is smaller than in the observations. A model sensitivity analysis for a severe storm shows that the near‐surface wind speed over sea can vary by 10% depending on the difference between the air temperature and the sea surface temperature. The results presented in this study indicate that even in conditions that are usually classified as ‘(near) neutral’, small variations in stability may have a significant impact on the wind profile. They also indicate that for high wind speeds, the sea‐to‐land wind speed ratio is dominated by the stability over sea as in these conditions the stability over land is close to neutral. Copyright © 2015 John Wiley & Sons, Ltd.
Recent advances in nanotechnology for diabetes treatment
Authors: DiSanto Rocco Michael , Subramanian Vinayak , Gu Zhen 
Published: January 2015

Nanotechnology in diabetes research has facilitated the development of novel glucose measurement and insulin delivery modalities which hold the potential to dramatically improve quality of life for diabetics. Recent progress in the field of diabetes research at its interface with nanotechnology is our focus. In particular, we examine glucose sensors with nanoscale components including metal nanoparticles and carbon nanostructures. The addition of nanoscale components commonly increases glucose sensor sensitivity, temporal response, and can lead to sensors which facilitate continuous in vivo glucose monitoring. Additionally, we survey nanoscale approaches to ‘closed‐loop’ insulin delivery strategies which automatically release insulin in response to fluctuating blood glucose levels (BGLs). ‘Closing the loop’ between BGL measurements and insulin administration by removing the requirement of patient action holds the potential to dramatically improve the health and quality of life of diabetics. Advantages and limitations of current strategies, as well as future opportunities and challenges are also discussed. WIREs Nanomed Nanobiotechnol 2015, 7:548–564. doi: 10.1002/wnan.1329This article is categorized under:

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology