bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concise Review: Emerging Role of CD44 in Cancer Stem Cells: A Promising Biomarker and Therapeutic Target
Authors: Yan Yongmin , Zuo Xiangsheng , Wei Daoyan 
Published: July 2015

Abstract

The reception and integration of the plethora of signals a cell receives from its microenvironment determines the cell's fate. CD44 functions as a receptor for hyaluronan and many other extracellular matrix components, as well as a cofactor for growth factors and cytokines, and thus, CD44 is a signaling platform that integrates cellular microenvironmental cues with growth factor and cytokine signals and transduces signals to membrane-associated cytoskeletal proteins or to the nucleus to regulate a variety of gene expression levels related to cell-matrix adhesion, cell migration, proliferation, differentiation, and survival. Accumulating evidence indicates that CD44, especially CD44v isoforms, are cancer stem cell (CSC) markers and critical players in regulating the properties of CSCs, including self-renewal, tumor initiation, metastasis, and chemoradioresistance. Furthermore, there is ample evidence that CD44, especially CD44v isoforms, are valuable prognostic markers in various types of tumors. Therefore, therapies that target CD44 may destroy the CSC population, and this holds great promise for the cure of life-threatening cancers. However, many challenges remain to determining how best to use CD44 as a biomarker and therapeutic target. Here we summarize the current findings concerning the critical role of CD44/CD44v in the regulation of cancer stemness and the research status of CD44/CD44v as biomarkers and therapeutic targets in cancer. We also discuss the current challenges and future directions that may lead to the best use of CD44/CD44v for clinical applications.

Significance
Mounting evidence indicates that cancer stem cells (CSCs) are mainly responsible for cancer aggressiveness, drug resistance, and tumor relapse. CD44, especially CD44v isoforms, have been identified as CSC surface markers for isolating and enriching CSCs in different types of cancers. The current findings concerning the critical role of CD44/CD44v in regulation of cancer stemness and the research status of CD44/CD44v as biomarkers and therapeutic targets in cancer are summarized. The current challenges and future directions that may lead to best use of CD44/CD44v for clinical applications are also discussed.
Mainstreaming Organic Agriculture through Innovation Policy– The Case of Organic Agriculture in Negros Occidental, Philippines
Authors: GASMEN ANDREW , BACONGUIS ROWENA DT. 
Published: July 2015

This paper highlights the innovation policies that facilitated the growth of the organic movement in Negros Occidental. The research is an intrinsic case study that employed in-depth data collection involving multiple sources of information. Organic agriculture started with the civil society because of the desire to produce healthy food and ensure environmental integrity. Health conscious businessmen saw the opportunity of a business built on the pillars of environmental integrity, health, partnership with the grassroots and the growing movement of organic agriculture supporters. In response, the provincial governments of Negros Occidental and Negros Oriental crafted a policy that envisioned the whole Negros Island as the “Organic Bowl in Asia”. Innovative responses of the provincial government included the development of ordinances, organizational adjustments and budget allocations. The innovations of the government legitimized the movement and facilitated the mainstreaming of organic agriculture. The collaboration model results from the active participation of the key stakeholders that was reinforced by forces such as increasing health and environmental consciousness of the populace. While the movement is now mainstreamed, the actors have to forward the movement to another level by increasing the market share of organic products. Keywords - Innovation policy, organizational innovation, organic agriculture, case study, Philippines
Cre Activated and Inactivated Recombinant Adeno‐Associated Viral Vectors for Neuronal Anatomical Tracing or Activity Manipulation
Authors: Saunders Arpiar , Sabatini Bernardo L. 
Published: July 2015

AbstractRecombinant adeno‐associated viruses (rAAVs) transcriptionally activated by Cre recombinase (Cre‐On) are powerful tools for determining the anatomy and function of genetically defined neuronal types in transgenic Cre driver mice. Here we describe how rAAVs transcriptionally inactivated by Cre (Cre‐Off) can be used in conjunction with Cre‐On rAAVs or genomic Cre‐reporter alleles to study brain circuits. Intracranial injection of Cre‐On/Cre‐Off rAAVs into spatially intermingled Cre+ and Cre‐ neurons allows these populations to be differentially labeled or manipulated within individual animals. This comparison helps define the unique properties of Cre+ neurons, highlighting the specialized role they play in their constituent brain circuits. This protocol touches on the conceptual and experimental background of Cre‐Off rAAV systems, including caveats and methods of validation. © 2015 by John Wiley & Sons, Inc.
Using Google Reverse Image Search to Decipher Biological Images
Authors: Mamrosh Jennifer L. , Moore David D. 
Published: July 2015

AbstractDespite the range of tasks performed by biological image‐processing software, current versions cannot find matches for the image in question among the huge range of biological images that exist in the literature and elsewhere on the Internet. Google's Reverse Image Search is designed for this, and it is a simple, yet powerful tool that can be applied to decipher the contents of biological images. For images that contain unfamiliar or unknown elements, for example, Reverse Image Search can identify similar features in published images. Here we describe general guidelines for using this freely available tool to search published images in National Center for Biotechnology Information's (NCBI's) image database. These guidelines can be applied to a variety of types of biological images, including immunohistochemistry and electron microscopy, to facilitate straightforward and rapid searches using Google's Reverse Image Search. © 2015 by John Wiley & Sons, Inc.
MARCC (Matrix‐Assisted Reader Chromatin Capture): An Antibody‐Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications
Authors: Su Zhangli , Denu John M. 
Published: July 2015

AbstractCombinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody‐free method named MARCC (Matrix‐Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin‐interacting protein modules, or so‐called reader domains, which can bind in a combinatorial modification‐dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co‐existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next‐generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. © 2015 by John Wiley & Sons, Inc.
Porphyria Diagnostics—Part 1: A Brief Overview of the Porphyrias
Authors: Ramanujam Vaithamanithi‐Mudumbai Sadagopa , Anderson Karl Elmo 
Published: July 2015

AbstractPorphyria diseases are a group of metabolic disorders caused by abnormal functioning of heme biosynthesis enzymes and characterized by excessive accumulation and excretion of porphyrins and their precursors. Precisely which of these chemicals builds up depends on the type of porphyria. Porphyria is not a single disease but a group of nine disorders: acute intermittent porphyria (AIP), hereditary coproporphyria (HCP), variegate porphyria (VP), δ‐aminolevulinic acid dehydratase deficiency porphyria (ADP), porphyria cutanea tarda (PCT), hepatoerythropoietic porphyria (HEP), congenital erythropoietic porphyria (CEP), erythropoietic protoporphyria (EPP), and X‐linked protoporphyria (XLP). Each porphyria results from overproduction of heme precursors secondary to partial deficiency or, in XLP, increased activity of one of the enzymes of heme biosynthesis. Taken together, all forms of porphyria afflict fewer than 200,000 people in the United States. Based on European studies, the most common porphyria, PCT, has a prevalence of 1 in 10,000, the most common acute porphyria, AlP, has a prevalence of ∼1 in 20,000, and the most common erythropoietic porphyria, EPP, is estimated at 1 in 50,000 to 75,000. CEP is extremely rare, with prevalence estimates of 1 in 1,000,000 or less. Only six cases of ADP are documented. The current porphyria literature is very exhaustive and a brief overview of porphyria diseases is essential in order for the reader to better appreciate the relevance of this area of research prior to undertaking biochemical diagnostics procedures. This unit summarizes the current knowledge on the classification, clinical features, etiology, pathogenesis, and genetics of porphyria diseases. © 2015 by John Wiley & Sons, Inc.
Finding Pathogenic Nucleic Acid Sequences in Next Generation Sequencing Data
Authors: Parfenov Michael , Seidman J.G. 
Published: July 2015

AbstractViruses and bacteria are established as one of the main causes of human diseases from hepatitis to cancer. Recently, the presence of such pathogens has been extensively studied using human whole genome and transcriptome sequencing data. However, detecting and studying pathogens via next generation sequencing data is a challenging task in terms of time and computational resources. In this protocol we give instructions for a simple and quick method to find pathogenic DNA or RNA and detect possible integration of the pathogen genome into the host genome. © 2015 by John Wiley & Sons, Inc.
Collection, Storage, and Preparation of Human Blood Cells
Authors: Dagur Pradeep K. , McCoy J. Philip 
Published: July 2015

AbstractHuman peripheral blood is often studied by flow cytometry in both the research and clinical laboratories. The methods for collection, storage, and preparation of peripheral blood will vary depending on the cell lineage to be examined as well as the type of assay to be performed. This unit presents protocols for collection of blood, separation of leukocytes from whole blood by lysis of erythrocytes, isolating mononuclear cells by density gradient separation, and assorted non‐flow sorting methods, such as magnetic bead separations, for enriching specific cell populations, including monocytes, T lymphocytes, B lymphocytes, neutrophils, and platelets, prior to flow cytometric analysis. A protocol is also offered for cryopreservation of cells, since clinical research often involves retrospective flow cytometric analysis of samples stored over a period of months or years. © 2015 by John Wiley & Sons, Inc.
Flow Cytometry of Extracellular Vesicles: Potential, Pitfalls, and Prospects
Authors: Nolan John P. 
Published: July 2015

AbstractEvidence suggests that extracellular vesicles (EVs) can play roles in physiology and pathology, providing impetus to explore their use as diagnostic and therapeutic targets. However, EVs are also small, heterogeneous, and difficult to measure, and so this potential has not yet been realized. The development of improved approaches to EV detection and characterization will be critical to further understanding their roles in physiology and disease. Flow cytometry has been a popular tool for measuring cell‐derived EVs, but has often been used in an uncritical manner in which fundamental principles and limitations of the instrument are ignored. Recent efforts to standardize procedures and document the effects of different methodologies have helped to address this shortcoming, but much work remains. In this paper, I address some of the instrument, reagent, and analysis considerations relevant to measurement of individual EVs in flow, with the aim of clarifying a path to quantitative and standardized measurement of these interesting and potentially important biological nanoparticles. © 2015 by John Wiley & Sons, Inc.
Water mass mixing: The dominant control on the zinc distribution in the North Atlantic Ocean
Authors: Roshan Saeed , Wu Jingfeng 
Published: July 2015

AbstractDissolved zinc (dZn) concentration was determined in the North Atlantic during the U.S. GEOTRACES 2010 and 2011 cruise (GOETRACES GA03). A relatively poor linear correlation (R2 = 0.756) was observed between dZn and silicic acid (Si), the slope of which was 0.0577 nM/µmol/kg. We attribute the relatively poor dZn‐Si correlation to the following processes: (a) differential regeneration of zinc relative to silicic acid, (b) mixing of multiple water masses that have different Zn/Si, and (c) zinc sources such as sedimentary or hydrothermal. To quantitatively distinguish these possibilities, we use the results of Optimum Multi‐Parameter Water Mass Analysis by Jenkins et al. (2015) to model the zinc distribution below 500 m. We hypothesized two scenarios: conservative mixing and regenerative mixing. The first scenario (conservative) could be modeled to results in a correlation with observations with a R2 = 0.846. In the second scenario, we took a Si‐related regeneration into account, which could model the observations with a R2 = 0.867. Through this regenerative mixing scenario, we estimated a Zn/Si = 0.0548 nM/µmol/kg that may be more realistic than linear regression slope due to accounting for process b. However, this did not improve the model substantially (R2 = 0.867 versus0.846), which may indicate the insignificant effect of remineralization on the zinc distribution in this region. The relative weakness in the model‐observation correlation (R2~0.85 for both scenarios) implies that processes (a) and (c) may be plausible. Furthermore, dZn in the upper 500 m exhibited a very poor correlation with apparent oxygen utilization, suggesting a minimal role for the organic matter‐associated remineralization process.
Unipolar and bipolar pulses emitted during the development of lightning flashes
Authors: Kašpar Petr , Santolík Ondřej , Kolmašová Ivana 
Published: July 2015

AbstractBoth unipolar and bipolar magnetic or electric field pulses have been observed during preparatory stages of a lightning flash. We introduce a new simple analytical model to describe both kinds of pulses. We show how the polarity overshoot depends on the parameters of the model, including the propagation velocity of the current pulse, the step length, and the injected current waveshape. We observe that the expression for the radiation part of the magnetic field can be decomposed into two time‐shifted terms with opposite polarities. The time shift of the two terms is determined by the overall propagation time of the current pulse. The model well corresponds not only to observations of the bipolar preliminary breakdown pulses at time scales of tens of microseconds but also to both unipolar and bipolar dart‐stepped leader pulses at submicrosecond time scales.
Comparison and evaluation of the MODIS Collection 6 aerosol data in China
Authors: Tao Minghui , Chen Liangfu , Wang Zifeng , Tao Jinhua , Che Huizheng , Wang Xinhui , Wang Yang 
Published: July 2015

AbstractSeveral important improvements have been made in recent Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 6 aerosol retrievals, but few regional validations are conducted. We compared Deep Blue (DB) and Dark Target (DT) retrievals over China and evaluated their performance with ground observations. Sampling frequency of DB was much higher than that of DT, which was mainly caused by unavailable retrieval of DT in bright surface and heavy pollution conditions. It is found that merged aerosol optical depth (AOD) will miss some cases if it was determined only by vegetation density. Collocated comparison shows that DT AOD was substantially higher than DB with seasonal difference exceeding 0.3–0.4 over eastern China. However, when all available retrievals were considered, DT AOD was obviously lower than DB in all the seasons except spring due to their large difference in spatial coverage in high‐AOD conditions. DB can well reveal spatial extent of the widespread haze pollution while there were few values in DT. More than one half of the situations with AOD > 1.0 was missed by DT, which largely underestimated the common regional haze pollution in eastern China. Ground validations show that DT tended to overestimate the aerosol loading by underestimation of the surface contribution and single scattering albedo of aerosols. DB performed generally well with higher accuracy in northern China but exhibited obvious underestimation in northwestern and southern China. Despite of slight decrease in accuracy, DB retrievals with all quality enable a large increase in spatial coverage, especially when dense haze clouds existed.
Estimating errors in cloud amount and cloud optical thickness due to limited spatial sampling using a satellite imager as a proxy for nadir‐view sensors
Authors: Liu Yinghui 
Published: July 2015

AbstractCloud climatologies from space‐based active sensors have been used in climate and other studies without their uncertainties specified. This study quantifies the errors in monthly mean cloud amount and optical thickness due to the limited spatial sampling of space‐based active sensors. Nadir‐view observations from a satellite imager, the Moderate Resolution Imaging Spectroradiometer (MODIS), serve as a proxy for those active sensors and observations within 10° of the sensor's nadir view serve as truth for data from 2003 to 2013 in the Arctic. June–July monthly mean cloud amount and liquid water and ice cloud optical thickness from MODIS for both observations are calculated and compared. Results show that errors increase with decreasing sample numbers for monthly means in cloud amount and cloud optical thickness. The root‐mean‐square error of monthly mean cloud amount from nadir‐view observations increases with lower latitudes, with 0.7% (1.4%) at 80°N and 4.2% (11.2%) at 60°N using data from 2003 to 2013 (from 2012). For a 100 km resolution Equal‐Area Scalable Earth Grid (EASE‐Grid) cell of 1000 sample numbers, the absolute differences in these two monthly mean cloud amounts are less than 6.5% (9.0%, 11.5%) with an 80 (90, 95)%chance; such differences decrease to 4.0% (5.0%, 6.5%) with 5000 sample numbers. For a 100 km resolution EASE‐Grid of 1000 sample numbers, the absolute differences in these two monthly mean cloud optical thicknesses are less than 2.7 (3.8) with a 90% chance for liquid water cloud (ice cloud); such differences decrease to 1.3 (1.0) for 5000 sample numbers. The uncertainties in monthly mean cloud amount and optical thickness estimated in this study may provide useful information for applying cloud climatologies from active sensors in climate studies and suggest the need for future spaceborne active sensors with a wide swath.
Matter‐antimatter asymmetry ‐ aspects at low energy
Authors: Willmann Lorenz , Jungmann Klaus 
Published: July 2015

The apparent dominance of matter over antimatter in our universe is an obvious and puzzling fact which cannot be adequately explained in present physical frameworks that assume matter‐antimatter symmetry at the big bang. However, our present knowledge of starting conditions and of known sources of CP violation are both insufficient to explain the observed asymmetry. Therefore ongoing research on matter‐antimatter differences is strongly motivated as well as attempts to identify viable new mechanisms that could create the present asymmetry. Here we concentrate on possible precision experiments at low energies towards a resolution of this puzzle.
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Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR‐Spektroskopie
Authors: Ardenkjaer‐Larsen Jan‐Henrik , Boebinger Gregory S. , Comment Arnaud , Duckett Simon , Edison Arthur S. , Engelke Frank , Griesinger Christian , Griffin Robert G. , Hilty Christian , Maeda Hidaeki , Parigi Giacomo , Prisner Thomas , Ravera Enrico , van Bentum Jan , Vega Shimon , Webb Andrew , Luchinat Claudio , Schwalbe Harald , Frydman Lucio 
Published: July 2015

AbstractIm Frühling 2013 versammelten sich NMR‐Spektroskopiker am Weizmann‐Institut in Israel, um neue Ansätze zur Verbesserung der Empfindlichkeit von NMR‐Experimenten zu diskutieren, besonders im Hinblick auf Experimente an biomolekularen Systemen. Der vorliegende Aufsatz ist von vielen Autoren mit unterschiedlichem fachlichem Hintergrund verfasst worden; er beschreibt den Stand der Forschung auf diesem Gebiet, wie er im Rahmen des Treffens diskutiert wurde. Es werden Ansätze für Ultra‐Hochfeld‐NMR‐Spektroskopie, für neuartige Techniken der NMR‐Detektion, für Prinzipien und Methoden der Kernhyperpolarisation, aber auch für neue Probenpräparationsmethoden diskutiert. Diese Ansätze verbessern die Empfindlichkeit von NMR‐Experimenten im Festkörper und in Lösung, sind voneinander unabhängig und können sich in ihren Auswirkungen multiplizieren. Auch wenn in allen genannten Bereichen bereits substanzielle Verbesserungen erzielt wurden, ist doch noch eine weite Strecke zu überwinden, um an die Empfindlichkeiten von optischen und elektronischen Spektroskopien heranzureichen. Diese Probleme und erste Lösungsansätze werden ebenfalls diskutiert.
Über die Rolle von Metallen in Elektrokatalysatoren auf Basis von stickstoffdotiertem Kohlenstoff für die Sauerstoffreduktion
Authors: Masa Justus , Xia Wei , Muhler Martin , Schuhmann Wolfgang 
Published: July 2015

AbstractDer Begriff des metallfreien Katalysators bezeichnet Kohlenstoffmaterialien, die mit nichtmetallischen Elementen modifiziert sind. Manche Katalysatoren, die als metallfrei gelten, werden jedoch unter Verwendung von metallhaltigen Vorstufen hergestellt. Spuren von Metallen in stickstoffdotiertem Kohlenstoff (“nitrogen‐doped carbon”, NC) spielen eine umstrittene Rolle bei der Sauerstoffreduktionsreaktion (ORR). Es wird eine Definition für tatsächlich metallfreie Katalysatoren vorgeschlagen, und der Unterschied zwischen stickstoffdotiertem Kohlenstoff und M‐Nx/C wird herausgearbeitet. Metallverunreinigungen, die typischerweise unterhalb der Nachweisgrenze von XPS, XRD und EDX liegen, beschleunigen deutlich die ORR. Durch Vergiftungstests, bei denen die Metallionen maskiert werden, wird deutlich, dass Metallreste die elektronische Struktur des NC verändern können oder selbst als aktive Zentren agieren. Die Vorzüge von sowohl M‐Nx/C‐ als auch NC‐Systemen werden diskutiert, um die Weiterentwicklung von Nicht‐Edelmetall‐Katalysatoren für die ORR voranzutreiben.
Transition‐Metal‐Free α‐Arylation of Enolizable Aryl Ketones and Mechanistic Evidence for a Radical Process
Authors: Pichette Drapeau Martin , Fabre Indira , Grimaud Laurence , Ciofini Ilaria , Ollevier Thierry , Taillefer Marc 
Published: July 2015

AbstractThe α‐arylation of enolizable aryl ketones can be carried out with aryl halides under transition‐metal‐free conditions using KOtBu in DMF. The α‐aryl ketones thus obtained can be used for step‐ and cost‐economic syntheses of fused heterocycles and Tamoxifen. Mechanistic studies demonstrate the synergetic role of base and solvent for the initiation of the radical process.