bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality control of nano‐LC‐MS systems using stable isotope‐coded peptides
Authors: Burkhart Julia Maria , Premsler Thomas , Sickmann Albert 
Published: January 2011

AbstractIn analytical sciences, there is a general need for quality control to assess whether a product or a process meets defined requirements. Especially in proteomics, which implies analysis of ten thousands of analytes within a complex mixture, quality control to validate LC‐MS performance and method setup is inevitable to achieve day‐to‐day‐, inter‐system‐, as well as inter‐user reproducibility. Thus, results deriving from LC‐MS analyses can be benchmarked and the need for system maintenance can be revealed. In particular with the advent of label‐free quantification of peptides and proteins, which above all depends on highly stable and reproducible LC separations, HPLC performance has to be appropriately monitored throughout the entire analytical procedure to assure quality and validity of the obtained data. Oftentimes, proteolytic digests of standard proteins are used in this context; however, this approach implies some limitations, such as inadequate batch‐to‐batch reproducibility, limited (if any) dynamic range and compositional inflexibility. Here, we present an alternative strategy of nano‐LC‐MS/MS quality control based on a mixture of synthetic peptides covering the entire LC‐gradient as well as a dynamic range of more than two orders of magnitude. Thus, (i) reproducibility of LC separation, (ii) MS performance (including limit of detection, identification and quantification), as well as (iii) overall nano‐LC‐MS system performance and reproducibility can be routinely monitored even in highly complex samples.
COMPASS: A suite of pre‐ and post‐search proteomics software tools for OMSSA
Authors: Wenger Craig D. , Phanstiel Douglas H. , Lee M. Violet , Bailey Derek J. , Coon Joshua J. 
Published: January 2011

AbstractHere we present the Coon OMSSA Proteomic Analysis Software Suite (COMPASS): a free and open‐source software pipeline for high‐throughput analysis of proteomics data, designed around the Open Mass Spectrometry Search Algorithm. We detail a synergistic set of tools for protein database generation, spectral reduction, peptide false discovery rate analysis, peptide quantitation via isobaric labeling, protein parsimony and protein false discovery rate analysis, and protein quantitation. We strive for maximum ease of use, utilizing graphical user interfaces and working with data files in the original instrument vendor format. Results are stored in plain text comma‐separated value files, which are easy to view and manipulate with a text editor or spreadsheet program. We illustrate the operation and efficacy of COMPASS through the use of two LC‐MS/MS data sets. The first is a data set of a highly annotated mixture of standard proteins and manually validated contaminants that exhibits the identification workflow. The second is a data set of yeast peptides, labeled with isobaric stable isotope tags and mixed in known ratios, to demonstrate the quantitative workflow. For these two data sets, COMPASS performs equivalently or better than the current de facto standard, the Trans‐Proteomic Pipeline.
Challenges for proteomics core facilities
Authors: Lilley Kathryn S. , Deery Michael J. , Gatto Laurent 
Published: January 2011

AbstractMany analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities.
iTRAQ protein quantification: A quality‐controlled workflow
Authors: Burkhart Julia M. , Vaudel Marc , Zahedi René P. , Martens Lennart , Sickmann Albert 
Published: January 2011

AbstractReporter ion‐based methods are among the major techniques to quantify peptides and proteins. Two main labels, tandem mass tag (TMT) and iTRAQ, are widely used by the proteomics community. They are, however, often applied as out‐of‐the‐box methods, without thorough quality control. Thus, due to undiscovered limitations of the technique, irrelevant results might be trusted. To address this issue, we here propose a step‐by‐step quality control of the iTRAQ workflow. From sample preparation to final ratio calculation we provide metrics and techniques assessing the actual effectiveness of iTRAQ quantification as well as a novel method for more reliable protein ratio estimation.
Bismuth‐metal nanocrystals self‐embedded in high‐k Bi‐based pyrochlore dielectrics grown at room temperature
Authors: Seong Nak‐Jin , Jung Hyun‐June , Yoon Soon‐Gil 
Published: January 2011

AbstractBismuth‐metal nanocrystals (NCs) are self‐embedded within high‐k Bi2Mg2/3Nb4/3O7 (BMNO) dielectrics grown at room temperature by rf magnetron sputtering were demonstrated for the low‐voltage nonvolatile memory device. The BMNO pyrochlore films grown in Ar/O2 ambient at room temperature showed the stable dielectric properties, together with high dielectric constant (∼45), small dielectric loss (0.2%), and improved leakage current. Bismuth nanocrystals (a mean size of 2–3 nm) and a high‐k BMNO films (∼50 nm thickness) as a control oxide layer were continuously in situ formed at room temperature in Ar and Ar/O2 ambient, respectively. A significant threshold voltage shift of 0.95 V is observed at a gate voltage of 5 V and the threshold voltage shift linearly increases with increasing gate voltage from 3 to 6 V. The self‐embedded bismuth nanocrystals in high‐k BMNO dielectrics at room temperature represent a viable candidate for low‐voltage NFGM device applications.
Piezoelectric properties and thermal stability of (Na0.53K0.47−xAgx)Nb1−xSbxO3 ceramics
Authors: Zheng Limei , Wang Jinfeng , Wu Qingzao , Zhang Rui , Wang Chunming , Gai Zhigang 
Published: January 2011

AbstractMany (K1−xNax)NbO3 (KNN)‐based ceramics with high piezoelectric performance exhibit undesirable strong temperature dependence due to the orthorhombic–tetragonal polymorphic phase transition near room temperature. In order to improve the temperature stability of the ceramics, many additives have been added into the KNN‐based ceramics to shift TO–T down to below room temperature. Contrary to the previous approach (Na0.53K0.47−xAgx)Nb1−xSbxO3 (NKANS) ceramics with TO–T well above room temperature have been prepared by a conventional solid‐state reaction method. The density and the electrical properties are effectively improved by the addition of AgSbO3, and optimum piezoelectric properties are found in the ceramics with 0.05 ≤ x ≤ 0.07, with maximum kp ∼ 0.46 for NKANS5 and maximum d33 ∼ 199 pC/N for NKANS7. More importantly, kp remains virtually almost unchanged up to the TO–T temperature (≥100 °C), indicating that the NKANS ceramics exhibit a much improved piezoelectric thermal stability. The analyses suggest that both the high TO–T value and diffuse orthorhombic–tetragonal phase transition should be responsible for the good temperature stability.
Carrier transport of diamond p+‐i‐n+ junction diode fabricated using low‐resistance hopping p+ and n+ layers
Authors: Oyama Kazuhiro , Ri Sung‐Gi , Kato Hiromitsu , Takeuchi Daisuke , Makino Toshiharu , Ogura Masahiko , Tokuda Norio , Okushi Hideyo , Yamasaki Satoshi 
Published: January 2011

AbstractWe have investigated the carrier transport of a single‐crystal diamond p+‐i‐n+ junction diode fabricated using low‐resistance hopping p+ and n+ layers, which showed high‐performance diode characteristics. By comparing the diode characteristics of the p+‐i‐n+ junction with those of the p+‐n+ diode and metal/n+/metal structure, the following results were obtained. The carrier transport of the p+‐i‐n+ junction is described using the band conduction caused by the free carriers, although the current transport in both p+ and n+ layers is mainly by the hopping conduction. The i‐layer in the p+‐i‐n+ junction provides a low‐resistance layer for the forward current and a good blocking layer for the reverse current. The contact resistance of the n+/metal layer affects the carrier transport of the p+‐i‐n+ diode, which lacks the ohmic property even with the phosphorous concentration around 1020 cm−3.
Finite size effects in ZnO nanoparticles: An electron paramagnetic resonance (EPR) analysis
Authors: Jakes Peter , Erdem Emre 
Published: January 2011

AbstractZnO nanoparticles were synthesized by solid coprecipitation method with consecutive high energy ball milling procedure. By reducing the particle size of ZnO to nano dimensions strong nano‐size effects were observed. In order to characterize the ZnO defect structure, EPR has been applied. It was observed that below 50 nm the surface defects play a dominant role in the electronic properties of ZnO. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Direct‐current nanogenerator based on ZnO nanotube arrays
Authors: Xi Y. , Lien D. H. , Yang R. S. , Xu C. , Hu C. G. 
Published: January 2011

AbstractDue to the special structure of a nanotube (NT), the different potential from piezoelectricity can be naturally divided by the hollow of the tube when the NT is bent or deformed. Furthermore, both the bent/deformed inner and outer wall can form a steady voltage/current, which might enhance the output voltage/current. We demonstrate a direct‐current nanogenerator (NG) based on zinc oxide (ZnO) NT arrays driven by an ultrasonic wave. The average output voltage is ca. 0.10 mV and the current density is ca. 0.069 μA/mm2. Our study shows that the maximum power output of the ZnO NT array NG is 0.112 nW and the power density is 1.4 nW/cm2. The success of energy harvesting from ZnO NTs reveals the potential of using nanogenerators for tubular piezoelectric materials. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Visualizing inhibition of fatty acid synthase through mass spectrometric analysis of mitochondria from melanoma cells
Authors: Zecchin Karina G. , Alberici Luciane C. , Riccio Maria Francesca , Eberlin Marcos N. , Vercesi Aníbal E. , Graner Edgard , Catharino Rodrigo R. 
Published: January 2011

AbstractFatty acid synthase (FASN) is the metabolic enzyme responsible for the endogenous synthesis of the saturated long‐chain fatty acid palmitate. In contrast to most normal cells, FASN is overexpressed in a variety of human cancers including cutaneous melanoma, in which its levels of expression are associated with a poor prognosis and depth of invasion. Recently, we have demonstrated the mitochondrial involvement in FASN inhibition‐induced apoptosis in melanoma cells. Herein we compare, via electrospray ionization mass spectrometry (ESI‐MS), free fatty acids (FFA) composition of mitochondria isolated from control (EtOH‐treated cells) and Orlistat‐treated B16‐F10 mouse melanoma cells. Principal component analysis (PCA) was applied to the ESI‐MS data and found to separate the two groups of samples. Mitochondria from control cells showed predominance of six ions, that is, those of m/z 157 (Pelargonic, 9:0), 255 (Palmitic, 16:0), 281 (Oleic, 18:1), 311 (Arachidic, 20:0), 327 (Docosahexaenoic, 22:6) and 339 (Behenic, 22:0). In contrast, FASN inhibition with Orlistat changes significantly mitochondrial FFA composition by reducing synthesis of palmitic acid, and its elongation and unsaturation products, such as arachidic and behenic acids, and oleic acid, respectively. ESI‐MS of mitochondria isolated from Orlistat‐treated cells presented therefore three major ions of m/z 157 (Pelargonic, 9:0), 193 (unknown) and 199 (Lauric, 12:0). These findings demonstrate therefore that FASN inhibition by Orlistat induces significant changes in the FFA composition of mitochondria. Copyright © 2011 John Wiley & Sons, Ltd.
A Study about the Influence of Carbon Content in the Steel on the Casting Behavior
Authors: Xia G. , Bernhard C. , Ilie S. , Fuerst C. 
Published: January 2011

AbstractIn the casting process of steels with a C‐content ranging from 0.09 to 0.53 mass%, austenite is formed as secondary crystal phase by peritectic reaction between crystal of δ ferrite and residual melt. For unalloyed or micro‐alloyed steels the C‐content or C‐equivalent influences the casting behavior of steel in the mould, such as strand shell growth, crack formation, heat transfer, temperature fluctuation in the copper plate, mould level fluctuation and oscillation marks formation. The negative casting behavior like the uneven strand shell growth, the deep oscillation mark formation, the high mould level fluctuation, the crack formation on the strand surface were found mostly for steel with C‐content or Cp between 0.10–0.13 mass%. The strand shell structure (strand shell growth, mushy zone, δ + γ phase transformation) and shrinkage of the strand shell were simulated depending on the C‐content by means of mathematical simulation. On the basis of the simulation results and of the measured high temperature strength of steel the dependence of stiffness and the irregularity of the shrinkage of strand shell on the C‐content was investigated. It was found that the stiffness and irregularity of the shrinkage of the strand shell reach the maximum value at a C‐content of about 0.12 mass%.
Genome-Wide Studies Reveal That Lin28 Enhances the Translation of Genes Important for Growth and Survival of Human Embryonic Stem Cells
Authors: Peng Shuping , Chen Ling-Ling , Lei Xin-Xiang , Yang Li , Lin Haifan , Carmichael Gordon G. , Huang Yingqun 
Published: January 2011

Abstract
Lin28 inhibits the expression of let-7 microRNAs but also exhibits let-7-independent functions. Using immunoprecipitation and deep sequencing, we show here that Lin28 preferentially associates with a small subset of cellular mRNAs. Of particular interest are those for ribosomal proteins and metabolic enzymes, the expression levels of which are known to be coupled to cell growth and survival. Polysome profiling and reporter analyses suggest that Lin28 stimulates the translation of many or most of these targets. Moreover, Lin28-responsive elements were found within the coding regions of all target genes tested. Finally, a mutant Lin28 that still binds RNA but fails to interact with RNA helicase A (RHA), acts as a dominant-negative inhibitor of Lin28-dependent stimulation of translation. We suggest that Lin28, working in concert with RHA, enhances the translation of genes important for the growth and survival of human embryonic stem cells.
Brief Report: Combined Chemical Treatment Enables Oct4-Induced Reprogramming from Mouse Embryonic Fibroblasts
Authors: Yuan Xu , Wan Haifeng , Zhao Xiaoyang , Zhu Saiyong , Zhou Qi , Ding Sheng 
Published: January 2011

Abstract
It has been established that exogenous expression of four transcription factors (Oct4, Klf4, Sox2, and c-Myc) can reprogram mammalian somatic cells to pluripotent states. Further studies demonstrated that such induced pluripotent stem cells (iPSCs) could be generated with fewer exogenous transcription factors, facilitated by endogenous expression of reprogramming factors and/or synthetic small molecules. Here, we reported identification of a new small molecule, a protein arginine methyltransferase inhibitor AMI-5, which enabled Oct4-induced reprogramming of mouse embryonic fibroblasts in combination with transforming growth factor (TGF)-β inhibitor A-83-01. The Oct4-induced iPSCs were shown similar to mouse embryonic stem cells with respect to typical pluripotency criteria. More importantly, they were shown to give rise to liveborn pups through tetraploid complementation assays, demonstrating the high quality of full reprogramming induced by this condition. Furthermore, this study suggests that regulation of protein arginine methylation might be involved in the reprogramming process.
Concise Review: Mesenchymal Tumors: When Stem Cells Go Mad
Authors: Mohseny Alexander B. , Hogendoorn Pancras C. W. 
Published: January 2011

Abstract
Sarcomas are nonepithelial, nonhematopoietic malignant tumors that arise from the embryonic mesoderm. Despite their rarity, less than 10% of all cancers, sarcomas are accountable for relatively high morbidity and mortality especially in children and adolescents. Although there are some hereditary conditions predisposing sarcoma, such as the Li-Fraumeni and Retinoblastoma syndrome, the vast majority of these tumors are sporadic. Based on their histological morphology, sarcomas have been divided into a broad spectrum of subtypes recognized in the 2002 WHO classification of tumors. This wide lineage range suggests that sarcomas originate from either many committed different cell types or from a multipotent cell, subsequently driven into a certain lineage. Mesenchymal stem cells (MSCs) are able to differentiate into many cell types needed to create mature structures like vessels, muscle, and bone. These multipotent cells can be isolated from several adult human tissues and massively expanded in culture, making them both of use for research as well as potential beneficial therapeutical agents. For this reason MSCs are being extensively studied, however, concerns have raised about whether they are the putative originating cells of sarcoma and their questionable role in cancer progression. Recent accomplishments in the field have broadened our knowledge of MSCs in relation to sarcoma origin, sarcoma treatment and the safety of MSCs usage in therapeutic settings.
The upstream flow of a wind turbine: blockage effect
Authors: Medici D. , Ivanell S. , Dahlberg J.‐Å. , Alfredsson P. H. 
Published: January 2011

AbstractThe flow upstream a wind turbine is studied in order to investigate blockage effects. We use rotating wind turbine models in a wind tunnel, where velocity measurements have been made both with hot‐wire anemometry up to approximately 4.5 diameters (D) upstream the turbine, as well as laser particle image velocimetry measurements close to the turbine rotor. Also, numerical simulations have been carried out by means of a finite volume code. The measurements show, among other things, that the flow is affected more than 3 D upstream the rotor plane. Copyright © 2011 John Wiley & Sons, Ltd.
Fractal (fractional) Brownian motion
Authors: Chow Winston C. 
Published: January 2011

AbstractFractal Brownian motion, also called fractional Brownian motion (fBm), is a class of stochastic processes characterized by a single parameter called the Hurst parameter, which is a real number between zero and one. fBm becomes ordinary standard Brownian motion when the parameter has the value of one‐half. In this manner, it generalizes ordinary standard Brownian motion. Here, we precisely define fBm, compare it with Brownian motion, and describe its unique mathematical and statistical properties, including fractal behavior. Ideas of how such properties make these stochastic processes useful models of natural or man‐made systems in life are described. We show how to use these processes as unique random noise representations in state equation models of some systems. We finally present statistical state equation estimation techniques where such processes replace traditional Gaussian white noises. WIREs Comp Stat 2011 3 149–162 DOI: 10.1002/wics.142This article is categorized under:

Data: Types and Structure > Time Series, Stochastic Processes, and Functional Data
A Model of Professional Development for Practicing Genetic Counselors: Adaptation of Communication Skills Training in Oncology
Authors: Dunlop Kate L. , Barlow‐Stewart Kristine , Butow Phyllis , Heinrich Paul 
Published: January 2011

AbstractOngoing professional development for practicing genetic counselors is critical in maintaining best practice. Communication skills training (CST) workshops for doctors in oncology, utilizing trained actors in role plays, have been implemented for many years to improve patient‐centred communication. This model was adapted to provide professional development in counseling skills for practicing genetic counselors, already highly trained in counseling skills. Detailed evidence based scenarios were developed. Evaluation of participants’ experience and perceived outcomes on practice included surveys immediately post workshops (2002, 2004, 2005, 2008 (×2); n = 88/97), 2–5 years later (2007; n = 21/38) and a focus group (2007; n = 7). All rated workshops as effective training. Aspects highly valued included facilitator feedback, actors rather than role‐playing with peers and being able to stop and try doing things differently. Perceived outcomes included the opportunity to reflect on practice; bring focus to communication; motivation and confidence. The high level of satisfaction is a strong endorsement for ongoing communication skills training in this format as part of professional development.
Reasons for Adult Referrals for Genetic Counseling at a Genetics Center in Izmir, Turkey: Analysis of 8965 Cases over an Eleven‐Year Period
Authors: Cogulu Ozgur , Ozkinay Ferda , Akin Haluk , Onay Huseyin , Karaca Emin , Durmaz Asude Alpman , Durmaz Burak , Aykut Ayca , Pariltay Erhan , Kirbiyik Ozgur , Gunduz Cumhur , Ozkinay Cihangir 
Published: January 2011

AbstractA limited numbers of published studies evaluate the referral reasons for genetic counseling services in the literature. These studies are focused on prenatal genetic counseling services, in particular, prenatal diagnosis. In order to provide the most effective and helpful genetic counseling services, genetics professionals need adequate knowledge about the profile of individuals referred for these services. In addition, physicians need increased awareness of the nature of genetic issues in order to make appropriate referrals. This study was intended to provide a descriptive analysis of the referral reasons of patients that received genetic counseling at a genetics center in Izmir, Turkey during an 11‐year period. A total of 8965 records generated between 1998 and 2008 from one genetic center (which consists of The Department of Medical Genetics and Division of Pediatric Genetics) were evaluated retrospectively. Of these, 6,258 involved referrals for prenatal reasons, and 2,707 involved referrals for postnatal reasons. Both prenatal and postnatal records were further classified into more specific categories of referral reasons. The most common reason for genetic counseling among the prenatal patients was advanced maternal age (42.0%), followed by high risk results on prenatal biochemical screening tests such as second trimester double test [(serum concentration of alphafetoprotein (AFP), beta‐human chorionic gonadotropin (beta‐HCG)], triple test (serum concentration of AFP, beta‐HCG, oestriol) and integrated test (26.5%). The most common indications for postnatal patients were recurrent miscarriages (28.2%) and infertility (19.7%). A significant increase in number of specific categories of referrals for genetic counseling was observed for the last 3 years after the establishment of the Medical Genetics Department. These data provide useful information about the frequency of referrals to the genetics department, and the feasibility of genetic services. Organization of genetic services and systematic procedures for genetic counseling and genetic testing may improve the public's awareness of genetics and ensure a high standard of patient care.