bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cysteine‐reactive covalent capture tags for enrichment of cysteine‐containing peptides
Authors: Giron Priscille , Dayon Loïc , Mihala Nikolett , Sanchez Jean‐Charles , Rose Keith 
Published: July 2010

AbstractConsidering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so‐called cysteine‐reactive covalent capture tags (C3T), for the isolation of Cys‐containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine‐containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins. Copyright © 2009 John Wiley & Sons, Ltd.
Groundwater Remediation and Aquifer Clean‐Up: A Case Study
Authors: Memon Bashir A. , George Lois D. , Mumtaz Azmeh M. 
Published: July 2010

AbstractGroundwater was being remediated with pump and treat technology at a facility where the groundwater was contaminated with commonly used degreaser solvents. Hydraulic conductivity of the heterogeneous residuum was beneficiated by applying pneumatic fracturing technology. The remedial system was controlled and monitored by a sophisticated remote telemetry system. A case history follows.
Remediation of MTBE‐Contaminated Water and Soil
Authors: Keller Arturo A. , Sirivithayapakorn Sanya , Kram Mark 
Published: July 2010

AbstractAs the number of leaking underground fuel tank sites with methyl tertiary butyl ehter (MTBE) contamination continues to grow, there is a need to develop cost‐effective solutions for treatment of soil and water contamination. MTBE poses special challenges because of its physicochemical properties, in particular high solubility and low Henry's constant, low affinity for sorption, and very slow rate of microbial degradation. Advanced oxidation processes tend to generate undesirable by‐products. Based on laboratory studies with hollow fiber membranes (HFM), a field‐scale unit was constructed and tested at a number of sites, to determine the effectiveness of this technology in dealing with MTBE contamination. In addition, to treat the soil contamination, the HFM unit was coupled with a Spray Aeration Vapor Extraction (SAVE) unit, which is based on an internal combustion engine. The engine provides the means to treat soil vapors, as well as organic vapors from the spray aeration and HFM units. The overall treatment objectives of 5μg/l for MTBE and 1 μg/l for benzene were achieved with a treatment train consisting of an ion exchange unit, a spray aeration system, a hollow fiber membrane module and two granular activated carbon (GAC) units, for flowrates ranging from 3.8 to 30 l/min (1 to 8 gal/min). The ion exchange unit sewed to reduce water hardness and avoid scaling in the subsequent treatment units, extending the run‐time of the entire system. Overall removal efficiencies for the spray aeration system and hollow fiber membrane module ranged from 85 to over 99 percent. High removal efficiencies (> 97%) were obtained at elevated water temperatures (54°C) or lower flowrates (up to 11 l/min). The GAC units were used only to polish the effluent and meet the discharge requirements. Soil, water, and gas phases are treated with this system. Cost estimates are provided for similar treatment processes, for water flowrates up to 38 l/min (10 gal/min). © 1999 John Wiley & Sons, Inc.
An Improved Technique for Determining Abundance of Polycyclic Aromatic Hydrocarbon Degrading Microbial Populations
Authors: Guerin Turlough F. 
Published: July 2010

AbstractThe current study describes an improved method for estimating the abundance of polycyclic aramatic hydrocarbon (PAH) degraders in contaminated soil and groundwater. Since the method is a simple incremental improvement to a commonly used approach, it can be easily introduced into the remediation practitioner's testing protocols by simply changing growth indicator dyes. The procedure described is relatively easy to conduct and provides an important addition to laboratories that are using conventional, nonmolecular techniques for microbial enumeration in their bioremediation programs. © 1999 John Wiley & Sons, Inc.
Excluding induced subgraphs: quadrilaterals
Authors: Prömel Hans JüRgen , Steger Angelika 
Published: July 2010

AbstractIn this note we determine the structure of “almost all” graphs not containing a quadrilateral (i.e., a cycle of length four) as an induced subgraph. In particular, it turns out that there are asymptotically twice as many graphs not containing an induced quadrilateral than there are bipartite graphs.
Regularity lemmas for hypergraphs and quasi‐randomness
Authors: Chung Fan R.K. 
Published: July 2010

AbstractWe give a simple proof for Szemerédi's Regularity Lemma and its generalization for k‐uniform hypergraphs. For fixed k, there are altogether k ‐1 different versions of the regularity lemma for k‐uniform hypergraphs. The connection between regularity lemmas for hypergraphs and quasi‐random classes of hypergraphs is also investigated.
The dimension of random ordered sets
Authors: Erdos P. , Kierstead H. A. , Trotter W. T. 
Published: July 2010

AbstractLet P = (X, <) be a finite ordered set and let |P| denote the cardinality of the universe X. Also let Δ(P) denote the maximum degree of P, i.e., the maximum number of points comparable to any one point of P. Füredi and Kahn used probabilistic methods to show that the dimension of P satisfies dim(P)≦ c1 Δ(P)log|P| and dim(P) ≦ c2Δ(P) log2Δ(P) where c, and c2 are positive absolute constants. In this article, we consider the probability space Ω(n, p) of bipartite ordered sets having n minimal elements and n maximal elements, where the events that any minimal element is less than any maximal element are independently distributed and each has probabilityp =p(n). We show that for every ϵ >0, there exist δ, c > 0 so that: (1) if (log1+ϵn)/n<p < 1/log n, then dim(P)∈ Ωpn log pn for almost all P∈ Δ(n, p); and (2) if 1/log n ≦ < 1 − n−1+ϵ, then dim(P) >n‐ cnlp log n for almost all P ∈Ω(n, p). The first inequality is best possible up to the value of the constant δ when p > (log2+en)/n. As to the accuracy of the second inequality, we have the trivial upper bound dim(P)≦n for all P∈Ω(n, p). We then develop a nontrivial upper bound which holds for almost all P ∈Ω(n, p), when p ≧ 1 /log n. This upper bound has the same form as the lower bound when p is constant. We also study the space ℒ︁(n) of all labelled ordered sets on n points and show that there exist positive constants c1, c2 so that n/4 ‐ c1n/log n < dim(P) <c2 n/4 ‐ c2n/log n for almost all P ∈ ℒ︁(n).
Stability properties of a flow process in graphs
Authors: Van Den Berg J. , Meester R. W. J. 
Published: July 2010

AbstractWe study a flow process in infinite graphs where vertices with large resources tend to attract resources from neighbors. The initial resources are random. An interesting question is whether in each finite region all motion stops after a finite time. Under certain assumptions, we prove that this is true. For some other cases, we prove a weaker stability result. We pay attention mostly to the case of Z2, but several results can be easily generalized to Zd.
An algorithmic approach to the Lovász local lemma. I
Authors: Beck József 
Published: July 2010

AbstractThe Lovász Local Lemma is a remarkable sieve method to prove the existence of certain structures without supplying any efficient way of finding these structures. In this article we convert some of the applications of the Local Lemma into polynomial time sequential algorithms (at the cost of a weaker constant factor in the “exponent”). Our main example is the following: assume that in an n‐uniform hypergraph every hyperedge intersects at most 2n/48 other hyperedges, then there is a polynomial time algorithm that finds a two‐coloring of the points such that no hyperedge is monochromatic.
Cycles in a random graph near the critical point
Authors: Luczak Tomasz 
Published: July 2010

AbstractLet G(n, M) be a graph chosen at random from the family of all labelled graphs with n vertices and M(n) = 0.5n + s(n) edges, where s3(n)n−2→∞ but s(n) = o(n). We find the limit distribution of the length of shortest cycle contained in the largest component of G(n, M), as well as of the longest cycle outside it. We also describe the block structure of G(n, M) and derive from this result the limit probability that G(n, M) contains a cycle with a diagonal. Finally, we show that the probability tending to 1 as n‐→∞ the length of the longest cycle in G(n, M) is of the order s2(n)/n.
A critical point for random graphs with a given degree sequence
Authors: Molloy Michael , Reed Bruce 
Published: July 2010

AbstractGiven a sequence of nonnegative real numbers λ0, λ1… which sum to 1, we consider random graphs having approximately λi n vertices of degree i. Essentially, we show that if Σ i(i ‐ 2)λi > 0, then such graphs almost surely have a giant component, while if Σ i(i ‐2)λ. < 0, then almost surely all components in such graphs are small. We can apply these results to Gn,p,Gn.M, and other well‐known models of random graphs. There are also applications related to the chromatic number of sparse random graphs.
Connectivity properties of random subgraphs of the cube
Authors: Bollobás B. , Kohayakawa Y. , Luczak T. 
Published: July 2010

AbstractThe n‐dimensional cube Qn is the graph whose vertices are the subsets of {1, n} where two such vertices are adjacent if and only if their symmetric difference is a singleton. Clearly Qn is an n‐connected graph of diameter and radius n. Write M = n2n−1 = e(Qn) for the size of Qn. Let Q̃ = (Qt)M0 be a random Q̃‐process. Thus Qt is a spanning subgraph of Qn of size t, and Qt is obtained from Qt‐1 by the random addition of an edge of Qn not in Qt‐1. Let t(k) = τ(Q̃ δ ≧ k) be the hitting time of the property of having minimal degree at least k. It is shown in [5] that, almost surely, at time t(1) the graph Qt becomes connected and that in fact the diameter of Qt at this point is n + 1. Here we generalize this result by showing that, for any fixed k≧2, almost surely at time t(k) the graph Qt acquires the extremely strong property that any two of its vertices are connected by k internally vertex‐disjoint paths each of length at most n, except for possibly one, which may have length n + 1. In particular, the hitting time of k‐connectedness is almost surely t(k). © 1995 John Wiley & Sons, Inc.
Maximal full subspaces in random projective spaces—thresholds and Poisson approximation
Authors: Kordecki Wojciech 
Published: July 2010

AbstractLet Gn, pdenote a random graph onnvertices. It is an interesting problem when small cliques arise and what distributions of the number of small cliques may occur. Matroids are natural generalization of graphs; therefore, we can try to investigate maximal flats of a small rank in random matroids. The most studied and most interesting seem to be “random projective geometries” introduced by Kelly and Oxley. Many of the theorems in our paper are based on the results published in a long paper of Barbour, Janson, Karoski, and Ruciski. However, proofs for projective geometries generally are more complicated.
The shape of stretched planar trees
Authors: Maier Robert S. 
Published: July 2010

AbstractWe study the asymptotics of a “stretched” model of unlabeled rooted planar trees, in which trees are not taken equiprobable but are weighted exponentially, according to their height. By using standard methods for computing the probabilities of large deviations of random processes, we show that, as the number of vertices tends to infinity, the normalized shape of a random tree converges in distribution to a deterministic limit. We compute this limit explicitly. © 1995 John Wiley & Sons, Inc.
Designing project‐based instruction to foster generative and mechanistic understandings in genetics
Authors: Duncan Ravit Golan , Tseng Katie Ann 
Published: July 2010

AbstractThe acquisition of scientific knowledge is fraught with difficulties and challenges for the learner. The very nature of some scientific domains contributes to the learning difficulties students' experience. Phenomena in these domains are composed of multiple organization levels featuring complicated interactions within and across these levels. Molecular genetics is a compelling example of such a domain. Current instructional practices in genetics leave students ill prepared to benefit from technological advances in genetics or to participate in public discussions about genetic issues. We argue that instruction in genetics needs to be refocused such that it promotes generative understandings of the genetic mechanisms that are at the core of modern genetics. This paper presents the early stages of design‐based research involving the development and study of a curriculum unit in genetics for high school students. We employed several design strategies to make the structure and mechanisms of genetic phenomena salient in the activities of the unit. Our findings suggest that the curriculum does, to a large extent, engender a deeper understanding of genetic phenomena. Specifically, we observed gains in students' understanding of the genetic information and the mechanisms that link genes to traits. © 2010 Wiley Periodicals, Inc. Sci Ed 95: 21–56, 2011
Exploring subcellular imaging on the buncher‐ToF J105 3D chemical imager
Authors: Rabbani S. , Fletcher J. S. , Lockyer N. P. , Vickerman J. C. 
Published: July 2010

AbstractImaging Mass Spectrometry is emerging as a promising technique to further the understanding of disease and treatment. ToF‐SIMS is also uniquely placed to become a powerful tool in this field due to its chemical specificity and the ability to perform high spatial resolution imaging. In this paper advances in single cell imaging at a sub‐cellular level in 2D and 3D are explored using a novel SIMS instrument based on a buncher‐ToF configuration, the J105 3D Chemical Imager. The data shows molecular localisation on a sub‐cellular scale, over a suitable timeframe, whilst sustaining high mass resolution. The cells are imaged using a 40 keV C60+ dc beam and a clear differentiation between the material within the nuclei and lipid membrane can be made. In addition challenges in data manipulation and interpretation are discussed. Investigation of cell preparation suggests that the frozen hydrated approach may be beneficial. Copyright © 2010 John Wiley & Sons, Ltd.
SIMS with highly excited primary beams for molecular depth profiling and imaging of organic and biological materials
Authors: Matsuo Jiro , Ninomiya Satoshi , Yamada Hideaki , Ichiki Kazuya , Wakamatsu Yoshinobu , Hada Masaki , Seki Toshio , Aoki Takaaki 
Published: July 2010

AbstractRecent developments in SIMS with both Ar cluster ions and swift heavy ions are presented. With these primary beams, the analysis of organic semiconductors and animal cells shows that one of the key factors to realizing the SIMS analysis of organic materials is high‐energy deposition near the surface. Molecular depth profiling and images of organic materials were demonstrated by using SIMS. Copyright © 2010 John Wiley & Sons, Ltd.
Surface studies of halloysite nanotubes by XPS and ToF‐SIMS
Authors: Ng Kai‐Mo , Lau Yiu‐Ting R. , Chan Chi‐Ming , Weng Lu‐Tao , Wu Jingshen 
Published: July 2010

AbstractThis report provides detailed experimental results of thermal and surface characterization on untreated and surface‐treated halloysite nanotubes (HNTs) obtained from two geographic areas. Surface characterization techniques, including XPS and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) were used. ToF‐SIMS surface analysis experiments were performed with both atomic and cluster ion beams. Higher ion yields and more high‐mass ions were obtained with the cluster ion beams. Static ToF‐SIMS spectra were analyzed with principal component analysis (PCA). Morphological diversities were observed in the samples although they mainly contained tubular structures. Thermogravimetric data indicated that aqueous hydrogen peroxide solution could remove inorganic salt impurities, such as alkali metal salts. The amount of grafting of benzalkonium chloride of HNT surface was determined by thermogravimetic analysis. PCA of ToF‐SIMS spectra could distinguish the samples mined from different geographical locations as well as among surface‐treated and untreated samples. Copyright © 2010 John Wiley & Sons, Ltd.
The chemical composition and bonding structure of amorphous hydrogenated carbon nitride film on aluminum surface deposited by electrodeposition
Authors: Yu Yuanlie , Zhang Junyan 
Published: July 2010

AbstractAmorphous hydrogenated carbon nitride films with excellent adhesion to the substrates were deposited on the surfaces of aluminum plates by electrodeposition with acetonitrile as carbon source. The as‐obtained films were detailed characterized by Raman, XPS and FTIR. The results show that the as‐obtained films are mainly made up of sp2 C, sp3 C, CN, CN bonds and a spot of sp3CH2, sp3CH3, sp3CH and sp2CH bonds. The atomic ratio of N/C is evaluated to be about 2.98 at.% by XPS. Raman analysis indicated that ID/IG ratios decreased from 0.827 to 0.675 when the deposition time increased from 10 to 20 h. At the end, on the basis of the detailed analysis, results of Raman, FTIR and XPS, the possible deposition mechanism was discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Complex interface and growth analysis of single crystalline epi‐Si(111)/Y2O3/ Pr2O3/Si(111) heterostructures: Strain engineering by oxide buffer control
Authors: Wilke A. , Yang J.‐M. , Kim J. W. , Seifarth O. , Dietrich B. , Giussani A. , Zaumseil P. , Storck P. , Schroeder T. 
Published: July 2010

AbstractComplex oxide heterostructures on Si gain in the field of engineered Si wafers increasing interest as flexible buffer systems for developing virtual Si substrates. Strain engineering of thin epitaxial Si thin films on insulating oxide buffers is of special interest to boost charge carrier mobility for Silicon‐on‐Insulator (SOI) technologies. The single crystalline Si(111)/Y2O3 (111)/Pr2O3 (111)/Si(111) heterostructure offers, in principle, the opportunity to grow strain‐engineered epitaxial Si(111) layers, realizing compressed, fully relaxed, as well as tensile‐strained Si films. This flexibility is based on a thickness‐dependence of the Y2O3 lattice constant in the oxide bi‐layer buffer: In theory, the Y2O3 buffer lattice constant on Pr2O3/Si(111) can change from pseudomorphism (bigger than Si) over the Si lattice constant towards a fully relaxed status (smaller than Si). By a detailed interface analysis, using TEM‐EELS in combination with an in‐situ RHEED–XPS study of the isomorphic Y2O3 growth on Pr2O3/Si(111), the physical origin of this Y2O3 buffer lattice constant variation is identified. It is possible to discriminate between the contributions from chemical mixing effects between the isomorphic oxides Y2O3 and Pr2O3 on the one hand and true misfit strain relaxation mechanisms in stoichiometric Y2O3 on the other hand. Copyright © 2010 John Wiley & Sons, Ltd.
Energy resolved XPS depth profile of (IrO2, RuO2, Sb2O5, SnO2) electrocatalyst powder to reveal core‐shell nanoparticle structure
Authors: Haverkamp Richard G. , Marshall Aaron T. , Cowie Bruce C. C. 
Published: July 2010

AbstractSynchrotron‐based energy resolved XPS was used to characterize the structure of IrO2RuO2‐coated Sb2O5SnO2 nanoparticles. Samples were heat treated at 300, 350, 400, 450 and 500 °C after chloride Ir and Ru precursors were added to Sb2O5SnO2. Photoelectron kinetic energies of 100, 350 and 1400 eV were employed to obtain an indication of the depth of elemental distributions and chemical shifts. It was shown that the electrocatalyst consists of a core of Sb2O5SnO2 enriched with Sb2O5 towards the surface, with a shell of IrO2RuO2 deposited on this core, and an outer layer of Sb2O5SnO2 over this shell. No significant chemical interaction occurs between IrO2RuO2 and Sb2O5SnO2. The energy resolved XPS depth profile technique is effective for studying core‐shell materials. Copyright © 2010 John Wiley & Sons, Ltd.
Tailoring the surface chemistry of carbon fiber and E‐glass composites for improved adhesion
Authors: Gilbert M. J. , Awaja F. , Kelly G. L. , Fox B. L. , Brynolf R. , Pigram P. J. 
Published: July 2010

AbstractThe main challenges in the manufacture of composite materials are low surface energy and the presence of silicon‐containing contaminants, both of which greatly reduce surface adhesive strength. In this study, carbon fiber (CF) and E‐glass epoxy resin composites were surface treated with the Accelerated Thermo‐molecular adhesion Process (ATmaP). ATmaP is a multiaction surface treatment process where tailored nitrogen and oxygen functionalities are generated on the surface of the sample through the vaporization and atomization of n‐methylpyrrolidone solution, injected via specially designed flame‐treatment equipment. The treated surfaces of the polymer composites were analyzed using XPS, time of flight secondary ion mass spectrometry (ToF‐SIMS), contact angle (CA) analysis and direct adhesion measurements. ATmaP treatment increased the surface concentration of polar functional groups while reducing surface contamination, resulting in increased adhesion strength. XPS and ToF‐SIMS showed a significant decrease in silicon‐containing species on the surface after ATmaP treatment. E‐glass composite showed higher adhesion strength than CF composite, correlating with higher surface energy, higher concentrations of nitrogen and CO functional groups (from XPS) and higher concentrations of oxygen and nitrogen‐containing functional groups (particularly C2H3O+ and C2H5NO+ molecular ions, from ToF‐SIMS). Copyright © 2010 John Wiley & Sons, Ltd.
Characterization of β‐cyclodextrin modified SiO2
Authors: Nielsen Ronnie , Kingshott Peter , Uyar Tamer , Hacaloglu Jale , Larsen Kim L. 
Published: July 2010

AbstractSilica particles containing a layer of β‐cyclodextrins were synthesized using a modified method of Armstrong (1985). The modified silica particles were extensively characterized to both the presence and amount of β‐cyclodextrin introduced onto the surface. Raman confirmed that β‐cyclodextrin was introduced onto the particle. The combination of thermogravmetric analysis (TGA) and direct pyrolysis mass spectroscopy were used to determine the amount and the chemical composition of organic material present on the silica, respectively. The two methods confirmed that β‐cyclodextrin was successfully introduced in amounts comparable to earlier literature values. The values obtained by TGA were compared to amounts found by elemental analysis and XPS. The elemental analysis and TGA found the same amount of β‐cyclodextrin, while the XPS values were in the region of 1.5 times higher. This suggests a heterogeneous distribution of the β‐cyclodextrin on the silica particles. Copyright © 2010 John Wiley & Sons, Ltd.