bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternative polyadenylation: less than meets the eye?
Authors: Neve Jonathan , Furger André
Published: August 2014

With the advances in deep-sequencing techniques over the last decade, the study of alternative cleavage and polyadenylation (APA) has shifted from individual gene to whole transcriptome analysis. Findings from such global studies have elevated APA to its currently accepted status as a major player in the regulation of eukaryotic gene expression. Although ~70% of human genes have been shown to contain multiple cleavage and polyadenylation sites, the extent of the consequences of APA and its role in regulating physiological processes are still largely unknown. The present review aims to summarize the experimental evidence that supports a physiological role of APA and highlights some of the shortcomings that need addressing to substantiate the widely proposed claim that APA is a key player in global gene regulation.
Human genetic variation and its effect on miRNA biogenesis, activity and function
Authors: Hogg Daniel R. , Harries Lorna W.
Published: August 2014

miRNAs are small non-coding regulators of gene expression that are estimated to regulate over 60% of all human genes. Each miRNA can target multiple mRNA targets and as such, miRNAs are responsible for some of the ‘fine tuning’ of gene expression and are implicated in regulation of all cellular processes. miRNAs bind to target genes by sequence complementarity, resulting in target degradation or translational blocking and usually a reduction in target gene expression. Like mRNA, miRNAs are transcribed from genomic DNA and are processed in several steps that are heavily reliant on correct secondary and tertiary structure. Secondary structure is determined by RNA sequence, which is in turn determined by the sequence of the genome. The human genome, however, like most eukaryotes is variable. Large numbers of SNPs (single nucleotide polymorphisms), small insertions and deletions (indels) and CNVs (copy number variants) have been described in our genome. Should this genetic variation occur in regions critical for the correct secondary structure or target binding, it may interfere with normal gene regulation and cause disease. In this review, we outline the consequences of genetic variation involving different aspects of miRNA biosynthesis, processing and regulation, with selected examples of incidences when this has potential to affect human disease.
ROS signalling, NADPH oxidases and cancer
Authors: Landry William D. , Cotter Thomas G.
Published: August 2014

ROS (reactive oxygen species) have long been regarded as a series of destructive molecules that have a detrimental effect on cell homoeostasis. In support of this are the myriad antioxidant defence systems nearly all eukaryotic cells have that are designed to keep the levels of ROS in check. However, research data emerging over the last decade have demonstrated that ROS can influence a range of cellular events in a manner similar to that seen for traditional second messenger molecules such as cAMP. Hydrogen peroxide (H2O2) appears to be the main ROS with such signalling properties, and this molecule has been shown to affect a wide range of cellular functions. Its localized synthesis by the Nox (NADPH oxidase) family of enzymes and how these enzymes are regulated is of particular interest to those who work in the field of tumour biology.
Redox regulation in the endoplasmic reticulum
Authors: Bulleid Neil J. , van Lith Marcel
Published: August 2014

The efficient folding, assembly and secretion of proteins from mammalian cells is a critically important process for normal cell physiology. Breakdown of the ability of cells to secrete functional proteins leads to disease pathologies caused by a lack of protein function or by cell death resulting from an aggravated stress response. Central to the folding of secreted proteins is the formation of disulfides which both aid folding and provide stability to the protein structure. For disulfides to form correctly necessitates the appropriate redox environment within the endoplasmic reticulum: too reducing and disulfides will not form, too oxidizing and non-native disulfides will not be resolved. How the endoplasmic reticulum maintains the correct redox balance is unknown. Although we have a good appreciation of the processes leading to a more oxidizing environment, our understanding of how any counterbalancing reductive pathway operates is limited. The present review looks at potential mechanisms for introducing reducing equivalents into the endoplasmic reticulum and discusses an approach to test these hypotheses.
Endogenous siRNAs: regulators of internal affairs
Authors: Piatek Monica J. , Werner Andreas
Published: August 2014

Endo-siRNAs (endogenous small-interfering RNAs) have recently emerged as versatile regulators of gene expression. They derive from double-stranded intrinsic transcripts and are processed by Dicer and associate with Argonaute proteins. In Caenorhabditis elegans, endo-siRNAs are known as 22G and 26G RNAs and are involved in genome protection and gene regulation. Drosophila melanogaster endo-siRNAs are produced with the help of specific Dicer and Argonaute isoforms and play an essential role in transposon control and the protection from viral infections. Biological functions of endo-siRNAs in vertebrates include repression of transposable elements and chromatin organization, as well as gene regulation at the transcriptional and post-transcriptional levels.
Novel flavonoids as anti-cancer agents: mechanisms of action and promise for their potential application in breast cancer
Authors: Martinez-Perez Carlos , Ward Carol , Cook Graeme , Mullen Peter , McPhail Donald , Harrison David J. , Langdon Simon P.
Published: August 2014

Flavonoids are a large group of ubiquitous polyphenolic secondary metabolites in plants with a wide range of properties, including a widely reported anti-cancer effect. The present review focuses on the different known mechanisms partaking in said anti-tumour effects, with particular emphasis on breast cancer. Their structure and reactivity allows flavonoids to work as antioxidant agents and phyto-oestrogens, modulating oestrogen signalling and metabolism to induce an overall anti-proliferative response. Other effects include the ability of flavonoids to modulate the CYP1 (cytochrome P450 1) and ABC (ATP-binding cassette) protein families, involved in carcinogenesis and drug delivery respectively. They can also induce apoptosis and cell cycle arrest and regulate other signalling pathways involved in the development and progression of cancer. In conclusion, there is accumulating evidence on the versatility of flavonoids and the numerous activities contributing to their anti-tumour effect. The complex, yet effective, mechanism of action of flavonoids, together with their interesting pharmacological properties, is the basis for their potential application in breast and other cancers. This rationale has led to the current interest in the application of flavonoids, including clinical trials currently underway and the development of novel flavonoids with improved properties, which hold great promise for tackling breast cancer.
The major urinary protein system in the rat
Authors: Gómez-Baena Guadalupe , Armstrong Stuart D. , Phelan Marie M. , Hurst Jane L. , Beynon Robert J.
Published: August 2014

The genomes of rats and mice both contain a cluster of multiple genes that encode small (18–20 kDa) eight-stranded β-barrel lipocalins that are expressed in multiple secretory tissues, some of which enter urine via hepatic biosynthesis. These proteins have been given different names, but are mostly generically referred to as MUPs (major urinary proteins). The mouse MUP cluster is increasingly well understood, and, in particular, a number of roles for MUPs in chemical communication between conspecifics have been established. By contrast, the literature on the rat orthologues is much less well developed and is fragmented. In the present review, we summarize current knowledge on the MUPs from the Norway (or brown) rat, Rattus norvegicus.
Exosome substrate targeting: the long and short of it
Authors: Mitchell Phil
Published: August 2014

The exosome ribonuclease complex functions in both the limited trimming of the 3′-ends of nuclear substrates during RNA processing events and the complete destruction of nuclear and cytoplasmic RNAs. The two RNases of the eukaryotic exosome, Rrp44 (rRNA-processing protein 44) and Rrp6, are bound at either end of a catalytically inert cylindrical core. RNA substrates are threaded through the internal channel of the core to Rrp44 by RNA helicase components of the nuclear TRAMP complex (Trf4–Air2–Mtr4 polyadenylation complex) or the cytoplasmic Ski (superkiller) complex. Recent studies reveal that Rrp44 can also associate directly with substrates via channel-independent routes. Although the substrates of the exosome are known, it is not clear whether specific substrates are restricted to one or other pathway. Data currently available support the model that processed substrates are targeted directly to the catalytic subunits, whereas at least some substrates that are directed towards discard pathways must be threaded through the exosome core.
Endothelial cell oxidative stress in diabetes: a key driver of cardiovascular complications?
Authors: Shaw Andrew , Doherty Mary K. , Mutch Nicola J. , MacRury Sandra M. , Megson Ian L.
Published: August 2014

Atherothrombotic disease is a well-recognized complication of diabetes and is a major contributor to the high morbidity and mortality associated with diabetes. Although there is substantial evidence linking diabetes with cardiovascular disease, the specific effect of hyper- (or hypo-) glycaemia is less well understood. The present review focuses on the impact that glycaemic dysregulation has on respiratory function and ROS (reactive oxygen species) generation in the endothelial cells that are critical in preventing several key steps in the atherothrombotic process. Endothelial cells are particularly susceptible to ROS-mediated dysfunction not only because of reduced cell viability and increased senescence, but also because one of the major endothelium-derived factors that help to protect against atherosclerosis, nitric oxide, is rapidly deactivated by superoxide radicals.
Regulation of the 2-oxoglutarate-dependent dioxygenases and implications for cancer
Authors: Vissers Margreet C.M. , Kuiper Caroline , Dachs Gabi U.
Published: August 2014

There is growing interest in the family of 2-OG (2-oxoglutarate)-dependent dioxygenase enzymes that catalyse the hydroxylation of a wide range of organic targets. Members of this family that regulate the cell's hypoxic response and epigenetic processes, particularly the demethylation of histones and DNA, have been identified in mammalian cells. The dependence of these enzymes on molecular oxygen and 2-OG as obligatory substrates, together with their need for iron and ascorbate as cofactors, has implications for their role as metabolic sensors. The oxygen-sensing property is utilized by the hydroxylases that regulate hypoxia-inducible factor and this has been well characterized, particularly with respect to tumour biology. However, the potential for metabolic sensing more generally is also of interest, and future research will expand our understanding of the effect of mitochondrial viability and nutrient (iron and ascorbate) supply on 2-OG-dependent dioxygenase activity.
Methods for measuring CoA and CoA derivatives in biological samples
Authors: Tsuchiya Yugo , Pham Uyen , Gout Ivan
Published: August 2014

CoA (coenzyme A) is a ubiquitous and essential cofactor that acts as an acyl group carrier in biochemical reactions. Apart from participating in numerous metabolic pathways as substrates and intermediates, CoA and a number of its thioester derivatives, such as acetyl-CoA, can also directly regulate the activity of proteins by allosteric mechanisms and by affecting protein acetylation reactions. Cellular levels of CoA and CoA thioesters change under various physiological and pathological conditions. Defective CoA biosynthesis is implicated in NBIA (neurodegeneration with brain iron accumulation). However, the exact role of CoA in the pathogenesis of NBIA is not well understood. Accurate and reliable assays for measuring CoA species in biological samples are essential for studying the roles of CoA and CoA derivatives in health and disease. The present mini-review discusses methods that are commonly used to measure CoA species in biological samples.
Coenzyme A biosynthetic machinery in mammalian cells
Authors: Martinez David Lopez , Tsuchiya Yugo , Gout Ivan
Published: August 2014

CoA (coenzyme A) is an essential cofactor in all living organisms. CoA and its thioester derivatives [acetyl-CoA, malonyl-CoA, HMG-CoA (3-hydroxy-3-methylglutaryl-CoA) etc.] participate in diverse anabolic and catabolic pathways, allosteric regulatory interactions and the regulation of gene expression. The biosynthesis of CoA requires pantothenic acid, cysteine and ATP, and involves five enzymatic steps that are highly conserved from prokaryotes to eukaryotes. The intracellular levels of CoA and its derivatives change in response to extracellular stimuli, stresses and metabolites, and in human pathologies, such as cancer, metabolic disorders and neurodegeneration. In the present mini-review, we describe the current understanding of the CoA biosynthetic pathway, provide a detailed overview on expression and subcellular localization of enzymes implicated in CoA biosynthesis, their regulation and the potential to form multi-enzyme complexes for efficient and highly co-ordinated biosynthetic process.
Coenzyme A, more than ‘just’ a metabolic cofactor
Authors: Srinivasan Balaji , Sibon Ody C.M.
Published: August 2014

In all organisms biomolecules play a vital role to enable proper cellular metabolism. Alteration of metabolite homoeostasis disrupts the physiology of cells, leading to various diseases [DeBerardinis and Thompson (2012) Cell, 148, 1132–1144]. Recent studies advances our understanding that some metabolites are not only involved in cellular metabolism, but also have other molecular functions. It has become evident that similar to multifunctional ‘moonlighting proteins’, ‘moonlighting metabolites’ also exists. One clear example is nicotinamide adenine dinucleotide (NAD). NAD is a ubiquitous molecule with a well-known function in many metabolic reactions, but it also has become clear that NAD is involved in the regulation of sirtuins. Sirtuins play a role in cancer, diabetes, and cardiovascular, neurodegenerative and other diseases [Donmez and Outeiro (2013) EMBO Mol. Med. 5, 344–352] and the deacetylation capacity of sirtuin proteins is NAD-dependent. This direct role of NAD in age-related diseases could not be anticipated when NAD was initially discovered as a metabolic cofactor [Donmez and Outeiro (2013) EMBO Mol. Med. 5, 344–352; Mouchiroud et al. (2013) Crit. Rev. Biochem. Mol. Biol. 48, 397–408]. Recent findings now also indicate that CoA (coenzyme A), another metabolic cofactor, can be considered as being more than ‘just’ a metabolic cofactor, and altered CoA levels lead to severe and complex effects.
Coenzyme A and its derivatives: renaissance of a textbook classic
Authors: Theodoulou Frederica L. , Sibon Ody C.M. , Jackowski Suzanne , Gout Ivan
Published: August 2014

In 1945, Fritz Lipmann discovered a heat-stable cofactor required for many enzyme-catalysed acetylation reactions. He later determined the structure for this acetylation coenzyme, or coenzyme A (CoA), an achievement for which he was awarded the Nobel Prize in 1953. CoA is now firmly embedded in the literature, and in students’ minds, as an acyl carrier in metabolic reactions. However, recent research has revealed diverse and important roles for CoA above and beyond intermediary metabolism. As well as participating in direct post-translational regulation of metabolic pathways by protein acetylation, CoA modulates the epigenome via acetylation of histones. The organization of CoA biosynthetic enzymes into multiprotein complexes with different partners also points to close linkages between the CoA pool and multiple signalling pathways. Dysregulation of CoA biosynthesis or CoA thioester homoeostasis is associated with various human pathologies and, although the biochemistry of CoA biosynthesis is highly conserved, there are significant sequence and structural differences between microbial and human biosynthetic enzymes. Therefore the CoA biosynthetic pathway is an attractive target for drug discovery. The purpose of the Coenzyme A and Its Derivatives in Cellular Metabolism and Disease Biochemical Society Focused Meeting was to bring together researchers from around the world to discuss the most recent advances on the influence of CoA, its biosynthetic enzymes and its thioesters in cellular metabolism and diseases and to discuss challenges and opportunities for the future.
Neutron tomography of axially symmetric objects using 14 MeV neutrons from a portable neutron generator
Authors: Andersson P. , Andersson-Sunden E. , Sjöstrand H. , Jacobsson-Svärd S.
Published: August 2014

In nuclear boiling water reactor cores, the distribution of water and steam (void) is essential for both safety and efficiency reasons. In order to enhance predictive capabilities, void distribution assessment is performed in two-phase test-loops under reactor-relevant conditions. This article proposes the novel technique of fast-neutron tomography using a portable deuterium-tritium neutron generator to determine the time-averaged void distribution in these loops. Fast neutrons have the advantage of high transmission through the metallic structures and pipes typically concealing a thermal-hydraulic test loop, while still being fairly sensitive to the water/void content. However, commercially available fast-neutron generators also have the disadvantage of a relatively low yield and fast-neutron detection also suffers from relatively low detection efficiency. Fortunately, some loops are axially symmetric, a property which can be exploited to reduce the amount of data needed for tomographic measurement, thus limiting the interrogation time needed. In this article, three axially symmetric test objects depicting a thermal-hydraulic test loop have been examined; steel pipes with outer diameter 24 mm, thickness 1.5 mm, and with three different distributions of the plastic material POM inside the pipes. Data recorded with the FANTOM fast-neutron tomography instrument have been used to perform tomographic reconstructions to assess their radial material distribution. Here, a dedicated tomographic algorithm that exploits the symmetry of these objects has been applied, which is described in the paper. Results are demonstrated in 20 rixel (radial pixel) reconstructions of the interior constitution and 2D visualization of the pipe interior is demonstrated. The local POM attenuation coefficients in the rixels were measured with errors (RMS) of 0.025, 0.020, and 0.022 cm−1, solid POM attenuation coefficient. The accuracy and precision is high enough to provide a useful indication on the flow mode, and a visualization of the radial material distribution can be obtained. A benefit of this system is its potential to be mounted at any axial height of a two-phase test section without requirements for pre-fabricated entrances or windows. This could mean a significant increase in flexibility of the void distribution assessment capability at many existing two-phase test loops.
Hydrodynamic tracer diffusion in suspensions of swimming bacteria
Authors: Kasyap T. V. , Koch Donald L. , Wu Mingming
Published: August 2014

We present theoretical predictions, simulations, and experimental measurements of the diffusion of passive, Brownian tracer particles in the bulk of three-dimensional suspensions of swimming bacteria performing run-tumble random walks. In the theory, we derive an explicit expression for the “hydrodynamic” tracer diffusivity that results from the fluid disturbances created by a slender-body model of bacteria by ensemble averaging the mass conservation equation of the tracer over the space of tracer-bacterium interactions which are assumed to be binary. The theory assumes that the orientations of the bacterium before and after a tumble are uncorrelated and the fluid velocity disturbance created by the bacterium is small compared to its swimming speed. The dependence of the non-dimensional hydrodynamic diffusivity \documentclass[12pt]{minimal}\begin{document}$\widetilde{D_h}$\end{document}Dh̃ obtained by scaling the dimensional hydrodynamic diffusivity by nL3UsL on the persistence in bacterial swimming and the Brownian diffusivity of the tracer are studied in detail through two nondimensional parameters—a Peclet number Pe = UsL/D which is the ratio of the time scale of bacterial swimming to the tracer diffusion time scale and a non-dimensional persistence time τ* = Usτ/L obtained by scaling the dimensional bacterial persistence time by the time that a bacterium takes to swim over a distance equal to its length. Here, n, Us, τ, and L are the concentration, swimming speed, tumbling time, and the overall length of the bacteria, respectively, and D is the Brownian diffusivity of the tracer. \documentclass[12pt]{minimal}\begin{document}$\widetilde{D_h}$\end{document}Dh̃ is found to be a monotonically increasing function of τ* and a non-monotonic function of Pe with a Pe1/2 scaling in the Pe ≪ 1 limit, an intermediate peak and a constant value in the Pe ≫ 1 limit for the typical case of wild-type bacteria with τ* = O(1). In the simulation study we compute the bacterial contribution to the tracer diffusivity from explicit numerical simulations of binary tracer-bacterium interactions to examine the validity of the weak disturbance assumption made in the theory, and to investigate the effects of correlations in the pre- and post-tumble bacterium orientations and the excluded volume (steric) interactions between the bacterium and the tracer. It is found that the weak disturbance assumption does not have a statistically significant effect on \documentclass[12pt]{minimal}\begin{document}$\widetilde{D_h}$\end{document}Dh̃ and correlations among pre- and post-tumble bacterium orientations and bacterium-tracer excluded volume interactions are found to enhance the tracer diffusivity by modest but statistically significant factors. Finally, we measure the effective diffusion coefficient of 1.01  μm diameter colloidal tracer particles in the bulk of a suspension of wild-type E. Coli cells and compare the experimental measurements with the predictions made by the theory and simulations.
Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)
Authors: Haigis Volker , Belkhodja Yacine , Coudert François-Xavier , Vuilleumier Rodolphe , Boutin Anne
Published: August 2014

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material.
Multiple branched adaptive steered molecular dynamics
Authors: Ozer Gungor , Keyes Thomas , Quirk Stephen , Hernandez Rigoberto
Published: August 2014

Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by “rare events” from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient “multiple branching” (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
Authors: Zubek Mariusz , Wasowicz Tomasz J. , Dąbkowska Iwona , Kivimäki Antti , Coreno Marcello
Published: August 2014

Formation of the excited NH(A3Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A3Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom (or proton) migration within the molecule prior to dissociation. The vertical excitation energies of the superexcited states were determined and the dissociation mechanisms of isoxazole are discussed. The density functional and ab initio quantum chemical calculations have been performed to study the mechanism of the NH formation.
A renormalized potential-following propagation algorithm for solving the coupled-channels equations
Authors: Karman Tijs , Janssen Liesbeth M. C. , Sprenkels Rik , Groenenboom Gerrit C.
Published: August 2014

We derive a general renormalized potential-following propagation method that efficiently solves the coupled-channels equations. The step size is variable, the method is compatible with reactive boundary conditions, and the algorithm may be combined with other renormalized algorithms, such as renormalized Numerov. We diagonalize the coupling matrix and consider piece-wise constant and linear reference potentials. The constant reference potential algorithm is very simple to implement, yet for multichannel problems almost as accurate as the linear reference potential method. The applicability of the proposed algorithms to realistic problems is demonstrated for cold collisions of NH radicals. The renormalized approach has the advantage of producing wave functions in a straightforward way, which is illustrated for a shape resonance in NH–NH collisions. These scattering wave functions can be used to study ultracold photoassociation and near-threshold photodissociation.
Locomotion in complex fluids: Integral theorems
Authors: Lauga Eric
Published: August 2014

The biological fluids encountered by self-propelled cells display complex microstructures and rheology. We consider here the general problem of low-Reynolds number locomotion in a complex fluid. Building on classical work on the transport of particles in viscoelastic fluids, we demonstrate how to mathematically derive three integral theorems relating the arbitrary motion of an isolated organism to its swimming kinematics in a non-Newtonian fluid. These theorems correspond to three situations of interest, namely, (1) squirming motion in a linear viscoelastic fluid, (2) arbitrary surface deformation in a weakly non-Newtonian fluid, and (3) small-amplitude deformation in an arbitrarily non-Newtonian fluid. Our final results, valid for a wide-class of swimmer geometry, surface kinematics, and constitutive models, at most require mathematical knowledge of a series of Newtonian flow problems, and will be useful to quantity the locomotion of biological and synthetic swimmers in complex environments.
Gibbs states on random configurations
Authors: Daletskii Alexei , Kondratiev Yuri , Kozitsky Yuri , Pasurek Tanja
Published: August 2014

Gibbs states of a spin system with the single-spin space $S=\mathbb {R}^{m}$S=Rm and unbounded pair interactions are studied. The spins are attached to the points of a realization γ of a random point process in $\mathbb {R} ^{n}$Rn. Under certain conditions on the model parameters we prove that, for almost all γ, the set $\mathcal {G}(S^{\gamma })$G(Sγ) of all Gibbs states is nonempty and its elements have support properties, explicitly described in the paper. We also show the existence of measurable selections $\gamma \mapsto \nu _{\gamma }\in \mathcal {G}(S^{\gamma })$γ↦νγ∈G(Sγ) (random Gibbs measures) and derive the corresponding averaged moment estimates.
Canonical form of three-fermion pure-states with six single particle states
Authors: Chen Lin , Ž Ðoković Dragomir , Grassl Markus , Zeng Bei
Published: August 2014

We construct a canonical form for pure states in \documentclass[12pt]{minimal}\begin{document}$\mathop {\wedge }\nolimits ^3({\mathbb {C}}^6)$\end{document}∧3(C6), the three-fermion system with six single particle states, under local unitary (LU) transformations, i.e., the unitary group U(6). We also construct a minimal set of generators of the algebra of polynomial U(6)-invariants on \documentclass[12pt]{minimal}\begin{document}$\mathop {\wedge }\nolimits ^3({\mathbb {C}}^6)$\end{document}∧3(C6). It turns out that this algebra is isomorphic to the algebra of polynomial LU-invariants of three-qubits which are additionally invariant under qubit permutations. As a consequence of this surprising fact, we deduce that there is a one-to-one correspondence between the U(6)-orbits of pure three-fermion states in \documentclass[12pt]{minimal}\begin{document}$\mathop {\wedge }\nolimits ^3({\mathbb {C}}^6)$\end{document}∧3(C6) and the LU orbits of pure three-qubit states when qubit permutations are allowed. As an important byproduct, we obtain a new canonical form for pure three-qubit states under LU transformations U(2) × U(2) × U(2) (no qubit permutations allowed).
In-situ high resolution transmission electron microscopy observation of silicon nanocrystal nucleation in a SiO2 bilayered matrix
Authors: Yang T. C.-J. , Kauffmann Y. , Wu L. , Lin Z. , Jia X. , Puthen-Veettil B. , Zhang T. , Conibeer G. , Perez-Wurfl I. , Rothschild A.
Published: August 2014

Solid-state nucleation of Si nanocrystals in a SiO2 bilayered matrix was observed at temperatures as low as 450 °C. This was achieved by aberration corrected high-resolution transmission electron microscopy (HRTEM) with real-time in-situ heating up to 600 °C. This technique is a valuable characterization tool especially with the recent interest in Si nanostructures for light emitting devices, non-volatile memories, and third-generation photovoltaics which all typically require a heating step in their fabrication. The control of size, shape, and distribution of the Si nanocrystals are critical for these applications. This experimental study involves in-situ observation of the nucleation of Si nanocrystals in a SiO2 bilayered matrix fabricated through radio frequency co-sputtering. The results show that the shapes of Si nanocrystals in amorphous SiO2 bilayered matrices are irregular and not spherical, in contrast to many claims in the literature. Furthermore, the Si nanocrystals are well confined within their layers by the amorphous SiO2. This study demonstrates the potential of in-situ HRTEM as a tool to observe the real time nucleation of Si nanocrystals in a SiO2 bilayered matrix. Furthermore, ideas for improvements on this in-situ heating HRTEM technique are discussed.
Precessed electron beam electron energy loss spectroscopy of graphene: Beyond channelling effects
Authors: Yedra Ll. , Torruella P. , Eljarrat A. , Darbal A. D. , Weiss J. K. , Peiró F. , Estradé S.
Published: August 2014

The effects of beam precession on the Electron Energy Loss Spectroscopy (EELS) signal of the carbon K edge in a 2 monolayer graphene sheet are studied. In a previous work, we demonstrated the use of precession to compensate for the channeling-induced reduction of EELS signal when in zone axis. In the case of graphene, no enhancement of EELS signal is found in the usual experimental conditions, as graphene is not thick enough to present channeling effects. Interestingly, though it is found that precession makes it possible to increase the collection angle, and, thus, the overall signal, without a loss of signal-to-background ratio.
Comparative study of the photodarkening relaxation-kinetics in amorphous selenium for above-bandgap and sub-bandgap illumination
Authors: Mishchenko A. , Lindberg G. P. , Weinstein B. A. , Reznik A.
Published: August 2014

The relaxation of photodarkening (PD) brought about by above-bandgap and sub-bandgap excitations is studied in a wide temperature range in amorphous selenium (a-Se) films designed for avalanche photodetectors. The experimental results suggest that in contrast to sub-bandgap excitation, above-bandgap excitation does not cause the formation of self-trapped excitons, viz., photoinduced transformation of the a-Se ground state configuration into a metastable higher-energy configuration. For above-bandgap excitation only transient PD is observed, and its subsequent relaxation can be explained by thermalization and energy relaxation of uncorrelated carriers through the band-tails in order to restore the ground state configuration. In contrast, sub-bandgap excitation causes both transient and reversible PD, with the latter controlled by the formation of self-trapped excitons, whose relaxation requires overcoming an energy barrier of 0.78 ± 0.02 eV either by thermal activation (at elevated temperatures) or by configurational tunneling (for temperatures below room temperature).
A new technique for analysis of human sperm morphology in unstained cells from raw semen
Authors: Soler Carles , García-Molina Almudena , Sancho María , Contell Jesús , Núñez Manuel , Cooper Trevor G.
Published: August 2014

Sperm morphology analysis is a fundamental component of semen analysis, but its real significance has been clouded by the plethora of techniques used for its evaluation. Most involve different fixation and staining procedures that induce artefacts. Herein we describe Trumorph (Proiser R+D, Paterna, Spain), a new method for sperm morphology analysis based on examination of wet preparations of spermatozoa immobilised, after a short 60°C shock, in narrow chambers and examined by negative phase contrast microscopy. A range of morphological forms was observed, similar to those found using conventional fixed and stained preparations, but other forms were also found, distinguishable only by the optics used. The ease of preparation makes the Trumorph a robust method applicable for the analysis of living unmodified spermatozoa in a range of situations. Subsequent studies on well-characterised samples are required to describe the morphology of spermatozoa with fertilising potential.
Inducing semantic roles
Authors: Cysouw Michael
Published: August 2014

Instead of defining semantic roles on the basis of the interpretation of lexical predicates, I will show that it is possible to induce semantic roles from the usage of case-like markers across a wide variety of languages. The assumptions behind this proposal are, first, that semantic roles are strongly contextually determined and, second, that similarity in coding of contextual roles across many different languages shows which contexts evoke the same (or better: very similar) semantic roles. This approach to the investigation of semantic roles will be exemplified by a study of case-like marking in a parallel text across a sample of fifteen languages. On this basis, a semantic map of contextual roles can be established, and it will be shown that higher-level abstractions, like semantic roles or even macro-roles, can be statistically derived from this diversity of marking across many languages. Further, a typology of alignment systems can be derived statistically. Keywords: Semantic roles; case; parallel text; linguistic typology; alignment
Diagnostic and Statistical Manual (DSM)
Authors: Widiger Thomas A. , Gore Whitney L.
Published: August 2014

This chapter provides a discussion of the American Psychiatric Association’s classification of mental disorders (DSM-I through DSM-5), with a particular emphasis on mood disorders and their classification and diagnosis. It begins with the rationale for having an official, authoritative diagnostic manual and then traces the history of the development of the first edition through the fourth edition (DSM-IV-TR, 2000). The authors then discuss fundamental issues concerning the fifth edition (DSM-5, 2013), including the definition of mental disorder, the empirical support for proposed revisions, the shift toward a dimensional model of classification, and the shift toward a neurobiologically-based classification.
Important Issues in Understanding Comorbidity Between Generalized Anxiety Disorder and Major Depressive Disorder
Authors: Mineka Susan , Anand Deepika , Sumner Jennifer A.
Published: August 2014

The comorbidity of anxiety and mood disorders has been of great interest to psychopathology researchers for the past 25 years. One topic––the comorbidity of generalized anxiety disorder (GAD) and major depressive disorder (MDD)––has received considerable attention, in part because it has raised fundamental nosological issues regarding whether GAD should continue to be categorized as an anxiety disorder or whether it should be recategorized as a mood disorder. We review the logic for reclassifying GAD with the mood disorders as well as what we believe to be even more compelling reasons for why it should be retained as an anxiety disorder. In doing so, we review three different kinds of comorbidity—cross-sectional, cumulative (lifetime), and sequential. We also discuss overlaps and distinctions in what is known about the etiology of GAD and MDD and how their somewhat different cognitive and affective profiles bear on these issues of classification. Finally, we briefly discuss what some of the treatment implications may be for individuals with comorbid GAD and MDD.
Sexual Dysfunction
Authors: Feldman Jamie , Larsen Karin
Published: August 2014

Sexual dysfunction covers a range of disturbances in sexual response affecting desire, arousal, and orgasm or involving pain with sexual activity. Depression and sexual dysfunction have long been known as comorbid conditions; however, some research suggests that depressed mood may not always be associated with specific sexual dysfunctions. Associations between sexual dysfunction and depression appears bidirectional, such that either one of these conditions may trigger or worsen the other, while improvement in one may also improve the other. This chapter examines the complex relationship between depression and male and female sexual dysfunctions. We explore the classification and prevalence of sexual dysfunction, the known interconnections involving neurobiology, and psychological issues. Finally, we summarize the core principles of evaluation and treatment of common sexual dysfunctions, particularly in the context of depressive illness.
Epilogue
Authors: O'Hara Michael W. , Richards C. Steven
Published: August 2014

The authors of the chapters in this volume have covered nearly every feature of depression comorbidity with other psychiatric disorders, chronic health conditions, and disturbed close relationships. Treatment implications are addressed both in chapters on individual disorders as well as comprehensively in separate chapters. This volume concludes with the “big picture” provided by Ronald Kessler and his colleagues. Several themes emerge. Depression comorbidity is pervasive. It touches to one degree or another almost every identifiable psychiatric condition, chronic health condition, and disturbed close relationship. There are numerous potential explanations for this pervasive comorbidity that depend in part on the comorbid disorder. Depression comorbidity is associated with greater disease burden, resistance to treatment, increased primary disease morbidity, and mortality relative to cases in which comorbid depression is not present. Although depression comorbidity is common across psychiatric disorders, it is especially common among the anxiety disorders, raising questions as whether these disorders are really distinct. The assessment and treatment of comorbid disorders is complicated and often requires interdisciplinary collaboration. Although great strides have been made in the study of depression comorbidity, there is much left to be learned, so that we will be able to provide the most effective possible care to our patients who suffer from comorbid depression.
The Purposes, Practices, and Principles of Autoethnographic Research
Authors: Ellis Carolyn , Adams Tony E.
Published: August 2014

This chapter details the authors’ approach to understanding and practicing autoethnography. It begins by defining autoethnography and describing its history and emergence within qualitative social research and within psychology. It then proposes general guiding principles for those seeking to do autoethnography, principles such as using personal experience, acknowledging existing research, understanding and critiquing cultural experience, using insider knowledge, breaking silence, and maneuvering through pain, confusion, anger, and uncertainty. It continues with a discussion of autoethnography as a process and as a product, and a method that can take a variety of representational forms. After offering ways to evaluate and critique autoethnography, it concludes with a discussion of autoethnography as an orientation to the living of life and an approach that has the potential of making life better—for the writer, reader, participant, and larger culture.
Content Analysis
Authors: Prior Lindsay
Published: August 2014

In this chapter, the focus is on ways in which content analysis can be used to investigate and describe interview and textual data. The chapter opens with a contextualization of the method and then proceeds to an examination of the role of content analysis in relation to both quantitative and qualitative modes of social research. Following the introductory sections, four kinds of data are subjected to content analysis. These include data derived from a sample of qualitative interviews (N = 54), textual data derived from a sample of health policy documents (N = 6), data derived from a single interview relating to a “case” of traumatic brain injury, and data gathered from 54 abstracts of academic papers on the topic of “well-being.” Using a distinctive and somewhat novel style of content analysis that calls upon the notion of semantic networks, the chapter shows how the method can be used either independently or in conjunction with other forms of inquiry (including various styles of discourse analysis) to analyze data, and also how it can be used to verify and underpin claims that arise out of analysis. The chapter ends with an overview of the different ways in which the study of “content”—especially the study of document content—can be positioned in social scientific research projects.
Critical Approaches to Qualitative Research
Authors: Bhavnani Kum-Kum , Chua Peter , Collins Dana
Published: August 2014

This chapter reflects on critical strategies in qualitative research. It examines the meanings and debates associated with the term “critical,” in particular, contrasting liberal and dialectical notions and practices in relation to social analysis and qualitative research. The chapter also explores how critical social research may be synonymous with critical ethnography in relation to issues of power, positionality, representation, and the production of situated knowledges. It uses Bhavnani’s framework to draw on Dana Collins’ research as a specific case to suggest how the notion of the “critical” relates to ethnographic research practices: ensuring feminist and queer accountability, resisting reinscription, and integrating lived experience.
Oral History Interviewing
Authors: Janesick Valerie J.
Published: August 2014

Oral history interviewing is a viable qualitative research orientation for many qualitative researchers in various disciplines. Oral history is the collection of stories, statements, and reminiscences of a person or persons who have firsthand knowledge of any number of experiences. It offers qualitative researchers a way to capture the lived experiences of participants. The techniques of oral history are those of the qualitative researcher, including interviews, document analysis, photographs, and video. The current digital era offers many opportunities to address issues and possibilities for the oral historian as qualitative researcher. Three major issues that emerge are those of social justice, arts-based approaches to oral history, and transdisciplinarity. Possibilities are endless in terms of using digital techniques for data presentation, data analysis, and dissemination. The power of oral history is the power of storytelling. By using current technology and working in a transdisciplinary context, oral history may now be more readily accessible and available to a wider population thus moving toward social justice.
Lineages
Authors: Zeller-Berkman Sarah M.
Published: August 2014

Participatory action research (PAR) in the twenty-first century asserts a democratization of who has the right to create knowledge, engage in participatory processes, research social conditions, and take action on issues that impact their lives. PAR is an approach to doing research that is based on a set of commitments. PAR theory and practice is a collective creation, benefiting from the thoughtful work of hundreds of people from more than sixty countries. This chapter traces three of PAR’s historical lineages, explores a current convergence of lineages called critical PAR, and offers some areas for future consideration.