bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-organization and control in stimulated Raman backscattering
Authors: ŠKORIĆ MILOŠ M. , NIKOLIĆ LJUBOMIR , ISHIGURO SEIJI
Published: November 2013

A stimulated Raman scattering (SRS) on electron plasma waves in underdense plasmas is of a big concern in laser fusion due to an energy loss and target preheating. Complex features of large Backward-SRS (BRS) in experiments and simulations with laser fusion targets are found. Recently, to reach ultra-high intensities at multi-exawatts and beyond, relevant to high-energy physics, Raman amplification based on BRS was proposed; still, with high sensitivity and a narrow operational window. Firstly, we revisit a standard three-coupled mode model of BRS to show that the condition for an absolute instability is readily satisfied in uniform plasmas which excites large Raman signals from a background noise. It sets in for interaction length L0 shorter than, both, the plasma length L and absorption length La. Further, we point out a generic BRS feature, which due to a nonlinear frequency shift in large electron plasma wave (relativistic/trapping effects), instead to a steady state, saturates via intermittent pulsations with incoherent spectral broadening. A ‘break up’ of Manley–Rowe invariants is shown to predict non-stationary BRS. Finally, an intermediate intensity regime is originally proposed for coherent femto-second pulse generation in a thin exploding foil plasma, with scalings investigated by theory and particle simulations.
Nutritional influences on age-related skeletal muscle loss
Authors: Welch Ailsa A.
Published: November 2013

Age-related muscle loss impacts on whole-body metabolism and leads to frailty and sarcopenia, which are risk factors for fractures and mortality. Although nutrients are integral to muscle metabolism the relationship between nutrition and muscle loss has only been extensively investigated for protein and amino acids. The objective of the present paper is to describe other aspects of nutrition and their association with skeletal muscle mass. Mechanisms for muscle loss relate to imbalance in protein turnover with a number of anabolic pathways of which the mechanistic TOR pathway and the IGF-1–Akt–FoxO pathways are the most characterised. In terms of catabolism the ubiquitin proteasome system, apoptosis, autophagy, inflammation, oxidation and insulin resistance are among the major mechanisms proposed. The limited research associating vitamin D, alcohol, dietary acid–base load, dietary fat and anti-oxidant nutrients with age-related muscle loss is described. Vitamin D may be protective for muscle loss; a more alkalinogenic diet and diets higher in the anti-oxidant nutrients vitamin C and vitamin E may also prevent muscle loss. Although present recommendations for prevention of sarcopenia focus on protein, and to some extent on vitamin D, other aspects of the diet including fruits and vegetables should be considered. Clearly, more research into other aspects of nutrition and their role in prevention of muscle loss is required.
Predicting response to cognitive behavioral therapy in contamination-based obsessive–compulsive disorder from functional magnetic resonance imaging
Authors: Olatunji B. O. , Ferreira-Garcia R. , Caseras X. , Fullana M. A. , Wooderson S. , Speckens A. , Lawrence N. , Giampietro V. , Brammer M. J. , Phillips M. L. , Fontenelle L. F. , Mataix-Cols D.
Published: November 2013

Background

Although cognitive behavioral therapy (CBT) is an effective treatment for obsessive–compulsive disorder (OCD), few reliable predictors of treatment outcome have been identified. The present study examined the neural correlates of symptom improvement with CBT among OCD patients with predominantly contamination obsessions and washing compulsions, the most common OCD symptom dimension.

Method

Participants consisted of 12 OCD patients who underwent symptom provocation with contamination-related images during functional magnetic resonance imaging (fMRI) scanning prior to 12 weeks of CBT.

Results

Patterns of brain activity during symptom provocation were correlated with a decrease on the Yale–Brown Obsessive Compulsive Scale (YBOCS) after treatment, even when controlling for baseline scores on the YBOCS and the Beck Depression Inventory (BDI) and improvement on the BDI during treatment. Specifically, activation in brain regions involved in emotional processing, such as the anterior temporal pole and amygdala, was most strongly associated with better treatment response. By contrast, activity in areas involved in emotion regulation, such as the dorsolateral prefrontal cortex, correlated negatively with treatment response mainly in the later stages within each block of exposure during symptom provocation.

Conclusions

Successful recruitment of limbic regions during exposure to threat cues in patients with contamination-based OCD may facilitate a better response to CBT, whereas excessive activation of dorsolateral prefrontal regions involved in cognitive control may hinder response to treatment. The theoretical implications of the findings and their potential relevance to personalized care approaches are discussed.
Food-derived bioactive peptides – a new paradigm
Authors: Moughan Paul J. , Rutherfurd Shane M. , Montoya Carlos A. , Dave Lakshmi A.
Published: November 2013

Food-derived bioactive peptides are regarded as important modulators of several physiological processes occurring both systemically and locally within the gastrointestinal tract (GIT). However, the concentrations of food-derived bioactive peptides in the GIT, and therefore attendant physiological effects, are likely to be highly variable given the wide variation in the type and amount of dietary protein consumed either during the day or on a day-to-day basis. In contrast, gut endogenous proteins (e.g. cell proteins, mucin, serum albumin and digestive enzymes) are a consistent and significant potential source of peptides for the GIT. With up to 80 % of gut endogenous proteins being digested in the GIT, it is possible that a wide range of peptides is generated, but until now the significance of the gut endogenous proteins as a source of bioactive peptides has not been considered. A hypothesis is promulgated that the gut endogenous proteins may have a hidden role as a consistent and quantitatively important source of bioactive peptides in the GIT.
The Media Archaeological Repairman
Authors: Riis Morten
Published: November 2013

This paper investigates how a contemporary constructed mechanical musical instrument driven by a steam engine can be used as an instrument that brings new knowledge and understanding to rudimentary conditions regarding electronic music. The investigation takes its starting point in the media archaeological repairman that digs out the malfunctioning music machine and gives the material physicality a pivotal role, in contrast to the otherwise more symbolic understanding of electronic music that seems to be predominant. This alternative conceptualisation of electronic music focuses on rudimentary understandings of physical and symbolic framings of machine-based music, which are unfolded through the notion of operative technology, and brings new knowledge regarding key epistemological issues regarding timing, malfunction and operation within electronic and machine-based music.
Provoking, Disturbing, Hacking: Media archaeology as a framework for the understanding of contemporary DIY composers’ instruments and ideas
Authors: Groth Sanne Krogh
Published: November 2013

The article is a discussion of works by two Danish composers who both, with self-constructed instruments, challenge computer music as genre, the understanding and use of conventional technology, and the music's relation to history. At first glance, the use of homemade instruments appears to be a common characteristic. But, when one takes a closer look, different discourses and various discussions of media and materiality are revealed. In the article the various positions are unfolded through discussions within the theoretical field of media archaeology – a science with its roots in media studies, but also an important framework for the production and understanding of a variety of DIY practices.

The overall purpose with the article is twofold: on the one hand it illustrates how theories from the field of media archaeology contribute interesting perspectives to discussions of artistic work within the area of DIY. On the other hand, it also serves as a critical discussion of media archaeology as not necessarily the solution to every aspect of artistic practices. The two artists are Morten Riis and Goodiepal.
Beyond DIY in Electronic Music
Authors: Richards John
Published: November 2013

Do-it-yourself (DIY) in electronic music represents a new paradigm that is not just about DIY. Doing-it-together (DIT) and the idea of community and shared experiences are at the root of DIY practice. This article discusses how the workshop and the event have become central to practitioners working in the field of DIY. Collective instrument building, the concept of the living installation, and performance are viewed as a holistic event. Some specific examples of the author's work known as Dirty Electronics are considered, where emphasis is placed upon experience rather than the ‘something to take home’ factor. These include the following works: ICA Solder a Score, Noise Shadow, Still and Cut & Thrust. Composing ‘outside’ electronics is regarded as a method for revealing processes that can be represented in other areas of the work beyond sound-generating circuits. The article also looks at how building circuits and sound devices acts as a way to create a tabula rasa, and how the idea of delegated performance, where instruments are played by ‘non-experts’, serves to establish a naïve approach and authenticity in performance. Through the sharing of information online and in workshops, the DIY community has become knowledgeable, which has resulted in a community ‘full of experts’ and the growth of custom-designed circuits. The rise of discrete hand-held music players, such as the Buddha Machine, and the boutique synthesiser are also discussed, and the physical artefact and sound object are seen as a vehicle for the dissemination of ideas. Finally, the question is asked: ‘In DIY practice, where does the authentic document of the work lie?’
A Manual Actions Expressive System (MAES)
Authors: Fischman Rajmil
Published: November 2013

This article describes amanual actions expressive system(MAES) which aims to enable music creation and performance using natural hand actions (e.g. hitting virtual objects, or shaking them). Gestures are fully programmable and result from tracking and analysing hand motion and finger bend, potentially allowing performers to concentrate on natural actions from our daily use of the hands (e.g. the physical movement associated with hitting and shaking). Work carried out focused on the development of an approach for the creation of gestures based on intuitive metaphors, their implementation as software for composition and performance, and their realisation within a musical composition through the choice of suitable mappings, sonic materials and processes.
Syntax–semantics mappings as a source of difficulty in Japanese speakers’ acquisition of the mass–count distinction in English
Authors: INAGAKI SHUNJI
Published: November 2013

This paper investigates Japanese speakers’ acquisition of the mass–count distinction in English. Learners judge whether two large objects/portions of stuff are more than six tiny objects/portions of stuff or vice versa. Results show that learners correctly base judgments on number for count nouns (judging that six small cups aremore cupsthan two large cups) and object-mass nouns (e.g.,furniture) and on volume for substance-mass nouns (judging that two large portions of mustard aremore mustardthan six tiny portions of it). For nouns that can be either mass or count in English (e.g.,string(s)) or cross-linguistically (e.g., “spinach”), learners fail to shift judgments according to the mass–count syntax in which the words appear. Results suggest that Japanese learners have difficulty using mass–count syntactic cues to disambiguate the meanings and thus fail to acquire the mass–count distinction in English.
The phenomenon of micronutrient deficiency among children in China: a systematic review of the literature
Authors: Wong Angel YS , Chan Esther W , Chui Celine SL , Sutcliffe Alastair G , Wong Ian CK
Published: November 2013

Objective

The present study aimed to review the literature on micronutrient deficiency and other factors influencing a deficiency status among children living in China.

Design

A systematic review was performed to analyse the literature.

Setting

Studies were identified through a search of PubMed and secondary references.

Subjects

Children living in China aged less than 18 years.

Results

Sixty-one articles were included. The prevalence of vitamin A deficiency decreased to approximately 10 % in 1995–2009. It increased with age but no significant difference was found between genders. The prevalence of thiamin and vitamin B12 deficiency was 10·5 % in Yunnan and 4·5 % in Chongqing provinces, respectively. Higher vitamin D deficiency rates were seen in spring and winter. The incidence of bleeding due to vitamin K deficiency was 3·3 % in 1998–2001 and more prevalent in rural areas. Both iodine deficiency and excess iodine intake were observed. Goitre rates were reported in Tibet, Jiangxi, Gansu and Hong Kong (3·5–46 %). Anaemia rates ranged from 20 % to 40 % in 2007–2011. High Se deficiency rates were found in Tibet, Shaanxi and Jiangsu. High Zn deficiency rates were also found (50–70 %) in 1995–2006. Few studies reported Ca deficiency rates (19·6–34·3 %). The degrees of deficiency for vitamin A, vitamin B12, Fe and Zn were more substantial in rural areas compared with urban areas.

Conclusions

The prevalence of micronutrient deficiency rates varied. Socio-economic status, environmental factors and the Chinese diet may influence micronutrient deficiency. Public health policies should consider implementing programmes of supplementation, food fortification and nutrition education to address these deficiencies among Chinese children.
Genetic diversity and population structure in a collection of roselle (Hibiscus sabdariffaL.) from Niger
Authors: Bakasso Y. , Zaman-Allah M. , Mariac C. , Billot C. , Vigouroux Y. , Zongo J. D. , Saadou M.
Published: November 2013

Roselle (Hibiscus sabdariffaL.) is an economically important plant in Niger. Little is known about its genetic diversity and population structure. In this study, we performed the first diversity assessment of a collection of 124 roselle accessions and 16 accessions of its close relativesHibiscuscannabinusandAbelmoschusesculentus. Our study was based on ten agromorphological traits and 267 amplified fragment length polymorphism markers. We identified two major distinct groups inH. sabdariffausing a Bayesian method. These two genetic groups were associated with statistical differences for three phenological characteristics: number of days to flowering, 100-seed weight and calyx size. However, the calyx colour, i.e. a morphological characteristic often used to classify different local ecotypes, did not superimpose this separation. Our findings suggested that roselle diversity is genetically structured; the two different groups were clearly associated with morphological differences but were not commonly used by farmers for their classification. The impact of the perceived ecotype structure and its consequence on farmer management is discussed.
The Effect of Client Case Complexity on Clinical Decision Making
Authors: Groenier Marleen , Pieters Jules M. , Witteman Cilia. L. M. , Lehmann Souja R. S.
Published: November 2013

In mental health care, clinicians’ treatment decisions are expected to be based on the formulation (i.e., exploration of the causing and maintaining mechanisms) of the client’s problems. Previous research showed two things: clinicians’ case formulations mainly contain descriptive information instead of explanatory information and it is unclear to what extent treatment decisions are actually based on case formulations. In this study, we tested whether the complexity of client problems influences case formulation quality and we investigated to what extent case formulations explain treatment decisions for simple and complex client problems. Results show that case formulations for complex problems were of lower quality than those for simple problems. Also, we found that case formulations are only weakly associated with treatment decisions, for both types of problems. We conclude that clinicians give higher quality case formulations when these may be least needed, that is: for simple cases, for which an empirically supported treatment is available. Clinicians appear to base treatment decisions on descriptions of overt client symptoms rather than on case formulations.
Germinal center‐independent, IgM‐mediated autoimmunity in sanroque mice lacking Obf1
Authors: Chevrier Stephane , Kratina Tobias , Emslie Dianne , Karnowski Alexander , Corcoran Lynn M
Published: November 2013

Mice homozygous for a point mutation in the Rc3h1 gene encoding Roquin1, designated sanroque mice, develop a severe antibody‐mediated autoimmune condition. The disease is T‐cell intrinsic, exacerbated by macrophage‐intrinsic defects and driven by excessive T follicular helper cell generation and spontaneous germinal centre (GC) formation. This culminates in abnormally high numbers of plasma cells secreting high‐affinity autoreactive immunoglobulin G (IgG). Obf1 is a transcriptional co‐activator required for normal T‐cell‐dependent antibody responses, and it is essential for GC formation under all circumstances so far tested. We crossed sanroque mice with Obf1‐null mice to determine whether the hyperactivity of sanroque T cells could drive Obf1−/− B cells to differentiate to GC B cells, or conversely, if Obf1 loss would prevent sanroque‐mediated autoimmune disease. Surprisingly, while sanroque/Obf1−/− mice did not form GC, they still developed autoimmune disease and succumbed even more rapidly than did sanroque mice. The disease was mediated by autoreactive IgM, which may have been derived from a pre‐existing population of autoreactive B cells in the Obf1−/− mice responding to the over‐exuberant activity of sanroque CD4 cells.
Dendritic cells treated with chloroquine modulate experimental autoimmune encephalomyelitis
Authors: Thomé Rodolfo , Issayama Luidy Kazuo , DiGangi Rosaria , Bombeiro Andre Luis , da Costa Thiago Alves , Ferreira Isadora Tassinari , de Oliveira Alexandre Leite Rodrigues , Verinaud Liana
Published: November 2013

Chloroquine (CQ), an antimalarial drug, has been shown to modulate the immune system and reduce the severity of experimental autoimmune encephalomyelitis (EAE). The mechanisms of disease suppression are dependent on regulatory T cell induction, although Tregs‐independent mechanisms exist. We aimed to evaluate whether CQ is capable to modulate bone marrow‐derived dendritic cells (DCs) both phenotypically and functionally as well as whether transfer of CQ‐modulated DCs reduces EAE course. Our results show that CQ‐treated DCs presented altered ultrastructure morphology and lower expression of molecules involved in antigen presentation. Consequently, T cell proliferation was diminished in coculture experiments. When transferred into EAE mice, DC‐CQ was able to reduce the clinical manifestation of the disease through the modulation of the immune response against neuroantigens. The data presented herein indicate that chloroquine‐mediated modulation of the immune system is achieved by a direct effect on DCs and that DC‐CQ adoptive transfer may be a promising approach for avoiding drug toxicity.
Rationally designed capsid and transgene cassette of AAV6 vectors for dendritic cell‐based cancer immunotherapy
Authors: Pandya Jheel , Ortiz Luis , Ling Chen , Rivers Angela E , Aslanidi George
Published: November 2013

Dendritic cell (DC)‐based immunotherapy has recently demonstrated a great potential for clinical applications; however, additional progress in the methods of tumor‐specific antigen delivery to DCs is necessary for the further development of anti‐tumor vaccines. To this end, a capsid‐optimized adeno‐associated virus serotype 6 (AAV6‐T492V+S663V) vector was developed by site‐directed mutagenesis of surface‐exposed serine (S) and threonine (T) residues, which have a critical role in intracellular trafficking of AAV vectors. This double‐mutant AAV6 vector had ∼5‐fold greater transduction efficiency in monocyte‐derived DCs (moDCs) compared with wild‐type (WT)‐AAV6 vectors. The increase in the transduction efficiency correlated with the improved nuclear translocation of AAV6‐T492V+S663V over that of the WT‐AAV6 vector. Additional studies of the CD11c promoter identified critical regulatory elements that fit into the AAV expression cassette and drive EGFP expression in moDCs. Development of a chimeric promoter (chmCD11c) that contains functional modules of CD11c and a Simian virus (SV40) enhancer element dramatically increased the EGFP expression in moDCs. MoDCs transduced by the capsid‐optimized AAV6 vector carrying human prostate‐specific antigen (hPSA) driven by CBA (AAV6‐T492V+S663V‐CBA‐hPSA) or chmCd11c (AAV6‐T492V+S663V‐chmCD11c‐hPSA) generated specific T‐cell clone proliferation and superior cytotoxic T lymphocytes (CTLs) with higher killing capability against human prostate adenocarcinoma cells, LNCaP, compared with WT‐AAV6 induced CTLs. Taken together, these studies suggest that optimization of capsid and promoter components of AAV vectors can be a useful approach for efficient targeting of moDCs and may prove to be a promising tool for cancer immunotherapy.
Chondroitin sulphate N-acetylgalactosaminyl-transferase-1 inhibits recovery from neural injury
Authors: Takeuchi Kosei , Yoshioka Nozomu , Higa Onaga Susumu , Watanabe Yumi , Miyata Shinji , Wada Yoshino , Kudo Chika , Okada Masayasu , Ohko Kentaro , Oda Kanako , Sato Toshiya , Yokoyama Minesuke , Matsushita Natsuki , Nakamura Masaya , Okano Hideyuki , Sakimura Kenji , Kawano Hitoshi , Kitagawa Hiroshi , Igarashi Michihiro
Published: November 2013

Extracellular factors that inhibit axon growth and intrinsic factors that promote it affect neural regeneration. Therapies targeting any single gene have not yet simultaneously optimized both types of factors. Chondroitin sulphate (CS), a glycosaminoglycan, is the most abundant extracellular inhibitor of axon growth. Here we show that mice carrying a gene knockout for CS N-acetylgalactosaminyltransferase-1 (T1), a key enzyme in CS biosynthesis, recover more completely from spinal cord injury than wild-type mice and even chondroitinase ABC-treated mice. Notably, synthesis of heparan sulphate (HS), a glycosaminoglycan promoting axonal growth, is also upregulated in TI knockout mice because HS-synthesis enzymes are induced in the mutant neurons. Moreover, chondroitinase ABC treatment never induces HS upregulation. Taken together, our results indicate that regulation of a single gene, T1, mediates excellent recovery from spinal cord injury by optimizing counteracting effectors of axon regeneration—an extracellular inhibitor of CS and intrinsic promoters, namely, HS-synthesis enzymes.
A cholinergic trigger drives learning-induced plasticity at hippocampal synapses
Authors: Mitsushima Dai , Sano Akane , Takahashi Takuya
Published: November 2013

Learning induces plastic changes in synapses. However, the regulatory molecules that orchestrate learning-induced synaptic changes are largely unknown. Although it is well established that cholinergic inputs from the medial septum modulate learning and memory, evidence for the cholinergic regulation of learning-induced synaptic plasticity is lacking. Here we find that the activation of muscarinic acetylcholine (ACh) receptors (mAChRs) mediates the contextual fear learning-driven strengthening of hippocampal excitatory pyramidal synapses through the synaptic incorporation of AMPA-type glutamate receptors (AMPARs). Contextual fear learning also enhances the strength of inhibitory synapses on hippocampal pyramidal CA1 neurons, in a manner mediated by the activation of, not mAChRs, but, nicotinic AChRs (nAChRs). We observe a significant correlation between the learning-induced increases in excitatory and inhibitory synaptic strength at individual pyramidal neurons. Understanding the mechanisms underlying cholinergic regulation of learning-induced hippocampal synaptic plasticity may help the development of new therapies for cognitive disorders.
Cheap glass fiber mats as a matrix of gel polymer electrolytes for lithium ion batteries
Authors: Zhu Yusong , Wang Faxing , Liu Lili , Xiao Shiyin , Yang Yaqiong , Wu Yuping
Published: November 2013

Lithium ion batteries (LIBs) are going to play more important roles in electric vehicles and smart grids. The safety of the current LIBs of large capacity has been remaining a challenge due to the existence of large amounts of organic liquid electrolytes. Gel polymer electrolytes (GPEs) have been tried to replace the organic electrolyte to improve their safety. However, the application of GPEs is handicapped by their poor mechanical strength and high cost. Here, we report an economic gel-type composite membrane with high safety and good mechanical strength based on glass fiber mats, which are separator for lead-acid batteries. The gelled membrane exhibits high ionic conductivity (1.13 mS cm−1), high Li+ ion transference number (0.56) and wide electrochemical window. Its electrochemical performance is evaluated by LiFePO4 cathode with good cycling. The results show this gel-type composite membrane has great attraction to the large-capacity LIBs requiring high safety with low cost.
NMR investigation of disulfide containing peptides and proteins
Authors: Kövér Katalin E. , Batta Gyula
Published: November 2013

Peptides and proteins with disulfide bonds are abundant in all kingdoms and play essential role in many biological events. Because small disulfide-rich peptides (proteins) are usually difficult to crystallize, nuclear magnetic resonance (NMR) is by far one of the most powerful techniques for the determination of their solution structure. Besides the “static” three-dimensional structure, NMR has unique opportunities to acquire additional information about molecular dynamics and folding at atomic resolution. Nowadays it is becoming increasingly evident, that “excited”, “disordered” or “fuzzy” protein states may exhibit biological function and disulfide proteins are also promising targets for such studies. In this short two-three years overview those disulfide peptides and proteins were cited from the literature that were studied by NMR. Though we may have missed some, their structural diversity and complexity as well as their wide repertoire of biological functions is impressive. We emphasised especially antimicrobial peptides and peptide based toxins in addition to some biologically important other structures. Besides the general NMR methods we reviewed some contemporary techniques suitable for disclosing the peculiar properties of disulfide bonds. Interesting dynamics and folding studies of disulfide proteins were also mentioned. It is important to disclose the essential structure, dynamics, function aspects of disulfide proteins since this aids the design of new compounds with improved activity and reduced toxicity. Undoubtedly, NMR has the potential to accelerate the development of new disulfide peptides/proteins with pharmacological activity.
Self-assembly of designed peptides and their nanomaterials applications
Authors: Tsutsumi Hiroshi , Mihara Hisakazu
Published: November 2013

Peptide self-assembling is one of the useful tools to fabricate various nanostructures including fibers, tubes, vesicles and spheres based on a supramolecular chemistry. Self-assembling peptides have various structural motifs including a β-sheet, an α-helical coiled-coil, a lipid/surfactant-like motif, a peptide amphiphile with an aliphatic tail and a diphenylalanine motif. Recent continuous studies for such self-assembling peptides give us much important information about the relationship between sequences and self-assembling properties. Self-assembled structures are applied to nanomaterials with various functional units and stimuli responsiveness by selective modification and peptide design. Self-assembling peptides are also utilized as potential scaffolds to construct hybrid nanomaterials for optical and electronic devices that involve controlled energy, light or charge transfer. Furthermore, their nanostructures with functionalized surfaces work as useful scaffolds for efficient mineralization of metallic/inorganic nanomaterials. Recent researches for self-assembling peptides spread to computational approaches for understanding of self-assembling mechanism and analyses of nanostructural properties. Computational techniques with improved designing works will encourage further development of self-assembling peptides and their nanomaterial applications.
Peptide and protein based pharmaceuticals
Authors: Mezo Gábor
Published: November 2013

It is predicted that in the 21st century there will be more and more new drug investments that violates the Lipinski's “rule-of-five”. Among them, peptides have received increased interest in the current drug therapies. Advantages of peptide-based pharmaceuticals are the high potency and selectivity as well as their low accumulation in tissues; thus, they have potentially lower toxicity than the small drug molecules. Furthermore, the high chemical and biological diversity of peptides provide a broad range of targets, which could represent a basis for personalized medication. Currently, there are more than 70 approved peptide drugs on the market, generating an annual sale close to USD 20 billion in 2012. About half of them are presented in this chapter, which ones are used for the treatment of diabetes, cancers, multiple sclerosis, HIV, hereditary angioedema, respiratory distress syndrome, prevention of thrombosis or relief pain. Next to the structures of the peptide-based pharmaceuticals, their biological activity on the mentioned diseases will be shortly discussed. An outlook for the new peptide-based drug development indicates high perspectives of this area.
Unprecedented organocatalytic reduction of lignin model compounds to phenols and primary alcohols using hydrosilanes
Authors: Feghali Elias , Cantat Thibault
Published: November 2013

The first metal-free reduction of lignin model compounds is described. Using inexpensive PMHS and TMDS hydrosilanes as reductants, α-O-4 and β-O-4 linkages are reduced to primary alcohols and phenols under mild conditions using B(C6F5)3as an efficient catalyst.
Tuning, inhibiting and restoring the enzyme mimetic activities of Pt–apoferritin
Authors: Carmona Unai , Zhang Lianbing , Li Le , Münchgesang Wolfram , Pippel Eckhard , Knez Mato
Published: November 2013

Selective inhibition of the enzyme mimetic activity of nanoparticles and a novel way to recover the inhibited activity.
Assessment of G3(MP2)//B3 theory including a pseudopotential for molecules containing first-, second-, and third-row representative elements
Authors: Rocha Carlos Murilo Romero , Pereira Douglas Henrique , Morgon Nelson Henrique , Custodio Rogério
Published: November 2013

G3(MP2)//B3 theory was modified to incorporate compact effective potential (CEP) pseudopotentials, providing a theoretical alternative referred to as G3(MP2)//B3-CEP for calculations involving first-, second-, and third-row representative elements. The G3/05 test set was used as a standard to evaluate the accuracy of the calculated properties. G3(MP2)//B3-CEP theory was applied to the study of 247 standard enthalpies of formation, 104 ionization energies, 63 electron affinities, 10 proton affinities, and 22 atomization energies, comprising 446 experimental energies. The mean absolute deviations compared with the experimental data for all thermochemical results presented an accuracy of 1.4 kcal mol−1 for G3(MP2)//B3 and 1.6 kcal mol−1 for G3(MP2)//B3-CEP. Approximately 75% and 70% of the calculated properties are found with accuracy between ±2 kcal mol−1 for G3(MP2)//B3 and G3(MP2)//B3-CEP, respectively. Considering a confidence interval of 95%, the results may oscillate between ±4.2 kcal mol−1 and ±4.6 kcal mol−1, respectively. The overall statistical behavior indicates that the calculations using pseudopotential present similar behavior with the all-electron theory. Of equal importance to the accuracy is the CPU time, which was reduced by between 10% and 40%.
Broken symmetry approach to density functional calculation of zero field splittings including anisotropic exchange interactions
Authors: Kessler Eva M. V. , Schmitt Sebastian , van Wüllen Christoph
Published: November 2013

The broken symmetry approach to the calculation of zero field splittings (or magnetic anisotropies) of multinuclear transition metal complexes is further developed. A procedure is suggested how to extract spin Hamiltonian parameters for anisotropic exchange from a set of broken symmetry density functional calculations. For isotropic exchange coupling constants Jij, the established procedure is retrieved, and anisotropic (or pseudodipolar) exchange coupling tensors Dij are obtained analogously. This procedure only yields the sum of the individual single-ion zero field splitting tensors Di. Therefore, a procedure based on localized orbitals has been developed to extract the individual single-ion contributions. With spin Hamiltonian parameters at hand, the zero field splittings of the individual spin multiplets are calculated by an exact diagonalization of the isotropic part, followed by a spin projection done numerically. The method is applied to the binuclear cation [LCr(OH)3CrL]3 + (L = 1,4,7-trimethyl-1,4,7-triazanonane) for which experimental zero field splittings for all low-energy spin states are known, and to the single-molecule magnet [Fe4(CH3C(CH2O)3)2(dpm)6] (Hdpm = 2,2,6,6-tetramethylheptane-3,5-dione). In both these 3d compounds, the single-ion tensors mainly come from the spin-orbit interaction. Anisotropic exchange is dominated by the spin-dipolar interaction only for the chromium compound. Despite the rather small isotropic exchange couplings in the iron compound, spin-orbit and spin-dipolar contributions to anisotropic exchange are of similar size here.
Investigation of new superhard carbon allotropes with promising electronic properties
Authors: Kvashnina Yulia A. , Kvashnin Alexander G. , Sorokin Pavel B.
Published: November 2013

During the systematic search for a new superhard carbon allotrope, we predicted three structures with promising physical properties. Our electronic structure calculations show that these materials have a semiconducting band gap and a high carrier mobility comparable with diamond. The simulated x-ray diffraction patterns of the proposed materials are in a good agreement with the experimental X-ray spectra. Evaluated phase transition pressures from graphite to the new proposed carbon phases are smaller than 25 GPa and close to the experimental values.
Temperature-driven motion of liquid crystals confined in a microvolume
Authors: Zakharov A. V. , Vakulenko A. A.
Published: November 2013

The theoretical description of the reorientational dynamics in microsized liquid crystal (LC) cell, where the nematic sample is confined by two horizontal and two lateral surfaces, under the influence of a temperature gradient ∇T, caused by a laser beam focused on the bounding surface with and without the orientational defect, whereas the rest of the bounding surfaces of the LC cell are kept at constant temperature, has been presented. Our calculations, based on the appropriate nonlinear extension of the classical Ericksen-Leslie theory, show that due to interaction between ∇T and the gradient of the director field \documentclass[12pt]{minimal}\begin{document}$\nabla \hat{{\hbox{\bf n}}}$\end{document}∇n̂ in the LC sample, a thermally excited vortical fluid flow is maintained in the vicinity of the orientational defect, with the motion in the positive sense (clockwise) around the middle part of that defect. In the case of the same LC cell, but without the orientational defect on the lower hotter boundary, the heating regime can also produce the vortical flow in the vicinity of the lower boundary, but with the motion in the negative sense (anti-clockwise) around the middle part of that boundary. At that, the second vortex is characterized by a much slower speed than the vortical flow in the first case.
Asymptotics for inhomogeneous Dirichlet initial-boundary value problem for the nonlinear Schrödinger equation
Authors: Kaikina Elena I.
Published: November 2013

We consider the inhomogeneous Dirichlet initial-boundary value problem for the nonlinear Schrödinger equation, formulated on a half-line. We study traditionally important problems of the theory of nonlinear partial differential equations, such as global in time existence of solutions to the initial-boundary value problem and the asymptotic behavior of solutions for large time.
Spatiotemporal heterogeneity of local free volumes in highly supercooled liquid
Authors: Shiba Hayato , Kawasaki Takeshi
Published: November 2013

We discuss the spatiotemporal behavior of local density and its relation to dynamical heterogeneity in a highly supercooled liquid by using molecular dynamics simulations of a binary mixture with different particle sizes in two dimensions. To trace voids heterogeneously existing with lower local densities, which move along with the structural relaxation, we employ the minimum local density for each particle in a time window whose width is set along with the structural relaxation time. Particles subject to free volumes correspond well to the configuration rearranging region of dynamical heterogeneity. While the correlation length for dynamical heterogeneity grows with temperature decrease, no growth in the correlation length of heterogeneity in the minimum local density distribution takes place. A comparison of these results with those of normal mode analysis reveals that superpositions of lower-frequency soft modes extending over the free volumes exhibit spatial correlation with the broken bonds. This observation suggests a possibility that long-ranged vibration modes facilitate the interactions between fragile regions represented by free volumes, to induce dynamical correlations at a large scale.
Shortcomings of the standard Lennard–Jones dispersion term in water models, studied with force matching
Authors: Nicolini Paolo , Guàrdia Elvira , Masia Marco
Published: November 2013

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r−6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.
Photon induced tunneling of electron through a graphene electrostatic barrier
Authors: Biswas R. , Sinha C.
Published: November 2013

The influence of an external intense laser field on the tunneling transport (ballistic) of the Dirac fermions through a monolayer graphene electrostatic barrier is studied in the framework of the Floquet approach for a continuous wave, linearly polarized, monochromatic laser. The Klein tunneling is shown to be suppressed by the irradiation of a strong laser field, arising due to breaking of chiral symmetry. The symmetric nature of the field free angular transmission spectrum around the normal to the well-barrier interface is destroyed due to the additional coupling between the pseudo-spin and the time dependent vector potential. The energy distribution of the tunneling spectrum displays Fano resonance which is absent for a laser assisted conventional electrostatic barrier but similar to the case of quantum well structures, providing an optical tool to identify field free quasi bound states inside the graphene nanostructures.
Rayleigh-Bénard convection at high Rayleigh number and infinite Prandtl number: Asymptotics and numerics
Authors: Vynnycky M. , Masuda Y.
Published: November 2013

The problem of fast viscous steady Rayleigh-Bénard convection in a rectangular enclosure is revisited using asymptotic and numerical methods. There are two generic cases: in the first, there is zero shear stress at all boundaries; in the second, there is zero shear stress at the vertical boundaries, but no slip at the horizontal ones. For the first case, we reconcile our new numerical solutions to the full equations with earlier asymptotic results for large Rayleigh number and effectively infinite Prandtl number. For the second case, we first derive the corresponding asymptotic theory and then reconcile it also with the relevant full numerical solutions. However, the latter also indicate behavior which the asymptotic theory does not predict, for Rayleigh numbers in excess of just over 106 and aspect ratios in excess of around 1.1.
Compact ultrahigh vacuum sample environments for x-ray nanobeam diffraction and imaging
Authors: Evans P. G. , Chahine G. , Grifone R. , Jacques V. L. R. , Spalenka J. W. , Schülli T. U.
Published: November 2013

X-ray nanobeams present the opportunity to obtain structural insight in materials with small volumes or nanoscale heterogeneity. The effective spatial resolution of the information derived from nanobeam techniques depends on the stability and precision with which the relative position of the x-ray optics and sample can be controlled. Nanobeam techniques include diffraction, imaging, and coherent scattering, with applications throughout materials science and condensed matter physics. Sample positioning is a significant mechanical challenge for x-ray instrumentation providing vacuum or controlled gas environments at elevated temperatures. Such environments often have masses that are too large for nanopositioners capable of the required positional accuracy of the order of a small fraction of the x-ray spot size. Similarly, the need to place x-ray optics as close as 1 cm to the sample places a constraint on the overall size of the sample environment. We illustrate a solution to the mechanical challenge in which compact ion-pumped ultrahigh vacuum chambers with masses of 1–2 kg are integrated with nanopositioners. The overall size of the environment is sufficiently small to allow their use with zone-plate focusing optics. We describe the design of sample environments for elevated-temperature nanobeam diffraction experiments demonstrate in situ diffraction, reflectivity, and scanning nanobeam imaging of the ripening of Au crystallites on Si substrates.
Shock-induced termination of reentrant cardiac arrhythmias: Comparing monophasic and biphasic shock protocols
Authors: Bragard Jean , Simic Ana , Elorza Jorge , Grigoriev Roman O. , Cherry Elizabeth M. , Gilmour Robert F. , Otani Niels F. , Fenton Flavio H.
Published: November 2013

In this article, we compare quantitatively the efficiency of three different protocols commonly used in commercial defibrillators. These are based on monophasic and both symmetric and asymmetric biphasic shocks. A numerical one–dimensional model of cardiac tissue using the bidomain formulation is used in order to test the different protocols. In particular, we performed a total of 4.8 × 106 simulations by varying shock waveform, shock energy, initial conditions, and heterogeneity in internal electrical conductivity. Whenever the shock successfully removed the reentrant dynamics in the tissue, we classified the mechanism. The analysis of the numerical data shows that biphasic shocks are significantly more efficient (by about 25%) than the corresponding monophasic ones. We determine that the increase in efficiency of the biphasic shocks can be explained by the higher proportion of newly excited tissue through the mechanism of direct activation.
Recording polarization gratings with a standing spiral wave
Authors: Vernon Jonathan P. , Serak Svetlana V. , Hakobyan Rafik S. , Aleksanyan Artur K. , Tondiglia Vincent P. , White Timothy J. , Bunning Timothy J. , Tabiryan Nelson V.
Published: November 2013

A scalable and robust methodology for writing cycloidal modulation patterns of optical axis orientation in photosensitive surface alignment layers is demonstrated. Counterpropagating circularly polarized beams, generated by reflection of the input beam from a cholesteric liquid crystal, direct local surface orientation in a photosensitive surface. Purposely introducing a slight angle between the input beam and the photosensitive surface normal introduces a grating period/orientation that is readily controlled and templated. The resulting cycloidal diffractive waveplates offer utility in technologies requiring diffraction over a broad range of angles/wavelengths. This simple methodology of forming polarization gratings offers advantages over conventional fabrication techniques.
Silicon technology compatible photonic molecules for compact optical signal processing
Authors: Barea Luis A. M. , Vallini Felipe , Jarschel Paulo F. , Frateschi Newton C.
Published: November 2013

Photonic molecules (PMs) based on multiple inner coupled microring resonators allow to surpass the fundamental constraint between the total quality factor (QT), free spectral range (FSR), and resonator size. In this work, we use a PM that presents doublets and triplets resonance splitting, all with high QT. We demonstrate the use of the doublet splitting for 34.2 GHz signal extraction by filtering the sidebands of a modulated optical signal. We also demonstrate that very compact optical modulators operating 2.75 times beyond its resonator linewidth limit may be obtained using the PM triplet splitting, with separation of ∼55 GHz.
Crystal nucleation in undercooled melts of PdZr2
Authors: Klein S. , Herlach D. M.
Published: November 2013

Crystal nucleation in undercooled melts of the stoichiometric PdZr2 compound is studied by measuring the nucleation undercooling of small droplets processed by containerless electrostatic and electromagnetic levitation. Owing to the avoidance of container walls usually acting as heterogeneous nuclei, large undercoolings are achieved. The statistics of crystal nucleation is investigated by measuring the nucleation undercooling of at least 100 melting and solidification cycles for both sets of experiments. The results are analyzed within a statistical approach based on the classical nucleation theory. Out of this two important parameters can be extracted. These are the activation energy, which needs to be overcome to form critical nuclei and, the pre-factor in the nucleation rate equation, which measures the number of potential nucleation sites per unit volume. The results are discussed with respect to the different experimental conditions, short-range order in the undercooled liquid state and its impact to the glass forming ability of this alloy.