bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Assessment of Social Cognition in Individuals with Multiple Sclerosis: A Pilot Study
Authors: Genova Helen M. , Cagna Christopher J. , Chiaravalloti Nancy D. , DeLuca John , Lengenfelder Jean
Published: November 2015

It has recently been reported that individuals with multiple sclerosis (MS) are impaired on tasks requiring emotional processing and social cognition, including tasks of Theory of Mind (ToM) and facial affect recognition. The current pilot study examined the ability of individuals with MS to understand and interpret lies and sarcasm using a dynamic task: The Awareness of Social Inference Test (TASIT). Fifteen individuals with MS and 15 healthy controls (HCs) performed the Social Inference-Enriched subtest of the TASIT, in which they viewed video-taped social interactions in which lies and sarcasm are presented. Additionally, tests of cognition were also administered to better understand the relationship between specific cognitive abilities and the ability to understand lies and sarcasm. The MS group showed impairments in the ability to interpret and understand lies and sarcasm relative to HCs. These impairments were correlated with several cognitive abilities including processing speed, working memory, learning and memory, and premorbid IQ. The results indicate that the TASIT is a sensitive measure of social cognition in individuals with MS. Furthermore, performance on the TASIT was related to cognitive abilities. Results are discussed in terms of social cognition deficits in MS and how they relate to cognitive abilities. (JINS, 2016, 22, 83–88)
Recovering function and surviving treatments are primary motivators for health behavior change in patients with head and neck cancer: Qualitative focus group study
Authors: Henry Melissa , Bdira Ala , Cherba Maria , Lambert Sylvie , Carnevale Franco A. , MacDonald Christina , Hier Michael , Zeitouni Anthony , Kost Karen , Mlynarek Alex , Black Martin , Rosberger Zeev , Frenkiel Saul
Published: November 2015

Objective:

Against medical advice, head and neck cancer (HNC) patients have been shown to continue to smoke and misuse alcohol post-diagnosis and treatment. This study aimed to better understand the barriers to and facilitators of health behavior change (HBC) in HNC patients.

Method:

We conducted nine focus groups following a standard protocol. Eligible patients were diagnosed less than three years previously with a primary HNC and selected using maximum variability sampling (gender, age, cancer stage, smoking, and alcohol misuse). Thematic analysis was conducted using NVivo 10 software.

Results:

Participants were mostly men (79%), 65 years of age (SD = 10.1), and married/common-law (52%, n = 15). Mean time from diagnosis was 19 months (SD = 12.3, range = 5.0–44.5), and most had advanced cancer (65.5%, n = 19). Participants provided a larger than anticipated definition of health behaviors, encompassing both traditional (smoking, drinking, diet, exercise, UV protection) and HNC-related (e.g., dental hygiene, skin care, speech exercises, using a PEG, gaining weight). The main emerging theme was patient engagement, that is, being proactive in rehabilitation, informed by the medical team, optimistic, flexible, and seeking support when needed. Patients were primarily motivated to stay proactive and engage in positive health behaviors in order to return to normal life and reclaim function, rather than to prevent a cancer recurrence. Barriers to patient engagement included emotional aspects (e.g., anxiety, depression, trauma, demoralization), symptoms (e.g., fatigue, pain), lack of information about HBC, and healthcare providers' authoritarian approach in counseling on HBC. We found some commonalities in barriers and facilitators according to behavior type (i.e., smoking/drinking/UV protection vs. diet/exercise).

Significance of Results:

This study underlines the key challenges in addressing health behaviors in head and neck oncology, including treatment-related functional impairments, symptom burden, and the disease's emotional toll. This delicate context requires health promotion strategies involving close rehabilitative support from a multidisciplinary team attentive to the many struggles of patients both during treatments and in the longer-term recovery period. Health promotion in HNC should be integrated into routine clinical care and target both traditional and HNC-related behaviors, emphasizing emotional and functional rehabilitation as key components.
Contribution of urban and periurban agriculture to household food and nutrition security along the urban–rural continuum in Ouagadougou, Burkina Faso
Authors: Chagomoka Takemore , Drescher Axel , Glaser Rüdiger , Marschner Bernd , Schlesinger Johannes , Nyandoro George
Published: November 2015

There is growing evidence of urban poverty in and around cities in sub-Saharan Africa in the form of food and nutrition insecurity. Although many studies have been done across sub-Saharan Africa on urban agriculture, food and nutrition insecurity, little is known about the association of urban agriculture to household food and nutrition insecurity along the urban–rural continuum, especially in West African cities. Therefore, a survey was carried out between August and September 2014 in and around Ouagadougou (Burkina Faso), using a transect approach to guide the data collection. The purpose of this study was to understand the dynamics of urban, periurban and rural agriculture and its association with household food and nutrition insecurity. A total of 240 households participated in the survey. From these households, data were collected on 179 women of reproductive age (15–49 yr) and 133 children under the age of 5 yr to compute Women's Dietary Diversity Scores (WDDS) and other anthropometric indices. The results of this study provide a general picture of crop production which is inclined to subsistence and income generation. Households in rural and periurban areas were more engaged in crop and livestock production compared with their urban area counterparts. Households in periurban areas had the highest relative proportion (54%) of food insecurity (household food insecurity access scale (HFIAS) > 11), compared with urban areas (39%) and rural areas (45%). At the same time the periurban households had the highest relative proportion of stunting and wasting prevalence compared with urban and rural households. Households in the rural areas had the highest dietary diversity (WDDS ≥ 6), compared with periurban and urban households. Households keeping livestock significantly experienced less wasting (weight-for-height index (WHZ)) (coef = −0.15;P= 0.008) by a factor of 0.15, and overweight (body mass index (BMI)-for-age (BAZ)) (coef = −0.12;P= 0.015) by a factor of 0.12 compared with households not doing livestock keeping. Households involved in crop production significantly experienced more food insecurity, HFIAS (coef. = 2.55;P= 0.042) by a factor of 2.55 compared with households without crop production. The complexity of periurban areas coupled with the scourge of food and nutrition insecurity will require more periurban agriculture and food policy consideration.
Novel star-shaped fractal antenna for multiband applications
Authors: Rao Neeraj , Malik Ankit , Kumar Rahul , Goel Shobhit , Kumar V Dinesh
Published: November 2015

Fractals have unique properties such as self-similarity and space-filling. The use of fractal geometry in antenna design provides a good method for achieving the desired miniaturization, multi-band, and wideband properties. In this communication, novel fractal geometry is proposed based on which a multiband antenna is designed. The proposed antenna has fractal patches which are shaped as different iterations of an eight-pointed star. The multiband behavior is in the frequency range from 4.50 to 17.00 GHz. The proposed antenna is designed on a dielectric substrate Roggers RO4003 lossy with a dielectric constant of εr = 3.55. The antenna has applications in commercial and military communication system.
Epigenome-Wide DNA Methylation Analysis of Monozygotic Twins Discordant for Diurnal Preference
Authors: Wong Chloe C. Y. , Parsons Michael J. , Lester Kathryn J. , Burrage Joe , Eley Thalia C. , Mill Jonathan , Dempster Emma L. , Gregory Alice M.
Published: November 2015

Diurnal preference is an individual's preference for daily activities and sleep timing and is strongly correlated with the underlying circadian clock and the sleep-wake cycle validating its use as an indirect circadian measure in humans. Recent research has implicated DNA methylation as a mechanism involved in the regulation of the circadian clock system in humans and other mammals. In order to evaluate the extent of epigenetic differences associated with diurnal preference, we examined genome-wide patterns of DNA methylation in DNA from monozygotic (MZ) twin-pairs discordant for diurnal preference. MZ twins were selected from a longitudinal twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. Fifteen pairs of MZ twins were identified in which one member scored considerably higher on the Horne–Ostberg Morningness–Eveningness Questionnaire (MEQ) than the other. Genome-wide DNA methylation patterns were assessed in twins’ buccal cell DNA using the Illumina Infinium HumanMethylation450 BeadChips. Quality control and data pre-processing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. Our data indicate that DNA methylation differences are detectable in MZ twins discordant for diurnal preference. Moreover, downstream gene ontology (GO) enrichment analysis on the top-ranked diurnal preference associated DMPs revealed significant enrichment of pathways that have been previously associated with circadian rhythm regulation, including cell adhesion processes and calcium ion binding.
Genetic and Environmental Stability of Neuroticism From Adolescence to Adulthood
Authors: Nivard Michel G. , Middeldorp Christel M. , Dolan Conor V. , Boomsma Dorret I.
Published: November 2015

Longitudinal studies of neuroticism have shown that, on average, neuroticism scores decrease from adolescence to adulthood. The heritability of neuroticism is estimated between 0.30 and 0.60 and does not seem to vary greatly as a function of age. Shared environmental effects are rarely reported. Less is known about the role of genetic and environmental influences on the rank order stability of neuroticism in the period from adolescence to adulthood. We studied the stability of neuroticism in a cohort sequential (classical) twin design, from adolescence (age 14 years) to young adulthood (age 32 years). A genetic simplex model that was fitted to the longitudinal neuroticism data showed that the genetic stability of neuroticism was relatively high (genetic correlations between adjacent age bins >0.9), and increased from adolescence to adulthood. Environmental stability was appreciably lower (environmental correlations between adjacent age bins were between 0.3 and 0.6). This low stability was largely due to age-specific environmental variance, which was dominated by measurement error. This attenuated the age-to-age environmental correlations. We constructed an environmental covariance matrix corrected for this error, under the strong assumption that all age-specific environmental variance is error variance. The environmental (co)variance matrix corrected for attenuation revealed highly stable environmental influences on neuroticism (correlations between adjacent age bins were between 0.7 and 0.9). Our results indicate that both genetic and environmental influences have enduring effects on individual differences in neuroticism.
Investigating Flight Crew Recovery Capabilities Regarding System	Failures in Highly Automated Fourth Generation Aircraft
Authors: Mohrmann Frederik , Lemmers Arjan , Stoop John
Published: November 2015

Abstract. This project aimed to understand rapid crew transitions from a monitoring to a decision-making role, when asserting manual control of aircraft subsystems. Ten crews unknowingly flew a semicritical failure scenario in a full flight simulator, forcing several crew decision moments. Observations of automation-related (diagnostic) behavior were correlated with respective flight performance, revealing that specific competencies (related to knowledge, procedures, attitude toward automation, and teamwork) with automated systems led to significant performance gains. More importantly, the absence of these behaviors severely deteriorated performance and should not be underestimated in its potency to affect flight safety. These findings may form a foundation for developing and evaluating near-future innovations in training, operations, and automation design, which could prove critical toward improving future accident rates.
Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation
Authors: Ballut Lionel , Violot Sébastien , Shivakumaraswamy Santosh , Thota Lakshmi Prasoona , Sathya Manu , Kunala Jyothirmai , Dijkstra Bauke W. , Terreux Raphaël , Haser Richard , Balaram Hemalatha , Aghajari Nushin
Published: November 2015

GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the GATase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. We suggest that conformational changes in helix 371–375 holding catalytic residues and in loop 376–401 along the rotation trajectory trigger the different steps of catalysis, and establish the central role of Glu374 in allostery and inter-domain crosstalk. These studies reveal the mechanism of domain rotation and inter-domain communication, providing a molecular framework for the function of all single polypeptide GMPSs and form a solid basis for rational drug design targeting this therapeutically important enzyme.
A bridge for accelerating materials by design
Authors: Sumpter Bobby G , Vasudevan Rama K , Potok Thomas , Kalinin Sergei V
Published: November 2015

Recent technical advances in the area of nanoscale imaging, spectroscopy and scattering/diffraction have led to unprecedented capabilities for investigating materials structural, dynamical and functional characteristics. In addition, recent advances in computational algorithms and computer capacities that are orders of magnitude larger/faster have enabled large-scale simulations of materials properties starting with nothing but the identity of the atomic species and the basic principles of quantum and statistical mechanics and thermodynamics. Along with these advances, an explosion of high-resolution data has emerged. This confluence of capabilities and rise of big data offer grand opportunities for advancing materials sciences but also introduce several challenges. In this perspective, we identify challenges impeding progress towards advancing materials by design (e.g., the design/discovery of materials with improved properties/performance), possible solutions and provide examples of scientific issues that can be addressed using a tightly integrated approach where theory and experiments are linked through big-deep data.
VenomKB, a new knowledge base for facilitating the validation of putative venom therapies
Authors: Romano Joseph D. , Tatonetti Nicholas P.
Published: November 2015

Animal venoms have been used for therapeutic purposes since the dawn of recorded history. Only a small fraction, however, have been tested for pharmaceutical utility. Modern computational methods enable the systematic exploration of novel therapeutic uses for venom compounds. Unfortunately, there is currently no comprehensive resource describing the clinical effects of venoms to support this computational analysis. We present VenomKB, a new publicly accessible knowledge base and website that aims to act as a repository for emerging and putative venom therapies. Presently, it consists of three database tables: (1) Manually curated records of putative venom therapies supported by scientific literature, (2) automatically parsed MEDLINE articles describing compounds that may be venom derived, and their effects on the human body, and (3) automatically retrieved records from the new Semantic Medline resource that describe the effects of venom compounds on mammalian anatomy. Data from VenomKB may be selectively retrieved in a variety of popular data formats, are open-source, and will be continually updated as venom therapies become better understood.
Self-assembled amyloid fibrils with controllable conformational heterogeneity
Authors: Lee Gyudo , Lee Wonseok , Lee Hyungbeen , Lee Chang Young , Eom Kilho , Kwon Taeyun
Published: November 2015

Amyloid fibrils are a hallmark of neurodegenerative diseases and exhibit a conformational diversity that governs their pathological functions. Despite recent findings concerning the pathological role of their conformational diversity, the way in which the heterogeneous conformations of amyloid fibrils can be formed has remained elusive. Here, we show that microwave-assisted chemistry affects the self-assembly process of amyloid fibril formation, which results in their conformational heterogeneity. In particular, microwave-assisted chemistry allows for delicate control of the thermodynamics of the self-assembly process, which enabled us to tune the molecular structure of β-lactoglobulin amyloid fibrils. The heterogeneous conformations of amyloid fibrils, which can be tuned with microwave-assisted chemistry, are attributed to the microwave-driven thermal energy affecting the electrostatic interaction during the self-assembly process. Our study demonstrates how microwave-assisted chemistry can be used to gain insight into the origin of conformational heterogeneity of amyloid fibrils as well as the design principles showing how the molecular structures of amyloid fibrils can be controlled.
Room temperature large-scale synthesis of layered frameworks as low-cost 4 V cathode materials for lithium ion batteries
Authors: Hameed A. Shahul , Reddy M. V. , Nagarathinam M. , Runčevski Tomče , Dinnebier Robert E , Adams Stefan , Chowdari B. V. R. , Vittal Jagadese J.
Published: November 2015

Li-ion batteries (LIBs) are considered as the best available technology to push forward the production of eco-friendly electric vehicles (EVs) and for the efficient utilization of renewable energy sources. Transformation from conventional vehicles to EVs are hindered by the high upfront price of the EVs and are mainly due to the high cost of LIBs. Hence, cost reduction of LIBs is one of the major strategies to bring forth the EVs to compete in the market with their gasoline counterparts. In our attempt to produce cheaper high-performance cathode materials for LIBs, an rGO/MOPOF (reduced graphene oxide/Metal-Organic Phosphate Open Framework) nanocomposite with ~4 V of operation has been developed by a cost effective room temperature synthesis that eliminates any expensive post-synthetic treatments at high temperature under Ar/Ar-H2. Firstly, an hydrated nanocomposite, rGO/K2[(VO)2(HPO4)2(C2O4)]·4.5H2O has been prepared by simple magnetic stirring at room temperature which releases water to form the anhydrous cathode material while drying at 90 °C during routine electrode fabrication procedure. The pristine MOPOF material undergoes highly reversible lithium storage, however with capacity fading. Enhanced lithium cycling has been witnessed with rGO/MOPOF nanocomposite which exhibits minimal capacity fading thanks to increased electronic conductivity and enhanced Li diffusivity.
A highly durable fuel cell electrocatalyst based on double-polymer-coated carbon nanotubes
Authors: Berber Mohamed R. , Hafez Inas H. , Fujigaya Tsuyohiko , Nakashima Naotoshi
Published: November 2015

Driven by the demand for the commercialization of fuel cell (FC) technology, we describe the design and fabrication of a highly durable FC electrocatalyst based on double-polymer-coated carbon nanotubes for use in polymer electrolyte membrane fuel cells. The fabricated electrocatalyst is composed of Pt-deposited polybenzimidazole-coated carbon nanotubes, which are further coated with Nafion. By using this electrocatalyst, a high FC performance with a power density of 375 mW/cm2 (at 70 ˚C, 50% relative humidity using air (cathode)/H2(anode)) was obtained and a remarkable durability of 500,000 accelerated potential cycles was recorded with only a 5% loss of the initial FC potential and 20% loss of the maximum power density, which were far superior properties compared to those of the membrane electrode assembly prepared using carbon black in place of the carbon nanotubes. The present study indicates that the prepared highly durable fuel cell electrocatalyst is a promising material for the next generation of PEMFCs.
The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K
Authors: Middleton Adam J. , Day Catherine L.
Published: November 2015

The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.
HdeB chaperone activity is coupled to its intrinsic dynamic properties
Authors: Ding Jienv , Yang Chengfeng , Niu Xiaogang , Hu Yunfei , Jin Changwen
Published: November 2015

Enteric bacteria encounter extreme acidity when passing through hosts’ stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2–3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4–5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes and therefore its functional mechanism is apparently different from HdeA.
Flicker-assisted localization microscopy reveals altered mitochondrial architecture in hypertension
Authors: Chalmers Susan , Saunter Christopher D. , Girkin John M. , McCarron John G.
Published: November 2015

Mitochondrial morphology is central to normal physiology and disease development. However, in many live cells and tissues, complex mitochondrial structures exist and morphology has been difficult to quantify. We have measured the shape of electrically-discrete mitochondria, imaging them individually to restore detail hidden in clusters and demarcate functional boundaries. Stochastic “flickers” of mitochondrial membrane potential were visualized with a rapidly-partitioning fluorophore and the pixel-by-pixel covariance of spatio-temporal fluorescence changes analyzed. This Flicker-assisted Localization Microscopy (FaLM) requires only an epifluorescence microscope and sensitive camera. In vascular myocytes, the apparent variation in mitochondrial size was partly explained by densely-packed small mitochondria. In normotensive animals, mitochondria were small spheres or rods. In hypertension, mitochondria were larger, occupied more of the cell volume and were more densely clustered. FaLM provides a convenient tool for increased discrimination of mitochondrial architecture and has revealed mitochondrial alterations that may contribute to hypertension.
Probing the character of ultra-fast dislocations
Authors: Ruestes C. J. , Bringa E. M. , Rudd R. E. , Remington B. A. , Remington T. P. , Meyers M. A.
Published: November 2015

Plasticity is often controlled by dislocation motion, which was first measured for low pressure, low strain rate conditions decades ago. However, many applications require knowledge of dislocation motion at high stress conditions where the data are sparse and come from indirect measurements dominated by the effect of dislocation density rather than velocity. Here we make predictions based on atomistic simulations that form the basis for a new approach to measure dislocation velocities directly at extreme conditions using three steps: create prismatic dislocation loops in a near-surface region using nanoindentation, drive the dislocations with a shockwave and use electron microscopy to determine how far the dislocations moved and thus their velocity at extreme stress and strain rate conditions. We report on atomistic simulations of tantalum that make detailed predictions of dislocation flow and find that the approach is feasible and can uncover an exciting range of phenomena, such as transonic dislocations and a novel form of loop stretching. The simulated configuration enables a new class of experiments to probe average dislocation velocity at very high applied shear stress.
Multiple Sources of Infection and Potential Endemic Characteristics of the Large Outbreak of Dengue in Guangdong in 2014
Authors: Shen Shu-Qun , Wei Hai-Xia , Fu Yong-Hang , Zhang Hao , Mo Qing-Yi , Wang Xiao-Jun , Deng Sheng-Qun , Zhao Wei , Liu Yu , Feng Xiao-Shuang , Chen Wei , Peng Hong-Juan
Published: November 2015

A large outbreak of dengue, with the most documented cases, occurred in Guangdong China in 2014. Epidemiological studies and phylogenetic analysis of the isolated dengue virus (DENV) showed this outbreak was attributed to multiple sources and caused by at least two genotypes of DENV-1 (Genotypes I and III) and two genotypes of DENV-2 (Cosmopolitan and Asian I Genotypes). A retrospective review and phylogenetic analysis of DENV isolated in Guangdong showed that DENV-1 Genotype I strains were reported continuously during 2004–2014, Genotype III strains were reported during 2009–2014 ; DENV-2 Cosmopolitan and Asian I Genotype strains were reported continuously during 2012–2014. At least 45,171 cases were reported in this outbreak, with 65.9% of the patients in the 21–55-year-old group. A trend toward a decrease in the daily newly emerged cases lagged by approximately 20 days compared with the mosquito density curve. Several epidemiological characteristics of this outbreak and the stably sustained serotypes and genotypes of DENV isolated in Guangdong suggest that Guangdong has been facing a threat of transforming from a dengue epidemic area to an endemic area. The high temperature, drenching rain, rapid urbanization and pandemic of dengue in Southeast Asia may have contributed to this large outbreak of dengue.
Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis
Authors: de Cima Sergio , Polo Luis M. , Díez-Fernández Carmen , Martínez Ana I. , Cervera Javier , Fita Ignacio , Rubio Vicente
Published: November 2015

Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain enzyme, catalyzes the first step of ammonia detoxification to urea requiring N-acetyl-L-glutamate (NAG) as essential activator to prevent ammonia/amino acids depletion. Here we present the crystal structures of CPS1 in the absence and in the presence of NAG, clarifying the on/off-switching of the urea cycle by NAG. By binding at the C-terminal domain of CPS1, NAG triggers long-range conformational changes affecting the two distant phosphorylation domains. These changes, concerted with the binding of nucleotides, result in a dramatic remodeling that stabilizes the catalytically competent conformation and the building of the ~35 Å-long tunnel that allows migration of the carbamate intermediate from its site of formation to the second phosphorylation site, where carbamoyl phosphate is produced. These structures allow rationalizing the effects of mutations found in patients with CPS1 deficiency (presenting hyperammonemia, mental retardation and even death), as exemplified here for some mutations.
Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes
Authors: Lam Tze Hau , Tay Matthew Zirui , Wang Bei , Xiao Ziwei , Ren Ee Chee
Published: November 2015

Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases.
Lipidomic Profiling of Liver Tissue from Obesity-Prone and Obesity-Resistant Mice Fed a High Fat Diet
Authors: Nam Miso , Choi Myung-Sook , Jung Sunhee , Jung Youngae , Choi Ji-Young , Ryu Do Hyun , Hwang Geum-Sook
Published: November 2015

Obesity is a multifactorial health problem resulting from genetic, environmental and behavioral factors. A particularly interesting aspect of obesity is the differences observed in response to the same high-fat diet (HFD). In this study, we performed lipidomic profiling on livers from HFD-fed C57BL/6J mice using ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry. Mice were divided into three groups: normal diet (ND), HFD-obesity prone (HFD-OP) and HFD-obesity resistant (HFD-OR). Principal components analyses showed a difference between the HFD-OP and HFD-OR groups. Individuals in the HFD-OR group were closer to those in the ND group compared with those in the HFD-OP group. In particular, phosphocholine (PC) and triglyceride (TG) levels differed significantly depending on the length of the acyl chain and degree of unsaturation, respectively. PC species were either positively or negatively correlated with concentrations of glucose, insulin, leptin and hepatic cholesterol according to the length of the acyl chain. Decreased expression of the scavenger receptor B1 and ATP-binding cassette A1 in HFD-OP mice indicated that the acyl chain length of PC species may be related to high-density lipoprotein cholesterol metabolism. This study demonstrates that lipidomic profiling is an effective approach to analyzing global lipid alterations as they pertain to obesity.
Identification of Bacillus strains by MALDI TOF MS using geometric approach
Authors: Starostin Konstantin V. , Demidov Evgeny A. , Bryanskaya Alla V. , Efimov Vadim M. , Rozanov Alexey S. , Peltek Sergey E.
Published: November 2015

Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to theBacillus pumilusgroup. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species,Bacillus pumilusandBacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available athttp://www.bionet.nsc.ru/mbl/database/database.html.
A high-density immunoblotting methodology for quantification of total protein levels and phosphorylation modifications
Authors: Mazet F. , Dunster J. L. , Jones C. I. , Vaiyapuri S. , Tindall M. J. , Fry M. J. , Gibbins J. M.
Published: November 2015

The components of many signaling pathways have been identified and there is now a need to conduct quantitative data-rich temporal experiments for systems biology and modeling approaches to better understand pathway dynamics and regulation. Here we present a modified Western blotting method that allows the rapid and reproducible quantification and analysis of hundreds of data points per day on proteins and their phosphorylation state at individual sites. The approach is of particular use where samples show a high degree of sample-to-sample variability such as primary cells from multiple donors. We present a case study on the analysis of >800 phosphorylation data points from three phosphorylation sites in three signaling proteins over multiple time points from platelets isolated from ten donors, demonstrating the technique’s potential to determine kinetic and regulatory information from limited cell numbers and to investigate signaling variation within a population. We envisage the approach being of use in the analysis of many cellular processes such as signaling pathway dynamics to identify regulatory feedback loops and the investigation of potential drug/inhibitor responses, using primary cells and tissues, to generate information about how a cell’s physiological state changes over time.
Scaling of decoherence for a system of uncoupled spin qubits
Authors: Jing Jun , Hu Xuedong
Published: November 2015

Significant experimental progresses in recent years have generated continued interest in quantum computation. A practical quantum computer would employ thousands if not millions of coherent qubits and maintaining coherence in such a large system would be imperative for its utility. As an attempt at understanding the quantum coherence of multiple qubits, here we study decoherence of a multi-spin-qubit state under the influence of hyperfine interaction and clearly demonstrate that the state structure is crucial to the scaling behavior of n-spin decoherence. Specifically, we find that coherence times of a multi-spin state at most scale with the number of qubits n as "Equation missing", while some states with higher symmetries have scale-free coherence with respect to n. Statistically, convergence to these scaling behavior is generally determined by the size of the Hilbert space m, which is usually much larger than n (up to an exponential function of n), so that convergence rate is very fast as we increase the number of qubits. Our results can be extended to other decoherence mechanisms, including in the presence of dynamical decoupling, which allow meaningful discussions on the scalability of spin-based quantum coherent technology.
Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli
Authors: Yang Chi , Chang Chuan-Hsiung
Published: November 2015

Modeling the binding of transcription factors helps to decipher the control logic behind transcriptional regulatory networks. Position weight matrix is commonly used to describe a binding motif but assumes statistical independence between positions. Although current approaches take within-motif dependence into account for better predictive performance, these models usually rely on prior knowledge and incorporate simple positional dependence to describe binding motifs. The inability to take complex within-motif dependence into account may result in an incomplete representation of binding motifs. In this work, we applied association rule mining techniques and constructed models to explore within-motif dependence for transcription factors in Escherichia coli. Our models can reflect transcription factor-DNA recognition where the explored dependence correlates with the binding specificity. We also propose a graphical representation of the explored within-motif dependence to illustrate the final binding configurations. Understanding the binding configurations also enables us to fine-tune or design transcription factor binding sites and we attempt to present the configurations through exploring within-motif dependence.
Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation
Authors: Schliep M. , Pernice M. , Sinutok S. , Bryant C. V. , York P. H. , Rasheed M. A. , Ralph P. J.
Published: November 2015

Seagrass meadows are threatened by coastal development and global change. In the face of these pressures, molecular techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) have great potential to improve management of these ecosystems by allowing early detection of chronic stress. In RT-qPCR, the expression levels of target genes are estimated on the basis of reference genes, in order to control for RNA variations. Although determination of suitable reference genes is critical for RT-qPCR studies, reports on the evaluation of reference genes are still absent for the major Australian speciesZostera muellerisubsp.capricorni(Z. muelleri). Here, we used three different software (geNorm, NormFinder and Bestkeeper) to evaluate ten widely used reference genes according to their expression stability inZ. muelleriexposed to light limitation. We then combined results from different software and used a consensus rank of four best reference genes to validate regulation in Photosystem I reaction center subunit IV B and Heat Stress Transcription factor A- gene expression inZ. muelleriunder light limitation. This study provides the first comprehensive list of reference genes inZ. muelleriand demonstrates RT-qPCR as an effective tool to identify early responses to light limitation in seagrass.
Towards a new class of heavy ion doped magnetic semiconductors for room temperature applications
Authors: Lee Juwon , Subramaniam Nagarajan Ganapathi , Agnieszka Kowalik Iwona , Nisar Jawad , Lee Jaechul , Kwon Younghae , Lee Jaechoon , Kang Taewon , Peng Xiangyang , Arvanitis Dimitri , Ahuja Rajeev
Published: November 2015

The article presents, using Bi doped ZnO, an example of a heavy ion doped oxide semiconductor, highlighting a novel p-symmetry interaction of the electronic states to stabilize ferromagnetism. The study includes both ab initio theory and experiments, which yield clear evidence for above room temperature ferromagnetism. ZnBixO1−x thin films are grown using the pulsed laser deposition technique. The room temperature ferromagnetism finds its origin in the holes introduced by the Bi doping and the p-p coupling between Bi and the host atoms. A sizeable magnetic moment is measured by means of x-ray magnetic circular dichroism at the O K-edge, probing directly the spin polarization of the O(2p) states. This result is in agreement with the theoretical predictions and inductive magnetometry measurements. Ab initio calculations of the electronic and magnetic structure of ZnBixO1−x at various doping levels allow to trace the origin of the ferromagnetic character of this material. It appears, that the spin-orbit energy of the heavy ion Bi stabilizes the ferromagnetic phase. Thus, ZnBixO1−x doped with a heavy non-ferromagnetic element, such as Bi, is a credible example of a candidate material for a new class of compounds for spintronics applications, based on the spin polarization of the p states.
Ultrathin niobium nanofilms on fiber optical tapers – a new route towards low-loss hybrid plasmonic modes
Authors: Wieduwilt Torsten , Tuniz Alessandro , Linzen Sven , Goerke Sebastian , Dellith Jan , Hübner Uwe , Schmidt Markus A.
Published: November 2015

Due to the ongoing improvement in nanostructuring technology, ultrathin metallic nanofilms have recently gained substantial attention in plasmonics, e.g. as building blocks of metasurfaces. Typically, noble metals such as silver or gold are the materials of choice, due to their excellent optical properties, however they also possess some intrinsic disadvantages. Here, we introduce niobium nanofilms (~10 nm thickness) as an alternate plasmonic platform. We demonstrate functionality by depositing a niobium nanofilm on a plasmonic fiber taper and observe a dielectric-loaded niobium surface-plasmon excitation for the first time, with a modal attenuation of only 3–4 dB/mm in aqueous environment and a refractive index sensitivity up to 15 μm/RIU if the analyte index exceeds 1.42. We show that the niobium nanofilm possesses bulk optical properties, is continuous, homogenous and inert against any environmental influence, thus possessing several superior properties compared to noble metal nanofilms. These results demonstrate that ultrathin niobium nanofilms can serve as a new platform for biomedical diagnostics, superconducting photonics, ultrathin metasurfaces or new types of optoelectronic devices.
Hydrophilic Magnetochromatic Nanoparticles with Controllable Sizes and Super-high Magnetization for Visualization of Magnetic Field Intensity
Authors: Zhuang Lin , Zhao Yongxin , Zhong Huixiang , Liang Jinhua , Zhou Jianhua , Shen Hui
Published: November 2015

Hydrophilic Fe3O4 nanoparticles with controllable size and shape have been fabricated using a facile solvothermal approach followed by surface modification with polyacrylic acid (PAA). The nanoparticles form one-dimension photonic crystal structure under external magnetic field ranging from 29.6 to 459 G. The reflection peaks of formed photonic crystals cover the entire visible spectrum, which indicates a good magnetochromatic property and prospect of wide applications. The size and shape of Fe3O4 nanoparticles are controlled by changing the ratio between ethylene glycol and diethylene glycol. In the process of surface modification, PAA synthesized by free radical polymerization was chemisorbed onto the surface of Fe3O4 particles with the aid of Fe3+ cations, which renders the particles well dispersed in aqueous solution with high thermo-stability. The Fe3O4 particles exhibit ferrimagnetism with a high saturation magnetization value of 88.0 emu/g. Both the high magnetization and the wide reflection spectrum under magnetic field make the magnetochromatic nanoparticles a promising material for visualization of the distribution of magnetic field intensity on microfluidic chips.
Influence of Humic Acid Complexation with Metal Ions on Extracellular Electron Transfer Activity
Authors: Zhou Shungui , Chen Shanshan , Yuan Yong , Lu Qin
Published: November 2015

Humic acids (HAs) can act as electron shuttles and mediate biogeochemical cycles, thereby influencing the transformation of nutrients and environmental pollutants. HAs commonly complex with metals in the environment, but few studies have focused on how these metals affect the roles of HAs in extracellular electron transfer (EET). In this study, HA-metal (HA-M) complexes (HA-Fe, HA-Cu and HA-Al) were prepared and characterized. The electron shuttle capacities of HA-M complexes were experimentally evaluated through microbial Fe(III) reduction, biocurrent generation and microbial azoreduction. The results show that the electron shuttle capacities of HAs were enhanced after complexation with Fe but were weakened when using Cu or Al. Density functional theory calculations were performed to explore the structural geometry of the HA-M complexes and revealed the best binding sites of the HAs to metals and the varied charge transfer rate constants (k). The EET activity of the HA-M complexes were in the order HA-Fe > HA-Cu > HA-Al. These findings have important implications for biogeochemical redox processes given the ubiquitous nature of both HAs and various metals in the environment.
A facile method for determining the Fe(0) content and reactivity of zero valent iron
Authors: Li Shaolin , Ding Yangyang , Wang Wei , Lei Hong
Published: November 2015

This work provides a facile and reliable way to assess the quality of metallic iron used for environmental clean-up.
A general approach to fabricate free-standing metal sulfide@carbon nanofiber networks as lithium ion battery anodes
Authors: Fei Ling , Williams Brian Patrick , Yoo Sang Ha , Carlin Joseph Michael , Joo Yong Lak
Published: November 2015

Fabrication of free-standing metal sulfide@CNF electrodes for lithium ion batteries.
High-affinity sequence-selective DNA binding by iridium(iii) polypyridyl organometallopeptides
Authors: Gamba Ilaria , Salvadó Iria , Brissos Rosa F. , Gamez Patrick , Brea José , Loza María Isabel , Vázquez M. Eugenio , López Miguel Vázquez
Published: November 2015

We demonstrate the application of solid-phase peptide synthesis methods for assembling polynuclear Ir(iii) organometallopeptides that exhibit high DNA-binding affinity, sequence selectivity, and high cytotoxic effect towards a set of cancer cell lines.
Spontaneous self-assembly and disassembly of colloidal gold nanoparticles induced by tetrakis(hydroxymethyl) phosphonium chloride
Authors: Gulka Christopher P. , Wong Alexis C. , Wright David W.
Published: November 2015

The mechanism behind self-assembly and disassembly of gold colloids driven by addition of a phosphonium was characterized using31P NMR.
Boronic acids for fluorescence imaging of carbohydrates
Authors: Sun Xiaolong , Zhai Wenlei , Fossey John S. , James Tony D.
Published: November 2015

Carbohydrate biomarkers are particularly important targets for fluorescence imaging given their pivotal role in numerous important biological events. This review highlights the development of fluorescence imaging agents based on boronic acids.
Gas-phase structure of 2,2,2-trichloroethyl chloroformate studied by electron diffraction and quantum-chemical calculations
Authors: Gil Diego M. , Tuttolomondo María E. , Blomeyer Sebastian , Reuter Christian G. , Mitzel Norbert W. , Altabef Aída Ben
Published: November 2015

The molecular structure and conformational properties of 2,2,2-trichloroethyl chloroformate, ClC(O)OCH2CCl3 were determined experimentally using gas-phase electron diffraction (GED) and theoretically based on quantum-chemical calculations at the MP2 and DFT levels of theory.