bluuebunny/crossref_metadata_2025 huggingface dataset:
CoSMoMVPA: multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave
Authors: Oosterhof Nikolaas N. , Connolly Andrew C. , Haxby James V.
Published: April 2016

Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto-and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens.

CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species.

It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets.

CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques.

CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality.

CoSMoMVPA comes with extensive documentation, including a variety of runnable demonstration scripts and analysis exercises (with example data and solutions). It uses best software engineering practices including version control, distributed development, an automated test suite, and continuous integration testing. It can be used with the proprietary Matlab and the free GNU Octave software, and it complies with open source distribution platforms such as NeuroDebian.

CoSMoMVPA is Free/Open Source Software under the permissive MIT license.

Website:https://cosmomvpa.org

Source code:https://github.com/CoSMoMVPA/CoSMoMVPA
Predictions shape confidence in right inferior frontal gyrus
Authors: Sherman Maxine T. , Seth Anil K. , Kanai Ryota
Published: April 2016

It is clear that prior expectations shape perceptual decision-making, yet their contribution to the construction of subjective decision confidence remains largely unexplored. We recorded fMRI data while participants made perceptual decisions and confidence judgements, controlling for potential confounds of attention. Results show that subjective confidence increases as perceptual prior expectations increasingly support the decision, and that this relationship is associated with BOLD activity in right inferior frontal gyrus (rIFG). Specifically, rIFG is sensitive to the discrepancy between expectation and decision (mismatch), and, crucially, higher mismatch responses are associated with lower decision confidence. Connectivity analyses revealed the source of the expectancy information to be bilateral orbitofrontal cortex (OFC) and the source of sensory signals to be intracalcarine sulcus. Altogether, our results indicate that predictive information is integrated into subjective confidence in rIFG, and reveal an occipital-frontal network that constructs confidence from top-down and bottom-up signals. This interpretation was further supported by exploratory findings that the white matter density of intracalcarine sulcus and OFC negatively predicted their respective contributions to the construction of confidence. Our findings advance our understanding of the neural basis of subjective perceptual processes by revealing an occipito-frontal functional network that integrates prior beliefs into the construction of confidence.
Potential for Zika virus to establish a sylvatic transmission cycle in the Americas
Authors: Althouse Benjamin M. , Vasilakis Nikos , Sall Amadou A. , Diallo Mawlouth , Weaver Scott C. , Hanley Kathryn A.
Published: April 2016

Zika virus (ZIKV) originated and continues to circulate in a sylvatic transmission cycle between non-human primate hosts and arboreal mosquitoes in tropical Africa. Recently ZIKV invaded the Americas, where it poses a threat to human health, especially to pregnant women and their infants. Here we examine the risk that ZIKV will establish a sylvatic cycle in the Americas, focusing on Brazil. We review the natural history of sylvatic ZIKV and present a mathematical dynamic transmission model to assess the probability of establishment of a sylvatic ZIKV transmission cycle in non-human primates and/or other mammals and arboreal mosquito vectors in Brazil. Brazil is home to multiple species of primates and mosquitoes potentially capable of ZIKV transmission, though direct assessment of host competence (ability to mount viremia sufficient to infect a feeding mosquito) and vector competence (ability to become infected with ZIKV and disseminate and transmit upon subsequent feedings) of New World species is lacking. Modeling reveals a high probability of establishment of sylvatic ZIKV across a large range of biologically plausible parameters. Probability of establishment is dependent on host population sizes and birthrates and ZIKV force of infection, but a network of as few as 6,000 primates with 10,000 mosquitoes is capable of supporting establishment of a ZIKV sylvatic cycle. Research on the susceptibility of New World monkeys or other small mammals to ZIKV, on the vector competence of New WorldAedes, Sabethes, andHaemagogusmosquitoes for ZIKV, and on the geographic range of these species is urgently needed. A sylvatic cycle of ZIKV would make future elimination efforts in the Americas practically impossible, and paints a dire situation for the epidemiology of ZIKV and ending the ongoing outbreak of congenital Zika syndrome.
Characterization of sterol synthesis in bacteria
Authors: Wei Jeremy H. , Yin Xinchi , Welander Paula V.
Published: April 2016

Sterols are essential components of eukaryotic cells whose biosynthesis and function in eukaryotes has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from 5 phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences revealed two potential lineages of the sterol pathway in bacteria indicating a complex evolutionary history of sterol synthesis in this domain. We characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of bacterial sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown. It is possible that bacteria have evolved distinct proteins for catalyzing sterol modifications and this could have significant implications for our understanding of the evolutionary history of this ancient biosynthetic pathway.
Genetic contributions to self-reported tiredness
Authors: Deary Vincent , Hagenaars Saskia P , Harris Sarah E , Hill W David , Davies Gail , Liewald David CM ,   International Consortium for Blood Pressure GWAS,   CHARGE consortium Aging and Longevity Group, McIntosh Andrew M , Gale Catharine R , Deary Ian J
Published: April 2016

Self-reported tiredness and low energy, often called fatigue, is associated with poorer physical and mental health. Twin studies have indicated that this has a heritability between 6% and 50%. In the UK Biobank sample (N = 108 976) we carried out a genome-wide association study of responses to the question, ″Over the last two weeks, how often have you felt tired or had little energy?″ Univariate GCTA-GREML found that the proportion of variance explained by all common SNPs for this tiredness question was 8.4% (SE = 0.6%). GWAS identified one genome-wide significant hit (Affymetrix id 1:64178756_C_T; p = 1.36 x 10-11). LD score regression and polygenic profile analysis were used to test for pleiotropy between tiredness and up to 28 physical and mental health traits from GWAS consortia. Significant genetic correlations were identified between tiredness and BMI, HDL cholesterol, forced expiratory volume, grip strength, HbA1c, longevity, obesity, self-rated health, smoking status, triglycerides, type 2 diabetes, waist-hip ratio, ADHD, bipolar disorder, major depressive disorder, neuroticism, schizophrenia, and verbal-numerical reasoning (absolute rg effect sizes between 0.11 and 0.78). Significant associations were identified between tiredness phenotypic scores and polygenic profile scores for BMI, HDL cholesterol, LDL cholesterol, coronary artery disease, HbA1c, height, obesity, smoking status, triglycerides, type 2 diabetes, and waist-hip ratio, childhood cognitive ability, neuroticism, bipolar disorder, major depressive disorder, and schizophrenia (standardised β′s between -0.016 and 0.03). These results suggest that tiredness is a partly-heritable, heterogeneous and complex phenomenon that is phenotypically and genetically associated with affective, cognitive, personality, and physiological processes.
Araport11: a complete reannotation of theArabidopsis thalianareference genome
Authors: Cheng Chia-Yi , Krishnakumar Vivek , Chan Agnes , Schobel Seth , Town Christopher D.
Published: April 2016

The flowering plantArabidopsis thalianais a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, noncoding RNA, and small RNA. The most recent annotation update (TAIR10) released more than five years ago had a profound impact onArabidopsisresearch. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-seq libraries from 113 datasets and constructed 48,359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of noncoding RNA including small RNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and microRNA using published datasets and in-house analytic results. Altogether, we identified 738 novel protein-coding genes, 508 novel transcribed regions, 5051 non-coding genes, and 35846 small-RNA loci that formerly eluded annotation. Analysis on the splicing events and RNA-seq based expression profile revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.
Effective Dynamic Models of Metabolic Networks
Authors: Vilkhovoy Michael , Minot Mason , Varner Jeffrey D.
Published: April 2016

Mathematical models of biochemical networks are useful tools to understand and ultimately predict how cells utilize nutrients to produce valuable products. Hybrid cybernetic models in combination with elementary modes (HCM) is a tool to model cellular metabolism. However, HCM is limited to reduced metabolic networks because of the computational burden of calculating elementary modes. In this study, we developed the hybrid cybernetic modeling with flux balance analysis or HCM-FBA technique which uses flux balance solutions instead of elementary modes to dynamically model metabolism. We show HCM-FBA has comparable performance to HCM for a proof of concept metabolic network and for a reduced anaerobicE. colinetwork. Next, HCM-FBA was applied to a larger metabolic network of aerobicE. colimetabolism which was infeasible for HCM (29 FBA modes versus more than 153,000 elementary modes). Global sensitivity analysis further reduced the number of FBA modes required to describe the aerobicE. colidata, while maintaining model fit. Thus, HCM-FBA is a promising alternative to HCM for large networks where the generation of elementary modes is infeasible.
Growth-Environment Dependent Modulation ofStaphylococcus aureusBranched-Chain to Straight-Chain Fatty Acid Ratio and Incorporation of Unsaturated Fatty Acids
Authors: Sen Suranjana , Johnson Seth R. , Song Yang , Sirobhushanam Sirisha , Tefft Ryan , Gatto Craig , Wilkinson Brian J.
Published: April 2016

The fatty acid composition of membrane glycerolipids is a major determinant ofStaphylococcus aureusmembrane biophysical properties that impacts key factors in cell physiology including susceptibility to membrane active antimicrobials, pathogenesis, and response to environmental stress. The fatty acids ofS. aureusare considered to be a mixture of branched-chain fatty acids (BCFAs), which increase membrane fluidity, and straight-chain fatty acids (SCFAs) that decrease it. The balance of BCFAs and SCFAs in strains USA300 and SH1000 was affected considerably by differences in the conventional laboratory medium in which the strains were grown with media such as Mueller-Hinton broth and Luria broth resulting in high BCFAs and low SCFAs, whereas growth in Tryptic Soy Broth and Brain-Heart Infusion broth led to reduction in BCFAs and an increase in SCFAs. Straight-chain unsaturated fatty acids (SCUFAs) were not detected. However, when the organism was grownex vivoin serum, the fatty acid composition was radically different with SCUFAs, which increase membrane fluidity, making up a substantial proportion of the total (<25%) with SCFAs (>37%) and BCFAs (>36%) making up the rest. Staphyloxanthin, an additional major membrane lipid component unique toS. aureus, tended to be greater in content in cells with high BCFAs or SCUFAs. Cells with high staphyloxanthin content had a lower membrane fluidity that was attributed to increased production of staphyloxanthin.S. aureussaves energy and carbon by utilizing host fatty acids for part of its total fatty acids when growing in serum. The fatty acid composition ofin vitrogrownS. aureusis likely to be a poor reflection of the fatty acid composition and biophysical properties of the membrane when the organism is growing in an infection in view of the role of SCUFAs in staphylococcal membrane composition and virulence.

Funding:

This work was funded in part by grant 1R15AI099977 to Brian Wilkinson and Craig Gatto and grant 1R15GM61583 to Craig Gatto from the National Institutes of Health
Pattern alteration of women’s suits based on ease distribution
Authors: Gu Bingfei , Su Junqiang , Liu Guolian , Xu Bugao
Published: April 2016

Purpose

The goal of this study was to realize pattern alterations for women’s suits by using the spatial distribution of distance ease in the body-garment interface.

Design/methodology/approach

An unclothed mannequin and the mannequin clothed with seven suits having different ease allowances were scanned by a 3D body scanner respectively. The image of the unclothed mannequin was then superimposed on that of each clothed mannequin (suit) to exhibit the differences in ease distribution among these suits. The distance eases at ten selected body landmarks were determined by measuring the gaps between the body and suit surfaces.

Findings

The mathematical models of ease distributions were built through the regression analysis to predict the distance ease with a given ease allowance. After the verification with the actual measurements, these ease distribution models could provide localized distance eases for alternating pattern pieces to ensure a specified ease allowance.

Originality/value

In order to realize the automatic generation of garment patterns, the ease distribution between a human body and a garment is crucial because ease is one of the determinants for garment fit. This study demonstrated a new approach of automatic pattern alteration based on 3D scanned data to accelerate the pattern making process for women’s suits with customized ease allowance.
Modification of Hogarth models on the stripe costume
Authors: Zhu Xuyun , Wen Xuming , Wang Jianping , Zhang Hang
Published: April 2016

Purpose

Beautiful and simple curves are most commonly employed in apparel design since they can not only simplify the manufacture process, but also significantly beautify the breast profile of customers. However, it is regularly difficult to choose the most suitable curve when producing the strip costume; this is due to the fact that the curve is a kind of aesthetics without any laws. The quantification and standardization to curves are necessary for fashion design. The purpose of this paper is to investigate the relationship between the stripe of costumes and the breast profiles of wearers.

Design/methodology/approach

Seven curves drawn derived from the Hogarth theory (Hogarth curves) were firstly diagrammatized by the central line technology using CorelDraw, and the format of bitmaps and quadratic functions of these selected curves were obtained respectively. Simulating formulas were subsequently used to interpret these curves. The standard of curves for apparel design was finally established after being evaluated by comparison between the different types of female breasts and the curves on the costumes.

Findings

The established models indicated that the fourth Hogarth curves was the most attractive one that combining the static state and the dynamic beauty, which could also help females to highlight the beautiful breast shapes.

Originality/value

This work provided the fundamentally understanding of the application of Hogarth curves in fashion design and the improvement on the effectiveness of the garment industry.
Analysis of surface metal fiber arrangement of electromagnetic shielding fabric and its influence on shielding effectiveness
Authors: Liu Zhe , Wang Xiuchen , Zhang Yongheng , Zhou Zhong
Published: April 2016

Purpose

No adequate study on scientific analysis of surface metal fiber (SMF) arrangement of electromagnetic shielding fabric (EMSF) and influence on shielding effectiveness (SE) is available at present.

Design/methodology/approach

This paper recognizes the SMF region and constructs a binary feature matrix according to edge condition, width condition and gray condition using the computer image analysis technique based on the construction of the surface digitized image of the EMSF. Three parameters of coverage, dispersion and uniformity are proposed to describe the SMF arrangement. Then experiments and testing samples are designed to analyze the relationship between the three parameters and the SE.

Findings

Results show that the proposed method can accurately recognize the SMF of the EMSF, the coverage, dispersion and uniformity can describe three aspects of the SMF arrangement of percentage content, porosity and orientation, and the three parameters are positively, negatively and positively correlated to the SE, respectively.

Originality/value

The research in this paper provides the basis for further description of the SMF arrangement of the EMSF, possesses the significance for the study of the shielding mechanism, transmission model, electromagnetic performance and rapid non-destructive evaluation of the EMSF and provide a new idea for the study on the shielding theory and application of the EMSF.
Design preferences on wearable e-nose systems for diabetes
Authors: Koo Helen S. , Michaelson Dawn , Teel Karla , Kim Dong-Joo , Park Hyejin , Park Minseo
Published: April 2016

Purpose

The purpose of this study is to investigate potential users’ preferences and expectations for fabric-based wearable e-nose system designs in order to develop painless and non-invasive monitoring systems for diabetes.

Design/methodology/approach

After developing a fabric-based wearable sensor, this study used an online survey with a mixture of closed- and open-ended questions about people’s desires and preferences for use-contexts, product types, design styles, and other key design factors.

Findings

This study investigated the preferences and expectations on designs of wearable e-nose systems for diabetes. The results showed that designers and developers need to consider important design components including sizes, shapes, and colors for practical wearable e-nose system designs. There were strong positive and significant correlations between participant characteristics and preferred wearable e-nose system design factors.

Research limitations/implications

Future research could compare differences between different age groups with different types of diabetes.

Practical implications

Understanding these differences will help designers and marketers target consumers and create diverse designs with different versions for success in the market.

Originality/value

There is lack of research for considering designs of wearable monitoring systems for diabetes. This research will be the first research to understand design preferences and expectations for developing wearable e-nose monitoring systems for diabetes.
The impact of FGM on Shangani women in Zimbabwe
Authors: Mutanda Darlington , Rukondo Howard
Published: April 2016

Purpose

– The purpose of this paper is to discuss the practice of female genital mutilation (FGM) in the context of gender and HIV/AIDS among the Shangani people in Zimbabwe. Broadly, the discussion ais to fcus on how FGM has been used as tool to maintain the subordinate position of women in the Shangani community.

Design/methodology/approach

– In addition to secondary material, the paper hugely benefited from interviews with Shangani women in order to appreciate the challenges of eradicating FGM in their society. The sources pointed to the fact that in addition to being exploitative, FGM has no direct health benefits to women.

Findings

– The paper confirms that eliminating FGM is difficult because it is deeply entrenched in the patriarchal establishment of the Shangani society. As a result of the patriarchal nature of the society, women find themselves subjected to positions of powerlessness as compared to their male counterparts.

Originality/value

– The paper confirms that FGM is a widespread practice in many African communities including Zimbabwe. As communities grapple with the challenges of eradicating or minimising the practice, it is important in the meantime to modernise cultural practices like FGM as a way of doing away with the spreading of HIV/AIDS. Indonesia has already taken that route. FGM as a cultural practice exposes young women to HIV infection because of blood conduct.
Temporary-Creep and Postcreep Properties of Aquaculture Netting Materials With UHMWPE Fibers
Authors: Moe-Føre Heidi , Endresen Per Christian , Jensen Østen
Published: April 2016

This paper presents test results on temporary-creep properties, recovery of strain postcreep and postcreep tensile properties of a Raschel knitted netting material with a combination of ultrahigh molecular weight polyethylene (UHMWPE) and polyester fibers. Specimens of the material were subjected to uniaxial loading over a period of 30 mins, at a constant creep target load of 10–90% of average tensile strength. The specimens were wet and tested in room temperature. The netting structure experienced creep strain with mean values in the range of 1.3–4.5%, increasing with increased creep target load. In addition, the netting experienced 2% creep strain during on-loading. The creep strains were elastic, while large proportions of the elongation accumulated during on-loading (structural strain of 8.8–27.8%) were long lasting and possibly permanent. Tensile tests showed that for the highest creep target load, strength, and elongation at break increased by 17%.
The Indirectly Heated Carbonate Looping Process for CO2 Capture—A Concept With Heat Pipe Heat Exchanger
Authors: Hoeftberger Daniel , Karl Juergen
Published: April 2016

The carbonate looping process using the reversible calcination/carbonation reaction of limestone is a promising way to reduce CO2 emissions of fossil fired power plants. This paper describes the concept of an indirectly heated version of this process in which heat pipes accomplish the heat transfer from an air-blown fluidized bed combustor to a bubbling fluidized bed calciner. It defines the calciner's specific heat demand which is a pendant to the heating value of coal. The dimensioning depends on the processes inside heat pipes as well as heat transfer of immersed heating surfaces. Experimental investigations in an electrically heated batch reactor with a similar pipe grid provide heat transfer coefficients under calcination conditions.
Exergy-Based Study of a Binary Rankine Cycle
Authors: Hofmann Mathias , Tsatsaronis George
Published: April 2016

The aim of this work is to study a binary Rankine process with a significantly higher efficiency compared to a conventional coal-fired power plant. This paper focuses on the design of the process and especially on an efficient combination of flue gas, potassium, and water streams in the components of the steam generator, such as economizers, evaporators, and superheaters, to decrease the overall exergy destruction. Based on a literature review, a base case for a coal-fired binary Rankine cycle with potassium and water as working fluids was developed and, in order to evaluate the thermodynamic quality of several variants, comparative exergy analyses were conducted. A simulation of the process and calculation of the values for the streams were carried out by using the flow-sheeting program CycleTempo, which simultaneously solves the mass and energy balances and contains property functions for the specific enthalpy and entropy of all the substances used. Necessary assumptions are predominantly based on literature data or they are discussed in the paper. We present the exergy analysis of the overall process that includes the flue gas streams as well as the potassium and water cycles. A design analysis and sensitivity studies show the effects of stream combinations and key parameters on the net efficiency, which is higher than 50%.
Active Control of a Rectangular Thin Plate Via Negative Acceleration Feedback
Authors: Bauomy H. S. , EL-Sayed A. T.
Published: April 2016

In this paper, the dynamic oscillation of a rectangular thin plate under parametric and external excitations is investigated and controlled. The motion of a rectangular thin plate is modeled by coupled second-order nonlinear ordinary differential equations. The formulas of the thin plate are derived from the von Kármán equation and Galerkin's method. A control law based on negative acceleration feedback is proposed for the system. The multiple time scale perturbation technique is applied to solve the nonlinear differential equations and obtain approximate solutions up to the second-order approximations. One of the worst resonance case of the system is the simultaneous primary resonances, where Ω1≅ω1 and  Ω2≅ω2. From the frequency response equations, the stability of the system is investigated according to the Routh–Hurwitz criterion. The effects of the different parameters are studied numerically. It is also shown that the system parameters have different effects on the nonlinear response of the thin plate. The simulation results are achieved using matlab 7.0 software. A comparison is made with the available published work.
Applications of ToF-SIMS for imaging and depth profiling commercial materials
Authors: Clark Paula A. , Hagenhoff Birgit , Kersting Reinhard , Tallarek Elke
Published: April 2016

The development of cluster primary ion sources such as Aun+, Bin+, SF5+, C60+, and Arn+ has been an exciting advancement in SIMS analysis. Relative to atomic primary ion sources, cluster ion sources provide higher secondary ion yields. Furthermore, C60+ and Arn+ impart significantly less chemical damage to the sample thus enabling molecular depth profiling. Molecular depth profiling using cluster primary ion sources is routinely used to characterize a wide range of commercially important materials, including organic light emitting diode, biomaterials and pharmaceuticals, adhesives, and architectural paints and coatings. This paper highlights the application of time of flight secondary ion mass spectrometry (ToF-SIMS) to study contact lenses and acrylic-based paints. In the first application, ToF-SIMS was used to investigate the surface composition of two commercial contact lenses. Lens material I is composed of 2-hydroxy-ethyl methacrylate (HEMA) and glycerol methacrylate while lens material II is composed of HEMA and 2-methacryloxyethyl phosphorylcholine cross-linked with ethyleneglycol dimethacrylate. The ToF-SIMS data confirm the presence of the 2-methacryloxyethyl phosphorylcholine on the surface of lens material II. ToF-SIMS was also used to characterize a HEMA-based contact lens which had been worn for about 4 weeks. The analysis reveals the presence of N-containing species, fatty acids, phosphorylcholine, and dioctyldecyl dimethyl ammonium. Arn+ gas cluster ion beams (GCIB) depth profiling indicates the N-containing species, the fatty acids, and the dioctyldecyl dimethyl ammonium are concentrated at the surface. In the second application, a combination of O2+ and Arn+ GCIB depth profiling was used to study the pigment levels in acrylic-based paints. The O2+ beam was used to profile into the bulk of the dried paint film and Arn+ gas cluster beam was then used to remove the damaged material. ToF-SIMS analysis of the crater bottom reveals differences in pigment levels. The combined O2+ and Arn+ GCIB depth profiling is an effective way of characterizing materials composed of both organic and inorganic components.
Use of slow sound to design perfect and broadband passive sound absorbing materials
Authors: Groby J.-P. , Pommier R. , Aurégan Y.
Published: April 2016

Perfect (100%) absorption by thin structures consisting of a periodic arrangement of rectangular quarter-wavelength channels with side detuned quarter-wavelength resonators is demonstrated. The thickness of these structures is 13–17 times thinner than the acoustic wavelength. This low frequency absorption is due to a slow sound wave propagating in the main rectangular channel. A theoretical model is proposed to predict the complex wavenumber in this channel. It is shown that the speed of sound in the channel is much lower than in the air, almost independent of the frequency in the low frequency range, and it is dispersive inside the induced transparency band which is observed. The perfect absorption condition is found to be caused by a critical coupling between the rectangular channel (sub-wavelength resonators) and the incoming wave. It is shown that the width of a large absorption peak in the frequency spectrum can be broadened if several rectangular channels in the unit cell are detuned. The detuning is achieved by varying the length of the side resonators for each channel. The predicted absorption coefficients are validated experimentally. Two resonant cells were produced with stereolithography which enabled the authors to incorporate curved side resonators.
Individualizing liver transplant immunosuppression using a phenotypic personalized medicine platform
Authors: Zarrinpar Ali , Lee Dong-Keun , Silva Aleidy , Datta Nakul , Kee Theodore , Eriksen Calvin , Weigle Keri , Agopian Vatche , Kaldas Fady , Farmer Douglas , Wang Sean E. , Busuttil Ronald , Ho Chih-Ming , Ho Dean
Published: April 2016

Postoperative liver transplant immunosuppression was personalized using a phenotypic, disease mechanism–independent and indication-agnostic approach.
Cultured networks of excitatory projection neurons and inhibitory interneurons for studying human cortical neurotoxicity
Authors: Xu Jin-Chong , Fan Jing , Wang Xueqing , Eacker Stephen M. , Kam Tae-In , Chen Li , Yin Xiling , Zhu Juehua , Chi Zhikai , Jiang Haisong , Chen Rong , Dawson Ted M. , Dawson Valina L.
Published: April 2016

A method to culture human cortical neurons that yielded a balanced network of excitatory and inhibitory neurons revealed that these cells die in a PARP-dependent manner after neurotoxic insult.
Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming
Authors: Zimmer Sebastian , Grebe Alena , Bakke Siril S. , Bode Niklas , Halvorsen Bente , Ulas Thomas , Skjelland Mona , De Nardo Dominic , Labzin Larisa I. , Kerksiek Anja , Hempel Chris , Heneka Michael T. , Hawxhurst Victoria , Fitzgerald Michael L. , Trebicka Jonel , Björkhem Ingemar , Gustafsson Jan-Åke , Westerterp Marit , Tall Alan R. , Wright Samuel D. , Espevik Terje , Schultze Joachim L. , Nickenig Georg , Lütjohann Dieter , Latz Eicke
Published: April 2016

The cyclic oligosaccharide 2-hydroxypropyl-β-cyclodextrin facilitates atheroprotective mechanisms through oxysterol-mediated reprogramming of macrophages.
Poster child: Ready for a close-up
Authors: Gill Saar
Published: April 2016

Resistance to PD1 inhibitors in melanoma is associated with a unique transcriptomic signature.
Desferrioxamine passes the sniff test
Authors: Martin Ian
Published: April 2016

An iron chelator delivered through the nose prevented neurodegeneration in a rodent model of Parkinson’s disease.
Rhythm fuels the adipose tissue fire
Authors: Brown J. Mark
Published: April 2016

Circadian utilization of glucose by human brown adipose tissue affects thermogenesis.
Cancer metastases: Are one and all the same?
Authors: Beltran Himisha
Published: April 2016

Most known tumor driver mutations and resistance mechanisms in metastatic prostate cancer are shared, suggesting that a single biopsy may be clinically representative of other dispersed metastases in a given patient.
Diversified
mcr-1
-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota
Authors: Ye Huiyan , Li Yihui , Li Zhencui , Gao Rongsui , Zhang Han , Wen Ronghui , Gao George F. , Hu Qinghua , Feng Youjun
Published: April 2016

Colistin is an ultimate line of refuge against multidrug-resistant Gram-negative pathogens. Very recently, the emergence of plasmid-mediated
mcr-1
colistin resistance has become a great challenge to global public health, raising the possibility that dissemination of the
mcr-1
gene is underestimated and diversified. Here, we report three cases of plasmid-carried MCR-1 colistin resistance in isolates from gut microbiota of diarrhea patients. Structural and functional analyses determined that the colistin resistance is conferred purely by the single
mcr-1
gene. Genetic and sequence mapping revealed that
mcr-1
-harbouring plasmid reservoirs are present in diversity. Together, the data represent the first evidence of diversity in
mcr-1
-harbouring plasmid reservoirs of human gut microbiota.

IMPORTANCE
The plasmid-mediated mobile colistin resistance gene (
mcr-1
) challenged greatly the conventional idea mentioned above that colistin is an ultimate line of refuge against lethal infections by multidrug-resistant Gram-negative pathogens. It is a possibility that diversified dissemination of the
mcr-1
gene might be greatly underestimated. We report three cases of plasmid-carried MCR-1 colistin resistance in isolates from gut microbiota of diarrhea patients and functionally define the colistin resistance conferred purely by the single
mcr-1
gene. Genetic and sequence mapping revealed unexpected diversity among the
mcr-1
-harbouring plasmid reservoirs of human gut microbiota.
The Importance of First Impressions: Early Events in Mycobacterium tuberculosis Infection Influence Outcome
Authors: Cadena Anthony M. , Flynn JoAnne L. , Fortune Sarah M.
Published: April 2016

Tuberculosis remains a major health threat in much of the world. New vaccines againstMycobacterium tuberculosisare essential for preventing infection, disease, and transmission. However, the host immune responses that need to be induced by an effective vaccine remain unclear. Increasingly, it has become clear that early events in infection are of major importance in the eventual outcome of the infection. Studying such events in humans is challenging, as they occur within the lung and thoracic lymph nodes, and any clinical signs of early infection are relatively nonspecific. Nonetheless, clinical studies and animal models of tuberculosis have provided new insights into the local events that occur in the first few weeks of tuberculosis. Development of an effective vaccine requires a clear understanding of the successful (and detrimental) early host responses againstM. tuberculosis, with the goal to improve upon natural immune responses and prevent infection or disease.
Scleral fixation of a posterior chamber intraocular lens combined with penetrating keratoplasty in an aphakic patient with microcornea and microphthalmia
Authors: Li He J , Tsaousis Konstantinos T , Tabin Geoffrey C
Published: April 2016

A 66-year-old man with microcornea and microphthalmia required a corneal transplant for bullous keratopathy. The patient suffered from congenital cataracts and was left aphakic at the time of the original surgery because of the special challenge of operating on his eye. To improve his vision, we elected to place an intraocular lens (IOL) into his eye as an ‘open sky’ procedure during corneal transplant. However, the implantation was difficult because of the small size of this eye. The surgeon used a novel approach to fixing the IOL to the sclera in which he penetrated the IOL and sutured the IOL through this hole. Following the procedure, the patient reported improvement in his vision and great satisfaction. This case report describes a manoeuvre of fixating an IOL to the sclera by piercing the IOL optic.
Medication-related osteonecrosis of the jaw: a dentist's nightmare
Authors: Muthukrishnan Arvind , Bijai Kumar Laliytha , Ramalingam Gomathi
Published: April 2016

Medication-related osteonecrosis of the jaw (MRONJ) is a complication in patients who are on anti-bone resorptive drugs. These drugs are prescribed for patients with multiple myeloma, osteoporosis, metastatic carcinoma and Paget's disease. Common anti-bone resorptive drugs such as bisphosphonate and monoclonal antibodies such as denosumab are prescribed for these patients to prevent bone resorption. Although very effective in preventing bone resorption, a complication arising from these groups of drugs is the development of osteomyelitis of the jaw. This medication-related osteonecrosis occurs only in the jaw bones. It could mimic a metastatic jaw tumour when a patient reports to the dental surgeon with pain and swelling in the jaw. This case report describes MRONJ in a 50-year-old Indian woman. This possible painful drug-induced complication of jaw bones can be prevented if proper medical history is taken and management protocol is followed in these patients.
New index of social deprivation during pregnancy: results from a national study in France
Authors: Opatowski Marion , Blondel Béatrice , Khoshnood Babak , Saurel-Cubizolles Marie-Josèphe
Published: April 2016

Objectives

To identify precariousness markers in pregnant women that differ from the usual socioeconomic variables.

Methods

Data were obtained from the National Perinatal Survey, a representative sample of women giving birth in France in 2010. From six indicators of social vulnerability, four were selected by multiple correspondence analysis. The first axis of this analysis was used, characterised by the following contributory variables: receiving RSA (Revenu de Solidarité Active) allowance; benefitting from the CMU (Couverture Maladie Universelle) system (French social security) or not being insured; not living in own accommodation; and not living with a partner. These four variables were summed to create a deprivation index.

Results

This index was strongly associated with social maternal characteristics and correctly identified women who were socially vulnerable. Furthermore, it was highly related to the psychosocial context, access to care, behaviours during pregnancy, and pregnancy outcomes. These associations remained significant after adjustment for social variables: compared with no deprivation (no factors), a high level of deprivation (≥3 factors) was associated with late prenatal care (OR 5.8, 95% CI 4.6 to 7.2) and small for gestational age (OR 1.5, 95% CI 1.1 to 1.9).

Conclusions

This index of social deprivation was associated with health issues and behaviours during pregnancy, even after adjustment for social variables, revealing a dimension not measured by the usual variables. Moreover, it is simple to use and easily reproducible.
Health and social consequences of an alcohol-related admission to critical care: a qualitative study
Authors: McPeake Joanne , Forrest Ewan , Quasim Tara , Kinsella John , O'Neill Anna
Published: April 2016

Objective

To examine the impact of critical care on future alcohol-related behaviour. Further, it aimed to explore patterns of recovery for patients with and without alcohol use disorders beyond the hospital environment.

Design

In-depth, semistructured interviews with participants (patients) 3–7 months post intensive care discharge.

Setting

The setting for this study was a 20-bedded mixed intensive care unit (ICU), in a large teaching hospital in Scotland. On admission, patients were allocated to one of the three alcohol groups: low risk, harmful/hazardous and alcohol dependency.

Participants

21 participants who received mechanical ventilation for greater than 3 days were interviewed between March 2013 and June 2014.

Interventions

None.

Measurements and main results

Four themes which impacted on recovery from ICU were identified in this patient group: psychological resilience, support for activities of daily living, social support and cohesion and the impact of alcohol use disorders on recovery. Participants also discussed the importance of personalised goal setting and appropriate and timely rehabilitation for alcohol-related behaviours during the critical care recovery period.

Conclusions

There is a significant interplay between alcohol misuse and recovery from critical illness. This study has demonstrated that at present, there is a haphazard approach to rehabilitation for patients after ICU. A more targeted rehabilitation pathway for patients leaving critical care, with specific emphasis on alcohol misuse if appropriate, requires to be generated.
Prenatal exposure to cannabis and maternal and child health outcomes: a systematic review and meta-analysis
Authors: Gunn J K L , Rosales C B , Center K E , Nuñez A , Gibson S J , Christ C , Ehiri J E
Published: April 2016

Objective

To assess the effects of use of cannabis during pregnancy on maternal and fetal outcomes.

Data sources

7 electronic databases were searched from inception to 1 April 2014. Studies that investigated the effects of use of cannabis during pregnancy on maternal and fetal outcomes were included.

Study selection

Case–control studies, cross-sectional and cohort studies were included.

Data extraction and synthesis

Data synthesis was undertaken via systematic review and meta-analysis of available evidence. All review stages were conducted independently by 2 reviewers.

Main outcomes and measures

Maternal, fetal and neonatal outcomes up to 6 weeks postpartum after exposure to cannabis. Meta-analyses were conducted on variables that had 3 or more studies that measured an outcome in a consistent manner. Outcomes for which meta-analyses were conducted included: anaemia, birth weight, low birth weight, neonatal length, placement in the neonatal intensive care unit, gestational age, head circumference and preterm birth.

Results

24 studies were included in the review. Results of the meta-analysis demonstrated that women who used cannabis during pregnancy had an increase in the odds of anaemia (pooled OR (pOR)=1.36: 95% CI 1.10 to 1.69) compared with women who did not use cannabis during pregnancy. Infants exposed to cannabis in utero had a decrease in birth weight (low birth weight pOR=1.77: 95% CI 1.04 to 3.01; pooled mean difference (pMD) for birth weight=109.42 g: 38.72 to 180.12) compared with infants whose mothers did not use cannabis during pregnancy. Infants exposed to cannabis in utero were also more likely to need placement in the neonatal intensive care unit compared with infants whose mothers did not use cannabis during pregnancy (pOR=2.02: 1.27 to 3.21).

Conclusions and relevance

Use of cannabis during pregnancy may increase adverse outcomes for women and their neonates. As use of cannabis gains social acceptance, pregnant women and their medical providers could benefit from health education on potential adverse effects of use of cannabis during pregnancy.