bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid and efficient removal of arsenic from water using electrospun CuO–ZnO composite nanofibers
Authors: Malwal Deepika , Gopinath P.
Published: December 2016

To remove arsenic effectively from water, we synthesized CuO–ZnO composite nanofibers using a simple electrospinning technique assisted by post-calcination.
Quantitative analysis of amyloid polymorphism using height histograms to correct for tip convolution effects in atomic force microscopy imaging
Authors: Lin Yi-Chih , Komatsu Hiroaki , Ma Jianqiang , Axelsen Paul H. , Fakhraai Zahra
Published: December 2016

Development of a statistical height analysis method to study amyloid polymorphism.
Iron catalyzed methylation and ethylation of vinyl arenes
Authors: Zhu Nengbo , Zhao Jianguo , Bao Hongli
Published: December 2016

Iron-catalyzed methyl, ethyl and propyl Heck reactions were developed using readily available alkyl peroxides as alkyl sources.
Application of carbon fibers to flexible, miniaturized wire/fiber-shaped energy conversion and storage devices
Authors: Cai Xin , Zhang Chaoqun , Zhang Shengsen , Fang Yueping , Zou Dechun
Published: December 2016

An overview of recent progress in wire/fiber-shaped flexible power devices made from micro-carbon fibers is given.
Surface-functionalized perovskite films for stable photoelectrochemical water splitting
Authors: Wang Chongwu , Yang Shuang , Chen Xiao , Wen Tianyu , Yang Hua Gui
Published: December 2016

Integration of Ni passivation and surface functionalization with hydrophobic ammonium cations has been demonstrated to enhance the stability of perovskite to moisture. The functionalized perovskite photoanode can perform steady water oxidation for more than 30 min.
Manipulating the hydrogen evolution pathway on composition-tunable CuNi nanoalloys
Authors: Lin Zhaoyong , Li Jiling , Li Lihua , Yu Lili , Li Weijia , Yang Guowei
Published: November 2016

CuNi nanoalloys with cocatalytic activities comparable to Pt for TiO2 photocatalytic H2 evolution were investigated based on the hydrogen evolution pathway.
Ethylenediamine functionalized fullerene nanoparticles as independent electron transport layers for high-efficiency inverted polymer solar cells
Authors: Li Jie , Zhao Fuwen , Wang Taishan , Nie Mingzhe , Li Jiangjun , Wei Zhixiang , Jiang Li , Wang Chunru
Published: December 2016

Ethylenediamine functionalized fullerene nanoparticles are preparedviaa facile solid–liquid reaction, and they are introduced as efficient independent electron transport layers for inverted polymer solar cells.
Correction: ZnO nanorods decorated with metal sulfides as stable and efficient counter-electrode materials for high-efficiency quantum dot-sensitized solar cells
Authors: Gopi Chandu V. V. M. , Venkata-Haritha Mallineni , Lee Young-Seok , Kim Hee-Je
Published: December 2016

Correction for ‘ZnO nanorods decorated with metal sulfides as stable and efficient counter-electrode materials for high-efficiency quantum dot-sensitized solar cells’ by Chandu V. V. M. Gopi et al., J. Mater. Chem. A, 2016, 4, 8161–8171.
Amphiphilic star-shaped poly(sarcosine)-block-poly(ε-caprolactone) diblock copolymers: one-pot synthesis, characterization, and solution properties
Authors: Cui Saide , Pan Xianfu , Gebru Hailemariam , Wang Xin , Liu Jiaqi , Liu Jingjing , Li Zhenjiang , Guo Kai
Published: December 2016

We firstly synthesized amphiphilic three-armed star-shaped poly(sarcosine)-block-poly(ε-caprolactone) diblock copolymers (s-PSar-b-PCLs), and investigated the solution properties and biocompatibility of the copolymers.
Implantable polymeric microneedles with phototriggerable properties as a patient-controlled transdermal analgesia system
Authors: Chen Mei-Chin , Chan Hao-An , Ling Ming-Hung , Su Liang-Cheng
Published: December 2016

Phototriggerable microneedles (MNs) can be quickly implanted into the skin as a depot for the on-demand delivery of pain medicines.
Modulation doping of transition metal dichalcogenide/oxide heterostructures
Authors: Xu Kang , Wang Yi , Zhao Yuda , Chai Yang
Published: December 2016

Control of carrier type and carrier density provides a way to tune the physical properties of two-dimensional (2D) semiconductors.
Do we know whether potential G-quadruplexes actually form in long functional RNA molecules?
Authors: Weldon Carika , Eperon Ian C. , Dominguez Cyril
Published: December 2016

The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding. Therefore, novel methods need to be developed to allow the characterization of G4s in long functional RNAs and in a cellular context. This need has in part been met by our recent development of a method based on a comparison of RNA and 7-deaza-RNA that provides a test for identifying RNA G4s in such conditions.
Novel biomarkers in kidney disease: roles for cilia, Wnt signalling and ATMIN in polycystic kidney disease
Authors: Goggolidou Paraskevi , Wilson Patricia D.
Published: December 2016

Biomarkers, the measurable indicators of biological conditions, are fast becoming a popular approach in providing information to track disease processes that could lead to novel therapeutic interventions for chronic conditions. Inherited, chronic kidney disease affects millions of people worldwide and although pharmacological treatments exist for some conditions, there are still patients whose only option is kidney dialysis and kidney transplantation. In the past 10 years, certain chronic kidney diseases have been reclassified as ciliopathies. Cilia in the kidney are antenna-like, sensory organelles that are required for signal transduction. One of the signalling pathways that requires the primary cilium in the kidney is Wnt signalling and it has three components such as canonical Wnt, non-canonical Wnt/planar cell olarity (PCP) and non-canonical Wnt/Ca2+ signalling. Identification of the novel role of ATM INteractor (ATMIN) as an effector molecule in the non-canonical Wnt/PCP pathway has intrigued us to investigate its potential role in chronic kidney disease. ATMIN could thus be an important biomarker in disease prognosis and treatment that might lighten the burden of chronic kidney disease and also affect on its progression.
PHLPPing through history: a decade in the life of PHLPP phosphatases
Authors: Grzechnik Agnieszka T. , Newton Alexandra C.
Published: December 2016

In the decade since their discovery, the PH domain leucine-rich repeat protein phosphatases (PHLPP) have emerged as critical regulators of cellular homeostasis, and their dysregulation is associated with various pathophysiologies, ranging from cancer to degenerative diseases, such as diabetes and heart disease. The two PHLPP isozymes, PHLPP1 and PHLPP2, were identified in a search for phosphatases that dephosphorylate Akt, and thus suppress growth factor signaling. However, given that there are over 200 000 phosphorylated residues in a single cell, and fewer than 50 Ser/Thr protein phosphatases, it is not surprising that PHLPP has many other cellular functions yet to be discovered, including a recently identified role in regulating the epigenome. Both PHLPP1 and PHLPP2 are commonly deleted in human cancers, supporting a tumor suppressive role. Conversely, the levels of one isozyme, PHLPP1, are elevated in diabetes. Thus, mechanisms to correctly control PHLPP activity in cells are critical for normal cellular homeostasis. This review summarizes the known functions of PHLPP and its role in disease.
Cellular functions of LRRK2 implicate vesicular trafficking pathways in Parkinson's disease
Authors: Cookson Mark R.
Published: December 2016

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene, associated with Parkinson's disease, have been shown to affect intracellular trafficking pathways in a variety of cells and organisms. An emerging theme is that LRRK2 can bind to multiple membranous structures in cells, and several recent studies have suggested that the Rab family of small GTPases might be important in controlling the recruitment of LRRK2 to specific cellular compartments. Once localized to membranes, LRRK2 then influences downstream events, evidenced by changes in the autophagy–lysosome pathway. Here, I will discuss available evidence that supports or challenges this outline, with a specific emphasis on those aspects of LRRK2 function that have been controversial or remain to be fully clarified.
Screening for chemical modulators for LRRK2
Authors: Mortiboys Heather
Published: December 2016

After the discovery of leucine-rich repeat kinase 2 (LRRK2) as a risk factor for sporadic Parkinson's disease (PD) and mutations in LRRK2 as a cause of some forms of familial PD, there has been substantial interest in finding chemical modulators of LRRK2 function. Most of the pathogenic mutations in LRRK2 are within the enzymatic cores of the protein; therefore, many screens have focused on finding chemical modulators of this enzymatic activity. There are alternative screening approaches that could be taken to investigate compounds that modulate LRRK2 cellular functions. These screens are more often phenotypic screens. The preparation for a screen has to be rigorous and enable high-throughput accurate assessment of a compound's activity. The pipeline to beginning a drug screen and some LRRK2 inhibitor and phenotypic screens will be discussed.
Neurotrophin signalling: novel insights into mechanisms and pathophysiology
Authors: Mitre Mariela , Mariga Abigail , Chao Moses V.
Published: December 2016

Neurotrophins, such as brain-derived neurotrophic factor (BDNF), are prominent regulators of neuronal survival, growth and differentiation during development. While trophic factors are viewed as well-understood but not innovative molecules, there are many lines of evidence indicating that BDNF plays an important role in the pathophysiology of many neurodegenerative disorders, depression, anxiety and other psychiatric disorders. In particular, lower levels of BDNF are associated with the aetiology of Alzheimer's and Huntington's diseases. A major challenge is to explain how neurotrophins are able to induce plasticity, improve learning and memory and prevent age-dependent cognitive decline through receptor signalling. This article will review the mechanism of action of neurotrophins and how BDNF/tropomyosin receptor kinase B (TrkB) receptor signaling can dictate trophic responses and change brain plasticity through activity-dependent stimulation. Alternative approaches for modulating BDNF/TrkB signalling to deliver relevant clinical outcomes in neurodegenerative and neuropsychiatric disorders will also be described.
Energy‐efficient relaying technique for two‐hop diamond networks
Authors: Aydin İbrahim , Aygölü Ümit
Published: December 2016

Energy‐efficiency (EE) is a critical metric in many types of wireless networks and is getting increasingly important for new technologies. In this paper, the authors propose an energy‐efficient decode‐and‐forward relaying strategy for two‐hop diamond networks where the source–destination communication is established by the help of two relays which have an inter‐relay link. The inter‐relay link gives the opportunity of correcting the data packet between relays if only one of them decodes the packet that is received from the source correctly. Hence, both relays are able to send the data packet to the destination with distributed Alamouti coding which provides multipath diversity. In addition, they introduce optimum data rate adaptation for each link separately to maximise EE for the considered network. By exploiting diversity and optimum rate adaptation, it is possible to transmit at higher rates with reasonable outage probability which has critical effects on EE and throughput. They show via computer simulations that the proposed technique is substantially more energy‐efficient and has a better throughput than the successive relaying technique given in the literature; moreover, more robust to the changes in system conditions, i.e. relay location and transmission power level.
Adaptive sliding mode control of non‐linear non‐minimum phase system with input delay
Authors: Hu Xiaoxiang , Wu Ligang , Si Xiaosheng , Xu Bin
Published: December 2016

This study proposes an adaptive sliding mode control (SMC) design method for multi‐input multi‐output non‐linear non‐minimum phase system with input delay. The problem is challenging, not only because of the unstable internal dynamics of the non‐minimum phase system, but also the existence of input delay. The partially linearised model of the original non‐linear system is obtained through input/output linearisation, and a state tracking model is constructed based on the computed ideal internal dynamics. A filtered tracking error is introduced to handle the input delay. A SMC strategy is proposed for the stability of filtered tracking error system, and an adaptive law is designed to estimate the upper bound of perturbations. Finally, comparison simulation results on vertical takeoff and landing aircraft are provided to verify the efficiency of the proposed method.
What’s in a name? Re-conceptualizing non-state armed groups in the Middle East
Authors: Berti Benedetta
Published: November 2016

In recent decades, the role and status of non-state armed groups (NSAGs)—generally defined as armed organizations operating outside the control of the state and willing and able to use force to achieve their objectives—has attracted growing scholarly and policy interest; mirroring these groups’ seemingly more prominent role in both war-making and post-conflict transitions. This is especially the case when it comes to the contemporary Middle East and North Africa, where a combination of state fragility, conflict and instability has further enhanced the military, political and social importance of NSAGs. But is there a mismatch between the organizational evolution of some NSAGs and the conceptual framework adopted to describe and analyze them? How can recognizing these limitations help better conceptualizing and analyzing violent non-state organizations? In the Middle East, organizations like Hamas or Hezbollah operate simultaneously as sophisticated armed organizations, complex political entities and as highly developed social movement organizations involved in administering and delivering social services at the grassroots level. Elsewhere in the region, the rise of the “Islamic State” offers an entirely distinct example of a socio-political project established by an actor commonly defined as a NSAG. Despite the significant ideological, organizational and strategic differences between these organizations, all three actors fall broadly within the “non-state armed groups” category. Yet, both in their use of armed force, as well in their relationship with the state, these organizations appear as characterized by multi-layered identities and strategies that defy simple labelling. Moreover, these groups’ different roles as alternative providers of governance de facto blur the line between state and non-state actor and create an evolving dynamic that simultaneously challenges, contests and redefines concepts like statehood and sovereignty. The article analyzes the organizational evolution of these three actors and, in doing so, it problematizes and challenges the way we currently conceptualize and think about non-state actors in general and non-state armed groups more specifically. This article is published as part of a collection on analyzing security complexes in a changing Middle East.
Switchable polarization rotation of visible light using a plasmonic metasurface
Authors: Earl Stuart K. , James Timothy D. , Gómez Daniel E. , Marvel Robert E. , Haglund Richard F. , Roberts Ann
Published: November 2016

A metasurface comprising an array of silver nanorods supported by a thin film of the phase change material vanadium dioxide is used to rotate the primary polarization axis of visible light at a pre-determined wavelength. The dimensions of the rods were selected such that, across the two phases of vanadium dioxide, the two lateral localized plasmon resonances (in the plane of the metasurface) occur at the same wavelength. Illumination with linearly polarized light at 45° to the principal axes of the rod metasurface enables excitation of both of these resonances. Modulating the phase of the underlying substrate, we show that it is possible to reversibly switch which axis of the metasurface is resonant at the operating wavelength. Analysis of the resulting Stokes parameters indicates that the orientation of the principal linear polarization axis of the reflected signal is rotated by 90° around these wavelengths. Dynamic metasurfaces such as these have the potential to form the basis of an ultra-compact, low-energy multiplexer or router for an optical signal.
A farm-scale framework to assess potential farm- and regional-scale implications of removing palm-kernel expeller as a supplementary feed for dairy cows
Authors: Vibart Ronaldo , Mackay Alec , Wall Andrew , Vogeler Iris , Beautrais Josef , Dalley Dawn
Published: December 2016

Farm-scale models were integrated with spatially discrete estimates of pasture production to examine the potential farm and regional implications of removing palm-kernel expeller (PKE) as a supplementary feed from dairy farms in Southland, New Zealand. The following two farm-production systems representing the majority of dairy farms in the region were modelled: a System 3 farm (D3; mid-intensification, with 10–20% of imported feed) and a System 4 farm (D4; mid- to high intensification, with 20–30% of imported feed). Within each system, the impact of the following four PKE options was explored: (1) a control with PKE (Baseline); (2) no PKE, with fewer cows producing the same amount of milk per cow as in Baseline; (3) no PKE, with the same number of cows producing less milk per cow than in Baseline; and (4) PKE replaced with barley grain. Barley grain provides for similar flexibility (timing of purchase and feeding), and can be sourced locally. Faced with the need to remove PKE as a dietary ingredient, farmers would benefit from adopting the second PKE option (no PKE, with fewer cows producing the same amount of milk per cow as in Baseline); farm-operating profits were reduced by only 3% (compared with 30% of System 4 farms adopting the third PKE option, i.e. no PKE, with the same number of cows producing less milk per cow than in Baseline) relative to the Baseline farms. The narrow range of mean annual nitrate-nitrogen (nitrate-N) leaching losses (estimates ranged from 30 to 33 kg N/ha) reflects similar estimates of N intake and N excreted in urine across the modelled options. Substantial amounts of barley grain would need to be transported into the region or produced locally to replace PKE.
Comparing the profitability of a dairy business with alternative investments
Authors: Heard J. W. , Lawrence K. R. , Ho C. K. M. , Malcolm B.
Published: December 2016

In the present study, the profitability of a dairy-farm case study evaluated over the period 2003–2004 to 2014–2015 was compared with the performance of other dairy farms and other non-agricultural investments over the same time. Investments are generally made on the expectation that a net return will be earned that justifies using capital in one particular way rather than an alternative way. The expected, and actual, returns from capital invested in different assets will differ according to the risks involved. Investors choose an investment, and mixes of investments, that align with their goals, preferences for risk and anticipated returns over time. Dairy farming involves investing in assets, such as land and improvements, water, livestock, plant and equipment, and people, which are managed to produce milk and ultimately to earn a competitive return on capital. With uncertain seasonal conditions, fluctuating costs and prices, declining terms of trade, wide ranges of equity and management abilities, and a steady decline in the number of commercial farm businesses, it may be tempting to presume that investing in farming, and dairy farming in particular, is a hard road, leading to lower and more variable returns than investing in non-agricultural investment opportunities in the economy. This need not be the case. Analysis of how a dairy business in northern Victoria performed from 2003–2004 to 2014–2015 showed that this farm did well compared with (i) other dairy businesses in Victoria and (ii) alternative investments, such as shares, bonds and property, over the same time. Compound annual return to capital for the dairy farm over the 12 years studied was 12.4% (real, before tax). Over half the return came from the farming operations and the remainder came from owning assets that appreciated in value, particularly in this case, water. The dairy business that was studied was well managed and earned higher annual average returns than the average returns of investments with similar risk elsewhere in the economy, such as shares, and matched it with the best performing of these alternative investments.
Directionality and the Role of Polarization in Electric Field Effects on Radical Stability
Authors: Gryn'ova Ganna , Coote Michelle L.
Published: December 2016

Accurate quantum-chemical calculations are used to analyze the effects of charges on the kinetics and thermodynamics of radical reactions, with specific attention given to the origin and directionality of the effects. Conventionally, large effects of the charges are expected to occur in systems with pronounced charge-separated resonance contributors. The nature (stabilization or destabilization) and magnitude of these effects thus depend on the orientation of the interacting multipoles. However, we show that a significant component of the stabilizing effects of the external electric field is largely independent of the orientation of external electric field (e.g. a charged functional group, a point charge, or an electrode) and occurs even in the absence of any pre-existing charge separation. This effect arises from polarization of the electron density of the molecule induced by the electric field. This polarization effect is greater for highly delocalized species such as resonance-stabilized radicals and transition states of radical reactions. We show that this effect on the stability of such species is preserved in chemical reaction energies, leading to lower bond-dissociation energies and barrier heights. Finally, our simplified modelling of the diol dehydratase-catalyzed 1,2-hydroxyl shift indicates that such stabilizing polarization is likely to contribute to the catalytic activity of enzymes.
Research challenges and conservation implications for urban cat management in New Zealand
Authors: Kikillus K. Heidy , Chambers Geoff K. , Farnworth Mark J. , Hare Kelly M.
Published: December 2016

Over the past 20 years, conservation efforts in New Zealand have moved from being concentrated in rural and isolated island locations, where exotic mammalian predators are often controlled, to begin to bring native fauna back to major cities. However, human–wildlife conflicts arise when conservation occurs in close proximity to cities. These are particularly intense when companion animals are involved either as potential predators or prey of high-value conservation animals. Within New Zealand, this conflict is particularly fraught around domestic cats (Felis catus) in the urban environment. Cats in New Zealand are recognised as major introduced predators of native fauna, but they also prey on small introduced predatory mammals. This dynamic causes much conflict between people with different attitudes towards animals; however, as yet, few studies have explored the role(s), either negative or positive, of urban cats in New Zealand. Here, we review current knowledge on domestic cats in urban New Zealand, identify gaps in knowledge and make suggestions for future research, which includes further social science research, citizen science-based research programs, market research, investigation into cat-management legislation, and more in-depth studies of cat diseases and zoonoses. These data are vital for informing the public and improving the management of urban cat populations, including mitigating conservation impacts. Urban ecologists will need to be versatile in the way they design and conduct experiments, exploiting multiple disciplines to both ensure scientific robustness, but also community and government support for uptake of results into management and legislation.
Molecular Genetics Informs Spatial Segregation of Two Desert Stream Gila Species
Authors: Marsh Paul C. , Clarkson Robert W. , Dowling Thomas E.
Published: December 2016

Headwater Chub Gila nigra and Roundtail Chub G. robusta are two distinct but morphologically similar cyprinid species that historically were parapatric in Fossil Creek (Gila River basin) in central Arizona. The creek was chemically treated in 2005 to eradicate nonnative fishes, and chubs salvaged before the treatment were repatriated afterward. Annual samples from multiple sites along a transect throughout the treated reach were characterized for mtDNA and microsatellites from 2008 to 2014. Genetic variation was compared within and among Fossil Creek samples and with reference material for Headwater Chub from Fossil Springs at the headwaters of the creek and for Roundtail Chub from the Verde River and West Clear Creek. Measures of mtDNA and microsatellite diversity identified significant differences among Headwater Chub from Fossil Springs, Roundtail Chub from the Verde River, and samples above and below Irving Falls, a natural fish barrier within the treatment reach. The frequency of Headwater Chub mtDNA was low at the most downstream sampling sites, progressively increasing upstream. There was also temporal variation, with Headwater Chub mtDNA generally becoming rarer in later samples. F‐statistic analysis of microsatellite data and Bayesian clustering of microsatellite genotypes with STRUCTURE were generally consistent and identified three groups: Headwater Chub and two forms of Roundtail Chub. Using the species assignments provided by STRUCTURE and mitotypes, we found 153 “pure” Headwater Chub and only a single pure Roundtail Chub above Irving Falls and 27 pure Headwater Chub and 398 pure Roundtail Chub below the falls. Tests of cytonuclear disequilibrium indicated nonrandom mating (with the rare species more likely to mate than the more common one) and/or selection against hybrids. These data support the recognition of the Headwater Chub as a distinct full species and demonstrate that conservation actions within the genus Gila should typically be carried out at the population level.

Received April 8, 2016; accepted August 16, 2016 Published online December 2, 2016
Status of the Shortnose Sturgeon Population in the Savannah River, Georgia
Authors: Bahr Derek L. , Peterson Douglas L.
Published: December 2016

The federally endangered Shortnose Sturgeon Acipenser brevirostrum was once abundant in all major coastal river systems from the Saint John River, Canada, to the St. Johns River, Florida. During much of the 20th century, however, populations suffered major declines throughout their range from the combined effects of overfishing, pollution, and habitat loss. Although the species was a charter member of the Endangered Species Act, quantified population assessments are still lacking for many river systems throughout their range. Because river‐specific assessments are critical for evaluating species recovery, the objective of this study was to quantify abundance and annual recruitment of Shortnose Sturgeon occupying the Savannah River, Georgia. Anchored gill nets and trammel nets fished during slack tides were used to sample juvenile and adult Shortnose Sturgeon in their summer holding areas during 2013–2015. Huggins closed‐capture models in RMark were used to derive abundance estimates for each demographic group. The best models estimated that the Savannah River contained 81 (95% CI = 27–264) age‐1 juveniles in 2013, 270 (162–468) in 2014, and 245 (104–691) in 2015. The models also estimated the river to contain 486 (198–1,273) age‐2+ juveniles in 2013, 123 (69–235) in 2014, and 187 (81–526) in 2015. Similarly, the adult population was estimated to be 1,865 (784–4,694) individuals in 2013, 1,564 (1,005–2,513) in 2014, and 940 (535–1,753) in 2015. The results of this study provide the first population estimates available for Shortnose Sturgeon in the Savannah River. Additionally, the results suggest that the Savannah River likely contains the second largest population of Shortnose Sturgeon in Georgia. Future studies are needed in the Savannah River and other South Atlantic river systems to better evaluate Shortnose Sturgeon recovery status and the effects of river‐specific anthropogenic modifications.

Received June 27, 2016; accepted September 29, 2016 Published online December 2, 2016
Vincenzo Danti’s Deceits
Authors: Cole Michael , Gamberini Diletta
Published: November 2016

The great sculptor Vincenzo Danti wrote one of the longest poems to have survived from a Renaissance artist, but the text’s close thematic and conceptual connections to its author’s art have gone entirely unnoticed. What Danti’s poem and sculpture share, this essay argues, is a concern with mystified identity. Danti’s poetic sensibility stands at odds with the biographical frameworks that typically guide the interpretation of Renaissance art and literature. At the same time, his example shows how much there is to be gained from an investigation of how artists learned to be writers, and of what came of those efforts.
The CCL-K11 ongoing key comparison. Final report for the year 2014
Authors: Matus Michael , Gavalyugov Veselin , Tamakyarska Denita , Alqahtani Nasser , Alfohaid Mohammad , Moona Girija , Sharma Rina , Hapiddin Asep , Boynawan Ahmad Mohamad , Ranusawud Monludee , Tonmueanwai Anusorn , Hong Feng-Lei , Ishikawa Jun , Robertsson Lennart
Published: November 2016

Lasers from four national metrological institutes (NMIs) were compared in 2014 as part of the CCL-K11 ongoing key comparison, initiated by the 13th meeting of the Comité Consultative des Longuers (CCL) in 2007. The absolute frequency of R(127) 11-5 transitions of molecular iodine was measured for these lasers following the technical protocol for CCL-K11. The results of these measurements are compiled in the present report. The comparison reports, as communicated by each participant, are included as appendices.

This document constitutes the sixth final report for the ongoing key comparison CCL-K11.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Maternal Blood Pressure Before Pregnancy and Sex of the Baby: A Prospective Preconception Cohort Study
Authors: Retnakaran Ravi , Wen Shi Wu , Tan Hongzhuan , Zhou Shujin , Ye Chang , Shen Minxue , Smith Graeme N. , Walker Mark C.
Published: December 2016

BACKGROUND

Population-level sociologic studies have suggested that adverse societal conditions may affect fetal viability in a sex-specific manner and thereby modify the ratio of male vs. female babies. This concept suggests that there may exist certain physiologic features in a woman that relate to her likelihood of delivering a boy or girl. We thus established a preconception cohort to prospectively evaluate the relationship between maternal pregravid health and sex of the baby.

METHODS

In this analysis nested within an observational cohort study, 1,411 newly married women in Liuyang, China, underwent pregravid cardiometabolic characterization (including anthropometry and measurement of blood pressure, cholesterol, triglycerides, and glucose) at median 26.3 weeks before a singleton pregnancy, delivering at 39.0 ± 1.3 weeks gestation.

RESULTS

Systolic blood pressure before pregnancy was higher in women who delivered a boy than in those who had a girl (112.5 ± 11.9 vs. 109.6 ± 12.0 mm Hg, P < 0.0001). The prevalence of a male baby progressively increased across quintiles of pregravid systolic blood pressure (P < 0.0001). After covariate adjustment, mean adjusted pregravid systolic blood pressure was higher in mothers of boys vs. girls (106.0 vs. 103.3 mm Hg, P = 0.0015). On logistic regression analysis, pregravid systolic blood pressure emerged as the only significant predictor of having a male baby (adjusted odds ratio = 1.017 per mm Hg, 95% confidence interval = 1.007–1.028). The pregravid difference in blood pressure between mothers of boys and girls was not present during any trimester of pregnancy.

CONCLUSION

Maternal blood pressure before pregnancy is a previously unrecognized factor that may be associated with the likelihood of delivering a boy or girl.
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
Authors: Leimeister Chris-André , Sohrabi-Jahromi Salma , Morgenstern Burkhard
Published: December 2016

Motivation

Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods.

Results

We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes.

Availability and Implementation

The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/

Supplementary information

Supplementary data are available at Bioinformatics online.
Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Authors: Jacox Edwin , Weller Mathias , Tannier Eric , Scornavacca Celine
Published: December 2016

Gene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is insufficient to determine them all. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. However finding a most parsimonious binary resolution of a non-binary tree obtained by contracting the unsupported branches is NP-hard if transfer events are considered as possible gene scale events, in addition to gene origination, duplication and loss. We propose an exact, parameterized algorithm to solve this problem in single-exponential time, where the parameter is the number of connected branches of the gene tree that show low support from the sequence alignment or, equivalently, the maximum number of children of any node of the gene tree once the low-support branches have been collapsed. This improves on the best known algorithm by an exponential factor. We propose a way to choose among optimal solutions based on the available information. We show the usability of this principle on several simulated and biological datasets. The results are comparable in quality to several other tested methods having similar goals, but our approach provides a lower running time and a guarantee that the produced solution is optimal.

Availability and Implementation

Our algorithm has been integrated into the ecceTERA phylogeny package, available at http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and which can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.

Supplementary information

Supplementary data are available at Bioinformatics online.
pHMM-tree: phylogeny of profile hidden Markov models
Authors: Huo Luyang , Zhang Han , Huo Xueting , Yang Yasong , Li Xueqiong , Yin Yanbin
Published: December 2016

Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families.

Availability and Implementation

This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/

Supplementary information

Supplementary data are available at Bioinformatics online.
HIV Infection, Immunosuppression, and Age at Diagnosis of Non-AIDS-Defining Cancers
Authors: Shiels Meredith S. , Althoff Keri N. , Pfeiffer Ruth M. , Achenbach Chad J. , Abraham Alison G. , Castilho Jessica , Cescon Angela , D’Souza Gypsyamber , Dubrow Robert , Eron Joseph J. , Gebo Kelly , John Gill M. , Goedert James J. , Grover Surbhi , Hessol Nancy A. , Justice Amy , Kitahata Mari , Mayor Angel , Moore Richard D. , Napravnik Sonia , Novak Richard M. , Thorne Jennifer E. , Silverberg Michael J. , Engels Eric A. ,   for the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiologic Databases to Evaluate AIDS (IeDEA)
Published: December 2016

Background.

It is unclear whether immunosuppression leads to younger ages at cancer diagnosis among people living with human immunodeficiency virus (PLWH). A previous study found that most cancers are not diagnosed at a younger age in people with AIDS, with the exception of anal and lung cancers. This study extends prior work to include all PLWH and examines associations between AIDS, CD4 count, and age at cancer diagnosis.

Methods.

We compared the median age at cancer diagnosis between PLWH in the North American AIDS Cohort Collaboration on Research and Design and the general population using data from the Surveillance, Epidemiology and End Results Program. We used statistical weights to adjust for population differences. We also compared median age at cancer diagnosis by AIDS status and CD4 count.

Results.

After adjusting for population differences, younger ages at diagnosis (P < .05) were observed for PLWH compared with the general population for lung (difference in medians = 4 years), anal (difference = 4), oral cavity/pharynx (difference = 2), and kidney cancers (difference = 2) and myeloma (difference = 4). Among PLWH, having an AIDS-defining event was associated with a younger age at myeloma diagnosis (difference = 4; P = .01), and CD4 count <200 cells/µL (vs ≥500) was associated with a younger age at lung cancer diagnosis (difference = 4; P = .006).

Conclusions.

Among PLWH, most cancers are not diagnosed at younger ages. However, this study strengthens evidence that lung cancer, anal cancer, and myeloma are diagnosed at modestly younger ages, and also shows younger ages at diagnosis of oral cavity/pharynx and kidney cancers, possibly reflecting accelerated cancer progression, etiologic heterogeneity, or risk factor exposure in PLWH.
Hepatitis C Infection and the Risk of Non-Liver-Related Morbidity and Mortality in HIV-Infected Persons in the Swiss HIV Cohort Study
Authors: Kovari Helen , Rauch Andri , Kouyos Roger , Rougemont Mathieu , Cavassini Matthias , Schmid Patrick , Stöckle Marcel , Bernasconi Enos , Weber Rainer , Ledergerber Bruno ,   for the Swiss HIV Cohort Study
Published: December 2016

Background.

Hepatitis C virus (HCV) infection has been associated with increased non-liver-related morbidity and mortality. However, studies have yielded inconsistent results.

Methods.

The incidence of clinical events in human immunodeficiency virus (HIV)–infected HCV-seropositive and incidence density–matched HCV-seronegative participants of the Swiss HIV Cohort Study from August 1994 to December 2014 was studied. We compared (1) HCV-seropositive with HCV-seronegative participants and (2) HCV-viremic with successfully treated nonviremic patients. Poisson regression was used to assess differences between these groups.

Results.

We included 2503 HCV-seropositive participants (540 with spontaneous HCV clearance, 1294 untreated HCV RNA positive, 345 treated with sustained virologic response [SVR], 43 during treatment, and 281 treated without SVR), and 2503 HCV-seronegative controls. After a mean follow-up of 8.2 years, we observed (HCV seropositive and HCV seronegative, respectively) 107 and 18 liver events, 41 and 14 kidney events, 230 and 121 osteoporosis/fractures, 82 and 94 diabetes mellitus, 114 and 129 cardiovascular events, 119 and 147 non-AIDS malignancies, 162 and 126 Centers for Disease Control and Prevention HIV category B/C events, 106 and 10 liver-related deaths, and 227 and 218 non-liver-related deaths. Compared with HCV-negative controls, HCV-seropositive participants had an increased risk of liver events (incidence rate ratio [IRR], 6.29 [95% confidence interval {CI}, 3.52–11.22]), liver-related death (IRR, 8.24 [95% CI, 3.61–18.83]), kidney events (IRR, 2.43 [95% CI, 1.11–5.33]), and osteoporosis/fracture (IRR, 1.43 [95% CI, 1.03–2.01]). Among HCV-seropositive individuals, treated participants without SVR vs those with SVR had a higher risk of liver events (IRR, 6.79 [95% CI, 2.33–19.81]), liver-related death (IRR, 3.29 [95% CI, 1.35–8.05]), and diabetes mellitus (IRR, 4.62 [95% CI, 1.53–13.96]). Similar but not statistically significant differences were found between untreated HCV RNA–positive patients and those with SVR.

Conclusions.

While HCV exposure was associated with an increased risk of kidney disease and osteoporosis/fracture, this risk did not seem to be dependent of persistent HCV RNA. Successful HCV treatment was associated with a lower incidence of liver disease, liver-related death, and diabetes mellitus, whereas the other conditions studied were less affected.
Incidence of myocardial infarction in pregnancy: a systematic review and meta-analysis of population-based studies
Authors: Gibson Paul , Narous Mariam , Firoz Tabassum , Chou Doris , Barreix Maria , Say Lale , James Matthew ,   on behalf of the WHO Maternal Morbidity Working Group
Published: December 2016

Aims

Cardiac disease is one of the leading causes of indirect maternal death, and myocardial infarction (MI) is one of its most common aetiologies. The objectives of this systematic review and meta-analysis were to characterize the incidence of pregnancy-associated MI (PAMI), as well as the maternal mortality and the case-fatality rates due to PAMI.

Methods and results

Articles were obtained by searching electronic databases, bibliographies and conference proceedings with no language or date restrictions. Two reviewers independently selected population-based cohort and case-control studies reporting on incidence, mortality and case-fatality rates for pregnancy-associated MI. Meta-analysis was performed to estimate pooled maternal incidence, mortality and case-fatality rates. Meta-regression was performed to explore heterogeneity. Based on 17 included studies, the pooled incidence of PAMI and maternal mortality from PAMI were 3.34 (2.09–4.58) and 0.20 (0.10–0.29) per 100 000 pregnancies, respectively. The case-fatality rate was 5.03% (3.78–6.27%). Country/region (meta-regression P = 0.006) and years of study (meta-regression P = 0.04) were potential explanations for the observed heterogeneity in the pooled incidence estimates of maternal MI and its associated mortality, with more recent studies and those conducted in the USA revealing the highest rates.

Conclusion

This article provides a global estimate of the incidence, mortality rate, and case fatality rate of pregnancy-associated MI. We identified higher rates of PAMI in the USA (relative to Canada and European countries) and rising rates over time. Further research regarding this population is needed, especially given rising maternal age and the increasing prevalence of cardiovascular risk factors.
The UCLA Health Resident Informaticist Program – A Novel Clinical Informatics Training Program
Authors: Singer Jennifer S , Cheng Eric M , Baldwin Kevin , Pfeffer Michael A ,   the UCLA Health Physician Informaticist Committee
Published: December 2016

Few opportunities exist for physician trainees to gain exposure to, and training in, the field of clinical informatics, an Accreditation Council for Graduate Medical Education–accredited, recently board-certified specialty. Currently, 21 approved programs exist nationwide for the formal training of fellows interested in pursuing careers in this discipline. Residents and fellows training in medical and surgical fields, however, have few avenues available to gain experience in clinical informatics. An early introduction to clinical informatics brings an opportunity to generate interest for future career trajectories. At University of California Los Angeles (UCLA) Health, we have developed a novel, successful, and sustainable program, the Resident Informaticist Program, with the goals of exposing physician trainees to the field of clinical informatics and its academic nature and providing opportunities to expand the clinical informatics workforce. Herein, we provide an overview of the development, implementation, and current state of the UCLA Health Resident Informaticist Program, with a blueprint for development of similar programs.
Adaptive and Network Sampling for Inference and Interventions in Changing Populations
Authors: Thompson Steven K
Published: December 2016

In this paper, I discuss some of the wider uses of adaptive and network sampling designs. Three uses of sampling designs are to select units from a population to make inferences about population values, to select units to use in an experiment, and to distribute interventions to benefit a population. The most useful approaches for inference from adaptively selected samples are design-based methods and Bayesian methods. Adaptive link-tracing network sampling methods are important for sampling populations that are otherwise hard to reach. Sampling in changing populations involves temporal network or spatial sampling design processes with units selected both into and out of the sample over time. Averaging or smoothing fast-moving versions of these designs provides simple estimates of network-related characteristics. The effectiveness of intervention programs to benefit populations depends a great deal on the sampling and assignment designs used in spreading the intervention.