bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Small-Scale Armoring and Residential Development on the Salt Marsh-Upland Ecotone
Authors: Gehman Alyssa-Lois M. , McLenaghan Natalie A. , Byers James E. , Alexander Clark R. , Pennings Steven C. , Alber Merryl
Published: August 2017

Small-scale armoring placed near the marsh-upland interface to protect single-family homes is widespread but understudied. Using a nested, spatially blocked sampling design on the coast of Georgia, USA, we compared the biota and environmental characteristics of 60 marshes adjacent to either a bulkhead, a residential backyard with no armoring, or an intact forest. We found that marshes adjacent to bulkheads were at lower tidal elevations and had features typical of lower elevation marsh habitats: high coverage of the marsh grass Spartina alterniflora, high density of crab burrows, and muddy sediments. Marshes adjacent to unarmored residential sites had higher soil water content and lower porewater salinities than the armored or forested sites, suggesting that there may be increased freshwater input to the marsh at these sites. Deposition of Spartina wrack on the marsh-upland ecotone was negatively related to elevation at armored sites and positively related at unarmored residential and forested sites. Armored and unarmored residential sites had reduced densities of the high marsh crab Armases cinereum, a species that moves readily across the ecotone at forested sites, using both upland and high marsh habitats. Distance from the upland to the nearest creek was longest at forested sites. The effects observed here were subtle, perhaps because of the small-scale, scattered nature of development. Continued installation of bulkheads in the southeast could lead to greater impacts such as those reported in more densely armored areas like the northeastern USA. Moreover, bulkheads provide a barrier to inland marsh migration in the face of sea level rise. Retaining some forest vegetation at the marsh-upland interface and discouraging armoring except in cases of demonstrated need could minimize these impacts.
Progressive changes in hippocampal cytoarchitecture in a neurodevelopmental rat model of epilepsy: implications for understanding presymptomatic epileptogenesis, predictive diagnosis, and targeted treatments
Authors: Bernard Paul B. , Ramsay Leslie A. , MacDonald Debra S. , Tasker R. Andrew
Published: August 2017

Epilepsies affect about 4% of the population and are frequently characterized by a prolonged “silent” period before the onset of spontaneous seizures. Most current animal models of epilepsy either involve acute seizure induction or kindling protocols that induce repetitive seizures. We have developed a rat model of epilepsy that is characterized by a slowly progressing series of behavioral abnormalities prior to the onset of behavioral seizures. In the current study, we further describe an accompanying progression of cytoarchitectural changes in the hippocampal formation. Groups of male and female SD rats received serial injections of a low dose of domoic acid (0.020 mg/kg) (or vehicle) throughout the second week of life. Postmortem hippocampal tissue was obtained on postnatal days 29, 64, and 90 and processed for glial fibrillary acidic protein (GFAP), NeuN, and calbindin expression. The data revealed no significant changes on postnatal day (PND) 29 but a significant increase in hilar NeuN-positive cells in some regions on PND 64 and 90 that were identified as ectopic granule cells. Further, an increase in GFAP positive cell counts and evidence of reactive astrogliosis was found on PND 90 but not at earlier time points. We conclude that changes in cellular expression, possibly due to on-going non-convulsive seizures, develop slowly in this model and may contribute to progressive brain dysfunction that culminates in a seizure-prone phenotype.
Migration, Mobility and Place in Ancient Italy
Authors: Isayev Elena
Published: August 2017

Migration, Mobility and Place in Ancient Italy challenges prevailing conceptions of a natural tie to the land and a demographically settled world. It argues that much human mobility in the last millennium BC was ongoing and cyclical. In particular, outside the military context 'the foreigner in our midst' was not regarded as a problem. Boundaries of status rather than of geopolitics were those difficult to cross. The book discusses the stories of individuals and migrant groups, traders, refugees, expulsions, the founding and demolition of sites, and the political processes that could both encourage and discourage the transfer of people from one place to another. In so doing it highlights moments of change in the concepts of mobility and the definitions of those on the move. By providing the long view from history, it exposes how fleeting are the conventions that take shape here and now.
Period Mappings and Period Domains
Authors: Carlson James , Müller-Stach Stefan , Peters Chris
Published: August 2017

This up-to-date introduction to Griffiths' theory of period maps and period domains focusses on algebraic, group-theoretic and differential geometric aspects. Starting with an explanation of Griffiths' basic theory, the authors go on to introduce spectral sequences and Koszul complexes that are used to derive results about cycles on higher-dimensional algebraic varieties such as the Noether–Lefschetz theorem and Nori's theorem. They explain differential geometric methods, leading up to proofs of Arakelov-type theorems, the theorem of the fixed part and the rigidity theorem. They also use Higgs bundles and harmonic maps to prove the striking result that not all compact quotients of period domains are Kähler. This thoroughly revised second edition includes a new third part covering important recent developments, in which the group-theoretic approach to Hodge structures is explained, leading to Mumford–Tate groups and their associated domains, the Mumford–Tate varieties and generalizations of Shimura varieties.
Variations and changes in snow depth at meteorological stations Barentsburg and Hornsund (Spitsbergen)
Authors: Osuch Marzena , Wawrzyniak Tomasz
Published: August 2017

In this study, seasonality and interannual variability of snow depth at two stations (Hornsund and Barentsburg) located in western Spitsbergen are investigated. For this purpose, the novel Moving Average over Shifting Horizon method combined with trend estimation was used. The Hornsund and Barentsburg stations exhibit similar snow depth trends during early autumn and late spring when statistically significant decreases were estimated at both stations (for August 1984–July 2016). In the remaining period, there are differences in outcomes between stations. The results for Barentsburg from October till the end of May are characterised by the lack of a trend while at Hornsund decreases of snow depth were estimated. The largest changes occur in May when the snow depth was at its maximum. Differences in the estimated tendencies were explained with the help of a trend analysis for air temperature and precipitation. An analysis of maximum snow depth, snow onset date, snow disappearance date and snow-cover duration is included. The results of the assessment depend on the location, with a lack of statistically significant changes in Barentsburg, and later snow onset date, shorter duration and decrease of maximum depth in Hornsund.
A COMPARATIVE STUDY OF TWO-POPULATION MODELS FOR THE ASSESSMENT OF BASIS RISK IN LONGEVITY HEDGES
Authors: Villegas Andrés M. , Haberman Steven , Kaishev Vladimir K. , Millossovich Pietro
Published: August 2017

Longevity swaps have been one of the major success stories of pension scheme de-risking in recent years. However, with some few exceptions, all of the transactions to date have been bespoke longevity swaps based upon the mortality experience of a portfolio of named lives. In order for this market to start to meet its true potential, solutions will ultimately be needed that provide protection for all types of members, are cost effective for large and smaller schemes, are tradable, and enable access to the wider capital markets. Index-based solutions have the potential to meet this need; however, concerns remain with these solutions. In particular, the basis risk emerging from the potential mismatch between the underlying forces of mortality for the index reference portfolio and the pension fund/annuity book being hedged is the principal issue that has, to date, prevented many schemes progressing their consideration of index-based solutions. Two-population stochastic mortality models offer an alternative to overcome this obstacle as they allow market participants to compare and project the mortality experience for the reference and target populations and thus assess the amount of demographic basis risk involved in an index-based longevity hedge. In this paper, we systematically assess the suitability of several multi-population stochastic mortality models for assessing basis risks and provide guidelines on how to use these models in practical situations paying particular attention to the data requirements for the appropriate calibration and forecasting of such models.
The Great East Japan Earthquake: Analyses of Disaster Impacts on Health Care Clinics
Authors: Ochi Sae , Kato Shigeaki , Kobayashi Ken-ichi , Kanatani Yasuhiro
Published: August 2017

Objective

Local health facilities play a critical role in mitigating the deterioration of health after catastrophic disasters. However, limited information is available on clinic damage. Therefore, the National Institute of Public Health conducted surveillance on clinic damage after the 2011 Great East Japan Earthquake (GEJE) to identify risk factors.

Methods

A cross-sectional study using a paper-based questionnaire was conducted that targeted 728 clinics located in coastal areas in the 3 prefectures most affected by the GEJE.

Results

The risk of building damage was inversely correlated with distance from the coast, whereas the risk of ceasing operations was significantly correlated with building damage and some specialties of clinics, namely, internal medicine and pediatrics.

Discussion

In mountainous countries like Japan, clinics often need to be built in coastal areas, where the majority of residents live. This surveillance revealed that clinics built in readily accessible locations and that provide care with high needs are more likely to get damaged by tsunamis. As clinics are often the frontline health facilities in disaster settings, local disaster plans need to include plans to reinforce disaster preparedness among clinics. For effective planning and resource allocation, nationwide hazard vulnerability analysis using a global standard will be helpful. (Disaster Med Public Health Preparedness. 2018; 12: 291–295)
Thermoacoustic instability as mutual synchronization between the acoustic field of the confinement and turbulent reactive flow
Authors: Pawar Samadhan A. , Seshadri Akshay , Unni Vishnu R. , Sujith R. I.
Published: August 2017

Thermoacoustic instability is the result of a positive coupling between the acoustic field in the duct and the heat release rate fluctuations from the flame. Recently, in several turbulent combustors, it has been observed that the onset of thermoacoustic instability is preceded by intermittent oscillations, which consist of bursts of periodic oscillations amidst regions of aperiodic oscillations. Quantitative analysis of the intermittency route to thermoacoustic instability has been performed hitherto using the pressure oscillations alone. We perform experiments on a laboratory-scale bluff-body-stabilized turbulent combustor with a backward-facing step at the inlet to obtain simultaneous data of acoustic pressure and heat release rate fluctuations. With this, we show that the onset of thermoacoustic instability is a phenomenon of mutual synchronization between the acoustic pressure and the heat release rate signals, thus emphasizing the importance of the coupling between these non-identical oscillators. We demonstrate that the stable operation corresponds to desynchronized aperiodic oscillations, which, with an increase in the mean velocity of the flow, transition to synchronized periodic oscillations. In between these states, there exists a state of intermittent phase synchronized oscillations, wherein the two oscillators are synchronized during the periodic epochs and desynchronized during the aperiodic epochs of their oscillations. Furthermore, we discover two different types of limit cycle oscillations in our system. We notice a significant increase in the linear correlation between the acoustic pressure and the heat release rate oscillations during the transition from a lower-amplitude limit cycle to a higher-amplitude limit cycle. Further, we present a phenomenological model that qualitatively captures all of the dynamical states of synchronization observed in the experiment. Our analysis shows that the times at which vortices that are shed from the inlet step reach the bluff body play a dominant role in determining the behaviour of the limit cycle oscillations.
Development and evaluation of a concise food list for use in a web-based 24-h dietary recall tool
Authors: Evans Katie , Hennessy Áine , Walton Janette , Timon Claire , Gibney Eileen , Flynn Albert
Published: August 2017

Foodbook24 is a self-administered web-based 24-h dietary recall tool developed to assess food and nutrient intakes of Irish adults. This paper describes the first step undertaken in developing Foodbook24 which was to limit participant burden by establishing a concise list of food items for inclusion in the tool. The aim of the present study was to evaluate whether using a concise food list (as opposed to an extensive list) with generic composition data would influence the estimates of nutrient intakes in a nationally representative sample of Irish adults. A 2319-item food list generated from the Irish National Adult Nutrition Survey (NANS) (2008–2010) (n1500) was used as the basis for a shortened food list for integration into the tool. Foods similar in nutritional composition were recoded with a generic type food code to produce a concise list of 751 food codes. The concise food list was applied to the NANS food consumption dataset and intake estimates of thirty-five nutrients were compared with estimates derived using the original extensive list. Small differences in nutrient intakes (<6 %) with limited effect size (Cohen'sd< 0·1) were observed between estimates from both food lists. The concise food list showed strong positive correlations (rs0·9–1·0,n1500,P< 0·001) and a high level of agreement with the extensive list (80–97 % of nutrient intakes classified into the same tertile; >90% of intakes similarly categorised according to dietary reference values). This indicates that a concise food list is suitable for use in a web-based 24-h dietary recall tool for Irish adults.
ASSESSMENT OF UNIVERSAL NEWBORN HEARING SCREENING AND INTERVENTION IN SHANGHAI, CHINA—ADDENDUM
Authors: Chen Xiuzhi , Yuan Min , Lu Jun , Zhang Qi , Sun Mei , Chang Fengshui
Published: August 2017

In the above publication by Chen et al. (2017), the authors neglected to include that Dr. Zhang was supported by the 111 Project (Grant Number B16031) as part of their financial support and conflicts of interest. The complete corrected conflicts of interest section is provided below:

The authors report grants from the National Natural Science Foundation of China, grants from the National Science & Technology Pillar Program during the Twelfth Five-year Plan Period, and grants from the Key Discipline in Shanghai during the conduct of the study. Dr. Zhang was supported by the 111 Project (Grant Number B16031).
Multi-agent credit assignment in stochastic resource management games
Authors: Mannion Patrick , Devlin Sam , Duggan Jim , Howley Enda
Published: August 2017

Multi-agent systems (MASs) are a form of distributed intelligence, where multiple autonomous agents act in a common environment. Numerous complex, real world systems have been successfully optimized using multi-agent reinforcement learning (MARL) in conjunction with the MAS framework. In MARL agents learn by maximizing a scalar reward signal from the environment, and thus the design of the reward function directly affects the policies learned. In this work, we address the issue of appropriate multi-agent credit assignment in stochastic resource management games. We propose two new stochastic games to serve as testbeds for MARL research into resource management problems: the tragic commons domain and the shepherd problem domain. Our empirical work evaluates the performance of two commonly used reward shaping techniques: potential-based reward shaping and difference rewards. Experimental results demonstrate that systems using appropriate reward shaping techniques for multi-agent credit assignment can achieve near-optimal performance in stochastic resource management games, outperforming systems learning using unshaped local or global evaluations. We also present the first empirical investigations into the effect of expressing the same heuristic knowledge in state- or action-based formats, therefore developing insights into the design of multi-agent potential functions that will inform future work.
Femoral vein homograft as Sano shunt results in improved pulmonary artery growth after Norwood operation
Authors: Briceno-Medina Mario , Kumar T. K. Susheel , Sathanandam Shyam , Boston Umar , Perez Michael , Allen Jerry , Zurakowski David , Ilbawi Michel , Knott-Craig Christopher J.
Published: August 2017

Objective

To evaluate differences in interstage growth of pulmonary arteries between use of polytetrafluoroethylene and femoral vein homograft as Sano shunt during stage-I Norwood palliation.

Methods

A retrospective review of all patients who survived to the second stage following Norwood–Sano operation at two institutions was performed. Either polytetrafluoroethylene or the valved segment of femoral vein homograft was used for construction of the Sano shunt. The size of pulmonary arteries was compared at pre-Glenn catheterisation.

Results

A total of 48 neonates with the diagnosis of hypoplastic left heart syndrome or its variants comprised the study population. Femoral vein homograft of 5–6 mm diameter was used in 14 and polytetrafluoroethylene graft of 5 mm was used in 34 patients. The two groups were comparable in terms of preoperative demographics and age at time of pre-Glenn catheterisation (3.9±0.7 versus 3.4±0.8 months, p=0.06). Patients who received femoral vein homograft demonstrated a significantly higher pre-Glenn Nakata index [264 (130–460) versus 165 (108–234) mm2/m2, p=0.004]. The individual branch pulmonary arteries were significantly larger in the femoral vein group (right, 7.8±3.6 versus 5.0±1.2, p=0.014; left, 7.2±2.1 versus 5.6±1.9, p=0.02). There were no differences in cardiac index, Qp:Qs, ventricular end-diastolic pressure or systemic oxygen saturations.

Conclusions

Utilisation of a valved segment of femoral vein homograft as right ventricle to pulmonary artery conduit during Norwood–Sano operation confers better interstage growth of the pulmonary arteries. Further studies are needed to evaluate the impact of femoral vein homograft on single ventricle function.
Utilisation of early intervention services in young children with hypoplastic left heart syndrome
Authors: Mussatto Kathleen A. , Hollenbeck-Pringle Danielle , Trachtenberg Felicia , Sood Erica , Sananes Renee , Pike Nancy A. , Lambert Linda M. , Mahle William T. , Goldberg David J. , Goldberg Caren S. , Dunbar-Masterson Carolyn , Otto Michelle , Marino Bradley S. , Bartle Bronwyn H. , Williams Ismee A. , Jacobs Jeffrey P. , Zyblewski Sinai C. , Pemberton Victoria L.
Published: August 2017

Objective

Children with hypoplastic left heart syndrome are at a risk for neurodevelopmental delays. Current guidelines recommend systematic evaluation and management of neurodevelopmental outcomes with referral for early intervention services. The Single Ventricle Reconstruction Trial represents the largest cohort of children with hypoplastic left heart syndrome ever assembled. Data on life events and resource utilisation have been collected annually. We sought to determine the type and prevalence of early intervention services used from age 1 to 4 years and factors associated with utilisation of services.

Methods

Data from 14-month neurodevelopmental assessment and annual medical history forms were used. We assessed the impact of social risk and geographic differences. Fisher exact tests and logistic regression were used to evaluate associations.

Results

Annual medical history forms were available for 302 of 314 children. Greater than half of the children (52–69%) were not receiving services at any age assessed, whereas 20–32% were receiving two or more therapies each year. Utilisation was significantly lower in year 4 (31%) compared with years 1–3 (with a range from 40 to 48%) (p<0.001). Social risk factors were not associated with the use of services at any age but there were significant geographic differences. Significant delay was reported by parents in 18–43% of children at ages 3 and 4.

Conclusion

Despite significant neurodevelopmental delays, early intervention service utilisation was low in this cohort. As survival has improved for children with hypoplastic left heart syndrome, attention must shift to strategies to optimise developmental outcomes, including enrolment in early intervention when merited.
Group independent component analysis reveals alternation of right executive control network in Internet gaming disorder
Authors: Wang Lingxiao , Zhang Yifen , Lin Xiao , Zhou Hongli , Du Xiaoxia , Dong Guangheng
Published: August 2017

Objective

Previous studies have demonstrated that individuals with Internet gaming disorder (IGD) showed attentional bias toward gaming-related cues and exhibited impaired executive functions. The purpose of this study was to explore the alternations in related functional brain networks underlying attentional bias in IGD subjects.

Methods

Eighteen IGD subjects and 19 healthy controls (HC) were scanned with functional magnetic resonance imaging while they were performing an addiction Stroop task. Networks of functional connectivity were identified using group independent component analysis (ICA).

Results

ICA identified 4 functional networks that showed differences between the 2 groups, which were related to the right executive control network and visual related networks in our study. Within the right executive control network, in contrast to controls, IGD subjects showed increased functional connectivity in the temporal gyrus and frontal gyrus, and reduced functional connectivity in the posterior cingulate cortex, temporal gyrus, and frontal gyrus.

Conclusion

These findings suggest that IGD is related to abnormal functional connectivity of the right executive control network, and may be described as addiction-related abnormally increased cognitive control processing and diminished response inhibition during an addiction Stroop task. The results suggest that IGD subjects show increased susceptibility towards gaming-related cues but weakened strength of inhibitory control.
Accuracy and acceptability of second-dialect performance on American television
Authors: KNOOIHUIZEN REMCO
Published: August 2017

This article analyses a case of second-dialect performance as an idealised instance of second-dialect acquisition, without mitigating factors such as access, analytical ability and motivation. It focuses on the Australian English and American English speech of three young Australian actors. An acoustic analysis of their short-vowel systems shows that they can successfully adapt to perform in an American English accent, but that their second-dialect system is less stable and more variable than their native system.

A foreign-accent rating experiment on the actors’ American English with American English judges shows that the actors on average are thought to sound slightly less American than the native American English-speaker controls. The discrepancy between the acoustic accuracy and listener acceptability may be explained by judges attending to different features from those included in the acoustic study.

This study of second-dialect performance shows what is maximally possible in second-dialect acquisition. Given the difference between the two measures of success, studies of second-dialect acquisition would benefit from including subjective measures in addition to acoustic accuracy.
Applying a food processing-based classification system to a food guide: a qualitative analysis of the Brazilian experience
Authors: Davies Vanessa Fernandes , Moubarac Jean-Claude , Medeiros Kharla Janinny , Jaime Patricia Constante
Published: August 2017

Objective

The present paper aimed to identify the stakeholders, as well as their arguments and recommendations, in the debate on the application of a food processing-based classification system to the new Brazilian Food Guide.

Design

Qualitative approach; an analysis was made of documents resulting from the consultation conducted for the development of the new Brazilian Food Guide, which uses the NOVA classification for its dietary recommendations. A thematic matrix was constructed and the resulting themes represented the main points for discussion raised during the consultation.

Setting

Brazil.

Subjects

Actors from academia, government and associations/unions/professional bodies/organizations related to the area of nutrition and food security; non-profit institutions linked to consumer interests and civil society organizations; organizations, associations and food unions linked to the food industry; and individuals.

Results

Four themes were identified: (i) conflicting paradigms; (ii) different perceptions about the role and need of individuals; (iii) we want more from the new food guide; and (iv) a sustainable guide.

Conclusions

There was extensive participation from different sectors of society. The debate generated by the consultation revealed two main conflicting opinions: a view aligned with the interests of the food industry and a view of healthy eating which serves the interests of the population. The first group was against the adoption of a food processing-based classification system in a public policy such as the new Brazilian Food Guide. The second group, although mostly agreeing with the new food guide, argued that it failed to address some important issues related to the food and nutrition agenda in Brazil.
Are Big Food’s corporate social responsibility strategies valuable to communities? A qualitative study with parents and children
Authors: Richards Zoe , Phillipson Lyn
Published: August 2017

Objective

Recent studies have identified parents and children as two target groups whom Big Food hopes to positively influence through its corporate social responsibility (CSR) strategies. The current preliminary study aimed to gain an in-depth understanding of parents and children’s awareness and interpretation of Big Food’s CSR strategies to understand how CSR shapes their beliefs about companies.

Design

Community-based qualitative semi-structured interviews.

Setting

New South Wales, Australia.

Subjects

Parents (n 15) and children aged 8–12 years (n 15).

Results

Parents and children showed unprompted recognition of CSR activities when shown McDonald’s and Coca-Cola brand logos, indicating a strong level of association between the brands and activities that target the settings of children. When discussing CSR strategies some parents and most children saw value in the activities, viewing them as acts of merit or worth. For some parents and children, the companies’ CSR activities were seen as a reflection of the company’s moral attributes, which resonated with their own values of charity and health. For others, CSR strategies were in conflict with companies’ core business. Finally, some also viewed the activities as harmful, representing a deceit of the public and a smokescreen for the companies’ ultimately unethical behaviour.

Conclusions

A large proportion of participants valued the CSR activities, signalling that denormalising CSR to sever the strong ties between the community and Big Food will be a difficult process for the public health community. Efforts to gain public acceptance for action on CSR may need greater levels of persuasion to gain public support of a comprehensive and restrictive approach.
Mapping Chemical Bonds in Semiconductor Devices by Monitoring the Shifts of EELS Edges
Authors: Potapov Pavel , Svistunova Elena L. , Gulyaev Alexander A.
Published: August 2017

Scanning transmission electron microscopy (STEM) in combination with electron energy-loss spectroscopy (EELS) can deliver information about variations of bonding at the nm scale. This is typically performed by analyzing the electron-loss near edge structure (ELNES) of given EELS edges. The present paper demonstrates an alternative way of a bonding examination through monitoring the EELS onset positions. Two conditions are essential for their accurate measurement. One (hardware) is using the dual EELS instrumentation that provides near simultaneous acquisition of low-loss and core-loss spectra. Another (software) is the least-square fitting of observed spectra to a reference spectrum. The combination of these hardware and software techniques reveals the positions of EELS onsets with the precision sufficient for mapping tiny variations of bonding. The paper shows that the method is capable of helping to solve practical tasks of nanoscale engineering like the analysis of modern CMOS devices.
Grant Will Advance Standards Promoting Open, High-Quality Data
Authors: Wendel JoAnna
Published: August 2017

Ensuring that data in the Earth and space sciences are findable, accessible, interoperable, and reusable (FAIR) lies at the heart of a new project funded by the Laura and John Arnold Foundation.
New insights into the vitamin D requirements during pregnancy
Authors: Hollis Bruce W , Wagner Carol L
Published: August 2017

Pregnancy represents a dynamic period with physical and physiological changes in both the mother and her developing fetus. The dramatic 2–3 fold increase in the active hormone 1,25(OH)2D concentrations during the early weeks of pregnancy despite minimal increased calcium demands during that time of gestation and which are sustained throughout pregnancy in both the mother and fetus suggests an immunomodulatory role in preventing fetal rejection by the mother. While there have been numerous observational studies that support the premise of vitamin D's role in maintaining maternal and fetal well-being, until recently, there have been few randomized clinical trials with vitamin D supplementation. One has to exhibit caution, however, even with RCTs, whose results can be problematic when analyzed on an intent-to-treat basis and when there is high non-adherence to protocol (as if often the case), thereby diluting the potential good or harm of a given treatment at higher doses. As such, a biomarker of a drug or in this case “vitamin” or pre-prohormone is better served. For these reasons, the effect of vitamin D therapies using the biomarker circulating 25(OH)D is a far better indicator of true “effect.” When pregnancy outcomes are analyzed using the biomarker 25(OH)D instead of treatment dose, there are notable differences in maternal and fetal outcomes across diverse racial/ethnic groups, with improved health in those women who attain a circulating 25(OH)D concentration of at least 100 nmol·L−1 (40 ng·mL−1). Because an important issue is the timing or initiation of vitamin D treatment/supplementation, and given the potential effect of vitamin D on placental gene expression and its effects on inflammation within the placenta, it appears crucial to start vitamin D treatment before placentation (and trophoblast invasion); however, this question remains unanswered. Additional work is needed to decipher the vitamin D requirements of pregnant women and the optimal timing of supplementation, taking into account a variety of lifestyles, body types, baseline vitamin D status, and maternal and fetal vitamin D receptor (VDR) and vitamin D binding protein (VDBP) genotypes. Determining the role of vitamin D in nonclassical, immune pathways continues to be a challenge that once answered will substantiate recommendations and public health policies.
Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Authors: Li Jun , Harata-Lee Yuka , Denton Matthew D , Feng Qianjin , Rathjen Judith R , Qu Zhipeng , Adelson David L
Published: August 2017

Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-β-d-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-β-d-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.
Genetically engineered red cells expressing single domain camelid antibodies confer long-term protection against botulinum neurotoxin
Authors: Huang Nai-Jia , Pishesha Novalia , Mukherjee Jean , Zhang Sicai , Deshycka Rhogerry , Sudaryo Valentino , Dong Min , Shoemaker Charles B. , Lodish Harvey F.
Published: August 2017

A short half-life in the circulation limits the application of therapeutics such as single-domain antibodies (VHHs). We utilize red blood cells to prolong the circulatory half-life of VHHs. Here we present VHHs against botulinum neurotoxin A (BoNT/A) on the surface of red blood cells by expressing chimeric proteins of VHHs with Glycophorin A or Kell. Mice whose red blood cells carry the chimeric proteins exhibit resistance to 10,000 times the lethal dose (LD50) of BoNT/A, and transfusion of these red blood cells into naive mice affords protection for up to 28 days. We further utilize an improved CD34+ culture system to engineer human red blood cells that express these chimeric proteins. Mice transfused with these red blood cells are resistant to highly lethal doses of BoNT/A. We demonstrate that engineered red blood cells expressing VHHs can provide prolonged prophylactic protection against bacterial toxins without inducing inhibitory immune responses and illustrates the potentially broad translatability of our strategy for therapeutic applications.
Charting the circuit QED design landscape using optimal control theory
Authors: Goerz Michael H. , Motzoi Felix , Whaley K. Birgitta , Koch Christiane P.
Published: August 2017

With recent improvements in coherence times, superconducting transmon qubits have become a promising platform for quantum computing. They can be flexibly engineered over a wide range of parameters, but also require us to identify an efficient operating regime. Using state-of-the-art quantum optimal control techniques, we exhaustively explore the landscape for creation and removal of entanglement over a wide range of design parameters. We identify an optimal operating region outside of the usually considered strongly dispersive regime, where multiple sources of entanglement interfere simultaneously, which we name the quasi-dispersive straddling qutrits regime. At a chosen point in this region, a universal gate set is realized by applying microwave fields for gate durations of 50 ns, with errors approaching the limit of intrinsic transmon coherence. Our systematic quantum optimal control approach is easily adapted to explore the parameter landscape of other quantum technology platforms.
Erratum: Clinical responses to ERK inhibition in BRAF
V600E-mutant colorectal cancer predicted using a computational model
Authors: Kirouac Daniel C. , Schaefer Gabriele , Chan Jocelyn , Merchant Mark , Orr Christine , Huang Shih-Min A. , Moffat John , Liu Lichuan , Gadkar Kapil , Ramanujan Saroja
Published: August 2017

A correction to this article has been published and is linked from the HTML version of this article.
Increase of vitamin D assays prescriptions and associated factors: a population-based cohort study
Authors: Caillet Pascal , Goyer-Joos Anne , Viprey Marie , Schott Anne-Marie
Published: August 2017

A worldwide increase in the frequency of testing for serum 25-hydroxyvitamin D (25OHD) levels has been observed over the last years. Our aim was to measure the evolution in the number of vitamin D assays performed in France from 2008 to 2013 and to investigate some of the drivers that may explain this increase. Patients within the representative 1/97th sample of the French health insurance system reimbursement database (EGBSdatabase) who had at least one 25OHD or 1-25(OH)2D assay between 2008 and 2013 were included. Trends over time in number of vitamin D assays were analysed globally and per year in a multivariable Poisson regression model with GEE. Among the 639,163 patients of theEGBSdatabase, 118,509 (18.5%) had at least one vitamin D assay over the 6-year study period. Among the individuals tested, 52.1% had only one test. The number of vitamin D assays (25OHD or 1-25(OH)2D) increased 7.5-fold from 9,620 in 2008 to 81,641 in 2013. This study confirms the rapid and dramatic increase in vitamin D assays prescriptions and shows that this is mostly due to a global increase of the proportion of patients tested rather than an increase in repetition of tests in some individual patients.
Vocal greeting during mother-infant reunions in a nocturnal primate, the gray mouse lemur (Microcebus murinus)
Authors: Scheumann Marina , Linn Sabrina , Zimmermann Elke
Published: August 2017

In human societies, ritualized greeting behavior includes gestural and vocal displays to signal the social acceptance of an encountering person. These displays are universal across cultures suggesting a pre-human origin. Vocal greeting displays are only reported for monkeys and apes with complex social systems, but none of these studies confirmed that greeting signals fulfill all criteria characterizing human greeting behavior. In this study, we analyzed for the first time whether vocal exchanges between mother and infants in a non-human primate fulfill the criteria of human greeting behavior and whether vocal greeting behavior is present in a basal primate with a less complex social system, the gray mouse lemur. By comparing spontaneous leave-takings and reunions, we found that vocal exchanges during mother-infant reunions fulfilled all six criteria characterizing human greeting behavior. Thus, predictable reciprocal vocal exchanges occurred at the start of the reunion (but not during leave-taking), when mother and infant had visual contact to each other. Thus, we argued that mother-infant vocal exchanges governing reunions are essential to establish social bonds and to ritualize the greeting function. Our findings suggest that ritualized vocal greeting has its origins deeply rooted in mammalian phylogeny and derives from vocal exchanges during parent-infant reunions.
Retrospective Analysis of Structural Disease Progression in Retinitis Pigmentosa Utilizing Multimodal Imaging
Authors: Cabral Thiago , Sengillo Jesse D. , Duong Jimmy K. , Justus Sally , Boudreault Katherine , Schuerch Kaspar , Belfort Rubens , Mahajan Vinit B. , Sparrow Janet R. , Tsang Stephen H.
Published: August 2017

In this report, we assess the natural progression rate of retinitis pigmentosa (RP) over an average of three years using spectral-domain optical coherence tomography (SD-OCT) and short wavelength fundus autofluorescence (SW-AF). Measurement of the ellipsoid zone (EZ) line width and hyperautofluorescent ring diameters was performed in 81 patients with RP in a retrospective, longitudinal fashion. Rate of structural disease progression, symmetry between eyes, and test-retest variability were quantified. We observed on average, EZ-line widths decreased by 140 µm (5.2%, p < 0.001) per year, and average horizontal and vertical hyperautofluorescent ring diameters decreased by 149 µm (3.6%, p < 0.001) and 120 µm (3.9%, p < 0.001) per year, respectively. The 95th percentile of this cohort had differences in progression slopes between eyes that were less than 154 µm, 118 µm, and 132 µm for EZ-line width and horizontal and vertical ring diameters, respectively. For all measures except horizontal ring diameter, progression rates were significantly slower at end-stage disease. From our data, we observed a statistically significant progression rate in EZ line width and SW-AF ring diameters over time, verifying the utility of these measurements for disease monitoring purposes. Additionally, calculated differences in progression slopes between eyes may prove useful for investigators evaluating the efficacy of unilateral treatments for RP in clinical trials.
A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei
Authors: Jones David B. , Jerry Dean R. , Khatkar Mehar S. , Raadsma Herman W. , Steen Hein van der , Prochaska Jeffrey , Forêt Sylvain , Zenger Kyall R.
Published: August 2017

The Pacific whiteleg shrimp,Litopenaeus vannamei, is the most farmed aquaculture species worldwide with global production exceeding 3 million tonnes annually.Litopenaeus vannameihas been the focus of many selective breeding programs aiming to improve growth and disease resistance. However, these have been based primarily on phenotypic measurements and omit potential gains by integrating genetic selection into existing breeding programs. Such integration of genetic information has been hindered by the limited available genomic resources, background genetic parameters and knowledge on the genetic architecture of commercial traits forL.vannamei. This study describes the development of a comprehensive set of genomic gene-based resources including the identification and validation of 234,452 putative single nucleotide polymorphismsin-silico, of which 8,967 high value SNPs were incorporated into a commercially available Illumina Infinium ShrimpLD-24 v1.0 genotyping array. A framework genetic linkage map was constructed and combined with locus ordering by disequilibrium methodology to generate an integrated genetic map containing 4,817 SNPs, which spanned a total of 4552.5 cM and covered an estimated 98.12% of the genome. These gene-based genomic resources will not only be valuable for identifying regions underlying importantL.vannameitraits, but also as a foundational resource in comparative and genome assembly activities.
Identify latent chromosomal aberrations relevant to myelodysplastic syndromes
Authors: Song Qibin , Chu Yuxin , Yao Yi , Peng Min , Yang Weihong , Li Xiaoqing , Huang Shiang
Published: August 2017

Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic malignancies. This study aims to identify latent chromosomal abnormalities relevant to MDS, which may optimize the current diagnosis of MDS. Affymetrix CytoScan 750 K microarray platform was utilized to perform a genome-wide detection of chromosomal aberrations in the bone marrow cells of the patients. The findings were compared with the results from traditional karyotypic analysis and FISH to reveal latent chromosomal aberrations. Chromosomal gain, loss, and UPD, and complex karyotypes were identified in those samples. In addition to established cytogenetic aberrations detected by karyotypic analysis, CytoScan 750 K microarray also detected cryptic chromosomal lesions in MDS. Those latent defects underlying multiple gene mutations may construe the clinical variability of MDS. In Conclusion, Affymetrix CytoScan 750 K microarray is efficient in identifying latent chromosomal aberrations in MDS.
The oceanic origin of path-independent carbon budgets
Authors: MacDougall Andrew H.
Published: August 2017

Virtually all Earth system models (ESM) show a near proportional relationship between cumulative emissions of CO2 and change in global mean temperature, a relationship which is independent of the emissions pathway taken to reach a cumulative emissions total. The relationship, which has been named the Transient Climate Response to Cumulative CO2 Emissions (TCRE), gives rise to the concept of a ‘carbon budget’. That is, a finite amount of carbon that can be burnt whilst remaining below some chosen global temperature change threshold, such as the 2.0 °C target set by the Paris Agreement. Here we show that the path-independence of TCRE arises from the partitioning ratio of anthropogenic carbon between the ocean and the atmosphere being almost the same as the partitioning ratio of enhanced radiative forcing between the ocean and space. That these ratios are so close in value is a coincidence unique to CO2. The simple model used here is underlain by many assumptions and simplifications but does reproduce key aspects of the climate system relevant to the path-independence of carbon budgets. Our results place TCRE and carbon budgets on firm physical foundations and therefore help validate the use of these metrics for climate policy.
Synthesis of Arbitrary Quantum Circuits to Topological Assembly: Systematic, Online and Compact
Authors: Paler Alexandru , Fowler Austin G. , Wille Robert
Published: August 2017

It is challenging to transform an arbitrary quantum circuit into a form protected by surface code quantum error correcting codes (a variant of topological quantum error correction), especially if the goal is to minimise overhead. One of the issues is the efficient placement of magic state distillation sub circuits, so-called distillation boxes, in the space-time volume that abstracts the computation’s required resources. This work presents a general, systematic, online method for the synthesis of such circuits. Distillation box placement is controlled by so-called schedulers. The work introduces a greedy scheduler generating compact box placements. The implemented software, whose source code is available at www.github.com/alexandrupaler/tqec, is used to illustrate and discuss synthesis examples. Synthesis and optimisation improvements are proposed.
Two-color pump-probe interferometry of ultra-fast light-matter interaction
Authors: Hayasaki Yoshio , Fukuda Shin-ichi , Hasegawa Satoshi , Juodkazis Saulius
Published: August 2017

Two-color side-view probing of light-matter interaction from minute focal volume of a tightly focused fs-laser pump pulse reveals charge dynamics with high 0.9 μm optical resolution and approximately ~45fs temporal resolution defined by pulse duration. Use of two colors is advantageous for probing optically excited plasma regions with different density. Holographical digital focusing and spatial filtering were implemented to obtain the same resolution images for subsequent Fourier analysis. Fast plasma density decay with time constant ~150 fs was resolved and is consistent with self-trapping. Potential applications of an optical control over light-induced defects with deep-sub-wavelength resolution is discussed.