bluuebunny/crossref_metadata_2025 huggingface dataset:
Faucet: streaming de novo assembly graph construction
Authors: Rozov Roye , Goldshlager Gil , Halperin Eran , Shamir Ron
Published: April 2017

Motivation

We present Faucet, a 2-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased.

Results

Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them. We show these metadata - coverage counts collected at junction k-mers and connections bridging between junction pairs - contain most salient information needed for assembly, and demonstrate they enable cleaning of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy. We compared Faucet’s resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers. Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers MetaSPAdes and Megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency - namely, Minia and LightAssembler. However, on metagenomes tested, Faucet’s outputs had 14-110% higher mean NGA50 lengths compared to Minia, and 2-11-foldhigher mean NGA50 lengths compared to LightAssembler, the only other streaming assembler available.

Availability

Faucet is available athttps://github.com/Shamir-Lab/Faucet

Contact

rshamir@tau.ac.il,eranhalperin@gmail.com

Supplementary information:

Supplementary data are available atBioinformaticsonline.
Elucidating dispersal ecology of reclusive species through genetic analyses of parentage and relatedness: the island night lizard (Xantusia riversiana) as a case study
Authors: Rice Stephen E , Clark Rulon W
Published: April 2017

Characterizing dispersal and movement patterns are vital to understanding the evolutionary ecology of species. For many reclusive species, such as reptiles, the observation of direct dispersal may be difficult or intractable. However, dispersal distances and patterns may be characterized through indirect genetic methods. We used genetic and capture data from the island night lizard (Xantusia riversiana) to estimate natal dispersal distances through indirect genetic methods, characterize movement and space use patterns, and compare these distances to previous estimates made from more traditional ecological approaches. We found that indirect estimates of natal dispersal were greater than previous field-based estimates of individual displacement of 3-5 m. Parent-offspring differences had a mean of approximately 14 m on Santa Barbara Island (SBI) and 41 m on San Clemente Island (SCI) whereas Wright’s σ was estimated at 16 m on SBI and 20 m for SCI. Spatial autocorrelation with correlograms of Moran’s I revealed large differences in the scale of autocorrelation between islands (SBI=375 m, SCI=1,813 m). Interpretation of these distances as average per generation distance of gene flow was incongruent with parentage analyses and σ. We also used variograms to evaluate the range of spatial autocorrelation among two inter-individual genetic differences. The range of spatial autocorrelation again identified different scales on the two islands (102 - 169 m on SBI and 955 - 1,424 m on SCI). No evidence of sex-biased dispersal was found on either island. However, a permutation logistic regression revealed that related individuals >0.8 years old were more likely to be captured together on both islands. Overall, our findings suggest that field-based estimates of individual displacement within this species may underestimate genetic dispersal. We suggest indirect inferences of natal dispersal distances should focus on parentage analyses and Wright’s σ for parameter estimation of individual movement, whereas the ranges identified by spatial autocorrelation and variograms are likely to be relevant at the metapopulation or patch scales. Furthermore, characterization of capture patterns and relatedness revealed kin-affiliative behavior inX. riversiana, which may be indicative of delayed dispersal and cryptic sociality. These results highlight the power of parentage- and relatedness-based analyses for characterizing aspects of the movement ecology of reclusive species that may be difficult to observe directly. These data can then be leveraged to support future conservation and population modeling efforts and assess extinction risks and management strategies.
Force generation by polymerizing filaments revisited: diffusive interaction leads to nonlinear force-number scaling
Authors: Valiyakath Jemseena , Gopalakrishnan Manoj
Published: April 2017

Polymers growing against a barrier generate force and push it forward. We study here force generation by a bundle ofNrigid polymers growing in parallel against a diffusing, rigid, flat barrier, resembling a bundle of microtubules. To estimate the polymerization force, the barrier is subjected to a forcefacting against the direction of growth of the polymers and the mean velocityVN(f) of the filament assembly is computed. The maximum polymerization force (aliasstall force)is deduced from the condition. This problem has been studied in the literature earlier, but two important aspects have escaped attention: (a) free diffusion of monomers is hindered by the barrier, even when it is far from the growing tips and (b) parallel filaments could interact through the monomer density field (“diffusive coupling”), leading to negative interference between them. In our model, both these effects are investigated in detail. A mathematical treatment based on a set of continuum Fokker-Planck equations for combined filament-wall dynamics suggests that the barrier reduces the influx of monomers to the growing polymer tip, thereby reducing the growth velocity and also the stall force, but it doesn’t affect the scaling of the stall force with number, i.e.,. However, Brownian dynamics simulations show that the linear scaling holds only when the filaments are far apart; when they are arranged close together, forming a bundle, sublinear scaling of force with number appears. We argue that the nonlinear scaling could be attributed to diffusive interaction between the growing tips which becomes significant when the tips are close together. These conclusions, initially established for simple flat-faced polymers, are also found to hold true for microtubules with their characteristic hollow cylindrical geometry and rugged tip structure. In particular, simulations show conclusively that the stall force of a single microtubule is a fraction of the combined stall force of the 13 protofilaments. This result is supported by a simple analytical estimate of the force using diffusive coupling theory, and is in agreement with earlier experimental observations.
Apremilast, an oral phosphodiesterase 4 inhibitor, in the treatment of Japanese patients with moderate to severe plaque psoriasis: Efficacy, safety and tolerability results from a phase 2b randomized controlled trial
Authors: Ohtsuki Mamitaro , Okubo Yukari , Komine Mayumi , Imafuku Shinichi , Day Robert M. , Chen Peng , Petric Rosemary , Maroli Allan , Nemoto Osamu
Published: April 2017

Apremilast, an oral, small‐molecule phosphodiesterase 4 inhibitor, works intracellularly within immune cells to regulate inflammatory mediators. This phase 2b randomized, placebo‐controlled study evaluated efficacy and safety of apremilast among Japanese patients with moderate to severe plaque psoriasis. In total, 254 patients were randomized to placebo, apremilast 20 mg b.i.d. (apremilast 20) or apremilast 30 mg b.i.d. (apremilast 30) through week 16; thereafter, all placebo patients were re‐randomized to apremilast 20 or 30 through week 68. Efficacy assessments included achievement of 75% or more reduction from baseline in Psoriasis Area and Severity Index score (PASI‐75; primary) and achievement of static Physician Global Assessment (sPGA; secondary) score of 0 (clear) or 1 (minimal) at week 16. Safety was assessed through week 68. At week 16, PASI‐75 response rates were 7.1% (placebo), 23.5% (apremilast 20; P = 0.0032 vs placebo) and 28.2% (apremilast 30; P = 0.0003 vs placebo); sPGA response rates (score of 0 or 1) were 8.8% (placebo), 23.9% (apremilast 20; P = 0.0165 vs placebo) and 29.6% (apremilast 30; P = 0.0020 vs placebo). Responses were maintained with apremilast through week 68. Most common adverse events (AEs) with placebo, apremilast 20 and apremilast 30 (0–16 weeks) were nasopharyngitis (8.3%, 11.8%, 11.8%), diarrhea (1.2%, 8.2%, 9.4%), and abdominal discomfort (1.2%, 1.2%, 7.1%), respectively. Exposure‐adjusted incidence of these AEs did not increase with continued apremilast treatment (up to 68 weeks). Apremilast demonstrated efficacy and safety in Japanese patients with moderate to severe plaque psoriasis through 68 weeks that was generally consistent with prior studies.
Identification of a heterozygous p.Gly568Val missense mutation in the TRPV3 gene in a Japanese patient with Olmsted syndrome: In silico analysis of TRPV3
Authors: Nagai Hiroshi , Takaoka Yutaka , Sugano Aki , Nakamachi Yuji , Kawano Seiji , Nishigori Chikako
Published: April 2017

Olmsted syndrome is a very rare congenital disorder, characterized by palmoplantar keratoderma and periorificial keratotic lesions. Recently, TRPV3 was reported to be a causative gene of Olmsted syndrome. We identified a heterozygous missense mutation of TRPV3, c.1703G>T, p.Gly568Val, in a Japanese patient with Olmsted syndrome. To the best of our knowledge, this is the first report of a Japanese patient with Olmsted syndrome harboring a missense mutation in TRPV3. We conducted in silico analysis of TRPV3 to evaluate whether the p.Gly568Val leads to structural changes in the TRPV3 selectivity filter. The selectivity filter was shown to become dilated and hyperpermeable as a result of genetic mutation (p.Gly573Ser, p.Tr692Gly or p.Gly568Val) as well as after a change in temperature (300 K to 310 K). In silico analysis of TRPV3 could be a useful approach in predicting mutation‐induced activated states of ion channels, and thus enrich our understanding of the pathogenesis of Olmsted syndrome.
Brexit and UK International Development Policy
Authors: Lightfoot Simon , Mawdsley Emma , Szent‐Iványi Balázs
Published: April 2017

In this article we explore the implications of Brexit for the UK and the EU's development policies and strategic directions, focusing on the former. While it is likely that the operational process of disentangling the UK from the various development institutions of the EU will be relatively straightforward, the choices that lie ahead about whether and how to cooperate thereafter are more complex. Aid and development policy touches on a wide range of interests—security, trade, climate change, migration, gender rights, and so on. We argue that Brexit will accelerate existing trends within UK development policy, notably towards the growing priority of private sector‐led economic growth strategies and blended finance tools. There are strong signals that UK aid will be cut, as successive secretaries of state appear unable to persuade a substantial section of the public and media that UK aid and development policy serves UK interests in a variety of ways.
Comparisons of cardioprotective efficacy between fibroblast growth factor 21 and dipeptidyl peptidase‐4 inhibitor in prediabetic rats
Authors: Tanajak Pongpan , Sa‐nguanmoo Piangkwan , Apaijai Nattayaporn , Wang Xiaojie , Liang Guang , Li Xiaokun , Jiang Chao , Chattipakorn Siriporn C. , Chattipakorn Nipon
Published: April 2017

Aims

Comparative efficacy between fibroblast growth factor 21 (FGF21) and vildagliptin on metabolic regulation, cardiac mitochondrial function, heart rate variability (HRV), and left ventricular (LV) function is not known. We hypothesized that FGF21 and vildagliptin share a similar efficacy in improving these parameters in high fat diet (HFD)‐induced obese‐insulin resistant rats.

Methods

Twenty‐four male Wistar rats were fed with either a normal diet (ND) or a HFD for 12 weeks. Then, ND rats were received vehicle (NDV). Rats in the HFD group were divided into three subgroups to receive either vehicle (HFV), recombinant human FGF21 (rhFGF21, 0.1 mg/kg/d, ip; HFF), or vildagliptin (3 mg/kg/d, PO; HFVil) for 28 days.

Results

HFV rats developed obese‐insulin resistance, increased serum tumor necrosis factors alpha (TNF‐α) level, impaired heart rate variability (HRV) together with cardiac mitochondrial dysfunction, and LV dysfunction. Cardiac apoptosis was markedly increased in HFV rats indicated by decreased B‐cell lymphoma 2 (Bcl‐2) with increased Bcl2‐associated X‐protein (Bax) and cleaved caspase 3 expression. Cardiac FGF21 signaling pathways were markedly decreased in HFV rats indicated by decreased phosphor‐fibroblast growth factor receptors 1 (p‐FGFR1), phosphor‐extracellular signal‐regulated protein kinases 1 (p‐ERK1/2), proliferator‐activated receptor gamma coactivator 1‐alpha (PGC‐1α), and carnitine palmitoyltransferase‐1 (CPT‐1) expression. Although both FGF21 and vildagliptin similarly attenuated these impairments, only HFF rats had decreased body weight, visceral fat, and serum TNF‐α levels.

Conclusions

FGF21 exerts better metabolic regulation and inflammation reduction than vildagliptin. However, FGF21 and vildagliptin shared a similar efficacy for cardioprotection by improving HRV and LV function.
Development Cost Capitalization During R&D Races
Authors: De Waegenaere Anja , Sansing Richard C. , Wielhouwer Jacco L.
Published: April 2017

We investigate the economic effects of capitalizing development costs during a race between two firms to discover and develop a new technology. Winning the race requires success in the research stage and success in the development stage. Development costs are expensed in some settings, but capitalized in others. Capitalization of development costs provides a credible signal regarding progress in the race, allowing the rival to make a more informed decision regarding whether to proceed with development. We study the effects of this signal on the firms’ investment decisions and social welfare. We show that if both firms capitalize instead of expense development costs, aggregate investment in research weakly increases but aggregate investment in development weakly decreases. We also characterize the accounting policies that the two rival firms would adopt if they could freely choose either an expensing policy or a capitalization policy.
Nitric oxide in the pathophysiology of retinopathy: evidences from preclinical and clinical researches
Authors: Opatrilova Radka , Kubatka Peter , Caprnda Martin , Büsselberg Dietrich , Krasnik Vladimir , Vesely Pavol , Saxena Sandeep , Ruia Surabhi , Mozos Ioana , Rodrigo Luis , Kruzliak Peter , dos Santos Katia Goncalves
Published: April 2017

Retinopathy is the leading cause of blindness and visual disability in working‐aged people. The pathogenesis of retinopathy is an actual and still open query. Alterations contributing to oxidative and nitrosative stress, including elevated nitric oxide and superoxide production, changes in the expression of different isoforms of nitric oxide synthase or endogenous antioxidant system, have been implicated in the mechanisms how this ocular disease develops. In addition, it was documented that renin–angiotensin system has been implicated in the progression of retinopathy. Based on comprehensive preclinical and clinical researches in this area, the role of above‐mentioned factors in the pathogenesis of diabetic retinopathy, hypertensive retinopathy and ischaemic proliferative retinopathy is reviewed in this study. Moreover, the genetic susceptibility factors involved in the development of the retinopathy and possible strategies that utilize antioxidants as additive therapy are also highlighted here.
Choroidal vascular changes in age‐related macular degeneration
Authors: Koh Lilian Hui Li , Agrawal Rupesh , Khandelwal Neha , Sai Charan Labishetty , Chhablani Jay
Published: April 2017

Purpose

To assess the choroidal vascular changes using choroidal vascularity index (CVI) in patients with age‐related macular degeneration (AMD) compared to controls.

Methods

Enhanced depth imaging (EDI) optical coherence tomography (OCT) scans of 64 patients with unilateral or bilateral AMD were obtained. Images with a poorly demarcated choroidal–scleral interface (CSI) were excluded from the analysis. Foveal scans of 63 AMD eyes and 35 ‘normal fellow’ eyes were analysed. Images of 30 eyes from 18 age‐matched healthy subjects were included as controls. Choroidal vascularity index (CVI) was derived from binarization of EDI OCT images, using fiji software.

Results

The mean age was 56.50 ± 5.50 years for AMD patients and 52.25 ± 6.75 years for controls. All patients were treatment naïve. Subfoveal choroidal thickness (SFCT) in AMD, ‘normal fellow’ eyes and controls was 314.02 ± 78.80 μm, 300.88 ± 53.85 μm and 278.5 ± 65.31 μm, respectively. Choroidal vascularity index (CVI) in AMD, ‘normal fellow’ eyes and controls was 64.04 ± 2.43%, 64.66 ± 2.25% and 66.07 ± 1.72%, respectively. Choroidal vascularity index (CVI) of both AMD and ‘normal fellow’ eyes was significantly lower compared to controls (p < 0.0001 and p = 0.007). The SFCT of AMD eye was not found to be significantly different from ‘normal fellow eyes’ (p = 0.45).

Conclusion

There was no statistical difference in SFCT, but CVI was significantly lower in patients with AMD. Choroidal vascularity index (CVI) was also lower in ‘normal fellow’ AMD eyes as compared to controls. This suggests possible reduction in choroidal vascularity in eyes with AMD and also to a certain extent in the ‘normal fellow’ eyes without phenotypical manifestations and may suggest underlying choroidal morphological change leading to wet AMD.
Preliminary study of a controllable device for subtenon drug infusion in a rabbit model
Authors: Duan Yiqin , Yang Yezhen , Huang Xuetao , Lin Ding
Published: April 2017

Background and objective

Conventional methods to treat intraocular diseases are invasive or associated with adverse effects. A minimally invasive means of sustained‐release drug delivery to the vitreous is required. This study evaluated a novel device for subtenon drug delivery to the vitreous, relative to a single subconjunctival injection.

Methods

Sixty adult New Zealand White rabbits were randomly assigned to receive demethylvancomycin (DMV) by continuous subtenon delivery with the flow rate of 0.1 ml/hr for 24 hr, or as a single 0.3 ml subconjunctival injection in the right eyes. Rabbits were killed in subgroups of six at 1, 3, 6, 12 and 24 hr. The DMV concentration of the vitreous humour of the right eye was analysed by high‐performance liquid chromatography.

Results

Overall, the vitreous DMV concentration of the subtenon group was significantly higher than that of the subconjunctival group (F = 25.928, p = 0.001). The DMV concentration of the subtenon group was also significantly higher than that of the subconjunctival group at 3, 6, 12 and 24 hr (t = 2.457, 5.064, 3.085, 4.207; p = 0.04, 0.01, 0.018, 0.004, respectively). In the subtenon group, the DMV concentration reached maximum (2.41 ± 0.67 μg/ml) at 6 hr, and at 24 hr was 2.37 ± 1.23 μg/ml. In the subconjunctival group, the DMV concentration reached maximum (0.48 ± 0.27 μg/ml) at 1 hr and declined to 0.09 ± 0.05 μg/ml at 24 hr.

Conclusion

Subtenon application with this novel minimally invasive design is an effective method for delivering an appropriate drug to the vitreous in a sustained and controllable amount.
Differential expression and localization of human tissue inhibitors of metalloproteinases in proliferative diabetic retinopathy
Authors: Abu El‐Asrar Ahmed M. , Ahmad Ajmal , Bittoun Emilie , Siddiquei Mohammad Mairaj , Mohammad Ghulam , Mousa Ahmed , De Hertogh Gert , Opdenakker Ghislain
Published: April 2017

Purpose

Tissue inhibitors of metalloproteinases (TIMPs) block the catalysis by matrix metalloproteinases (MMPs) and have additional biologic activities, including regulation of cell growth and differentiation, apoptosis, angiogenesis and oncogenesis. We investigated the expression levels of all the four human TIMPs and correlated these levels with those of MMP‐9 and vascular endothelial growth factor (VEGF) in proliferative diabetic retinopathy (PDR).

Methods

Vitreous samples from 38 PDR and 21 nondiabetic control patients and epiretinal membranes from 14 patients with PDR and 10 patients with proliferative vitreoretinopathy (PVR) were studied by enzyme‐linked immunosorbent assay, Western blot analysis and immunohistochemistry.

Results

Tissue inhibitor of metalloproteinases‐1, TIMP‐4, MMP‐9 and VEGF levels were significantly higher in vitreous samples from PDR patients than in nondiabetic controls (p < 0.0001 for all comparisons), whereas TIMP‐2 and TIMP‐3 levels did not differ significantly. TIMP‐1, TIMP‐4, MMP‐9 and VEGF levels in PDR with active neovascularization were significantly higher than those in inactive PDR (p < 0.0001, 0.001, 0.013, 0.004, respectively). Significant positive correlations existed between levels of TIMP‐1 and levels of TIMP‐4 (r = 0.37; p = 0.004), MMP‐9 (r = 0.65; p < 0.0001) and VEGF (r = 0.59; p < 0.0001), between levels of TIMP‐4 and levels of MMP‐9 (r = 0.61; p < 0.0001) and VEGF (r = 0.62; p < 0.0001) and between levels of MMP‐9 and VEGF (r = 0.62; p < 0.0001). TIMP‐1 and TIMP‐3 were expressed in vascular endothelial cells in PDR epiretinal membranes and in myofibroblasts and leucocytes in PDR and PVR epiretinal membranes.

Conclusion

The differential expression of TIMPs in PDR suggests that among the 4 TIMPs, TIMP‐1 and TIMP‐4 may be possible biomarkers of disease activity.
Can the SENSIMED Triggerfish® lens data be used as an accurate measure of intraocular pressure?
Authors: Vitish‐Sharma Parveen , Acheson Austin G. , Stead Richard , Sharp John , Abbas Ali , Hovan Marta , Maxwell‐Armstrong Charles , Guo Boliang , King Anthony J.
Published: April 2017

Purpose

The SENSIMED Triggerfish® contact lens sensor (CLS) has an embedded micro‐sensor that captures spontaneous circumferential changes at the corneoscleral junction and transmits them via an antenna to a device where these measurements are stored. During laparoscopic colorectal surgery, patients are placed in Trendelenburg position which has been shown to increase intraocular pressure (IOP). Laparoscopic colorectal surgery requires both pneumoperitoneum and Trendelenburg positioning; therefore, IOP can vary significantly. We aimed to assess whether circumferential changes in the corneoscleral area can be correlated to IOP changes measured using Tono‐pen® XL applanation tonometer during laparoscopic colorectal surgery.

Method

Patients undergoing laparoscopic colorectal resections were included. On the day of surgery, baseline IOP was taken and the SENSIMED Triggerfish® CLS was then set up in one eye of the patient. During surgery (whilst under general anaesthetic), IOP measurements were taken in the contralateral eye using a Tono‐pen® XL applanation tonometer every hour and any time the table was moved to record the fluctuations of IOP during surgery and any association with position change. The timings of these readings were documented.

Results

Twenty patients were included in this study (six males, 14 females). Average age was 64.6 years (SD = 16.3). The fluctuation in IOP measured in the reference eye ranged between 6.3 and 46.7 mmHg. The mean correlation coefficient between CLS output measurements and these IOP measurements was r = 0.291 (95% CI).

Conclusion

Our results showed a weak correlation between the SENSIMED Triggerfish® CLS data output and IOP measurements taken using the Tono‐pen® XL applanation tonometer.
Material migrations of performance
Authors: Rogers Amanda
Published: April 2017

This paper examines the multiple materialities of the performing arts and their transnational migration. In contrast to the majority of scholarship on the geographies of performance, which focuses on the space of the body, this paper provides an analysis of performance and materiality that encompasses, but also extends beyond, the corporeal through its attention to the material qualities of costumes, scripts and performance form. In conducting this analysis, the paper draws attention to the differential movement of performance work more widely by focusing on their composite materialities. Such an approach extends our apprehension of what the geographies of performance, and the geographies of art more widely, might be, and draws attention to under‐investigated spheres of creative activity.
Social anxiety and interpretation bias: examining clinical and subclinical components in adolescents
Authors: Loscalzo Yura , Giannini Marco , Miers Anne C.
Published: April 2017

Background

This study aimed to examine whether different components of interpretation bias are clinical or dimensional features of adolescent social anxiety. The study analyzed the components of this bias at a subclinical level of Social Anxiety Disorder (SAD) and compared these with a clinical sample of adolescents with SAD.

Method

Adolescents in the age range 13–17 years participated. A group with SAD (n = 30) was compared with a group with subclinical SAD (n = 60), and a non‐socially anxious group (n = 95).

Results

Negative interpretation bias for social situations was found to be a dimensional aspect of social anxiety. In contrast, belief in negative interpretations of social situations appears to be a clinical feature. Contrary to expectations, endorsement of positive interpretations did not differ between the three groups.

Conclusions

The results suggest that a screening instrument based on negative interpretations of social situations could be useful to detect adolescents at‐risk of developing SAD. In a clinical setting, the belief in negative interpretations and the presence of the bias in nonsocial situations should also be considered.
Children's experiences of managing Type 1 diabetes in everyday life: a thematic synthesis of qualitative studies
Authors: Rankin D. , Harden J. , Jepson R. , Lawton J.
Published: April 2017

Aims

To explore the everyday experiences of children (aged ≤ 12 years) with Type 1 diabetes to identify factors that help or hinder diabetes self‐management practices.

Methods

Eight databases (Embase, Medline, CINAHL, Web of Science, PsychInfo, ASSIA, ERIC and ProQuest Dissertations) were searched in 2016 to identify qualitative studies exploring children's views about self‐managing diabetes. Data were extracted, coded and analysed using thematic synthesis.

Results

Eighteen studies from five countries were included in the review. Synthesis of studies’ findings resulted in the identification of three overarching analytical themes. The first theme, ‘Understandings of diabetes and involvement in self‐management’, outlines ways in which children understand diabetes and develop self‐management responsibilities. The second theme, ‘Disruption to life and getting on with it’, reports children's frustrations at disruptions to everyday life when managing diabetes, and how attempts to appear normal to family and friends affect self‐management practices. The third theme, ‘Friends’ support’, describes how friends’ reactions and responses to diabetes affect children's ability to appear normal and willingness to disclose information about diabetes, and support provided by ‘informed friends’, or peers with diabetes.

Conclusions

Although the synthesis has identified how children's everyday life experiences inform ways in which they undertake diabetes self‐management, it was not possible to determine new ways to provide support. To help children optimise their glycaemic control, further work should be undertaken to identify their need for support and which takes into account the potential ways in which parents, friends and peers can offer assistance.
Myths and realities about input subsidies in sub‐Saharan Africa
Authors: Ghins Léopold , Mas Aparisi Alban , Balié Jean
Published: April 2017

Using a recent public expenditure dataset, this article proposes a ‘reality check’ of the level and composition of input subsidies in nine African countries between 2006 and 2013. Results show that input subsidies (1) received close to 35% of agricultural‐specific expenditure on average and (2) cover a variety of interventions, including investments in capital, such as on‐farm irrigation, and in on‐farm services, such as inspection or training. Further, the figures show that input subsidies tended to become entrenched in agricultural budgets over time, leading to sub‐optimal execution rates, and were primarily funded by the national taxpayer, while donors invested more in public goods. Findings confirm that input subsidies crowded out other spending categories likely to be more supportive of long‐term agricultural development objectives. The article concludes that the political economy of input subsidies should be directed to making more concrete efforts to attain a better balance of public expenditure on agriculture. Furthermore, policy‐makers should aim to increase the efficiency and policy coherence of input subsidies, since merely abolishing them is likely to be unfeasible in the short term.
The livelihood challenges of resettled communities of the Bui dam project in Ghana and the role of Chinese dam‐builders
Authors: Yankson Paul W. K. , Asiedu Alex B. , Owusu Kwadwo , Urban Frauke , Siciliano Giuseppina
Published: April 2017

Emerging issues from the Bui hydropower project suggest that the experiences of two earlier hydropower projects in Ghana failed to prevent challenges related to resource access and livelihoods. This article examines the nature of the challenges, their causes, why they were not avoided and the role of the Chinese builders. We conducted 43 interviews and 11 focus group discussions and analyzed qualitative data by themes using narrative analysis. Our findings show that the livelihoods of the resettled communities are, on balance, negatively impacted by the construction of the dam. While Chinese dam‐builders played a major role in financing and enabling the dam's construction, the Ghanaian governance arrangements were found to be more important in addressing the livelihood challenges.
Probabilistic vs. deterministic fiber tracking and the influence of different seed regions to delineate cerebellar‐thalamic fibers in deep brain stimulation
Authors: Schlaier Juergen R. , Beer Anton L. , Faltermeier Rupert , Fellner Claudia , Steib Kathrin , Lange Max , Greenlee Mark W. , Brawanski Alexander T. , Anthofer Judith M.
Published: April 2017

This study compared tractography approaches for identifying cerebellar‐thalamic fiber bundles relevant to planning target sites for deep brain stimulation (DBS). In particular, probabilistic and deterministic tracking of the dentate‐rubro‐thalamic tract (DRTT) and differences between the spatial courses of the DRTT and the cerebello‐thalamo‐cortical (CTC) tract were compared. Six patients with movement disorders were examined by magnetic resonance imaging (MRI), including two sets of diffusion‐weighted images (12 and 64 directions). Probabilistic and deterministic tractography was applied on each diffusion‐weighted dataset to delineate the DRTT. Results were compared with regard to their sensitivity in revealing the DRTT and additional fiber tracts and processing time. Two sets of regions‐of‐interests (ROIs) guided deterministic tractography of the DRTT or the CTC, respectively. Tract distances to an atlas‐based reference target were compared. Probabilistic fiber tracking with 64 orientations detected the DRTT in all twelve hemispheres. Deterministic tracking detected the DRTT in nine (12 directions) and in only two (64 directions) hemispheres. Probabilistic tracking was more sensitive in detecting additional fibers (e.g. ansa lenticularis and medial forebrain bundle) than deterministic tracking. Probabilistic tracking lasted substantially longer than deterministic. Deterministic tracking was more sensitive in detecting the CTC than the DRTT. CTC tracts were located adjacent but consistently more posterior to DRTT tracts. These results suggest that probabilistic tracking is more sensitive and robust in detecting the DRTT but harder to implement than deterministic approaches. Although sensitivity of deterministic tracking is higher for the CTC than the DRTT, targets for DBS based on these tracts likely differ.
Estimates of heritability of atrial fibrillation in the Standardbred racehorse
Authors: Kraus M. , Physick‐Sheard P. W. , Brito L. F. , Schenkel F. S.
Published: April 2017

Background

The number of Standardbred racehorses admitted to the Ontario Veterinary College Teaching Hospital (Guelph, Canada) for treatment of atrial fibrillation (AF) has been on the rise since the early 1990s. A small number of sires have been contributing to a large proportion of cases, indicating there may be a genetic predisposition to the arrhythmia in this breed.

Objectives

The objectives of this study were to determine the heritability of AF in Standardbred horses and whether heritability of the arrhythmia differs across gaits and/or sexes.

Study design

Heritability study based on retrospective review of clinical records and publicly available pedigree and racing records.

Methods

Standardbred horses admitted to hospital for treatment of AF that were born between 1978 and 2007 comprised the affected case population (n = 204). Five randomly selected racing contemporaries for each case, assumed to not suffer from the arrhythmia, comprised the control population (n = 1017). Racing contemporaries were identified by examining the race records of affected horses within the 6 months prior to their admission, and randomly selecting sex‐ and gait‐matched horses from these races. Heritability was estimated from the sampled horses as a whole (n = 1221), as well as for both sexes and gaits, using a generalised linear mixed model.

Results

Heritability of AF on the underlying liability scale was estimated to be (±s.e.) 0.30±0.04 in the entire data set; 0.30±0.06 in males; 0.24±0.08 in females; and 0.32±0.05 in pacers. After conversion to the observed scale, heritability estimates were 0.14, 0.15, 0.09 and 0.15, respectively.

Main limitations

There were insufficient data to estimate heritability of AF for trotters.

Conclusions

Modest heritability estimates were found for AF in the Standardbred horse, particularly in males and pacers, which support the hypothesis that there is a genetic contribution to the arrhythmia in this breed.

The Summary is available in Chinese – See Supporting Information.
CHI3L1 regulation of inflammation and the effects on osteogenesis in a Staphylococcus aureus‐induced murine model of osteomyelitis
Authors: Chen XueQiu , Jiao Jian , He XiaoQing , Zhang JianPing , Wang Hai , Xu YongQing , Jin Tao
Published: April 2017

Osteomyelitis is an inflammation of the bone and bone marrow that occurs as a consequence of infections mainly attributed to Staphylococcus aureus. In a previous study, we found that expression of the chitinase 3‐like 1 (CHI3L1) gene affected mineralization of MC3T3‐E1 cells infected with S. aureus and there was increased expression of CHI3L1 in the blood of osteomyelitis patients. In the present study, to further investigate the role of CHI3L1 in osteomyelitis, we developed an S. aureus‐induced murine model of the disease. We found that the expression of CHI3L1 was significantly up‐regulated in femurs of mice infected with S. aureus compared with mice inoculated with a PBS control. To investigate these results further, we performed a CHI3L1 knock‐down by lentivirus‐mediated RNA interference in mice. Micro‐computed tomography of infected femurs revealed that S. aureus triggers profound alterations in bone turnover, and femurs of CHI3L1 short hairpin RNA (shRNA‐CHI3L1)‐injected mice infected with S. aureus have significantly less cortical bone destruction when compared with control mice infected with S. aureus. Inhibition of CHI3L1 also decreased inflammation by reducing levels of proinflammatory cytokines and promoted the process of osteogenesis. The Notch signaling pathway has been shown to play an important role in modulating the differentiation of osteoblasts and osteoclasts. Our study showed that Notch1, Jagged1 and Hes1 expression significantly decreased in mice infected with S. aureus compared with the control, and shRNA‐CHI3L1 could increase their level in S. aureus‐infected mice. This research indicates that inhibition of CHI3L1 can reduce the debilitating effects of S. aureus in a murine model of osteomyelitis.
Structural features of Aspergillus niger β‐galactosidase define its activity against glycoside linkages
Authors: Rico‐Díaz Agustín , Ramírez‐Escudero Mercedes , Vizoso‐Vázquez Ángel , Cerdán M. Esperanza , Becerra Manuel , Sanz‐Aparicio Julia
Published: April 2017

β‐Galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of β‐galactosides. Among them, the Aspergillus niger β‐galactosidase (AnβGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity which is used to degrade lactose. We present here its three‐dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304, and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnβGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnβGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto‐oligosaccharides production than the Aspergillus oryzae β‐galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 β‐galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design.

Database

Structural data are available in PDB database under the accession numbers 5IFP (native form), 5IHR (in complex with 6GalGlu), 5IFT (in complex with 3GalGlu), 5JUV (in complex with 6GalGal), 5MGC (in complex with 4GalLac), and 5MGD (in complex with 6GalLac).
Point stresses during reproductive stage rather than warming seasonal temperature determine yield in temperate rice
Authors: Espe Matthew B. , Hill Jim E. , Hijmans Robert J. , McKenzie Kent , Mutters Randall , Espino Luis A. , Leinfelder‐Miles Michelle , van Kessel Chris , Linquist Bruce A.
Published: April 2017

Climate change is predicted to shift temperature regimes in most agricultural areas with temperature changes expected to impact yields of most crops, including rice. These temperature‐driven effects can be classified into point stresses, where a temperature event during a sensitive stage drives a reduction in yield, or seasonal warming losses, where raised temperature is thought to increase maintenance energy demands and thereby decrease available resources for yield formation. Simultaneous estimation of the magnitude of each temperature effect on yield has not been well documented due to the inherent difficulty in separating their effects. We simultaneously quantified the magnitude of each effect for a temperate rice production system using a large data set covering multiple locations with data collected from 1995 to 2015, combined with a unique probability‐based modeling approach. Point stresses, primarily cold stress during the reproductive stages (booting and flowering), were found to have the largest impact on yield (over 3 Mg/ha estimated yield losses). Contrary to previous reports, yield losses caused by increased temperatures, both seasonal and during grain‐filling, were found to be small (approximately 1–2% loss per °C). Occurrences of cool temperature events during reproductive stages were found to be persistent over the study period, and within season, the likelihood of a cool temperature event increased when flowering occurred later in the season. Short and medium grain types, typically recommended for cool regions, were found to be more tolerant of cool temperatures but more sensitive to heat compared to long grain cultivars. These results suggest that for temperate rice systems, the occurrence of periodic stress events may currently overshadow the impacts of general warming temperature on crop production.
Enhanced evapotranspiration was observed during extreme drought from Miscanthus, opposite of other crops
Authors: Joo Eva , Zeri Marcelo , Hussain Mir Zaman , DeLucia Evan H. , Bernacchi Carl J.
Published: April 2017

The impact of extreme drought and heat stress that occurred in the Midwestern U.S. in 2012 on evapotranspiration (ET), net ecosystem productivity (NEP), and water‐use efficiency (WUE) of three perennial ecosystems (switchgrass, miscanthus, prairie) and a maize/soybean agroecosystem was studied as part of a long‐term experiment. Miscanthus had a slower initial response but an eventually drastic ET as drought intensified, which resulted in the largest water deficit among the crops. The substantially higher ET at peak drought was likely supplied by access to deep soil water, but suggests that stomatal conductance of miscanthus during the drought may respond differently than the other ecosystems, consistent with an anisohydric strategy. While there was a discrepancy in the water consumption of maize and switchgrass/prairie in the early time of drought, all these ecosystems followed a water‐saving strategy when drought intensified. The gross primary production (GPP) of miscanthus dropped, but was reversible, when temperature reached 40 °C and still provided the largest total GPP among the ecosystems. Increased ET for miscanthus during 2012 resulted a large decline in ecosystem WUE compared to what was observed in other years. The biophysical responses of miscanthus measured during an extreme, historic drought suggest that this species can maintain high productivity longer than other ecosystems during a drought at the expense of water use. While miscanthus maintained productivity during drought, recovery lagged associated with depleted soil moisture. The enhanced ET of miscanthus may intensify droughts through increase supply of deep soil moisture to the atmosphere.
Experimental investigation of the LiAlSi2O6‐MgSiO3 and LiAlSi2O6‐CaMgSi2O6 isopleths at 1 atm
Authors: Konar Bikram , Hudon Pierre , Jung In‐Ho
Published: April 2017

The phase diagrams of the LiAlSi2O6‐MgSiO3 and LiAlSi2O6‐CaMgSi2O6 isopleths were experimentally investigated at 1 atm using the quenching method and differential scanning calorimetry and the phases produced were characterized with the help of X‐ray diffraction and electron probe microanalysis. With the help of thermodynamic optimization, the phase diagrams of both systems were more accurately reported. No detectable solubility of Li2O in diopside and enstatite was found. However, both systems are not simple binary eutectic systems because their phase equilibria are somewhat complex due to the presence of some β‐spodumene solid solution. In the β‐spodumene solid solution, no notable solubility of MgO and CaO was detected; evidence of significant solubility of SiO2 was confirmed.
Hydrothermal formation and up‐conversion luminescence of Er3+‐doped GdNbO4
Authors: Hirano Masanori , Ishikawa Katsuya
Published: April 2017

The effect of concentration of Er3+ on the up‐conversion and photoluminescence properties of Gd1.00−xErxNbO4, x=0‐0.50 which has monoclinic fergusonite‐type structure as a main phase has been investigated, using a processing technique based on hydrothermal method. Under weakly basic hydrothermal condition at 240°C for 5 hours, a single phase of fergusonite‐type Gd1.00−xErxNbO4 solid solution was directly formed as nanocrystals by the substitutional incorporation of Er3+ into GdNbO4 because of the gradual and linear decrease in the lattice parameters of the monoclinic phase corresponding to the Vegard's Law. The gadolinium niobate doped with 2 mol% Er3+, Gd0.98Er0.02NbO4 after heating at 1300°C for 1 hour, which has nanocrystalline structure whose crystallite size is around 29 nm, exhibits the highest photoluminescence intensity in the green spectral region, 515‐560 nm under excitation at wavelength of 254 nm. On the other hand, the up‐converted luminescence intensity of the niobate nanocrystals becomes the maximum at the concentration of 20 mol% Er3+, Gd0.80Er0.20NbO4 under excitation at 980 nm. These results demonstrate that the material, Er3+‐doped GdNbO4 nanocrystals prepared through hydrothermal route and postheating has potential for up‐converting phosphor.
Low‐temperature aging of baddeleyite‐based Ca‐TZP ceramics
Authors: Zhigachev Andrey O. , Umrikhin Alexey V. , Korenkov Viktor V. , Golovin Yuri I.
Published: April 2017

The aging kinetics during low‐temperature aging of calcia‐stabilized tetragonal zirconia polycrystal (Ca‐TZP) ceramics prepared by high‐energy milling of natural zirconia mineral (baddeleyite) was studied by X‐ray diffraction under hydrothermal treatment conditions. Aging kinetics was investigated for ceramics with different contents of calcia. It was found that the kinetics may be well‐described within Johnson‐Mehl‐Avrami‐Kolmogorov model. Model parameters were determined by data fitting procedure. Change in exponential factor within Johnson‐Mehl‐Avrami‐Kolmogorov model with time is shown. Analytical model to describe aging kinetics is proposed. The transformation nucleation rate, initial diameter, and depth of the transformed areas and their growth rates are estimated. Degradation of hardness and fracture toughness is also reported for Ca‐TZP after low‐temperature aging for different contents of the stabilizer.