bluuebunny/crossref_metadata_2025 huggingface dataset:
Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers
Authors: Heidaritabar M. , Calus M.P.L. , Megens H‐J. , Vereijken A. , Groenen M.A.M. , Bastiaansen J.W.M.
Published: January 2016

There is an increasing interest in using whole‐genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole‐genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole‐genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non‐synonymous and non‐coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non‐synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.
Not all Treaties are Created Equal: The Effects of Treaty Changes on Legislative Efficiency in the EU
Authors: Bølstad Jørgen , Cross James P.
Published: January 2016

One of the key motives behind recent reforms of the EU's legislative process has been to increase efficiency. This study examines whether the Amsterdam, Nice and Lisbon treaties have successfully increased the speed with which the EU creates new laws. An interrupted time series approach is utilized to detect the total effects of treaty change on the decision‐making process. This study thus complements existing research on the effects of decision‐making rules, by employing a design more robust to the challenge of endogeneity. The findings suggest that the Amsterdam treaty was very successful at increasing legislative efficiency. In contrast, the Nice treaty does not appear to have had a notable impact, and, more interestingly, neither does the Lisbon treaty.
Evolutionary history of the little fire ant Wasmannia auropunctata before global invasion: inferring dispersal patterns, niche requirements and past and present distribution within its native range
Authors: Chifflet L. , Rodriguero M. S. , Calcaterra L. A. , Rey O. , Dinghi P. A. , Baccaro F. B. , Souza J. L. P. , Follett P. , Confalonieri V. A.
Published: January 2016

The evolutionary history of invasive species within their native range may involve key processes that allow them to colonize new habitats. Therefore, phylogeographic studies of invasive species within their native ranges are useful to understand invasion biology in an evolutionary context. Here we integrated classical and Bayesian phylogeographic methods using mitochondrial and nuclear DNA markers with a palaeodistribution modelling approach, to infer the phylogeographic history of the invasive ant Wasmannia auropunctata across its native distribution in South America. We discuss our results in the context of the recent establishment of this mostly tropical species in the Mediterranean region. Our Bayesian phylogeographic analysis suggests that the common ancestor of the two main clades of W. auropunctata occurred in central Brazil during the Pliocene. Clade A would have differentiated northward and clade B southward, followed by a secondary contact beginning about 380 000 years ago in central South America. There were differences in the most suitable habitats among clades when considering three distinct climatic periods, suggesting that genetic differentiation was accompanied by changes in niche requirements, clade A being a tropical lineage and clade B a subtropical and temperate lineage. Only clade B reached more southern latitudes, with a colder climate than that of northern South America. This is concordant with the adaptation of this originally tropical ant species to temperate climates prior to its successful establishment in the Mediterranean region. This study highlights the usefulness of exploring the evolutionary history of invasive species within their native ranges to better understand biological invasions.
The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird
Authors: Bertrand J. A. M. , Delahaie B. , Bourgeois Y. X. C. , Duval T. , García‐Jiménez R. , Cornuault J. , Pujol B. , Thébaud C. , Milá B.
Published: January 2016

Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients.
A new species of philometrid parasite (Nematoda, Philometridae) and histopathological lesions in juvenile whitemouth croakers, Micropogonias furnieri (Desmarest)
Authors: Montes M M , Plaul S E , Martorelli S R
Published: January 2016

A new species of nematode parasite, Philometroides tahieli sp. nov. is described. The juvenile whitemouth croaker, Micropogonias furnieri Desmarest, was collected during the spring and summer of the years 2008–2010 from estuarial environments of Argentina. During investigations of the parasite fauna a nematode encapsulated in the musculature of the operculum was found. The nematodes were removed from the host's muscle tissue and slide‐mounted in lactophenol solution to clarify the specimens. Opercular muscle with the parasite was processed for histopathological examination. Philometroides tahieli sp. nov. can be identified by the location of gravid females in the host, presence of anterior oesophageal bulb, bosses on the surface of the body, presence of transversal mounds and 14 cephalic papillae in two circular rows. The pathogenicity of the parasite is low in the natural environment, but lesions are consistent with a chronic process. The appearance of caseous necrosis suggests the presence of a locally acting substance. Philometroides tahieli sp. nov. is the second species of this genera described from brackish waters, and since the discovery of Philometroides maplestoni in 1928, is the first species of this genus recorded for South America.
Morphological diversity of Paramoeba perurans trophozoites and their interaction with Atlantic salmon, Salmo salar L., gills
Authors: Wiik‐Nielsen J , Mo T A , Kolstad H , Mohammad S N , Hytterød S , Powell M D
Published: January 2016

Amoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans affects several cultured marine fish species worldwide. In this study, the morphology and ultrastructure of P. perurans in vitro and in vivo was investigated using scanning and transmission electron microscopy (SEM and TEM, respectively). Amoebae cultures contained several different morphologies ranging from a distinct rounded cell structure and polymorphic cells with pseudopodia of different lengths and shapes. SEM studies of the gills of AGD‐affected Atlantic salmon, Salmo salar L., revealed the presence of enlarged swellings in affected gill filaments and fusion of adjacent lamellae. Spherical amoebae appeared to embed within the epithelium, and subsequently leave hemispherical indentations with visible fenestrations in the basolateral surface following their departure. These fenestrated structures corresponded to the presence of pseudopodia which could be seen by TEM to penetrate into the epithelium. The membrane–membrane interface contained an amorphous and slightly fibrous matrix. This suggests the existence of cellular glycocalyces and a role for extracellular products in mediating pathological changes in amoebic gill disease.
Essential oils to control ichthyophthiriasis in pacu, Piaractus mesopotamicus (Holmberg): special emphasis on treatment with Melaleuca alternifolia
Authors: Valladão G M R , Gallani S U , Ikefuti C V , da Cruz C , Levy‐Pereira N , Rodrigues M V N , Pilarski F
Published: January 2016

In vitro effect of the Melaleuca alternifolia, Lavandula angustifolia and Mentha piperita essential oils (EOs) against Ichthyophthirius multifiliis and in vivo effect of M. alternifolia for treating ichthyophthiriasis in one of the most important South American fish, Piaractus mesopotamicus (Holmberg), were evaluated. The in vitro test consisted of three EOs, each at concentrations of 57 μL L−1, 114 μL L −1, 227 μL L−1 and 455 μL L −1, which were assessed once an hour for 4 h in microtitre plates (96 wells). The in vitro results demonstrated that all tested EOs showed a cytotoxic effect against I. multifiliis compared to control groups (P < 0.05). The in vivo treatment for white spot disease was performed in a bath for 2 h day−1 for 5 days using the M. alternifolia EO (50 μL L −1). In this study, 53.33% of the fish severely infected by I. multifiliis survived after the treatment with M. alternifolia (50 μL L −1) and the parasitological analysis has shown an efficacy of nearly 100% in the skin and gills, while all the fish in the control group died. Furthermore, the potential positive effect of M. alternifolia EO against two emergent opportunistic bacteria in South America Edwardsiella tarda and Citrobacter freundii was discussed.
Development, validation and implementation of a quantitative food frequency questionnaire to assess habitual vitamin D intake
Authors: Kiely M. , Collins A. , Lucey A. J. , Andersen R. , Cashman K. D. , Hennessy Á.
Published: January 2016

Background

A well‐designed, validated quantitative food frequency questionnaire (FFQ) could offer an efficient and cost‐effective method for assessing habitual vitamin D intake. The present study aimed to describe the development, validation and implementation of a vitamin D FFQ.

Methods

National food consumption survey data obtained from Irish adults (18–64 years) were used to identify foods that contribute 95% of vitamin D intake. A winter‐based validation study was carried out for the resulting FFQ in 120 females, including 98 women [mean (SD) 65.0 (7.3) years] and 22 girls [12.2 (0.8) years], using a 14‐day diet history (DH) as a comparator. Serum 25(OH)D concentrations were analysed. Validity coefficients were calculated using the method of triads. Cross‐classification and Bland–Altman analysis were also performed.

Results

Median (interquartile range) vitamin D intakes (including the contribution from nutritional supplements) were 5.4 (3.7) and 3.7 (5.9) μg day−1 from the FFQ and DH, respectively and intakes of vitamin D from food sources were 3.6 (3.1) and 2.4 (2.2) μg day−1. The FFQ and DH classified 86% and 87% of individuals into the same and adjacent thirds of wintertime serum 25(OH)D status, respectively. There was a strong association (r = 0.71, P < 0.0001) and no significant systematic or proportional bias observed for the difference between estimates from the FFQ and DH. The validity coefficient for the FFQ was 0.92 (95% confidence interval = 0.80–0.97). Repeatability analysis (n = 56) performed 6–12 months later showed no significant difference in estimates of vitamin D between administrations.

Conclusions

The data obtained in the present study indicate high validity and good reproducibility of a short, interviewer‐administered FFQ for vitamin D.
Medicinal and cosmetics soap production from Jatropha oil
Authors: Shahinuzzaman M. , Yaakob Zahira , Moniruzzaman M.
Published: January 2016

Soap is the most useful things which we use our everyday life in various cleansing and cosmetics purposes. Jatropha oil is nonedible oil which has more benefits to soap making. It has also cosmetics and medicinal properties. But the presence of toxic Phorbol esters in Jatropha oil is the main constrains to use it. So it is necessary to search a more suitable method for detoxifying the Jatropha oil before the use as the main ingredient of soap production. This review implies a more suitable method for removing phorbol esters from Jatropha oil. Several parameters such as the % yield of pure Jatropha oil soap, TFM value of soap, total alkali content, free caustic alkalinity content, pH, the antimicrobial activity, and CMC value of general soap should be taken into consideration for soap from detoxified Jatropha oil.
Senile lower lid entropion successfully treated with botulinum toxin A
Authors: Iozzo Ivano , Tengattini Vera , Antonucci Valentina A
Published: January 2016

Background

Spasmodic senile entropion (SE) is characterized by the inward turning of the eyelid. SE typically occurs spontaneously, but sometimes after ocular surgery. As of today, it is still lacking a gold standard technique.

Aims

To report the results of 11 cases of involutional entropion of the lower lid successfully treated with an injection of botulinum toxin, to evaluate the clinical results, and to document the duration of relief.

Methods

Eleven patients with senile entropion were treated with abobotulinum toxin A. The orbicularis oculi muscle was injected with 35 Su units of botulinum toxin. The procedures required an average of 5 min to complete. The follow‐up period was 24 months.

Results

The average age of the patients was 68.09 years (ranging between 62 and 75). About 7 days after the treatment, the entropion had resolved and there was only one recurrence at the 3‐month visit. The recurrence rate was 27% after 6 months, and 27% after 9 months. Of note, the patients with recurrence repeated the injection and showed an increasingly long wellness period.

Conclusions

Injection of botulinum toxin can treat entropion and resulted in a significantly high success rate.
Staff attitudes and reactions towards residents’ masturbation in Spanish long‐term care facilities
Authors: Villar Feliciano , Serrat Rodrigo , Celdrán Montserrat , Fabà Josep
Published: January 2016

Aims and objectives

To explore staff attitudes and reactions towards masturbation in long‐term care facilities.

Background

Staff attitudes and reactions towards the expression of sexuality in long‐term care facilities may be influenced by the nature of the sexual behaviour being expressed. Staff attitudes towards masturbation, a common sexual behaviour in such settings, have gone largely unexplored so far.

Design

An exploratory, descriptive, qualitative research design.

Methods

Fifty‐three staff members working in five different long‐term care facilities participated in the study. They were asked about what they would think, how they would react, and what possible reactions they might expect from workmates if they entered a room and found a resident masturbating.

Results

The majority of participants considered that masturbation was acceptable and avoiding interference was by far the most common reaction, although other reactions also arose. When asked about reactions attributed to workmates, mentions to reprimanding the resident and gossiping/joking about the issue were more frequent than acceptance.

Conclusions

The discrepancy between professionals’ own reported attitudes and those attributed to workmates suggests the existence of widespread negative reactions towards sexual activity in later life.

Relevance to clinical practice

In the light of these results, we underline the necessity of developing explicit policies regarding sexual issues. Formal training offered to staff would also help to recognise and preserve resident's sexual rights and needs.
Creating facades of conformity in the face of job insecurity: A study of consequences and conditions
Authors: Hewlin Patricia Faison , Kim Sung Soo , Song Young Ho
Published: January 2016

This study investigates creating facades of conformity (i.e., suppressing personal values and pretending to embrace organizational values) as a coping strategy associated with perceived job insecurity in workplace. In two survey‐based studies, we examined the conditions under which such a strategy is more likely, and the consequences of its use. The results show in Study 1 (N = 404) and in Study 2 (N = 622) that facades of conformity, although employed as an agentic response to protect one's status, is paradoxically associated with negative employee outcomes including increased intention to leave and reduced affective commitment. Furthermore, the results show that age attenuates the relationship between perceived job insecurity and facades of conformity, such that older workers are less likely than younger workers to engage in facades under higher job insecurity. Our research contributes to theory on job insecurity, authenticity, and lifespan development. Managerial implications are discussed.

Practitioner points

The current study found that employees who feel their job security threatened were more likely to suppress personal values and pretend to embrace organizational values, and such responses were linked to their intention to leave and reduced affective commitment.

The results from this study highlight the importance of fostering organizational environments that encourage authenticity such that members are not compelled to suppress personal values and pretend to embrace organizational values in job‐insecure environments.

The results also highlight how employees will enact their careers at different stages of their lives. In job‐insecure environments, older workers are more likely than younger workers to express divergent points of view.
IL‐1β‐regulating angiogenic factors expression in perforated temporomandibular disk cells via NF‐κB pathway
Authors: Xu Jie , Cai Hengxing , Meng Qinggong , Li Yingjie , Chen Guoxin , Fang Wei , Long Xing
Published: January 2016

Background

A high density of blood vessels is observed in the perforated disks of temporomandibular joint (TMJ), but the underlying mechanism is unknown. This study aimed to explore the regulation of disk angiogenesis in the perforated disks.

Methods

Expressions of vascular endothelial growth factor (VEGF), angiogenin‐1 (Ang‐1), chondromodulin‐1 (ChM‐1), and thrombospondins‐1 (TSP‐1) were compared between healthy and perforated TMJ disk cells with or without interleukin‐1β (IL‐1β) incubation. The tube formation, cell migration, and expressions of matrix‐metalloproteinases (MMPs) in human umbilical vein endothelial cell line (HUV‐EC‐C) were investigated in conditional media of disk cells. Western blot was performed to determine protein level of VEGF, Ang‐1, ChM‐1 and TSP‐1 in IL‐1β‐induced disk cells cultured by NF‐κB‐ or P38‐specific pathway inhibitors, respectively.

Results

Conditional media from perforated disk cells induced more tube formation, cell migration, and MMPs’ expression in HUV‐EC‐C. Expressions of VEGF and Ang‐1 were significantly higher, and ChM‐1 and TSP‐1 were lower in perforated disks compared to healthy disks. The VEGFA concentration was 291.1 ± 36.09 pg/ml in perforated disk cell conditioned media, markedly larger than that in NDCCM (144.9 ± 33.69 pg/ml). IL‐1β induced VEGF through NF‐κB signaling pathway and Ang‐1 through p38 MAPK pathway, while repressed expression of ChM‐1 and TSP‐1 was through NF‐κB pathway. Blockade of each pathway markedly restrained inducing effect of cultural media on HUV‐EC‐C tube formation and migration.

Conclusions

Perforated disk cells secreted more angiogenic factors which might induced via NF‐κB pathway.
Diagnosing autism: Australian paediatric research network surveys
Authors: Randall Melinda , Albein‐Urios Natalia , Brignell Amanda , Gulenc Alisha , Hennel Sabine , Coates Cathy , Symeonides Christos , Hiscock Harriet , Marraffa Catherine , Silove Natalie , Bayl Vivian , Woolfenden Susan , Williams Katrina
Published: January 2016

Aim

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with reported prevalence of more than 1/100. In Australia, paediatricians are often involved in diagnosing ASD and providing long‐term management. However, it is not known how paediatricians diagnose ASD. This study aimed to investigate whether the way Australian paediatricians diagnose ASD is in line with current recommendations.

Methods

Members of the Australian Paediatric Research Network were invited to answer questions about their ASD diagnostic practice in a multi‐topic survey and also as part of a study about parents needs around the time of a diagnosis of ASD.

Results

The majority of the 124 paediatricians who responded to the multi‐topic survey and most who responded to the parent needs survey reported taking more than one session to make a diagnosis of ASD. Most paediatricians included information from preschool, child care or school when making a diagnosis, and over half included information from speech pathology or psychology colleagues more than 50% of the time. The main reasons for not including assessment information in the diagnostic process were service barriers such as no regular service available or long waiting lists. More than 70% reported ordering audiology and genetic tests more than half of the time.

Conclusion

Not all paediatricians are following current recommendations for diagnosing ASD more than 50% of the time. While there are good reasons why current diagnostic approaches may fall short of expected standards, these need to be overcome to ensure diagnostic validity and optimal services for all children and their families.
Prescribed fire alters surface activity and movement behavior of a terrestrial salamander
Authors: O'Donnell K. M. , Thompson F. R. , Semlitsch R. D.
Published: January 2016

Prescribed fire has become a commonly used forest management tool for reducing the occurrence of severe wildfires, decreasing fuel loads and reestablishing the historic ecological influences of fire. Investigating population‐level wildlife responses to prescribed fire is important for evaluating the effects of fire management on animals, but in order to predict and simulate wildlife responses to potential management actions, mechanistic studies that elucidate individual‐level responses are also necessary. We used radio‐frequency identification to investigate individual‐level responses of western slimy salamanders Plethodon albagula to prescribed fire. We compared the salamander home‐range sizes [minimum convex polygons (MCP)], movement behaviors, and activity levels before and after prescribed fire using a randomized block experiment. We initiated the study at three plots in 2011, and added two new plots in 2012. We captured, tagged and released ≥38 salamanders at each plot from May 2011–May 2012 (total N = 205). We recorded 918 total recaptures of 142 unique salamanders; 31% of tagged salamanders were never recaptured. Across all years and treatments, only 14% of relocations were surface‐active (i.e. visually confirmed) salamanders; the others were underground. Following prescribed fire, the surface‐active proportion of recaptures was nearly seven times greater in control versus burned areas, which indicates that P. albagula respond to post‐prescribed fire conditions by spending more time belowground. We did not find evidence of direct mortality of salamanders from fires; the proportion of known‐alive individuals did not differ between treatments. Maximum daily displacement was 43.3% higher among burn‐area than control‐area salamanders, and MCP varied in a similar pattern; this may indicate salamanders were attempting to find more hospitable microenvironments or other resources, such as prey. Together, these individual‐level observations corroborate our findings from a population‐level study of a congeneric terrestrial salamander and contribute to our understanding of the behavioral mechanisms underlying population dynamics.
Romantic Anarchism: Asceticism, Aestheticism, and Education
Authors: Jun Nathan
Published: January 2016

Many anarchists of the late 19th and early 20th expressed a deeply anti‐romantic – one might even say chauvinistic – attitude marked by hostility toward artists, intellectuals, bohemians, and other “sentimentalists”; an unwavering commitment to austerity and personal self‐denial; and contempt for non‐political feelings and relationships, including family relationships. To this extent, many anarchists were simultaneously “romantic” (in the sense of being idealistic) as well as “anti‐romantic” (in the sense of being austere, pragmatic, and opposed to sentimentality). In this essay, I argue that the “anti‐romantic” tendency exemplified by some anarchists – which I will call “Romantic asceticism” – is actually profoundly Romantic (upper‐case ‘R’) insofar as it draws upon various political and philosophical ideas associated with 19th‐century Romanticism. At the same time, I will explore the existence of an alternative and countervailing tendency – which I will call “Romantic aestheticism” – which, although it is at least as indebted to Romanticism, stands in fundamental opposition to the former tendency. Further, I will argue that the latter tendency is not only more prevalent among the anarchists of this period but also more influential and significant in the history of anarchist thought and practice.
Under History's Changing Climate: Anarchism's Romantic Moods
Authors: Cohn Jesse
Published: January 2016

Is anarchism itself a form of what Jerome J. McGann called “romantic ideology,” privileging passion over reason, the affective over the cognitive? An answer is more difficult to give than might be readily apparent. On the one hand, anarchists have defined their political identity against romanticism as the literature of “tender, delicate, distinguished souls, aspiring to heaven, and living on earth as if in spite of themselves (Bakunin).” However, the anarchist tradition does betray a certain romantic genealogy, and anarchists such as Louise Michel, Gustav Landauer, and Rudolf Rocker have often evinced fascination with what Proudhon lambasted as a “literature of decadence.” Ultimately, rather than rendering a definitive political judgment on romanticism, anarchists come to enlist elements of its poetry and philosophy to organize affects in response to changing historical conditions.
High antiviral activity of NS5A inhibitor ABT‐530 with paritaprevir/ritonavir and ribavirin against hepatitis C virus genotype 3 infection
Authors: Poordad Fred , Landis Charles S. , Asatryan Armen , Jackson Daniel F. , Ng Teresa I. , Fu Bo , Lin Chih‐Wei , Yao Betty , Kort Jens
Published: January 2016

Background & Aims

ABT‐530 is a next‐generation hepatitis C virus (HCV) NS5A inhibitor with potent pangenotypic antiviral activity in vitro. Paritaprevir is an NS3/4A protease inhibitor codosed with ritonavir that displays in vitro activity against HCV genotypes 1–4 and 6.

Methods

Efficacy, pharmacokinetics and safety of ABT‐530 with paritaprevir/ritonavir and ribavirin were evaluated in this phase 2, open‐label, multicentre study in treatment‐naïve non‐cirrhotic patients with genotype 3 infection. Ten patients, all genotype 3a, received 120 mg ABT‐530 and 150/100 mg paritaprevir/ritonavir once daily with ribavirin for 12 weeks.

Results

Nine (90%) patients achieved a sustained virological response at post‐treatment weeks 12 and 24. One patient experienced virological failure at treatment week 6. Sequence analyses for HCV variants in samples from this patient identified A166S in NS3 at baseline and after breakthrough, as well as A30K at baseline and linked S24F+M28K+A30K variants in NS5A after breakthrough. Neither genotype 3 NS3 A166S nor NS5A A30K variant confers any resistance to paritaprevir or ABT‐530 respectively. However, genotype 3 NS5A S24F+M28K+A30K‐linked variant confers a >5000‐fold increase in ABT‐530 EC50 relative to that of the wild‐type replicon. This patient's ABT‐530 exposure was comparable to the cohort, while paritaprevir and ritonavir exposures were the lowest of all patients. No serious or severe adverse events and adverse events leading to early discontinuation were reported.

Conclusions

Results from this study show that ABT‐530 holds promise as part of a direct‐acting antiviral treatment regimen for HCV genotype 3 infection.
A longitudinal study of human milk composition in the second year postpartum: implications for human milk banking
Authors: Perrin Maryanne T. , Fogleman April D. , Newburg David S. , Allen Jonathan C.
Published: January 2016

While the composition of human milk has been studied extensively in the first year of lactation, there is a paucity of data regarding human milk composition beyond one year postpartum. Policies vary at milk banks around the world regarding how long lactating women are eligible to donate their milk. The primary purpose of this study is to describe longitudinal changes in human milk composition in the second year postpartum to support the development of evidence based guidelines regarding how long lactating women can donate human milk to a milk bank. Nineteen lactating women in North Carolina provided monthly milk samples from 11 months to 17 months postpartum (N = 131), and two non‐profit milk banks provided (N = 33) pooled, unpasteurized milk samples from 51 approved donors less than one year postpartum. There was a significant increase (P < 0.05) in the concentration of total protein, lactoferrin, lysozyme, Immunoglobulin A, oligosaccharides and sodium in longitudinal samples of mother's milk between 11 and 17 months postpartum, while zinc and calcium concentrations declined, and no changes were observed in lactose, fat, iron and potassium. Human milk in the second year postpartum contained significantly higher concentrations of total protein, lactoferrin, lysozyme and Immunoglobulin A, than milk bank samples, and significantly lower concentrations of zinc, calcium, iron and oligosaccharides. Accepting milk bank donations beyond one year postpartum is a potential strategy for increasing the supply of donor milk, but may require mineral fortification.
Identifying interventions to help rural Kenyan mothers cope with food insecurity: results of a focused ethnographic study
Authors: Pelto Gretel H. , Armar‐Klemesu Margaret
Published: January 2016

An ethnographic study was conducted in two areas in southern and western Kenya to identify potential interventions to improve the quality, availability and affordability of foods consumed by infants and young children. A cultural–ecological model of determinants of nutrition identified the sectors of information for data collection related to infant and young child (IYC) diet and feeding‐related behaviours, and the focused ethnographic study manual was used to guide the research. The results provide qualitative evidence about facilitators and constraints to IYC nutrition in the two geographical areas and document their inter‐connections. We conclude with suggestions to consider 13 potential nutrition‐sensitive interventions. The studies provide empirical ethnographic support for arguments concerning the importance of combining nutrition‐specific and nutrition‐sensitive interventions through a multi‐sectoral, integrated approach to improve the nutrition of infants and young children in low‐income, resource‐constrained populations. They also document the value of ethnography as a component of landscape analysis in nutrition programme and policy planning.

In addition to constraints on infant and young child diet that originate in environmental and technological conditions in both agro‐ecological zones, other factors that affect feeding practices include features of social organisation, household access to social support, caregivers income‐earning activities and their own health.

The results of the ethnographies, which highlight the importance of obtaining the knowledge and perspectives of caregivers of infants and young children, reveal the interactions of the multiple factors that affect child nutrition and the need for simultaneous nutrition‐sensitive interventions to complement nutrition‐specific intervention actions.

Most caregivers in both areas not only understood the importance of diet and food quality for child survival, they also regarded it as essential for child growth and development. This indicates that caregivers in these rural Kenyan communities have adopted the basic biomedical interpretation of the importance of child nutrition as an integral part of their ‘knowledge frameworks’.
Using ethnography in implementation research to improve nutrition interventions in populations
Authors: Tumilowicz Alison , Neufeld Lynnette M. , Pelto Gretel H.
Published: January 2016

‘Implementation research in nutrition’ is an emerging area of study aimed at building evidence‐based knowledge and sound theory to design and implement programs that will effectively deliver nutrition interventions. This paper describes some of the basic features of ethnography and illustrates its applications in components of the implementation process. We review the central purpose of ethnography, which is to obtain the emic view – the insider's perspective – and how ethnography has historically interfaced with nutrition. We present examples of ethnographic studies in relation to an analytic framework of the implementation process, situating them with respect to landscape analysis, formative research, process evaluation and impact evaluation. These examples, conducted in various parts of the world by different investigators, demonstrate how ethnography provided important, often essential, insights that influenced programming decisions or explained programme outcomes.

Designing, implementing and evaluating interventions requires knowledge about the populations and communities in which interventions are situated, including knowledge from the ‘emic’ (insider's) perspective.

Obtaining emic perspectives and analysing them in relation to cultural, economic and structural features of social organisation in societies is a central purpose of ethnography.

Ethnography is an essential aspect of implementation research in nutrition, as it provides important insights for making decisions about appropriate interventions and delivery platforms; determining how best to fit aspects of programme design and implementation into different environmental and cultural contexts; opening the ‘black box’ in interventions to understand how delivery and utilisation processes affect programme outcomes or impacts; and understanding how programme impacts were achieved, or not.
Acceptability of locally produced ready‐to‐use therapeutic foods in Ethiopia, Ghana, Pakistan and India
Authors: Weber Jacklyn M. , Ryan Kelsey N. , Tandon Rajiv , Mathur Meeta , Girma Tsinuel , Steiner‐Asiedu Matilda , Saalia Firibu , Zaidi Shujaat , Soofi Sajid , Okos Martin , Vosti Stephen A. , Manary Mark J.
Published: January 2016

Successful treatment of severe acute malnutrition has been achieved with ready‐to‐use therapeutic food (RUTF), but only 15% of children with severe acute malnutrition receive RUTF. The objective of this study was to determine whether new formulations of RUTF produced using locally available ingredients were acceptable to young children in Ethiopia, Ghana, Pakistan and India. The local RUTFs were formulated using a linear programming tool that allows for inclusion of only local ingredients and minimizes cost. The study consisted of 4 two‐arm, crossover, site‐randomized food acceptability trials to test the acceptability of an alternative RUTF formula compared with the standard peanut‐based RUTF containing powdered milk. Fifty children with moderate wasting in each country were enrolled in the 2‐week study. Acceptability was measured by overall consumption, likeability and adverse effects reported by caregivers. Two of the four RUTFs did not include peanut, and all four used alternative dairy proteins rather than milk. The ingredient cost of all of the RUTFs was about 60% of standard RUTF. In Ethiopia, Ghana and India, the local RUTF was tolerated well without increased reports of rash, diarrhoea or vomiting. Children consumed similar amounts of local RUTF and standard RUTF and preferred them similarly as well. In Pakistan, local RUTF was consumed in similar quantities, but mothers perceived that children did not enjoy it as much as standard RUTF. Our results support the further investigation of these local RUTFs in Ethiopia, Ghana and India in equivalency trials and suggest that local RUTFs may be of lower cost.
Absence of Cu–Zn superoxide dismutase BCSOD1 reduces Botrytis cinerea virulence in Arabidopsis and tomato plants, revealing interplay among reactive oxygen species, callose and signalling pathways
Authors: López‐Cruz Jaime , Óscar Crespo‐Salvador , Emma Fernández‐Crespo , Pilar García‐Agustín , Carmen González‐Bosch
Published: January 2016

Plants activate responses against pathogens, including the oxidative burst. Necrotrophic pathogens can produce reactive oxygen species (ROS) that benefit the colonization process. Previously, we have demonstrated that tomato plants challenged with Botrytis cinerea accumulate ROS and callose, together with the induction of genes involved in defence, signalling and oxidative metabolism. Here, we studied the infection phenotype of the Δbcsod1 strain in both tomato and Arabidopsis plants. This mutant lacks bcsod1, which encodes Cu–Zn superoxide dismutase (SOD). This enzyme catalyses the conversion of superoxide ion (
) into hydrogen peroxide (H2O2). ROS play a protective role and act as signals in plants. Δbcsod1 displayed reduced virulence compared with wild‐type B05.10 in both species. Plants infected with Δbcsod1 accumulated less H2O2 and more
than those infected with B05.10, which is associated with an increase in the defensive polymer callose. This supports a major role of fungal SOD in H2O2 production during the plant–pathogen interaction. The early induction of the callose synthase gene PMR4 suggested that changes in ROS altered plant defensive responses at the transcriptional level. The metabolites and genes involved in signalling and in response to oxidative stress were differentially expressed on Δbcsod1 infection, supporting the notion that plants perceive changes in ROS balance and activate defence responses. A higher O2–/H2O2 ratio seems to be beneficial for plant protection against this necrotroph. Our results highlight the relevance of callose and the oxylipin 12‐oxo‐phytodienoic acid (OPDA) in the response to changes in the oxidative environment, and clarify the mechanisms that underlie the responses to Botrytis in Arabidopsis and tomato plants.
A Network Perspective on Negotiation: What Is New and Why It Matters
Authors: Mouzas Stefanos
Published: January 2016

The resources that individual negotiators need to solve their problems are not available in a single, concentrated form, and they are certainly not available only within an isolated dyad itself. Instead, the necessary resources are widely dispersed among many actors within networks of business relationships. The best deal is unlikely to be fixed or predetermined, but is rather the outcome of long and time‐consuming negotiations that will then affect further negotiations. In this article, I describe a network perspective on negotiation that considers the relevance and impact of three phenomena that I call (1) vast connectivity, (2) multiple constitutions, and (3) ongoing consent. I further illustrate the applicability of these three factors using examples of real‐life negotiations.
Creating Stable Agreements in Marine Policy: Learning from the California South Coast Marine Life Protection Act Initiative
Authors: McCreary Scott , Grifman Phyllis , Cowart Meredith
Published: January 2016

In this article, we examine the California South Coast Marine Life Protection Act Initiative stakeholder process, evaluate its shortcomings, and consider what could have been done differently. Our objective is to make recommendations to improve future multi‐stakeholder marine policy processes. In our view, while the South Coast stakeholder process had many positive outcomes, it failed to reach what we call here a “stable agreement.” Our analysis is based on two of the authors’ involvement (one as a facilitator and the other as a stakeholder representative) in the process and a post‐hoc survey of participants. We find that several ill‐advised process design and management choices significantly destabilized the negotiations, leading to an ultimately unstable agreement.

We highlight four major problematic process design and management decisions, including the following: representation on the multi‐stakeholder group was imbalanced, the pre‐meeting caucuses were not paired with training in interest‐based negotiation, adequate incentives to negotiate toward a consensus agreement were not provided, and the use of straw voting at one point in the process was unclear and inconsistent. As a result of these and other process design and management flaws, many stakeholders believed that the process was biased and that their ends would be better achieved by anchoring negotiations and engaging in positional bargaining. Ultimately, this meant that near‐consensus on a single cross‐interest marine protected area proposal was not reached, the scientific guidelines put forth were not fully met, the process was not and is not viewed as fair by the stakeholders directly or indirectly involved, and the marine protected area regulations lack broad‐scale support.

These pitfalls of the South Coast stakeholder process could have been avoided had the management and facilitation team consistently followed best practices in dispute resolution. We recommend that future marine planning processes learn from this example, particularly those occurring in highly complex, urban ocean environments.
BK virus nephropathy in renal transplant recipients
Authors: Jamboti Jagadish S
Published: January 2016

BK virus nephropathy (BKVN) occurs in up to 10% of renal transplant recipients and can result in graft loss. The reactivation of BK virus in renal transplant recipients is largely asymptomatic, and routine surveillance especially in the first 12–24 months after transplant is necessary for early recognition and intervention. Reduced immunosuppression and anti‐viral treatment in the early stages may be effective in stopping BK virus replication. Urinary decoy cells, although highly specific, lack sensitivity to diagnose BKVN. Transplant biopsy remains the gold standard to diagnose BKVN, good surrogate markers for surveillance using quantitative urinary decoy cells, urinary SV40 T immunochemical staining or polyoma virus‐Haufen bodies are offered by recent studies. Advanced BKVN results in severe tubulo‐interstitial damage and graft failure. Retransplantation after BKVN is associated with good outcomes. Newer treatment modalities are emerging.
Online CO2 and H2O oxygen isotope fractionation allows estimation of mesophyll conductance in C4 plants, and reveals that mesophyll conductance decreases as leaves age in both C4 and C3 plants
Authors: Barbour Margaret M. , Evans John R. , Simonin Kevin A. , von Caemmerer Susanne
Published: January 2016

Mesophyll conductance significantly, and variably, limits photosynthesis but we currently have no reliable method of measurement for C4 plants.

An online oxygen isotope technique was developed to allow quantification of mesophyll conductance in C4 plants and to provide an alternative estimate in C3 plants. The technique is compared to an established carbon isotope method in three C3 species.

Mesophyll conductance of C4 species was similar to that in the C3 species measured, and declined in both C4 and C3 species as leaves aged from fully expanded to senescing. In cotton leaves, simultaneous measurement of carbon and oxygen isotope discrimination allowed the partitioning of total conductance to the chloroplasts into cell wall and plasma membrane versus chloroplast membrane components, if CO2 was assumed to be isotopically equilibrated with cytosolic water, and the partitioning remained stable with leaf age.

The oxygen isotope technique allowed estimation of mesophyll conductance in C4 plants and, when combined with well‐established carbon isotope techniques, may provide additional information on mesophyll conductance in C3 plants.
UNDERSTANDING MULTIPLE SPECIES ECOSYSTEM DYNAMICS USING A CONSUMER RESOURCE MODEL
Authors: COLLINS OBIORA C. , DUFFY KEVIN J.
Published: January 2016

Most ecological systems comprise multiple species coexisting and the dynamics of these multiple species can be important for understanding, management, and conservation. One method to study such ecological system dynamics is the use of heterogeneous models. Here we formulate and analyze a multiple species (n patches or groups) consumer resource model. Initial insights are gained by analyzing the special cases and . A threshold consumption number C0 is used to investigate system stability and hence the long‐term dynamics of the system. It is shown how this threshold consumption number can measure the effects and extent of multiple species coexistence in the system.
Clinical effectiveness of very‐low‐energy diets in the management of weight loss: a systematic review and meta‐analysis of randomized controlled trials
Authors: Parretti H. M. , Jebb S. A. , Johns D. J. , Lewis A. L. , Christian‐Brown A. M. , Aveyard P.
Published: January 2016

Guidelines suggest that very‐low‐energy diets (VLEDs) should be used to treat obesity only when rapid weight loss is clinically indicated because of concerns about rapid weight regain.

Literature databases were searched from inception to November 2014. Randomized trials were included where the intervention included a VLED and the comparator was no intervention or an intervention that could be given in a general medical setting in adults that were overweight. Two reviewers characterized the population, intervention, control groups, outcomes and appraised quality. The primary outcome was weight change at 12 months from baseline.

Compared with a behavioural programme alone, VLEDs combined with a behavioural programme achieved −3.9 kg [95% confidence interval (CI) −6.7 to −1.1] at 1 year. The difference at 24 months was −1.4 kg (95%CI −2.6 to −0.2) and at 38–60 months was −1.3 kg (95%CI −2.9 to 0.2). Nineteen per cent of the VLED group discontinued treatment prematurely compared with 20% of the comparator groups, relative risk 0.96 (0.56 to 1.66). One serious adverse event, hospitalization with cholecystitis, was reported in the VLED group and none in the comparator group.

Very‐low‐energy diets with behavioural programmes achieve greater long‐term weight loss than behavioural programmes alone, appear tolerable and lead to few adverse events suggesting they could be more widely used than current guidelines suggest.