bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional diversity of EF‐hand proteins: Evolutionary perspectives
Authors: Kawasaki Hiroshi , Kretsinger Robert H. 
Published: July 2017

AbstractWe have classified 865 sequences of EF‐hand proteins from five proteomes into 156 subfamilies. These subfamilies were put into six groups. Evolutionary relationships among subfamilies and groups were analyzed from the inferred ancestral sequence for each subfamily. CTER, CPV, and PEF groups arose from a common EF‐lobe (pair of adjacent EF‐hands). They have two or more EF‐lobes; the relative positions of their EF‐lobes differ from each other. Comparisons of the ancestral sequences and the inferred structures of the EF‐lobes of these groups indicate that the mutual positions of EF‐lobes were established soon after divergence of an EF‐lobe for each group and before the duplication and fusion of EF‐lobe gene(s). These ancestral sequences reveal that some subfamilies in low similarity and isolated groups did not evolve from the EF‐lobe precursor, even if their conformations are similar to the canonical EF‐hand. This is an example of convergent evolution.
Removal of a consensus proline is not sufficient to allow tetratricopeptide repeat oligomerization
Authors: Bakkum Amber L. , Hill R. Blake 
Published: July 2017

AbstractTetratricopeptide repeat (TPR) domains are ubiquitous protein interaction domains that adopt a modular antiparallel array of α‐helices. The TPR fold typically adopts a monomeric state, and consensus TPRs sequences successfully fold into the expected monomeric topology. The versatility of the TPR fold also supports different quaternary structures, which may function as regulatory switches. One example is yeast mitochondrial fission 1 (Fis1) that appears to interconvert between monomer and dimer states in regulating division of peroxisomes and mitochondria. Whether human Fis1 can also interconvert like the yeast molecule is unknown. A TPR consensus proline residue present in human Fis1 is absent in the yeast molecule and, when added, prevents yeast Fis1 dimerization suggesting that the TPR consensus proline might have persisted to prevent TPR oligomerization. Here, we address this question with human Fis1 and the consensus TPR protein CTPR3. We demonstrate that human Fis1 does not form a noncovalent dimer via its TPR domain, despite conditions that favor dimerization of the yeast protein. We also show that the presence of the consensus proline is not sufficient to forbid TPR dimerization. Lastly, an analysis of all available TPR protein structures (22 nonredundant structures, totaling 64 TPRs—42 with the consensus proline and 22 without) revealed that the consensus proline is not necessary for turn formation, but does favor shorter turns. This work suggests the TPR consensus proline is not to prevent oligomerization, but to favor tight turns between repeats.
Ratio of ellipticities between 192 and 208 nm (R1): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides
Authors: Banerjee Raja , Sheet Tridip 
Published: July 2017

AbstractCircular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between
and
((R2) ≅ [θ]222/[θ]208), along with
and
((R1) ≅ [θ]192/[θ]208), may be utilized towards identifying the peptide/protein conformation (especially 310‐ and α‐helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2‐trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R1 parameter can characterize better the individual helices, while the other parameter R2 and the signal intensity do not always converge. We emphasize the use of the R1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources.
Evaluation of free or anchored antimicrobial peptides as candidates for the prevention of orthopaedic device‐related infections
Authors: D'Este Francesca , Oro Debora , Boix‐Lemonche Gerard , Tossi Alessandro , Skerlavaj Barbara 
Published: July 2017

The prevention of implant‐associated infection, one the most feared complications in orthopaedic surgery, remains a major clinical challenge and urges development of effective methods to prevent bacterial colonization of implanted devices. Alpha‐helical antimicrobial peptides (AMPs) may be promising candidates in this respect due to their potent and broad‐spectrum antimicrobial activity, their low tendency to elicit resistance and possible retention of efficacy in the immobilized state.The aim of this study was to evaluate the potential of five different helical AMPs, the cathelicidins BMAP‐27 and BMAP‐28, their (1–18) fragments and the rationally designed, artificial P19(9/G7) peptide, for the prevention of orthopaedic implant infections. Peptides were effective at micromolar concentrations against 22 Staphylococcus and Streptococcus isolates from orthopaedic infections, while only BMAP‐28 and to a lesser extent BMAP‐27 were active against Enterococcus faecalis. Peptides in solution showed activities comparable to those of cefazolin and linezolid, on a molar basis, and also a variable capacity to neutralize bacterial lipopolysaccharide, while devoid of adverse effects on MG‐63 osteoblast cells at concentrations corresponding to the MIC. The (1–18) BMAP fragments and P19(9/G7) were selected for further examination, based on better selectivity indices, and showed effectiveness in the presence of hyaluronic acid and in synovial fluid, while human serum affected their activity to variable extents, with BMAP‐27(1–18) best retaining activity. This peptide was immobilized on streptavidin–resin beads and retained activity against reference Staphylococcus epidermidis and Staphylococcus aureus strains, with negligible toxicity towards osteoblasts, underlining its potential for the development of infection‐resistant biomaterials for orthopaedic application. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
Efficacy of a Proprietary Trigonella foenum‐graecum L. De‐Husked Seed Extract in Reducing Menopausal Symptoms in Otherwise Healthy Women: A Double‐Blind, Randomized, Placebo‐Controlled Study
Authors: Steels E. , Steele M.L. , Harold M. , Coulson S. 
Published: July 2017

Trigonella foenum‐graecum seed extract has demonstrated hormone modulatory activity, providing biological plausibility for relieving menopausal symptoms. The study aimed to assess efficacy of a standardized T. foenum‐graecum de‐husked seed extract in reducing menopausal symptoms in healthy aging women. The study was a double‐blind, randomized, placebo‐controlled trial that recruited 115 women aged 40 to 65 years of which 59 were allocated to active (n = 54 completed) and 56 to placebo (n = 50 completed). Active treatment was T. foenum‐graecum de‐husked seed extract, 600 mg per day for 12 weeks. Outcome measures included Menopause‐Specific Quality of Life (MENQOL) questionnaire, frequency of hot flushes and night sweats and serum estradiol levels. There was a significant reduction in menopausal symptoms in the active group compared with placebo as assessed by total MENQOL score (p < 0.001); reflected by significant improvements in the vasomotor (p < 0.001), psychosocial (p < 0.001), physical (p < 0.001) and sexual symptoms (p < 0.001) domains. Vasomotor outcomes correlated with hot flushes, the active group reporting significantly less daytime hot flushes and night sweats at 12 weeks (p < 0.001). The average estradiol levels were similar in both the active group and placebo group after treatment. This study demonstrated that this proprietary T. foenum‐graecum de‐husked seed extract may reduce menopausal symptoms in healthy women. Copyright © 2017 John Wiley & Sons, Ltd.
Differences between polydioxanone and poliglactin in intestinal anastomoses – a comparative study of intestinal anastomoses
Authors: Santos Carlos Henrique Marques dos , Santos Filho Kerginaldo Gondim dos , Cassino Pedro Carvalho , Chiquetti Camila Vieira , Mello Alvaro Pereira de , Dourado Doroty Mesquita 
Published: July 2017

Abstract
Introduction Intestinal anastomosis is a surgical practice constantly realized by surgeons worldwide. When the option is to perform manual anastomosis, which is still widely used for its low cost, the question arises as to the best material to be applied.
Objective To compare polydioxanone and polyglactin threads for healing and tensile strength in intestinal anastomosis in rats.
Method We used 25 rats Wistar; after anesthesia, in groups A and B (10 rats each), laparotomy was performed, transection of the ileum at 5 and 10 cm proximally to the ileocecal valve; in group A, anastomosis was performed with 4 separate extra mucosal sutures with polidioxanone; in group B, anastomosis was performed with polyglactin; in group C (5 rats), laparotomy and manipulation of the ileum were performed. After 21 days, the animals were anesthetized and submitted to euthanasia. The specimens were sent for histopathological study and tensile strength analysis. Statistical analysis was performed using the Turkey and Student's t tests, with a significance of p < 0.05.
Results The results showed that in the tensile strength analysis, there were no significant differences between them. The histological analysis showed significant differences between the cicatrization pattern, where polydioxanone caused less fibrosis than polyglactin.
Conclusion Polydioxanone caused less fibrosis than polyglactin in intestinal anastomoses of rats.
“Set Them to the Cyphering Schoole”: Reading, Writing, and Arithmetical Education, circa 1540–1700
Authors: Otis Jessica 
Published: July 2017

AbstractDuring the late sixteenth and seventeenth centuries, English men and women replaced their existing oral and object-based arithmetical practices with literate practices based on Arabic numerals. While the adoption of Arabic numerals was incentivized by continental commercial developments, this article argues that England's increasing literacy rates and the development of vernacular arithmetic textbooks enabled changing arithmetical practices. By exploring the qualities of printed books, analyzing marginalia in arithmetic textbooks, and examining changing educational advertisements and curricula over time, we can demonstrate the importance of literacy and literature to early modern arithmetical education.
State Formation from the Vantage of Early English Jamaica: The Neglect of Edward Doyley
Authors: Gardina Pestana Carla 
Published: July 2017

AbstractEdward Doyley led English Jamaica for most of its first decade. Sent as part of a military force intent on conquering the island, he rose to a position of command in the army as a result of his survival and seniority. Eventually he took charge of the navy and civilian affairs as well. Wielding theoretically vast powers he lacked official authorization from any central authority for much of his tenure. His correspondence requesting support for the island reveals the needs of a newly conquered colony, enumerating the requirements that an expanding imperial center must fill as England moved more decisively toward engagement in the wider world. Scholarly debates over state building that emphasize military and naval expansion as a driving force, and debates about state formation focusing on negotiations between central and local authorities, speak to the experience of early Jamaica. Doyley's circumstances place him in a position between the two ideal situations described in that literature.
Fleets of Fodder: The Ecological Orchestration of Agrarian Improvement in New South Wales and the Cape of Good Hope, 1780–1830
Authors: Capps Maura 
Published: July 2017

AbstractThis article challenges the dominant historical paradigms used to analyze imperial plant and animal transfers by examining the role of fodder crops in early colonial development in New South Wales and the Cape of Good Hope. In Alfred Crosby's enduring formulation of ecological imperialism—that is, the ecological transformation of temperate colonies of settlement by European plants, animals, and pathogens—was a largely independent process. To Crosby's critics, his grand narrative fails to acknowledge the technocratic management of plant and animal transfers on the part of increasingly long-armed colonial states from the mid-nineteenth century. Yet neither approach can adequately explain the period between the decline of Britain's Atlantic empire in the 1780s and the rise of its global empire in the 1830s, a period dominated by an aggressive ethos of agrarian improvement but lacking the institutional teeth of a more evolved imperial state. Traveling fodder crops link these embryonic antipodean colonies to the luminaries of the Agricultural Revolution in Britain. The attempt to transfer fodder-centric mixed husbandry to these colonies points to an emerging coalition of imperial ambition and scientific expertise in the late eighteenth-century British Empire.
“In Ten Years There Is an Increase of 450 Priests of Antichrist”: Quantification, Anti-Catholicism, and theBulwark
Authors: Burstein Miriam Elizabeth 
Published: July 2017

AbstractThe Scottish Reformation Society'sThe Bulwark(1851–present) was the Victorian era's most influential anti-Catholic periodical, a reputation based on its self-proclaimed devotion to “facts.” Attempting to counter a unified Catholic Church in a period of pronounced intra-Protestant conflict, theBulwarksought to root religious controversy in the increasingly popular phenomenon of statistical inquiry. TheBulwark’s obsession with collating and interpreting religion-based numbers was unique not for its existence, but for its sheer extent. It thus exemplifies how “official” statistical documents, methods, and conclusions were translated into the concerns of popular religious culture. In particular, theBulwark’s ongoing surveys of Catholicism's “progress,” intended to frighten Protestants into action, weaponized statistical discourses that were used in more measured fashion elsewhere. To that end, theBulwarkargued that only Protestants had the right mindset to put religious statistics into a proper explanatory framework, whereas Catholics manipulated their own data for dishonest rhetorical purposes that theBulwarkdisclaimed. TheBulwark’s statistical turn, which bypassed the sectarianism of its theological articles, positioned it as a voice uniting the interests of all Protestant readers against Parliament's dangerously tolerant brand of liberalism.
Identifying the metabolomic fingerprint of high and low flavonoid consumers
Authors: Ivey Kerry L. , Rimm Eric B. , Kraft Peter , Clish Clary B. , Cassidy Aedin , Hodgson Jonathan , Croft Kevin , Wolpin Brian , Liang Liming 
Published: July 2017

AbstractHigh flavonoid consumption can improve vascular health. Exploring flavonoid–metabolome relationships in population-based settings is challenging, as: (i) there are numerous confounders of the flavonoid–metabolome relationship; and (ii) the set of dependent metabolite variables are inter-related, highly variable and multidimensional. The Metabolite Fingerprint Score has been developed as a means of approaching such data. This study aims to compare its performance with that of more traditional methods, in identifying the metabolomic fingerprint of high and low flavonoid consumers. This study did not aim to identify biomarkers of intake, but rather to explore how systemic metabolism differs in high and low flavonoid consumers. Using liquid chromatography–tandem MS, 174 circulating plasma metabolites were profiled in 584 men and women who had complete flavonoid intake assessment. Participants were randomised to one of two datasets: (a) training dataset, to determine the models for the discrimination variables (n 399); and (b) validation dataset, to test the capacity of the variables to differentiate higher from lower total flavonoid consumers (n 185). The stepwise and full canonical variables did not discriminate in the validation dataset. The Metabolite Fingerprint Score successfully identified a unique pattern of metabolites that discriminated high from low flavonoid consumers in the validation dataset in a multivariate-adjusted setting, and provides insight into the relationship of flavonoids with systemic lipid metabolism. Given increasing use of metabolomics data in dietary association studies, and the difficulty in validating findings using untargeted metabolomics, this paper is of timely importance to the field of nutrition. However, further validation studies are required.
The National Health Service at a Critical Moment: when Brexit means Hectic
Authors: COSTA-FONT JOAN 
Published: July 2017

AbstractLeaving the European Union (so-called ‘Brexit’) is a ‘critical moment’ for health policy reform which can pave the way to different pathways, including, a ‘critical juncture’. Given that Brexit cannot be undone without a second referendum, it opens up opportunities to elude European constraints for reform along the lines of equity, employment rights and patient choice. Brexit deepens the financial crisis of the National Health Service (NHS) by increasing hiring costs and imposing new transaction costs to accommodate patient cross-border mobility and international public health needs. Given the weak sustainability of the NHS, it could lead to major system reform.
Self-reported use of nutrition labels to make food choices is associated with healthier dietary behaviours in adolescents
Authors: Haidar Amier , Carey Felicia R , Ranjit Nalini , Archer Natalie , Hoelscher Deanna 
Published: July 2017

AbstractObjectiveThe study aimed to examine nutrition label use and dietary behaviours among ethnically diverse middle- and high-school students, in Texas, USA.DesignThe School Physical Activity and Nutrition (SPAN) survey is a cross-sectional statewide study using a self-administered questionnaire to assess nutrition and physical activity behaviours. Height and weight measurements were used to determine BMI. Multivariable logistic regression was used to determine associations between nutrition label use and dietary behaviours, with gender, grade, ethnicity, BMI, parent education, socio-economic status and nutrition knowledge as covariates.SettingParticipants from 283 schools, weighted to represent Texas youth.SubjectsSPAN 2009–2011 included 6716 8th and 11th graders (3465 girls and 3251 boys). The study population consisted of 39·83 % White/Other, 14·61 % African-American and 45·56 % Hispanic adolescents; with a mean age of 14·9 years, and 61·95 % at a healthy weight, 15·71 % having overweight and 22·34 % having obesity.ResultsAdolescents who did not use nutrition labels had 1·69 times greater odds of consuming ≥1 sugary beverages/d (P<0·05). Adolescents who used nutrition labels had 2·13 times greater odds of consuming ≥1 fruits and vegetables/d (P<0·05). Adolescents who used nutrition labels had significantly higher healthy eating scores than those who did not (P<0·001). For every 1-point increase in nutrition knowledge, adolescents had 1·22 greater odds of using nutrition labels.ConclusionsNutrition label use is associated with healthier dietary behaviours in adolescents. Intervention strategies for youth should include efforts to teach adolescents to use labels to make healthy food choices.
The unprecedented 2015/16 Tasman Sea marine heatwave
Authors: Oliver Eric C. J. , Benthuysen Jessica A. , Bindoff Nathaniel L. , Hobday Alistair J. , Holbrook Neil J. , Mundy Craig N. , Perkins-Kirkpatrick Sarah E. 
Published: July 2017

AbstractThe Tasman Sea off southeast Australia exhibited its longest and most intense marine heatwave ever recorded in 2015/16. Here we report on several inter-related aspects of this event: observed characteristics, physical drivers, ecological impacts and the role of climate change. This marine heatwave lasted for 251 days reaching a maximum intensity of 2.9 °C above climatology. The anomalous warming is dominated by anomalous convergence of heat linked to the southward flowing East Australian Current. Ecosystem impacts range from new disease outbreaks in farmed shellfish, mortality of wild molluscs and out-of-range species observations. Global climate models indicate it is very likely to be that the occurrence of an extreme warming event of this duration or intensity in this region is respectively ≥330 times and ≥6.8 times as likely to be due to the influence of anthropogenic climate change. Climate projections indicate that event likelihoods will increase in the future, due to increasing anthropogenic influences.
Implementing a universal gate set on a logical qubit encoded in an oscillator
Authors: Heeres Reinier W. , Reinhold Philip , Ofek Nissim , Frunzio Luigi , Jiang Liang , Devoret Michel H. , Schoelkopf Robert J. 
Published: July 2017

AbstractA logical qubit is a two-dimensional subspace of a higher dimensional system, chosen such that it is possible to detect and correct the occurrence of certain errors. Manipulation of the encoded information generally requires arbitrary and precise control over the entire system. Whether based on multiple physical qubits or larger dimensional modes such as oscillators, the individual elements in realistic devices will always have residual interactions, which must be accounted for when designing logical operations. Here we demonstrate a holistic control strategy which exploits accurate knowledge of the Hamiltonian to manipulate a coupled oscillator-transmon system. We use this approach to realize high-fidelity (98.5%, inferred), decoherence-limited operations on a logical qubit encoded in a superconducting cavity resonator using four-component cat states. Our results show the power of applying numerical techniques to control linear oscillators and pave the way for utilizing their large Hilbert space as a resource in quantum information processing.
A 3 °C global RCP8.5 emission trajectory cancels benefits of European emission reductions on air quality
Authors: Fortems-Cheiney A. , Foret G. , Siour G. , Vautard R. , Szopa S. , Dufour G. , Colette A. , Lacressonniere G. , Beekmann M. 
Published: July 2017

AbstractDespite the international agreement to reduce global warming to below 2 °C, the Intended Nationally Determined Contributions submitted for the COP21 would lead to a global temperature rise of about 3 °C. The relative consequences of such a one-degree additional warming have not yet been investigated for regional air quality. Here we found that a + 3 °C global pollutant emission trajectory with respect to pre-industrial climate (reached along the 2040–2069 period under a RCP8.5 scenario) would significantly increase European ozone levels relative to a 2 °C one (reached along the 2028–2057 period under a RCP4.5 scenario). This increase is particularly high over industrial regions, large urban areas, and over Southern Europe and would annihilate the benefits of emission reduction policies. The regional ozone increase mainly stems from the advection of ozone at Europe’s boundaries, themselves due to high global methane concentrations associated with the RCP8.5 emission scenario. These results make regional emission regulation, combined with emissions-reduction policies for global methane, of crucial importance.