bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil nitrogen dynamics as an indicator for longleaf pine restoration
Authors: McCaskill George L. , Jose Shibu , Chauhan Ashvini , Ogram Andrew V.
Published: October 2017

Assessing the status of soil nutrients with their corresponding microbial communities provides important information about degraded soils during the restoration of coastal wet pine forests. Net nitrogen mineralization, nitrogen‐oxidizing bacteria (NOB), and soil microbial biomass were compared with patch‐derived volume along a 110‐year longleaf pine (Pinus palustrisMill.) chronosequence for identifying a trajectory and ecological benchmark during forest restoration. Net nitrogen mineralization rates decreased significantly in the maturing‐aged, pine patches, driven by a larger drop in net nitrification. Net nitrification and abundance ofNOBwere higher in young pine patches compared to soils from the maturing (86–110 years) pine patches. Gross nitrate fluxes followed the nonfungal portion of the soil microbial biomass along the chronosequence, declining in 64‐year‐old pine patches. Microbial biomass peaked in patches 17–34 years of age, but significantly declined in the older patches. Fungal biomass leveled off without decline. Ammonium was the major source of nitrogen within the maturing pine patches as well as the wetland patches, indicating that ammonium maintains longleaf pine during growth‐limiting conditions. Nitrate dominated during rapid tree growth, optimally in mesic conditions. The relative amounts of available ammonium to nitrate can be used to model nitrogen cycling in facultative‐wetland pine forests of the coastal United States as soils alternate between wet and mesic conditions. A key restoration benchmark occurred after 86 years of pine development when pine patch growth rates slowed, with lower numbers ofNOB, when the nonfungal biomass leveled off, and net nitrification rates are at a minimum, during pine maturation.
Managing patients with interstitial lung disease: Two more pieces of the puzzle
Authors: Macagno Francesco , Leone Paolo Maria , Richeldi Luca
Published: October 2017

See related Article, See related Article
Higher Price, Lower Costs? Minimum Prices in the EU Emissions Trading Scheme
Authors: Abrell Jan , Rausch Sebastian , Yonezawa Hidemichi
Published: October 2017

In this paper, we examine the introduction of a price floor in an emissions trading system (ETS) when some emissions are regulated outside the ETS. We theoretically characterize the conditions under which a price floor enhances welfare. Using a numerical simulation model of the European Union (EU), we find that moderate minimum prices in the EU ETS can reduce the costs of EU climate policy by up to 30 percent. We also find that, because of tax‐interaction effects, the optimal minimum price in the EU ETS should be about four times higher than the average marginal abatement cost in non‐ETS sectors.
Exercise physiology and nutritional perspectives of elite soccer refereeing
Authors: Schenk K. , Bizzini M. , Gatterer H.
Published: October 2017

Referees are an integral part of soccer, and their performance is fundamental for regular match flow, irrespective of the competition level or age classes. So far, scientific interest was mainly limited to aspects of exercise physiology and match performance of soccer referees, whereas recommendations for nutrition were adopted from active professional soccer. In contrast to elite soccer players, most referees are non‐professional and engaged in different occupations. Furthermore, elite referees and soccer players differ in regard to age, body composition, aerobic capacity, and training load. Thus, referees' caloric needs and recommended daily carbohydrate intake may generally be lower compared to active soccer players, with higher intakes limited to periods of increased training load and match days or for referees engaged in physical demanding occupations. With respect to fluid intake, pre‐match and in‐match hydration strategies generally valid in sports are recommended also for referees to avoid cognitive and physical performance loss, especially when officiating in extreme climates and altitude. In contrast to elite soccer, professional assistance concerning nutrition and training is rarely available for national elite referees of most countries. Therefore, special attention on education about adequate nutrition and fluid intake, about the dietary prevention of deficiencies (iron in female referees, vitamin D irrespective of sex and age), and basic precautions for travels abroad is warranted. In conclusion, the simple adoption of nutritional considerations from active soccer for referees may not be appropriate. Recommendations should respect gender differences, population‐specific physical characteristics, and demands just as well as individual characteristics and special needs.
Family as a Socio‐economic Actor in the Political Economies of East and South East Asian Welfare Capitalisms
Authors: Papadopoulos Theodoros , Roumpakis Antonios
Published: October 2017

In this article, we revisit Karl Polanyi's concept of ‘oikos’ in order to reconceptualize the role of the family as both a welfare provider and an economic actor in the social reproduction of East and South East Asian welfare capitalisms. Our article is structured in four parts. First, we critically review existing approaches on the characteristics of welfare capitalism in East and South East Asia. We argue that existing approaches tend to isolate family as a welfare provider and neglect how the role of the family is institutionalized as a collective actor. The second part focuses on the role of the family in the social reproduction of welfare capitalism, and explores how, in East and South East Asia, the specific conditions for family's role as an economic actor were institutionalized historically. The third part revisits Polanyi's concept of ‘oikos’ and how ‘householding’ constitutes one of the most important forms of economic action allowing us to examine the family as a socio‐economic actor. In the fourth section, we provide an analysis of families' available strategies and discuss evidence related to private education expenditure, household debt and labour market income share. We conclude by highlighting the need to re‐articulate the importance of family as a collective socio‐economic actor that, despite recent reforms and path departures, remains at the epicentre of East and South East Asian welfare capitalisms.
To Be or Not to Be Part of Greater China: Social Development in the Post‐Ma Taiwan
Authors: Ku Yeun‐wen , Chang Yu‐fang
Published: October 2017

Since the beginning of the 21st century, Taiwan has transitioned towards democratization. In 2000, the young opposition party, the Democratic Progressive Party (DPP), defeated and replaced the authoritarian ruling party, the Kuomintang (KMT), for the first time. However, this critical political change failed to meet the social reform expectations of the people, which resulted in the triumph of the KMT in the presidential election in 2008. The same story was repeated in 2016 when the KMT and President Ma Ying‐jeou lost their legitimacy to the public, and they were replaced by the current President Tsai Ing‐wen, the DPP leader. This article interprets the extremely difficult policy choice of Taiwan towards China and how its relationship with China shapes social development issues behind these political changes. Democratization has long been regarded as the main driving force for East Asian welfare development, especially with the cases of Taiwan and Korea. However, in conclusion, this article argues the importance of globalization in shaping domestic politics and managing welfare expectations.
Peruvian Food Chain Jenga: Learning Ecosystems with an Interactive Model
Authors: Hartweg Beau , Biffi Daniella , de la Fuente Yohanis , Malkoc Ummuhan , Patterson Melissa E. , Pearce Erin , Stewart Morgan A. , Weinburgh Molly
Published: October 2017

A pilot study was conducted on a multimodal educational tool, Peruvian Food Chain Jenga (PFCJ), with 5th‐grade students (N = 54) at a public charter school. The goal was to compare the effectiveness of the multimodal tool to a more traditional presentation of the same materials (food chain) using an experimental/control design. Data collection included a pretest/posttest and a “What I Did/What I Learned” response sheet. Quantitative analysis of pretest/posttest results showed both groups improved from pretest to posttest; however, there was no statistically significant difference between posttest results of experimental and control groups. Qualitative analysis of student open‐ended responses indicated a difference between students who used the PFCJ and students in the control. The most striking difference occurred in how the students perceived the connectedness of species and the awareness of human impact. Our findings suggest that using a model such as PFCJ as a means of teaching and connecting scientific content with practices related to ecosystems is an effective method of engaging students in intelligent discussions about these topics.
How Picture Books on the National Science Teacher's Association Recommend List Portray Scientists
Authors: Farland‐Smith Donna , Finson Kevin D. , Arquette Cecile M.
Published: October 2017

This study utilized the Draw‐A‐Scientist Test Checklist (DAST‐C) to assess the illustrations of scientists in the most recent three years of NSTA Recommends book lists. A total of 15,778 images were contained in the 148 books from those lists, of which 1,676 were of scientists. ANOVA procedures revealed no significant differences in stereotypical elements across the three years of books. However, three notable stereotypical elements were present in large percentages in books from all years: predominance of male images, non‐minority scientists, and scientists who were not youthful.
Greenscreen teaching: Institutional instability and classroom innovation
Authors: Perkins Miriam Y.
Published: October 2017

“Greenscreen Teaching” explores how the stresses of institutional and social change impact teaching and learning, and the creative resourcefulness born out of instability. In precarious institutions and social contexts, relevant outcomes for theological learning include developing attentiveness, robust moral discernment, and courageous speech seasoned by maturing convictions and pastoral sensitivities. I utilize greenscreen acting as a suggestive metaphor for describing four creative teaching strategies targeting these outcomes. Subsections gather insights from:

Etymology of disaster‐related words: Capitalize on the moment and “go big.”

Creative method: Improvise and keep it sharp.

Ritual theory: Creatively repurpose familiar but underutilized traditions.

Service learning: Widen the networks of community connection.

Each subsection also revisits moments and learning activities from a graduate course in feminist theology. Navigating constant transition impacts every aspect of the classroom. Nevertheless, a teaching scholar can resource this precariousness as creative agency for voice, solidarity, and mutual learning.
Proteomic characterization of hierarchical megacomplex formation in Arabidopsis thylakoid membrane
Authors: Rantala Marjaana , Tikkanen Mikko , Aro Eva‐Mari
Published: October 2017

Conversion of solar energy into chemical energy in plant chloroplasts concomitantly modifies the thylakoid architecture and hierarchical interactions between pigment–protein complexes. Here, the thylakoids were isolated from light‐acclimated Arabidopsis leaves and investigated with respect to the composition of the thylakoid protein complexes and their association into higher molecular mass complexes, the largest one comprising both photosystems (PSII and PSI) and light‐harvesting chlorophyll a/b‐binding complexes (LHCII). Because the majority of plant light‐harvesting capacity is accommodated in LHCII complexes, their structural interaction with photosystem core complexes is extremely important for efficient light harvesting. Specific differences in the strength of LHCII binding to PSII core complexes and the formation of PSII supercomplexes are well characterized. Yet, the role of loosely bound L‐LHCII that disconnects to a large extent during the isolation of thylakoid protein complexes remains elusive. Because L‐LHCII apparently has a flexible role in light harvesting and energy dissipation, depending on environmental conditions, its close interaction with photosystems is a prerequisite for successful light harvesting in vivo. Here, to reveal the labile and fragile light‐dependent protein interactions in the thylakoid network, isolated membranes were subjected to sequential solubilization using detergents with differential solubilization capacity and applying strict quality control. Optimized 3D‐lpBN‐lpBN‐sodium dodecyl sulfate–polyacrylamide gel electrophoresis system demonstrated that PSII–LHCII supercomplexes, together with PSI complexes, hierarchically form larger megacomplexes via interactions with L‐LHCII trimers. The polypeptide composition of LHCII trimers and the phosphorylation of Lhcb1 and Lhcb2 were examined to determine the light‐dependent supramolecular organization of the photosystems into megacomplexes.
China's exports, export tax rebates and exchange rate policy
Authors: Xu Zhenhui
Published: October 2017

This paper examines the relationship between China's exports, export tax rebates and exchange rate policy. It offers an explanation for why China's exports continued to rise under RMB real appreciations during the Asian financial crisis. Based on a traditional export demand model, we test our hypothesis that the counteracting effects of China's export tax rebate policy have diminished the effectiveness of real exchange rates in facilitating the resolution of trade imbalances under the current pegged exchange rate regime. We find evidence that RMB real appreciations during the crisis negatively affected China's exports, but the negative effects were mitigated by the positive effects of export tax rebates. We also find evidence of a long‐run relationship between China's exports and the other explanatory variables. The empirical evidence suggests that under the pegged exchange rate regime with limited adjustments, real exchange rate movements alone cannot resolve China's external imbalances. The policy implication of this study is that China needs to redirect its decades‐long export‐oriented development strategy to one that emphasises domestic demand‐oriented development and to replace the current pegged exchange rate regime with a market‐oriented more flexible exchange rate regime.
Analysis of the Thermodynamic Potential of Supercritical Carbon Dioxide Cycles: A Systematic Approach
Authors: Crespi Francesco , Gavagnin Giacomo , Sánchez David , Martínez Gonzalo S.
Published: October 2017

After the renewed interest in supercritical carbon dioxide cycles, a large number of cycle layouts have been proposed in literature. These works, which are essentially theoretical, consider different operating conditions and modeling assumptions, and thus, the results are not comparable. There are also works that aim to provide a fair comparison between different cycles in order to assess which one is most efficient. These analyses are very interesting but, usually, they combine thermodynamic and technical restrictions, which make it difficult to draw solid and general conclusions with regard to which the cycle of choice in the future should be. With this background, the present work provides a systematic thermodynamic analysis of 12 supercritical carbon dioxide cycles under similar working conditions, with and without technical restriction in terms of pressure and/or temperature. This yields very interesting conclusions regarding the most interesting cycles in the literature. Also, useful recommendations are extracted from the parametric analysis with respect to the directions that must be followed when searching for more efficient cycles. The analysis is based on efficiency and specific work diagrams with respect to pressure ratio and turbine inlet temperature in order to enhance its applicability to plant designs driven by fuel economy and/or footprint.
Boundary Layer Flashback in Premixed Hydrogen–Air Flames With Acoustic Excitation
Authors: Hoferichter Vera , Sattelmayer Thomas
Published: October 2017

Lean premixed combustion is prevailing in gas turbines to minimize nitrogen oxide emissions. However, this technology bears the risk of flame flashback and thermoacoustic instabilities. Thermoacoustic instabilities induce velocity oscillations at the burner exit which, in turn, can trigger flame flashback. This article presents an experimental study at ambient conditions on the effect of longitudinal acoustic excitation on flashback in the boundary layer of a channel burner. The acoustic excitation simulates the effect of thermoacoustic instabilities. Flashback limits are determined for different excitation frequencies characterizing intermediate frequency dynamics in typical gas turbine combustors (100–350 Hz). The excitation amplitude is varied from 0% to 36% of the burner bulk flow velocity. For increasing excitation amplitude, the risk of flame flashback increases. This effect is strongest at low frequencies. For increasing excitation frequency, the influence of the velocity oscillations decreases as the flame has less time to follow the changes in bulk flow velocity. Two different flashback regimes can be distinguished based on excitation amplitude. For low excitation amplitudes, flashback conditions are reached if the minimum flow velocity in the excitation cycle falls below the flashback limit of unexcited unconfined flames. For higher excitation amplitudes, where the flame starts to periodically enter the burner duct, flashback is initiated if the maximum flow velocity in the excitation cycle is lower than the flashback limit of confined flames. Consequently, flashback limits of confined flames should also be considered in the design of gas turbine burners as a worst case scenario.
Phase-Change Heat Transfer Measurements Using Temperature-Sensitive Paints
Authors: Al Hashimi Husain , Hammer Caleb F. , Lebon Michel T. , Zhang Dan , Kim Jungho
Published: October 2017

Techniques based on temperature-sensitive paints (TSP) to measure time-resolved temperature and heat transfer distributions at the interface between a wall and fluid during pool and flow boiling are described. The paints are excited using ultraviolet (UV) light emitting diodes (LEDs), and changes in fluorescence intensity are used to infer local temperature differences across a thin insulator from which heat flux distribution is obtained. Advantages over infrared (IR) thermometry include the ability to use substrates that are opaque to IR (e.g., glass, plexiglass and plastic films), use of low-cost optical cameras, no self-emission from substrates to complicate data interpretation, high speed, and high spatial resolution. TSP-based methods to measure wall heat transfer distributions are validated and then demonstrated for pool and flow boiling.
A Fermi-degenerate three-dimensional optical lattice clock
Authors: Campbell S. L. , Hutson R. B. , Marti G. E. , Goban A. , Darkwah Oppong N. , McNally R. L. , Sonderhouse L. , Robinson J. M. , Zhang W. , Bloom B. J. , Ye J.
Published: October 2017

Making a denser optical lattice clock

Some of today's most advanced clocks are made up of large numbers of atoms lined up in a one-dimensional (1D) optical lattice. The numbers improve clock stability, but atomic interactions can limit accuracy. Campbell
et al.
loaded their fermionic strontium atoms into a 3D optical lattice. The low temperatures and strong interactions ensured that the atoms avoided one another, resulting in a neat pattern where each lattice site was occupied by exactly one atom. This ordering reduced the influence of interactions on the clock's accuracy, whereas the high density of atoms enabled by the 3D geometry improved the precision.

Science
, this issue p.
90
Interactions between brain and spinal cord mediate value effects in nocebo hyperalgesia
Authors: Tinnermann A. , Geuter S. , Sprenger C. , Finsterbusch J. , Büchel C.
Published: October 2017

Price modulates early pain processing

Patients in randomized clinical trials frequently stop taking their drug, complaining of side effects. However, it turns out that some of these subjects are part of the placebo group and thus never received any active medication. This is a case of the nocebo effect seriously interfering with medical treatment. Tinnermann
et al.
investigated whether value information such as the price of a medication can further modulate behavioral nocebo effects and the underlying neural network dynamics (see the Perspective by Colloca). They used brain imaging to characterize the circuits involved in nocebo hyperalgesia within the descending pain pathway from the prefrontal cortex to the spinal cord. Their findings revealed how value information increased the nocebo effect.

Science
, this issue p.
105
; see also p.
44
Survival of the spineless
Squid Empire: The Rise and Fall of the Cephalopods
Danna Staaf
ForeEdge, 2017. 253 pp.
Authors: McAnulty Sarah J.
Published: October 2017

Fossils aren't your forte? A charming tale of cephalopod evolution may change your mind
Fun and games
Game Changers: Stories of the Revolutionary Minds Behind Game Theory
Rudolf Taschner
Prometheus Books, 2017. 237 pp.
Authors: Phillips Christopher J.
Published: October 2017

Blending fact and fiction, a mathematics professor aims to breathe new life into the history of game theory
Nerve agents in honey
Authors: Connolly Christopher N.
Published: October 2017

Analysis of local honey samples shows global landscape contamination by pesticides
Neutrophils take a round-trip
Authors: Garner Hannah , de Visser Karin E.
Published: October 2017

Imaging sheds light on neutrophil dynamics in sterile inflammation
U.S.-Iran science exchange
Authors: Schweitzer Glenn
Published: October 2017

If the Iran nuclear deal unravels, U.S. visa restrictions increase, and/or Americans who travel to Iran are subjected to unwarranted security harassment, opportunities for scientific engagement between the two countries, which are currently limited, will decline to a very low level. This would be a substantial loss to the global scientific community.
A perspective on AKT 25-plus years after its discovery
Authors: Paraskevopoulou Maria D. , Tsichlis Philip N.
Published: October 2017

A look at AKT shows that there is still much more to learn about this central signaling kinase.
A nap a day keeps the pain away?
Authors: Ferrarelli Leslie K.
Published: October 2017

Getting more sleep or increasing caffeine intake during the day may relieve chronic pain better than typical pain-killers.
Papers of note in
Nature
546
(7659)
Authors: VanHook Annalisa M.
Published: October 2017

This week’s articles describe engineered exosomes for treating pancreatic cancer, the role of the endoplasmic reticulum in cancer cell apoptosis, the priming of brown fat for cold-induced thermogenesis, synapse loss in a mouse model of lupus, and communication between cells of different lineages during liver development.
Papers of note in
Science
356
(6345)
Authors: VanHook Annalisa M.
Published: October 2017

This week’s articles address the release of volatile organic compounds from plant cells, a gene regulatory network that ensures proper neural patterning despite variability in morphogen gradients, and a role for adenosine signaling in the plasticity of an auditory circuit.
Detection of Colistin-Resistant MCR-1-Positive Escherichia coli by Use of Assays Based on Inhibition by EDTA and Zeta Potential
Authors: Esposito Fernanda , Fernandes Miriam R. , Lopes Ralf , Muñoz Maria , Sabino Caetano P. , Cunha Marcos P. , Silva Ketrin C. , Cayô Rodrigo , Martins Willames M. B. S. , Moreno Andrea M. , Knöbl Terezinha , Gales Ana C. , Lincopan Nilton
Published: October 2017

The emergence and rapid dissemination of colistin-resistant
Escherichia coli
carrying the plasmid-mediated
mcr-1
gene have created an urgent need to develop specific screening methods. In this study, we evaluated four assays based on the inhibition of MCR-1 activity by EDTA: (i) a combined-disk test (CDT) comparing the inhibition zones of colistin and colistin (10 μg) plus EDTA (100 mM); (ii) reduction of colistin MIC (CMR) in the presence of EDTA (80 μg/ml); (iii) a modified rapid polymyxin Nordmann/Poirel test (MPNP); and (iv) alteration of zeta potential (R
ZP
= ZP
+EDTA
/ZP
−EDTA
). We obtained encouraging results for the detection of MCR-1 in
E. coli
isolates recovered from human, food, and animal samples, using the following assay parameters: ≥3 mm difference in the inhibition zones between colistin disks without and with EDTA; ≥4-fold colistin MIC decrease in the presence of EDTA; R
ZP
of ≥2.5; and the absence of metabolic activity and proliferation, indicated by unchanged color of phenol red in the presence of colistin-EDTA, in the MPNP test. In this regard, the CDT, CMR, R
ZP
, and MPNP assays exhibited sensitivities of 96.7, 96.7, 95.1, and 96.7% and specificities of 89.6, 83.3, 100, and 100%, respectively, for detecting MCR-1-positive
E. coli
. Our results demonstrate that inhibition by EDTA and zeta potential assays may provide simple and inexpensive methods for the presumptive detection of MCR-1-producing
E. coli
isolates in human and veterinary diagnostic laboratories.
Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses
Authors: Zhou Bin , Deng Yi-Mo , Barnes John R. , Sessions October M. , Chou Tsui-Wen , Wilson Malania , Stark Thomas J. , Volk Michelle , Spirason Natalie , Halpin Rebecca A. , Kamaraj Uma Sangumathi , Ding Tao , Stockwell Timothy B. , Salvatore Mirella , Ghedin Elodie , Barr Ian G. , Wentworth David E.
Published: October 2017

Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe, and influenza A viruses intermittently cause pandemics. Sequence information from influenza virus genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance. However, due to sequence diversity and the dynamics of influenza virus evolution, rapid and high-throughput sequencing of influenza viruses remains a challenge. We developed a single-reaction influenza A/B virus (FluA/B) multiplex reverse transcription-PCR (RT-PCR) method that amplifies the most critical genomic segments (hemagglutinin [HA], neuraminidase [NA], and matrix [M]) of seasonal influenza A and B viruses for next-generation sequencing, regardless of viral type, subtype, or lineage. Herein, we demonstrate that the strategy is highly sensitive and robust. The strategy was validated on thousands of seasonal influenza A and B virus-positive specimens using multiple next-generation sequencing platforms.
High-Stringency Evaluation of the Automated BD Phoenix CPO Detect and Rapidec Carba NP Tests for Detection and Classification of Carbapenemases
Authors: Thomson Gina , Turner David , Brasso William , Kircher Susan , Guillet Thierry , Thomson Kenneth
Published: October 2017

There is an urgent need for rapid, accurate detection and classification of carbapenemases. The current study evaluated the automated BD Phoenix CPO Detect and the manual bioMérieux Rapidec Carba NP tests for meeting these needs. Both tests were challenged with 294 isolates of
Enterobacteriaceae
spp.,
Pseudomonas aeruginosa
, and
Acinetobacter baumannii
chosen to provide extreme diagnostic difficulty. Carbapenemases such as KPC, NMC-A, IMI, SME, NDM, SPM, IMP, VIM, and OXA-23, 40, 48, 58, 72, 181, and 232 were produced by 243 isolates and 51 carbapenemase-negative isolates included porin mutants and producers of extended-spectrum β-lactamases (ESBLs), AmpCs, K1, and broad-spectrum β-lactamases. Both tests exhibited high sensitivity of carbapenemase detection (>97%). Due to the highly challenging carbapenemase-negative isolates, specificities were lower than typical for evaluations involving mostly routine clinical isolates. BD Phoenix CPO Detect was 68.6% specific and Rapidec Carba NP was 60.8% to 78.4% specific, depending on how borderline results were interpreted. Only BD Phoenix CPO Detect classified carbapenemases. It correctly classified 85.0% of class A, 72.4% of class B, and 88.6% of class D carbapenemases. Importantly with respect to empirical therapy with new β-lactamase inhibitor combinations such as ceftazidime/avibactam, no class B carbapenemases were misclassified as class A carbapenemases. Both tests offer advantages. Used alone, without initial susceptibility tests, Rapidec Carba NP can provide positive results for some isolates after only 10 to 30 min incubation. BD Phoenix CPO Detect provides novel advantages such as automated carbapenemase detection, inclusion in susceptibility panels to eliminate delays and subjectivity in initiating carbapenemase tests, and classification of most carbapenemases.
The Trypomastigote Small Surface Antigen from Trypanosoma cruzi Improves Treatment Evaluation and Diagnosis in Pediatric Chagas Disease
Authors: Balouz Virginia , Melli Luciano J. , Volcovich Romina , Moscatelli Guillermo , Moroni Samanta , González Nicolás , Ballering Griselda , Bisio Margarita , Ciocchini Andrés E. , Buscaglia Carlos A. , Altcheh Jaime
Published: October 2017

Chagas disease is caused by the protozoan parasite
Trypanosoma cruzi
. Assessment of parasitological cure upon treatment with available drugs relies on achieving consistent negative results in conventional parasitological and serological tests, which may take years to assess. Here, we evaluated the use of a recombinant
T. cruzi
antigen termed trypomastigote small surface antigen (TSSA) as an early serological marker of drug efficacy in
T. cruzi
-infected children. A cohort of 78 pediatric patients born to
T. cruzi
-infected mothers was included in this study. Only 39 of the children were infected with
T. cruzi
, and they were immediately treated with trypanocidal drugs. Serological responses against TSSA were evaluated in infected and noninfected populations during the follow-up period using an in-house enzyme-linked immunosorbent assay (ELISA) and compared to conventional serological methods. Anti-TSSA antibody titers decreased significantly faster than anti-whole parasite antibodies detected by conventional serology both in
T. cruzi
-infected patients undergoing effective treatment and in those not infected. The differential kinetics allowed a significant reduction in the required follow-up periods to evaluate therapeutic responses or to rule out maternal-fetal transmission. Finally, we present the case of a congenitally infected patient with an atypical course in whom TSSA provided an early marker for
T. cruzi
infection. In conclusion, we showed that TSSA was efficacious both for rapid assessment of treatment efficiency and for early negative diagnosis in infants at risk of congenital
T. cruzi
infection. Based upon these findings we propose the inclusion of TSSA for refining the posttherapeutic cure criterion and other diagnostic needs in pediatric Chagas disease.
Functional Stability of HIV-1 Envelope Trimer Affects Accessibility to Broadly Neutralizing Antibodies at Its Apex
Authors: Gift Syna Kuriakose , Leaman Daniel P. , Zhang Lei , Kim Arthur S. , Zwick Michael B.
Published: October 2017

The trimeric envelope glycoprotein spike (Env) of HIV-1 is the target of vaccine development to elicit broadly neutralizing antibodies (bnAbs). Env trimer instability and heterogeneity in principle make subunit interfaces inconsistent targets for the immune response. Here, we investigate how functional stability of Env relates to neutralization sensitivity to V2 bnAbs and V3 crown antibodies that engage subunit interfaces upon binding to unliganded Env. Env heterogeneity was inferred when antibodies neutralized a mutant Env with a plateau of less than 100% neutralization. A statistically significant correlation was found between the stability of mutant Envs and the MPN of V2 bnAb, PG9, as well as an inverse correlation between stability of Env and neutralization by V3 crown antibody, 447-52D. A number of Env-stabilizing mutations and V2 bnAb-enhancing mutations were identified in Env, but they did not always overlap, indicating distinct requirements of functional stabilization versus antibody recognition. Blocking complex glycosylation of Env affected V2 bnAb recognition, as previously described, but also notably increased functional stability of Env. This study shows how instability and heterogeneity affect antibody sensitivity of HIV-1 Env, which is relevant to vaccine design involving its dynamic apex.

IMPORTANCE
The Env trimer is the only viral protein on the surface of HIV-1 and is the target of neutralizing antibodies that reduce viral infectivity. Quaternary epitopes at the apex of the spike are recognized by some of the most potent and broadly neutralizing antibodies to date. Being that their glycan-protein hybrid epitopes are at subunit interfaces, the resulting heterogeneity can lead to partial neutralization. Here, we screened for mutations in Env that allowed for complete neutralization by the bnAbs. We found that when mutations outside V2 increased V2 bnAb recognition, they often also increased Env stability-of-function and decreased binding by narrowly neutralizing antibodies to the V3 crown. Three mutations together increased neutralization by V2 bnAb and eliminated binding by V3 crown antibodies. These results may aid the design of immunogens that elicit antibodies to the trimer apex.
Coxsackievirus B Escapes the Infected Cell in Ejected Mitophagosomes
Authors: Sin Jon , McIntyre Laura , Stotland Aleksandr , Feuer Ralph , Gottlieb Roberta A.
Published: October 2017

Coxsackievirus B (CVB) is a common enterovirus that can cause various systemic inflammatory diseases. Because CVB lacks an envelope, it has been thought to be inherently cytolytic, wherein CVB can escape from the infected host cell only by causing it to rupture. In recent years, however, we and others have observed that various naked viruses, such as CVB, can trigger the release of infectious extracellular microvesicles (EMVs) that contain viral material. This mode of cellular escape has been suggested to allow the virus to be masked from the adaptive immune system. Additionally, we have previously reported that these viral EMVs have LC3, suggesting that they originated from autophagosomes. We now report that CVB-infected cells trigger DRP1-mediated fragmentation of mitochondria, which is a precursor to autophagic mitochondrial elimination (mitophagy). However, rather than being degraded by lysosomes, mitochondrion-containing autophagosomes are released from the cell. We believe that CVB localizes to mitochondria, induces mitophagy, and subsequently disseminates from the cell in an autophagosome-bound mitochondrion-virus complex. Suppressing the mitophagy pathway in HL-1 cardiomyocytes with either small interfering RNA (siRNA) or Mdivi-1 caused marked reduction in virus production. The findings in this study suggest that CVB subverts mitophagy machinery to support viral dissemination in released EMVs.

IMPORTANCECoxsackievirus B (CVB) can cause a number of life-threatening inflammatory diseases. Though CVB is well known to disseminate via cytolysis, recent reports have revealed a second pathway in which CVB can become encapsulated in host membrane components to escape the cell in an exosome-like particle. Here we report that these membrane-bound structures derive from mitophagosomes. Blocking various steps in the mitophagy pathway reduced levels of intracellular and extracellular virus. Not only does this study reveal a novel mechanism of picornaviral dissemination, but also it sheds light on new therapeutic targets to treat CVB and potentially other picornaviral infections.
Coat Protein Mutations That Alter the Flux of Morphogenetic Intermediates through the ϕX174 Early Assembly Pathway
Authors: Blackburn Brody J. , Li Shuaizhi , Roznowski Aaron P. , Perez Alexis R. , Villarreal Rodrigo H. , Johnson Curtis J. , Hardy Margaret , Tuckerman Edward C. , Burch April D. , Fane Bentley A.
Published: October 2017

Two scaffolding proteins orchestrate ϕX174 morphogenesis. The internal scaffolding protein B mediates the formation of pentameric assembly intermediates, whereas the external scaffolding protein D organizes 12 of these intermediates into procapsids. Aromatic amino acid side chains mediate most coat-internal scaffolding protein interactions. One residue in the internal scaffolding protein and three in the coat protein constitute the core of the B protein binding cleft. The three coat gene codons were randomized separately to ascertain the chemical requirements of the encoded amino acids and the morphogenetic consequences of mutation. The resulting mutants exhibited a wide range of recessive phenotypes, which could generally be explained within a structural context. Mutants with phenylalanine, tyrosine, and methionine substitutions were phenotypically indistinguishable from the wild type. However, tryptophan substitutions were detrimental at two sites. Charged residues were poorly tolerated, conferring extreme temperature-sensitive and lethal phenotypes. Eighteen lethal and conditional lethal mutants were genetically and biochemically characterized. The primary defect associated with the missense substitutions ranged from inefficient internal scaffolding protein B binding to faulty procapsid elongation reactions mediated by external scaffolding protein D. Elevating B protein concentrations above wild-type levels via exogenous, cloned-gene expression compensated for inefficient B protein binding, as did suppressing mutations within gene B. Similarly, elevating D protein concentrations above wild-type levels or compensatory mutations within gene D suppressed faulty elongation. Some of the parental mutations were pleiotropic, affecting multiple morphogenetic reactions. This progressively reduced the flux of intermediates through the pathway. Accordingly, multiple mechanisms, which may be unrelated, could restore viability.

IMPORTANCE
Genetic analyses have been instrumental in deciphering the temporal events of many biochemical pathways. However, pleiotropic effects can complicate analyses. Vis-à-vis virion morphogenesis, an improper protein-protein interaction within an early assembly intermediate can influence the efficiency of all subsequent reactions. Consequently, the flux of assembly intermediates cumulatively decreases as the pathway progresses. During morphogenesis, ϕX174 coat protein participates in at least four well-defined reactions, each one characterized by an interaction with a scaffolding or structural protein. In this study, genetic analyses, biochemical characterizations, and physiological assays, i.e., elevating the protein levels with which the coat protein interacts, were used to elucidate pleiotropic effects that may alter the flux of intermediates through a morphogenetic pathway.
Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination
Authors: Vashee Sanjay , Stockwell Timothy B. , Alperovich Nina , Denisova Evgeniya A. , Gibson Daniel G. , Cady Kyle C. , Miller Kristofer , Kannan Krishna , Malouli Daniel , Crawford Lindsey B. , Voorhies Alexander A. , Bruening Eric , Caposio Patrizia , Früh Klaus
Published: October 2017

The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. To overcome these limitations, we used synthetic biology tools to capture genomic fragments from viral DNA and assemble full-length genomes in yeast. Using an early passage of the HCMV isolate Toledo containing a mixture of wild-type and tissue culture-adapted virus. we directly cloned the majority sequence and recreated the minority sequence by simultaneous modification of multiple genomic regions. Thus, our novel approach provides a paradigm to not only efficiently engineer HCMV and other large DNA viruses on a genome-wide scale but also facilitates the cloning and genetic manipulation of primary isolates and provides a pathway to generating entirely synthetic genomes.
Validity of triage systems for paediatric emergency care: a systematic review
Authors: de Magalhães-Barbosa Maria Clara , Robaina Jaqueline Rodrigues , Prata-Barbosa Arnaldo , Lopes Claudia de Souza
Published: October 2017

Aim

To present a systematic review on the validity of triage systems for paediatric emergency care.

Methods

Search in MEDLINE, Cochrane Library, Latin American and Caribbean Health Sciences Literature (LILACS), Scientific Electronic Library Online (SciELO), Nursing Database Index (BDENF) and Spanish Health Sciences Bibliographic Index (IBECS) for articles in English, French, Portuguese or Spanish with no time limit. Validity studies of five-level triage systems for patients 0–18 years old were included. Two reviewers performed data extraction and quality assessment as recommended by PRISMA statement.

Results

We found 25 studies on seven triage systems: Manchester Triage System (MTS); paediatric version of Canadian Triage and Acuity Scale (PedCTAS) and its adaptation for Taiwan (paediatric version of the Taiwan Triage and Acuity System); Emergency Severity Index version 4 (ESI v.4); Soterion Rapid Triage System and South African Triage Scale and its adaptation for Bostwana (Princess Marina Triage Scale). Only studies on the MTS used a reference standard for urgency, while all systems were evaluated using a proxy outcome for urgency such as admission. Over half of all studies were low quality. The MTS, PedCTAS and ESI v.4 presented the largest number of moderate and high quality studies. The three tools performed better in their countries or near them, showing a consistent association with hospitalisation and resource utilisation. Studies of all three tools found that patients at the lowest urgency levels were hospitalised, reflecting undertriage.

Conclusions

There is some evidence to corroborate the validity of the MTS, PedCTAS and ESI v.4 for paediatric emergency care in their own countries or near them. Efforts to improve the sensitivity and to minimise the undertriage rates should continue. Cross-cultural adaptation is necessary when adopting these triage systems in other countries.
‘Nothing can be done until everything is done’: the use of complexity arguments by food, beverage, alcohol and gambling industries
Authors: Petticrew Mark , Katikireddi Srinivasa Vittal , Knai Cécile , Cassidy Rebecca , Maani Hessari Nason , Thomas James , Weishaar Heide
Published: October 2017

Background

Corporations use a range of strategies to dispute their role in causing public health harms and to limit the scope of effective public health interventions. This is well documented in relation to the activities of the tobacco industry, but research on other industries is less well developed. We therefore analysed public statements and documents from four unhealthy commodity industries to investigate whether and how they used arguments about complexity in this way.

Methods

We analysed alcohol, food, soda and gambling industry documents and websites and minutes of reports of relevant health select committees, using standard document analysis methods.

Results

Two main framings were identified: (i) these industries argue that aetiology is complex, so individual products cannot be blamed; and (ii) they argue that population health measures are ‘too simple’ to address complex public health problems. However, in this second framing, there are inherent contradictions in how industry used ‘complexity’, as their alternative solutions are generally not, in themselves, complex.

Conclusion

The concept of complexity, as commonly used in public health, is also widely employed by unhealthy commodity industries to influence how the public and policymakers understand health issues. It is frequently used in response to policy announcements and in response to new scientific evidence (particularly evidence on obesity and alcohol harms). The arguments and language may reflect the existence of a cross-industry ‘playbook’, whose use results in the undermining of effective public health policies – in particular the undermining of effective regulation of profitable industry activities that are harmful to the public’s health.
The role of suppression of hepatic SCD1 expression in the metabolic effects of dietary methionine restriction
Authors: Forney Laura A. , Stone Kirsten P. , Wanders Desiree , Ntambi James M. , Gettys Thomas W.
Published: October 2017

Dietary methionine restriction (MR) produces concurrent increases in energy intake and expenditure, but the proportionately larger increase in energy expenditure (EE) effectively limits weight gain and adipose tissue accretion over time. Increased hepatic fibroblast growth factor-21 (FGF21) is essential to MR-dependent increases in EE, but it is unknown whether the downregulation of hepatic stearoyl-coenzyme A desaturase-1 (SCD1) by MR could also be a contributing factor. Global deletion of SCD1 mimics cold exposure in mice housed at 23 °C by compromising the insular properties of the skin. The resulting cold stress increases EE, limits fat deposition, reduces hepatic lipids, and increases insulin sensitivity by activating thermoregulatory thermogenesis. To examine the efficacy of MR in the absence of SCD1 and without cold stress, the biological efficacy of MR in Scd1−/−mice housed near thermoneutrality (28 °C) was evaluated. Compared with wild-type mice on the control diet, Scd1−/−mice were leaner, had higher EE, lower hepatic and serum triglycerides, and lower serum leptin and insulin. Although dietary MR increased adipose tissue UCP1 expression, hepatic Fgf21 messenger RNA, 24 h EE, and reduced serum triglycerides in Scd1−/−mice, it failed to reduce adiposity or produce any further reduction in hepatic triglycerides, serum insulin, or serum leptin. These findings indicate that even when thermal stress is minimized, global deletion of SCD1 mimics and effectively masks many of the metabolic responses to dietary MR. However, the retention of several key effects of dietary MR in this model indicates that SCD1 is not a mediator of the biological effects of the diet.
Estimating primary energy of cosmic rays by calculating secondary particles density in optimum distance from shower core
Authors: Rastegarzadeh G. , Rafezi L.
Published: October 2017

Optimum distance (R[Formula: see text]) is a distance from the shower core in which the density calculated by lateral distribution function, has its minimum uncertainty. In this paper, using CORSIKA code, proton, carbon and iron primary in the energy range between 10[Formula: see text]–[Formula: see text][Formula: see text]eV are simulated to find R[Formula: see text] for Alborz-I array located at an altitude of 1200[Formula: see text]m above sea level. It is shown that R[Formula: see text] is approximately independent of characteristics of primary particle and it is only dependent to array configuration. Dependency of R[Formula: see text] on layout and detector spacing for 20 Alborz-I array detectors, are studied. It is shown that the Alborz-I array layout and its detector spacing result into the best (minimum uncertainty) R[Formula: see text] for its number of detectors. In this work, R[Formula: see text] for Alborz-I array is obtained about [Formula: see text][Formula: see text]m (from NKG function) and [Formula: see text][Formula: see text]m (from NKG type function). In addition, it is shown that, by finding dependency of primary energy to density in optimum distance, energy of primary particle can be estimated well. An energy estimation function is suggested and the function is examined by another set of simulated showers.