bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress intensity factors for corner cracks in single‐edge notch bend specimen by a three‐dimensional weight function method
Authors: Zhao X. C. , Wu X. R. , Newman J. C. , Tong D. H.
Published: August 2016

A three‐dimensional (3D) weight function method is employed to calculate stress intensity factors of quarter‐elliptical corner cracks at a semi‐circular notch in the newly developed single‐edge notch bend specimen. Corner cracks covering a wide range of geometrical parameters under pin‐loading and remote tension conditions are analysed. Stress intensity factors from the 3D weight function analysis agree well with ABAQUS‐Franc3D finite element results. An engineering similitude approach previously developed for the half‐elliptical surface crack in single‐edge notch bend specimen is also applied to the present corner crack configuration. The results compare well with those from the present weight function analysis.
Functional conservation of MBD proteins: MeCP2 and Drosophila MBD proteins alter sleep
Authors: Gupta T. , Morgan H. R. , Bailey J. A. , Certel S. J.
Published: August 2016

Proteins containing a methyl‐CpG‐binding domain (MBD) bind 5mC and convert the methylation pattern information into appropriate functional cellular states. The correct readout of epigenetic marks is of particular importance in the nervous system where abnormal expression or compromised MBD protein function, can lead to disease and developmental disorders. Recent evidence indicates that the genome of Drosophila melanogaster is methylated and two MBD proteins, dMBD2/3 and dMBD‐R2, are present. Are Drosophila MBD proteins required for neuronal function, and as MBD‐containing proteins have diverged and evolved, does the MBD domain retain the molecular properties required for conserved cellular function across species? To address these questions, we expressed the human MBD‐containing protein, hMeCP2, in distinct amine neurons and quantified functional changes in sleep circuitry output using a high throughput assay in Drosophila. hMeCP2 expression resulted in phase‐specific sleep loss and sleep fragmentation with the hMeCP2‐mediated sleep deficits requiring an intact MBD domain. Reducing endogenous dMBD2/3 and dMBD‐R2 levels also generated sleep fragmentation, with an increase in sleep occurring upon dMBD‐R2 reduction. To examine if hMeCP2 and dMBD‐R2 are targeting common neuronal functions, we reduced dMBD‐R2 levels in combination with hMeCP2 expression and observed a complete rescue of sleep deficits. Furthermore, chromosomal binding experiments indicate MBD‐R2 and MeCP2 associate on shared genomic loci. Our results provide the first demonstration that Drosophila MBD‐containing family members are required for neuronal function and suggest that the MBD domain retains considerable functional conservation at the whole organism level across species.
Geriatric problems correlated with cognitive decline using a screening test named “Dr. SUPERMAN” for comprehensive geriatric assessment in elderly inpatients
Authors: Namioka Nayuta , Sakurai Hirofumi , Terayama Hideyuki , Iwamoto Toshihiko , Fujihira Teruaki , Tsugehara Hiromi , Tsuchida Akihiko , Hanyu Haruo
Published: August 2016

Aim

We have recently developed and validated a screening test for comprehensive geriatric assessment (CGA). We investigated the prevalence of geriatric problems in elderly inpatients using CGA, and determined the relationship between geriatric problems and cognitive decline.

Methods

We enrolled consecutive elderly inpatients aged >65 years who were admitted to all of the hospital departments at Tokyo Medical University Hospital, Tokyo, Japan, between July and December 2013. We investigated the prevalence of specific geriatric problems or situations in elderly inpatients using a screening test for CGA named “Dr. SUPERMAN.” We examined 3969 elderly inpatients (2211 men and 1758 women; mean age 75.5 ± 6.7 years) using CGA. Inpatients were divided into three groups by age, namely, 65–74 years, 75–84 years and ≥85 years. Inpatients were divided into the two groups of “internal medicine” and “other departments.”

Results

Geriatric problems were more frequently found in patients who were aged ≥85 years and admitted to “internal medicine” departments. Furthermore, multiple regression analysis found cognitive decline significantly correlated with ADL decline, age, poor medication adherence, upper and lower extremity function disorder, visual/auditory disorder, and urinary disorder. In particular, cognitive decline strongly correlated with a decline in activities of daily living.

Conclusions

CGA should be considered for the treatment of elderly inpatients, particularly those with cognitive decline and admitted to “internal medicine” departments. Geriatr Gerontol Int 2017; 17: 1252–1256.
Urban Governance in Africa Today: Reframing, Experiences, and Lessons
Authors: Obeng‐Odoom Franklin
Published: August 2016

Progress in analysing the instrumental view of governance as an engine for growth, poverty reduction, and inclusive development has been held back by the difficulty in framing governance. This essay seeks to address this problem by 1) reframing urban governance 2) evaluating its aims, processes, and outcomes, and 3) explaining those outcomes on the basis of which some lessons are teased out. Using examples from Africa and an institutional political economy approach (based on institutional economics, Marxist political economics, Georgist political economics, and Polanyian political economy), I show that, overall, while urban economies are growing; both urban poverty and inequality levels have risen substantially. Urban governance has paved the way for new forms of urban development that only benefit the few. Not only are there differences in how urban services and resources are experienced, accessed, and controlled but the varieties are also socially differentiated. I argue that the underlying reasons for this disjuncture between “urban governance” in theory and “actually existing urban governance” are 1) difficulties in implementing urban governance theory consistently in practice, 2) problems arising because urban governance theory has been implemented in practice, 3) tensions that would entangle most policies which do not address historical and structural economic issues, 4) restrictive assumptions, and 5) incoherence among the different dimensions of urban governance. To resolve these contradictions, I put the case for major structural and institutional change involving: 1) the re‐ordering of the roles of the state, market, and society as institutions of change; 2) re‐working the relationships that bind together land, labour, capital, and the state, and 3) re‐organising the channels for keeping the attainment of the ends of urban governance in check.
Career Pathways into Retirement in the UK: Linking Older Women's Pasts to the Present
Authors: Duberley Joanne , Carmichael Fiona
Published: August 2016

Understanding of how women's experiences in retirement are shaped by their pre‐retirement lives is limited. In this paper we utilize an innovative mix of measures to examine the link between career histories and expectations and experiences of retirement. Analysis of timeline data capturing the long working lives of a sample of older women identifies five different pathways into retirement. We explore these trajectories in detail to determine how they are shaped and their links to different outcomes in later life. The analysis shows how different career histories unfold and how they shape expectations and experiences of retirement. Long, professional career pathways leave women feeling enabled in retirement, women following more fragmented pathways are more constrained, and some trajectories, including pathways involving transitions into professional careers in later life, can leave older women financially and emotionally vulnerable in older age.
Miniaturized fibre‐top cantilevers on etched fibres
Authors: CUI MOXI , VAN HOORN CAMIEL H. , IANNUZZI DAVIDE
Published: August 2016

Fibre‐top probes are self‐aligned, all optical devices obtained by carving a cantilever on top of a 125‐m diameter single‐mode optical fibre. In this paper, we show that this design can be adapted to smaller fibres as well. We evaluated the performance of a 20‐m diameter probe in contact mode atomic force microscopy (AFM) and that of a 50‐m diameter probe in nanoindentation measurements. AFM images proved to be accurate both in air and water, although some distortion was observed because of the mechanical bending of the fibre during scanning. Indentation curves resembled those obtained with larger devices. The maximum indentation depth, however, is limited by the small dimensions of the cantilever.
Outcomes in Diabetic Patients Undergoing Orbital Atherectomy System
Authors: Lee Michael S. , Shlofmitz Evan , Nguyen Heajung , Shlofmitz Richard A.
Published: August 2016

Objectives

We evaluated the angiographic and clinical outcomes of orbital atherectomy to treat severely calcified coronary lesions in diabetic and non‐diabetic patients.

Background

Diabetics have increased risk for death, myocardial infarction, and target vessel revascularization after percutaneous coronary intervention. Severely calcified coronary lesions are associated with increased cardiac events. Orbital atherectomy facilitates stent delivery and optimizes stent expansion by modifying severely calcified plaque. Outcomes in diabetic patients who undergo orbital atherectomy have not been reported.

Methods

Our retrospective multicenter registry included 458 consecutive real‐world patients with severely calcified coronary arteries who underwent orbital atherectomy. The primary safety endpoint was the rate of major adverse cardiac and cerebrovascular events at 30 days.

Results

Diabetics represented 42.1% (193/458) of the entire cohort. The primary endpoint was similar in diabetics and non‐diabetics (1.0% vs. 3.0%%, P = 0.20), as were 30‐day rates of death (0.5% vs. 1.9%, P = 0.41), myocardial infarction (0.5% vs. 1.5%, P = 0.40), target vessel revascularization (0% vs. 0%, P = 1), and stroke (0% vs. 0.4%, P > 0.9). Angiographic complications and stent thrombosis rate were low and did not differ between the 2 groups.

Conclusion

Diabetics represented a sizeable portion of patients who underwent orbital atherectomy. Diabetics who had severely calcified coronary arteries and underwent orbital atherectomy had low event rates that were similar to non‐diabetics. Orbital atherectomy appears to be a viable treatment strategy for diabetic patients. Randomized trials with longer‐term follow‐up are needed to determine the ideal treatment strategy for diabetics.
Papain‐like cysteine proteases as hubs in plant immunity
Authors: Misas‐Villamil Johana C. , van der Hoorn Renier A. L. , Doehlemann Gunther
Published: August 2016

Plants deploy a sophisticated immune system to cope with different microbial pathogens and other invaders. Recent research provides an increasing body of evidence for papain‐like cysteine proteases (PLCPs) being central hubs in plant immunity. PLCPs are required for full resistance of plants to various pathogens. At the same time, PLCPs are targeted by secreted pathogen effectors to suppress immune responses. Consequently, they are subject to a co‐evolutionary host–pathogen arms race. When activated, PLCPs induce a broad spectrum of defense responses including plant cell death. While the important role of PLCPs in plant immunity has become more evident, it remains largely elusive how these enzymes are activated and which signaling pathways are triggered to orchestrate different downstream responses.

Contents

Summary
902

I.
Introduction
902

II.
Depletion of PLCPs hampers plant immunity
903

III.
PLCPs are common targets of pathogen effectors
903

IV.
PLCPs induce defense responses and cell death
903

V.
PLCPs can act as co‐receptors
905

VI.
Natural variation in PLCPs is caused by arms races and host adaptation
905

VII.
Conclusion: how do PLCPs activate immunity?
905

Acknowledgements
906

References
906
POLICY CHANGE INCH BY INCH: POLICY ENTREPRENEURS IN THE HOLY BASIN OF JERUSALEM
Authors: SHPAIZMAN ILANA , SWED ORI , PEDAHZUR AMI
Published: August 2016

Facing barriers to change, policy entrepreneurs often shift their activities to a more favourable venue. In the new venue they either pressure the system from the outside, leading to policy punctuation, or make incremental changes within the existing system which over time will accumulate to a significant change in the status quo. This article aims to expand our understanding of policy entrepreneurs' role in the policy process by examining the strategies they use in the incremental path. Specifically, it focuses on one gradual change strategy, conversion – redirection of existing institutions to new purposes. Based on the case of policy entrepreneurs in the Holy Basin of Jerusalem, the findings indicate that when the entrepreneurs shift the venue to the bureaucracy they can establish cooperative relations with the government that will provide them with the needed capacities to exploit the gaps in the existing rules and redirect them to serve their aim.
Age‐related susceptibility ofEucalyptusspecies toPhytophthora boodjera
Authors: Simamora A. V. , Stukely M. J. C. , Barber P. A. , Hardy G. E. StJ. , Burgess T. I.
Published: August 2016

Phytophthora boodjerais a newly described pathogen causing damping off and mortality ofEucalyptusseedlings in Western Australian nurseries. This study evaluated the age‐related susceptibility of several taxa of malleeEucalyptustoP.boodjerain sterilized washed river sand‐infestation pot trials.Phytophthora cinnamomiandP.arenariawere included for comparison. Seedlings ofEucalyptustaxa were inoculated at 0, 2, 4, 12 and 88 weeks with individualPhytophthoraisolates. Pre‐emergent mortality in the presence ofPhytophthorawas almost 100%. Post‐emergent mortality was 50–100%, depending on isolate, compared to 0% for the control. Mortality was also high for inoculated 1 month‐old seedlings (46–68%) and root length of surviving seedlings was severely reduced. Death from root infection was not observed for seedlings inoculated at 12 and 88 weeks, but they developed root necrosis and reduced root dry weight compared to non‐inoculated controls.Phytophthora boodjerais a pre‐ and post‐emergent pathogen of mallee eucalypts. These eucalypts are susceptible toP. boodjeraat all life stages tested, but the mortality rates declined with plant age. Similar results were obtained forP. cinnamomiandP. arenaria. The events leading to its recent appearance in the nurseries remain unknown and further investigations are underway to determine if this is an introduced or endemic pathogen. The approach used here to understand the impact of aPhytophthoraspecies on multiple hosts at different seedling ages is novel and sets a benchmark for future work.
The Evolution of Social Mobility: Norway during the Twentieth Century
Authors: Pekkarinen Tuomas , Salvanes Kjell G. , Sarvimäki Matti
Published: August 2016

We document trends in social mobility in Norway using intergenerational income elasticities, the associations between the income percentiles of fathers and sons, and brother correlations. The results of all approaches suggest that social mobility increased substantially between cohorts born in the early 1930s and the early 1940s. Father–son associations remained stable for cohorts born after World War II, while brother correlations continued to decline. The relationship between father and son income percentile ranks is highly non‐linear for early cohorts, but it approaches linearity over time. We discuss increasing educational attainment among low‐ and middle‐income families as a possible mechanism underlying these trends.
Verbal Agreement with Partitive Noun Phrases
Authors: Leclercq Benoît , Depraetere Ilse
Published: August 2016

This paper provides empirical evidence in favour of Martí Girbau's (2003, 2010) quantifier phrase analysis (QP of N) of the partitive construction, which is based on the analysis of verbal agreement in a large data set from the BNC (British National Corpus) and COCA (Corpus of Contemporary American English). The competing binominal N of NP analysis, advocated by some, predicts that there is number agreement with the first nominal element. In order to account for verbal agreement along these lines, two further principles, that of proximal agreement and possibly that of notional agreement, are needed. The agreement patterns with the partitive construction as observed in the corpus can be explained in a more elegant way when the NP is analysed in terms of a quantifier phrase followed by a nominal head (QP of N): verb number is predicted in 95.74% of the cases (compared to 54.24% when the binominal analysis is adopted), agreement in the remaining 4.26% exceptional cases falling out of further semantic and lexical considerations.
IMAGING DIAGNOSIS—RADIOGRAPHY AND ULTRASONOGRAPHY OF BILATERAL CONGENITAL URETEROVESICAL JUNCTION STENOSIS CAUSING HYDRONEPHROSIS AND HYDROURETER IN A FERRET (MUSTELA PUTORIUS FURO)
Authors: Vilalta Laura , Dominguez Elisabet , Altuzarra Raul , Sibera Neus , Espada Yvonne , Novellas Rosa , Martorell Jaime
Published: August 2016

An 8‐month‐old neutered male ferret was presented for vaccination and preventive treatment for adrenal gland disease. Abdominal ultrasound revealed severe bilateral hydronephrosis and hydroureter. Excretory urography and negative contrast cystography showed bilateral ureterovesical junction stenosis. Positive retrograde cystography demonstrated right ureteral reflux. A subcutaneous ureteral bypass was placed in the left kidney; however, it had to be removed 3 months later due to an obstruction and persistent urinary tract infection. Bilateral ureteroneocystotomy was performed. Although congenital strictures are uncommon in veterinary patients, they should be included in the differential diagnosis in ferrets presenting with hydronephrosis and hydroureter of undetermined cause.
IMAGING DIAGNOSIS—MAGNETIC RESONANCE IMAGING FEATURES OF A MULTIFOCAL OLIGODENDROGLIOMA IN THE SPINAL CORD AND BRAIN OF A DOG
Authors: Schkeeper Amy E. , Moon Rachel , Shrader Stephanie , Koehler Jey W. , Linden Daniel , Taylor Amanda R.
Published: August 2016

An 8‐year‐old neutered male Toy Poodle was presented with chronic, progressive tetraparesis, and possible seizures. Magnetic resonance images demonstrated an extensive, T1 and T2 hyperintense contrast enhancing mass in the cervical spinal cord. Three nodules were present on the surface of the thalamus, with enhancement most evident on delayed images. A diagnosis of high‐grade oligodendroglioma was confirmed with postmortem histopathology and immunohistochemical labeling. Oligodendroglioma should be considered as a differential for T1 hyperintense intraaxial or intramedullary lesions with contrast enhancement. If enhancement is not visualized on postcontrast images, delayed images may be beneficial.
Large‐scale analysis reveals populational contributions of cortical spike rate and synchrony to behavioural functions
Authors: Kimura Rie , Saiki Akiko , Fujiwara‐Tsukamoto Yoko , Sakai Yutaka , Isomura Yoshikazu
Published: August 2016

Key points

There have been few systematic population‐wide analyses of relationships between spike synchrony within a period of several milliseconds and behavioural functions.

In this study, we obtained a large amount of spike data from > 23,000 neuron pairs by multiple single‐unit recording from deep layer neurons in motor cortical areas in rats performing a forelimb movement task.

The temporal changes of spike synchrony in the whole neuron pairs were statistically independent of behavioural changes during the task performance, although some neuron pairs exhibited correlated changes in spike synchrony.

Mutual information analyses revealed that spike synchrony made a smaller contribution than spike rate to behavioural functions.

The strength of spike synchrony between two neurons was statistically independent of the spike rate‐based preferences of the pair for behavioural functions.

Spike synchrony within a period of several milliseconds in presynaptic neurons enables effective integration of functional information in the postsynaptic neuron. However, few studies have systematically analysed the population‐wide relationships between spike synchrony and behavioural functions. Here we obtained a sufficiently large amount of spike data among regular‐spiking (putatively excitatory) and fast‐spiking (putatively inhibitory) neuron subtypes (> 23,000 pairs) by multiple single‐unit recording from deep layers in motor cortical areas (caudal forelimb area, rostral forelimb area) in rats performing a forelimb movement task. After holding a lever, rats pulled the lever either in response to a cue tone (external‐trigger trials) or spontaneously without any cue (internal‐trigger trials). Many neurons exhibited functional spike activity in association with forelimb movements, and the preference of regular‐spiking neurons in the rostral forelimb area was more biased toward externally triggered movement than that in the caudal forelimb area. We found that a population of neuron pairs with spike synchrony does exist, and that some neuron pairs exhibit a dependence on movement phase during task performance. However, the population‐wide analysis revealed that spike synchrony was statistically independent of the movement phase and the spike rate‐based preferences of the pair for behavioural functions, whereas spike rates were clearly dependent on the movement phase. In fact, mutual information analyses revealed that the contribution of spike synchrony to the behavioural functions was small relative to the contribution of spike rate. Our large‐scale analysis revealed that cortical spike rate, rather than spike synchrony, contributes to population coding for movement.
Thermal atomic layer etching of crystalline aluminum nitride using sequential, self-limiting hydrogen fluoride and Sn(acac)2 reactions and enhancement by H2 and Ar plasmas
Authors: Johnson Nicholas R. , Sun Huaxing , Sharma Kashish , George Steven M.
Published: August 2016

Thermal atomic layer etching (ALE) of crystalline aluminum nitride (AlN) films was demonstrated using sequential, self-limiting reactions with hydrogen fluoride (HF) and tin(II) acetylacetonate [Sn(acac)2] as the reactants. Film thicknesses were monitored versus number of ALE reaction cycles at 275 °C using in situ spectroscopic ellipsometry (SE). A low etch rate of ∼0.07 Å/cycle was measured during etching of the first 40 Å of the film. This small etch rate corresponded with the AlOxNy layer on the AlN film. The etch rate then increased to ∼0.36 Å/cycle for the pure AlN films. In situ SE experiments established the HF and Sn(acac)2 exposures that were necessary for self-limiting surface reactions. In the proposed reaction mechanism for thermal AlN ALE, HF fluorinates the AlN film and produces an AlF3 layer on the surface. The metal precursor, Sn(acac)2, then accepts fluorine from the AlF3 layer and transfers an acac ligand to the AlF3 layer in a ligand-exchange reaction. The possible volatile etch products are SnF(acac) and either Al(acac)3 or AlF(acac)2. Adding a H2 plasma exposure after each Sn(acac)2 exposure dramatically increased the AlN etch rate from 0.36 to 1.96 Å/cycle. This enhanced etch rate is believed to result from the ability of the H2 plasma to remove acac surface species that may limit the AlN etch rate. The active agent from the H2 plasma is either hydrogen radicals or radiation. Adding an Ar plasma exposure after each Sn(acac)2 exposure increased the AlN etch rate from 0.36 to 0.66 Å/cycle. This enhanced etch rate is attributed to either ions or radiation from the Ar plasma that may also lead to the desorption of acac surface species.
NSF tries two-step review, drawing praise—and darts
Authors: Mervis Jeffrey
Published: August 2016

Brief preliminary proposals can't do justice to innovative research, scientists complain.
Dispute over president's age tears Pasteur Institute apart
Authors: Rabesandratana Tania
Published: August 2016

Center's board of directors was sent home after denying Christian Bréchot, who's almost 65, a second term.
The storyteller
Authors: Cho Adrian
Published: August 2016

With Rainer Weiss, gravitational wave hunter and likely Nobel laureate, there's the story—and there's the subtext.
Grain-resolved analysis of localized deformation in nickel-titanium wire under tensile load
Authors: Sedmák P. , Pilch J. , Heller L. , Kopeček J. , Wright J. , Sedlák P. , Frost M. , Šittner P.
Published: August 2016

Bend it, shape it, remember it

Shape-memory alloys have the useful property of returning to their original shape after being greatly deformed. This process depends on the collective behavior of many small mineral grains in the metal. Using three-dimensional x-ray diffraction, Sedmák
et al.
tracked over 15,000 grains in a nickel-titanium shape-memory alloy as it moved through this transformation, thus linking microscopic changes to the bulk deformation.

Science
, this issue p.
559
Comment on “Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments”
Authors: Cronin Thomas W. , Gagnon Yakir Luc , Johnsen Sönke , Marshall N. Justin , Roberts Nicholas W.
Published: August 2016

Brady
et al
. (Reports, 20 November 2015, p. 965) claimed that the silvery sides of certain fish are cryptic when viewed by animals with polarization sensitivity, which they termed “polarocrypsis.” After examining their evidence, we find this claim to be unsupported due to (i) pseudoreplication, (ii) confounding polarization contrast with intensity contrast, and (iii) measurements taken at very shallow depths.
Tuning the valley and chiral quantum state of Dirac electrons in van der Waals heterostructures
Authors: Wallbank J. R. , Ghazaryan D. , Misra A. , Cao Y. , Tu J. S. , Piot B. A. , Potemski M. , Pezzini S. , Wiedmann S. , Zeitler U. , Lane T. L. M. , Morozov S. V. , Greenaway M. T. , Eaves L. , Geim A. K. , Fal'ko V. I. , Novoselov K. S. , Mishchenko A.
Published: August 2016

Teasing out chirality in graphene

A chiral elementary particle has its spin pointing in either the same or the opposite direction as its momentum. In graphene, electrons have an analogous chirality, but observing it in electrical transport experiments is tricky. To do this, Wallbank
et al.
studied how electrons tunnel between two slightly misaligned graphene sheets separated by a layer of insulating hexagonal boron nitride. The chiral nature of the electrons imposed restrictions on the tunneling, which made it possible to discern the signatures of chirality in the data.

Science
, this issue p.
575
Metabolic engineering of microbial competitive advantage for industrial fermentation processes
Authors: Shaw A. Joe , Lam Felix H. , Hamilton Maureen , Consiglio Andrew , MacEwen Kyle , Brevnova Elena E. , Greenhagen Emily , LaTouf W. Greg , South Colin R. , van Dijken Hans , Stephanopoulos Gregory
Published: August 2016

Xenobiotics to the rescue

Contaminating microorganisms can be highly detrimental to the large-scale fermentation of complex low-cost feedstocks, such as sugarcane or dry-milled corn for biofuels or other industrial purposes. The challenge is that foreign organisms have to be inhibited without using antibiotics because of concerns about spreading antibiotic resistance. Shaw
et al.
engineered bacteria and yeast to use rare compounds as sources of nutrients (see the Perspective by Lennen). Engineering the common biocatalyst
Escherichia coli
, for example, to consume melamine as a nitrogen source allowed it to outcompete contaminating organisms. Similarly, engineering yeast to use cyanamide for nitrogen or phosphite for phosphorus also improved competitive fitness.

Science
, this issue p.
583
; see also p.
542
Macromolecular recognition directs calcium ions to coccolith mineralization sites
Authors: Gal Assaf , Wirth Richard , Kopka Joachim , Fratzl Peter , Faivre Damien , Scheffel André
Published: August 2016

Many organisms form elaborate mineralized structures, constituted of highly organized arrangements of crystals and organic macromolecules. The localization of crystals within these structures is presumably determined by the interaction of nucleating macromolecules with the mineral phase. Here we show that, preceding nucleation, a specific interaction between soluble organic molecules and an organic backbone structure directs mineral components to specific sites. This strategy underlies the formation of coccoliths, which are highly ordered arrangements of calcite crystals produced by marine microalgae. On combining the insoluble organic coccolith scaffold with coccolith-associated soluble macromolecules in vitro, we found a massive accretion of calcium ions at the sites where the crystals form in vivo. The in vitro process exhibits profound similarities to the initial stages of coccolith biogenesis in vivo.
Direct conversion of methane to aromatics in a catalytic co-ionic membrane reactor
Authors: Morejudo S. H. , Zanón R. , Escolástico S. , Yuste-Tirados I. , Malerød-Fjeld H. , Vestre P. K. , Coors W. G. , Martínez A. , Norby T. , Serra J. M. , Kjølseth C.
Published: August 2016

Membranes to make benzene from methane

Methane gas is expensive to ship. It is usually converted into carbon monoxide and hydrogen and then liquefied. This is economically feasible only on very large scales. Hence, methane produced in small amounts at remote locations is either burned or not extracted. A promising alternative is conversion to benzene and hydrogen with molybdenumzeolite catalysts. Unfortunately, these catalysts deactivate because of carbon buildup; plus, hydrogen has to be removed to drive the reaction forward. Morejudo
et al.
address both of these problems with a solid-state BaZrO
3
membrane reactor that electrochemically removes hydrogen and supplies oxygen to suppress carbon buildup.

Science
, this issue p.
563
Bombs away?
Almighty Courage, Resistance, and Existential Peril in the Nuclear Age
Dan Zak
Blue Rider Press, 2016. 402 pp.
Authors: Wellerstein Alex
Published: August 2016

A journalist probes the morality of nuclear weapons in the 21st century
Bringing order to the expanding fermion zoo
Authors: Beenakker Carlo
Published: August 2016

Crystallographic classification provides an inventory of the electronlike particles that emerge in a lattice world
Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method
Authors: Brown Julianne R. , Roy Sunando , Ruis Christopher , Yara Romero Erika , Shah Divya , Williams Rachel , Breuer Judy
Published: August 2016

Norovirus full-genome sequencing is challenging due to sequence heterogeneity among genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and transcriptome sequencing (RNA-Seq), which nonspecifically sequences all RNA, including host and bacterial RNA, in stool specimens. Target enrichment uses a panel of custom-designed 120-mer RNA baits that are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, which overcomes the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimize the sequencing of nontarget RNA. SureSelect target enrichment and Illumina sequencing were used to sequence full genomes from 507 norovirus-positive stool samples with reverse transcription–real-time PCR cycle threshold (

C
T

) values of 10 to 43. Sequencing on an Illumina MiSeq system in batches of 48 generated, on average, 81% on-target reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, and GII.17. When outliers were accounted for, we generated >80% genome coverage for all positive samples, regardless of

C
T

values. A total of 164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain; 164/164 samples were successfully sequenced, compared to 158/164 samples that were amplified by PCR. Four of the samples that failed capsid PCR analysis had low titers, which suggests that target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity among norovirus genomes.
Spatiotemporal Expression Patterns and Antibody Reactivity of Taeniidae Endophilin B1
Authors: Ahn Chun-Seob , Bae Young-An , Kim Seon-Hee , Kim Jeong-Geun , Yu Jae-Ran , Yang Hyun-Jong , Eom Keeseon S. , Wang Hu , Kang Insug , Yang Yichao , Kong Yoon
Published: August 2016

Larval Taeniidae, such as metacestodes of
Taenia solium
,
Echinococcus granulosus
, and
Echinococcus multilocularis
, produce chronic and fatal helminthic diseases. Proper identification of these zoonotic cestodiases is often challenging and is hampered in some clinical settings. Endophilin B1 plays critical roles in the maintenance of membrane contours and endocytosis. We isolated proteins homologous to endophilin B1 from
T. solium
,
Taenia saginata
, and
Taenia asiatica
. The three Taeniidae endophilin B1 proteins shared 92.9 to 96.6% sequence identity. They harbored a Bin1/amphiphysin/Rvs (BAR) domain and residues for a dimeric interface but lacked a SRC homology 3 (SH3) domain. Endophilin B1 showed a unique immunological profile and was abundantly expressed in the tegumental syncytium of Taeniidae metacestodes and adults. Bacterially expressed recombinant
T. solium
endophilin B1 (rTsMEndoB1) demonstrated a sensitivity of 79.7% (345/433 cases) for serodiagnosis of larval Taeniidae infections. The protein showed strong immune recognition patterns against sera from patients with chronic neurocysticercosis, cystic echinococcosis, or advanced-stage alveolar echinococcosis. Adult Taeniidae infections exhibited moderate degrees of positive antibody responses (65.7% [23/35 samples]). rTsMEndoB1 showed some cross-reactivity with sera from patients infected with Diphyllobothriidae (23.6% [25/106 samples]) but not with sera from patients with other parasitic diseases or normal controls. The specificity was 91.7% (256/301 samples). The positive and negative predictive values were 93.6% and 73.4%, respectively. Our results demonstrate that Taeniidae endophilin B1 may be involved in the control of membrane dynamics, thus contributing to shaping and maintaining the tegumental curvature. rTsMEndoB1 may be useful for large-scale screening, as well as for individual diagnosis and follow-up surveillance of Taeniidae infections.
Characterization of Vibrio cholerae Strains Isolated from the Nigerian Cholera Outbreak in 2010
Authors: Dupke Susann , Akinsinde Kehinde A. , Grunow Roland , Iwalokun Bamidele A. , Olukoya Daniel K. , Oluwadun Afolabi , Velavan Thirumalaisamy P. , Jacob Daniela
Published: August 2016

We examined clinical samples from Nigerian patients with acute watery diarrhea for
Vibrio cholerae
during the 2010 cholera outbreak. A total of 109 suspected isolates were characterized, but only 57
V. cholerae
strains could be confirmed using multiplex real-time PCR as well as
rpoB
sequencing and typed as
V. cholerae
O:1 Ogawa biotype El Tor. This finding highlighted the need for accurate diagnosis of cholera in epidemic countries to implement life-saving interventions.
Human Choline Kinase-α Promotes Hepatitis C Virus RNA Replication through Modulation of Membranous Viral Replication Complex Formation
Authors: Wong Mun-Teng , Chen Steve S.
Published: August 2016

Hepatitis C virus (HCV) infection reorganizes cellular membranes to create an active viral replication site named the membranous web (MW). The role that human choline kinase-α (hCKα) plays in HCV replication remains elusive. Here, we first showed that hCKα activity, not the CDP-choline pathway, promoted viral RNA replication. Confocal microscopy and subcellular fractionation of HCV-infected cells revealed that a small fraction of hCKα colocalized with the viral replication complex (RC) on the endoplasmic reticulum (ER) and that HCV infection increased hCKα localization to the ER. In the pTM-NS3-NS5B model, NS3-NS5B expression increased the localization of the wild-type, not the inactive D288A mutant, hCKα on the ER, and hCKα activity was required for effective trafficking of hCKα and NS5A to the ER. Coimmunoprecipitation showed that hCKα was recruited onto the viral RC presumably through its binding to NS5A domain 1 (D1). hCKα silencing or treatment with CK37, an hCKα activity inhibitor, abolished HCV-induced MW formation. In addition, hCKα depletion hindered NS5A localization on the ER, interfered with NS5A and NS5B colocalization, and mitigated NS5A-NS5B interactions but had no apparent effect on NS5A-NS4B and NS4B-NS5B interactions. Nevertheless, hCKα activity was not essential for the binding of NS5A to hCKα or NS5B. These findings demonstrate that hCKα forms a complex with NS5A and that hCKα activity enhances the targeting of the complex to the ER, where hCKα protein, not activity, mediates NS5A binding to NS5B, thereby promoting functional membranous viral RC assembly and viral RNA replication.

IMPORTANCE
HCV infection reorganizes the cellular membrane to create an active viral replication site named the membranous web (MW). Here, we report that human choline kinase-α (hCKα) acts as an essential host factor for HCV RNA replication. A fraction of hCKα colocalizes with the viral replication complex (RC) on the endoplasmic reticulum (ER) in HCV-infected cells. NS3-NS5B expression increases ER localization of wild-type, but not D288A mutant, hCKα, and hCKα activity facilitates the transport of itself and NS5A to the ER. Silencing or inactivation of hCKα abrogates MW formation. Moreover, hCKα is recruited by NS5A independent of hCKα activity, presumably through binding to NS5A D1. hCKα activity then mediates the ER targeting of the hCKα-NS5A complex. On the ER membrane, hCKα protein,
per se
, induces NS5A binding to NS5B, thereby promoting membranous RC formation and viral RNA replication. Our study may benefit the development of hCKα-targeted anti-HCV therapeutics.
Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis
Authors: Mojardín Laura , Salas Margarita
Published: August 2016

The study of phage-host relationships is essential to understanding the dynamic of microbial systems. Here, we analyze genome-wide interactions of
Bacillus subtilis
and its lytic phage ϕ29 during the early stage of infection. Simultaneous high-resolution analysis of virus and host transcriptomes by deep RNA sequencing allowed us to identify differentially expressed bacterial genes. Phage ϕ29 induces significant transcriptional changes in about 0.9% (38/4,242) and 1.8% (76/4,242) of the host protein-coding genes after 8 and 16 min of infection, respectively. Gene ontology enrichment analysis clustered upregulated genes into several functional categories, such as nucleic acid metabolism (including DNA replication) and protein metabolism (including translation). Surprisingly, most of the transcriptional repressed genes were involved in the utilization of specific carbon sources such as ribose and inositol, and many contained promoter binding-sites for the catabolite control protein A (CcpA). Another interesting finding is the presence of previously uncharacterized antisense transcripts complementary to the well-known phage ϕ29 messenger RNAs that adds an additional layer to the viral transcriptome complexity.

IMPORTANCE
The specific virus-host interactions that allow phages to redirect cellular machineries and energy resources to support the viral progeny production are poorly understood. This study provides, for the first time, an insight into the genome-wide transcriptional response of the Gram-positive model
Bacillus subtilis
to phage ϕ29 infection.
Infectious Progression of Canine Distemper Virus from Circulating Cerebrospinal Fluid into the Central Nervous System
Authors: Takenaka Akiko , Sato Hiroki , Ikeda Fusako , Yoneda Misako , Kai Chieko
Published: August 2016

In the current study, we generated recombinant chimeric canine distemper viruses (CDVs) by replacing the hemagglutinin (H) and/or phosphoprotein (P) gene in an avirulent strain expressing enhanced green fluorescent protein (EGFP) with those of a mouse-adapted neurovirulent strain. An
in vitro
experimental infection indicated that the chimeric CDVs possessing the H gene derived from the mouse-adapted CDV acquired infectivity for neural cells. These cells lack the CDV receptors that have been identified to date (SLAM and nectin-4), indicating that the H protein defines infectivity in various cell lines. The recombinant viruses were administered intracerebrally to 1-week-old mice. Fatal neurological signs of disease were observed only with a recombinant CDV that possessed both the H and P genes of the mouse-adapted strain, similar to the parental mouse-adapted strain, suggesting that both genes are important to drive virulence of CDV in mice. Using this recombinant CDV, we traced the intracerebral propagation of CDV by detecting EGFP. Widespread infection was observed in the cerebral hemispheres and brainstems of the infected mice. In addition, EGFP fluorescence in the brain slices demonstrated a sequential infectious progression in the central nervous system: CDV primarily infected the neuroependymal cells lining the ventricular wall and the neurons of the hippocampus and cortex adjacent to the ventricle, and it then progressed to an extensive infection of the brain surface, followed by the parenchyma and cortex. In the hippocampal formation, CDV spread in a unidirectional retrograde pattern along neuronal processes in the hippocampal formation from the CA1 region to the CA3 region and the dentate gyrus. Our mouse model demonstrated that the main target cells of CDV are neurons in the acute phase and that the virus spreads via neuronal transmission pathways in the hippocampal formation.

IMPORTANCE
CDV is the etiological agent of distemper in dogs and other carnivores, and in many respects, the pathogenesis of CDV infection in animals resembles that of measles virus infection in humans. We successfully generated a recombinant CDV containing the H and P genes from a mouse-adapted neurovirulent strain and expressing EGFP. The recombinant CDV exhibited severe neurovirulence with high mortality, comparable to the parental mouse-adapted strain. The mouse-infectious model could become a useful tool for analyzing CDV infection of the central nervous system subsequent to passing through the blood-cerebrospinal fluid barrier and infectious progression in the target cells in acute disease.
Replacement of Glycoprotein B in Alcelaphine Herpesvirus 1 by Its Ovine Herpesvirus 2 Homolog : Implications in Vaccine Development for Sheep-Associated Malignant Catarrhal Fever
Authors: Cunha Cristina W. , Taus Naomi S. , Dewals Benjamin G. , Vanderplasschen Alain , Knowles Donald P. , Li Hong
Published: August 2016

Vaccine development is a top priority in malignant catarrhal fever (MCF) research. In the case of sheep-associated MCF (SA-MCF) caused by ovine herpesvirus 2 (OvHV-2), progress toward this objective has been hindered by the absence of methods to attenuate or modify the virus, since it cannot be propagated
in vitro
. As an alternative for vaccine development, in this study, we tested the hypothesis that one of the SA-MCF vaccine candidate targets, OvHV-2 glycoprotein B (gB), could be expressed by a nonpathogenic alcelaphine herpesvirus 1 (AlHV-1) and then evaluated the potential of the AlHV-1/OvHV-2 chimera to be used as a vaccine and a diagnostic tool.
Interleukin-1β and tumour necrosis factor-α levels in conjunctiva of diabetic patients with symptomatic moderate dry eye: case–control study
Authors: Zhang Chen , Xi Lei , Zhao Shaozhen , Wei Ruihua , Huang Yue , Yang Ruibo , Su Long , Liu Xun
Published: August 2016

Objectives

To compare expression of interleukin (IL)-1β and tumour necrosis factor (TNF)-α in the conjunctiva of diabetic and non-diabetic patients with symptomatic moderate dry eye.

Setting and participants

Nineteen diabetic patients with dry eye, 15 non-diabetic patients with dry eye and 14 diabetic patients without dry eye were recruited. The relative expression of IL-1β and TNF-α in conjunctival impression cytology (CIC) specimens was evaluated using immunofluorescent staining and in conjunctival biopsy specimens using immunohistochemical staining.

Results

The diabetic dry eye group showed significantly higher grades of metaplasia than the non-diabetic dry eye and diabetic without dry eye groups (both p<0.05). There was no significant difference in the concentration of IL-1β and TNF-α in CIC specimens between the three groups (p=0.504 and p=0.310, respectively). The mean levels of IL-1β and TNF-α in conjunctival biopsy specimens from the diabetic dry eye group was significantly increased compared with the non-diabetic dry eye and diabetic without dry eye groups (p=0.002, p<0.001; p=0.001, p<0.001, respectively). Interestingly, IL-1β- and TNF-α-positive cells were mainly located in the basal layer of the conjunctival epithelium, and rarely seen in the apical conjunctival epithelium in the three groups. The levels of both IL-1β and TNF-α did not correlate with conjunctival squamous metaplasia grades.

Conclusions

Levels of IL-1β and TNF-α in conjunctival biopsy specimens were increased in diabetic patients with dry eye, while levels of IL-1β and TNF-α in apical conjunctival epithelium were similar in the CIC specimens. These findings suggest that the inflammatory response is not limited to the surface of conjunctival epithelial cells, and is more serious in the basal layer of the epithelium, which may play an important role in the pathogenesis of dry eye in diabetic patients.
Bibliometric analysis of scientific publications in transplantation journals from Mainland China, Japan, South Korea and Taiwan between 2006 and 2015
Authors: Pu Qiang-Hong , Lyu Qiu-Ju , Su Huai-Yu
Published: August 2016

Objectives

The aim of this study is to compare the quantity and quality of scientific publications in transplantation fields that were written by researchers from Mainland China, Japan, South Korea and Taiwan in the East Asia region.

Settings

East Asia.

Participants and outcome measures

Articles except editorials, conference abstracts, letters, news and corrections published in 25 transplantation journals from 2006 to 2015 were screened with the Web of Science database. The number of total and annual articles, article types (study design and transplantation site), impact factor, citations and articles in the high-impact journals was determined to assess the quantity and quality of transplantation research from East Asia. The correlation of socioeconomic factors and annual publications was also analysed.

Results

From 2006 to 2015, there were 47 141 articles published in transplantation journals, of which researchers from Japan published 3694 articles, followed by Mainland China, South Korea and Taiwan with 2778, 1643 and 951 articles, respectively. Similar trends were observed in accumulated impact factor, accumulated citations, articles in the high-impact journals and articles on transplantation site. Publications from Japan had the highest average impact factor and citation, while those from Mainland China had the lowest. Additionally, in terms of study design, authors from Mainland China contributed to most clinical trials and randomised controlled trials, but authors from Japan contributed to most case reports. The annual numbers of articles from Mainland China and South Korea increased linearly (p<0.05), but those from Japan and Taiwan remained stable for the period studied. The annual numbers of articles from Mainland China and South Korea were positively correlated with gross domestic product (p<0.05).

Conclusions

Transplantation research productivity in East Asia is highly skewed, with gross domestic product having a significant positive correlation. Mainland China still lags far behind Japan in most bibliometric indicators; thus, there is vast room for improvement.