bluuebunny/crossref_metadata_2025 huggingface dataset:
Semantic Knowledge, Semantic Guidance, and Kripke's Wittgenstein
Authors: Green Derek
Published: November 2015

Saul Kripke's influential ‘sceptical paradox’ of semantic rule‐following alleges that speakers cannot have any justification for using a word one way rather than another. If it is correct, there can be no such thing as meaning anything by a word. I argue that the paradox fails to undermine meaning. Kripke never adequately motivates its excessively strict standard for the justified use of words. The paradox lacks the resources to show that its standard is truly mandatory or that speakers do not frequently satisfy the well‐motivated competitor I offer. So the paradox fails.
AsHSP17, a creeping bentgrass small heat shock protein modulates plant photosynthesis and ABA‐dependent and independent signalling to attenuate plant response to abiotic stress
Authors: Sun Xinbo , Sun Chunyu , Li Zhigang , Hu Qian , Han Liebao , Luo Hong
Published: November 2015

Heat shock proteins (HSPs) are molecular chaperones that accumulate in response to heat and other abiotic stressors. Small HSPs (sHSPs) belong to the most ubiquitous HSP subgroup with molecular weights ranging from 12 to 42 kDa. We have cloned a new sHSP gene, AsHSP17 from creeping bentgrass (Agrostis stolonifera) and studied its role in plant response to environmental stress. AsHSP17 encodes a protein of 17 kDa. Its expression was strongly induced by heat in both leaf and root tissues, and by salt and abscisic acid (ABA) in roots. Transgenic Arabidopsis plants constitutively expressing AsHSP17 exhibited enhanced sensitivity to heat and salt stress accompanied by reduced leaf chlorophyll content and decreased photosynthesis under both normal and stressed conditions compared to wild type. Overexpression of AsHSP17 also led to hypersensitivity to exogenous ABA and salinity during germination and post‐germinative growth. Gene expression analysis indicated that AsHSP17 modulates expression of photosynthesis‐related genes and regulates ABA biosynthesis, metabolism and ABA signalling as well as ABA‐independent stress signalling. Our results suggest that AsHSP17 may function as a protein chaperone to negatively regulate plant responses to adverse environmental stresses through modulating photosynthesis and ABA‐dependent and independent signalling pathways.
Beyond Psoriasis: Novel Uses for Biologic Response Modifiers in Pediatric Dermatology
Authors: Bellodi‐Schmidt Fernanda , Shah Kara N.
Published: November 2015

Dermatologists have witnessed the increasing availability of novel biologic response modifiers for the treatment of inflammatory and autoimmune diseases in recent years. The most common dermatologic indication for the use of biologic response modifiers in adults is psoriasis, but the U.S. Food and Drug Administration has not approved any of these agents for use in any dermatologic disease in children with the exception of omalizumab, and as such, use in this population is considered off‐label. In this review, we focus on the use of these agents in children to treat inflammatory skin diseases other than psoriasis, including atopic dermatitis, hidradenitis suppurativa, pemphigus vulgaris, bullous pemphigoid, and toxic epidermal necrolysis, with an emphasis on the use of etanercept, infliximab, rituximab, omalizumab, and ustekinumab. By highlighting novel uses of these agents, particularly for the treatment of dermatologic conditions for which optimal therapies are yet to be established, we hope to raise awareness of the potential use of this class of medications to treat inflammatory skin diseases in children.
Abnormal cardiac axis as a prenatal marker of left pulmonary artery sling
Authors: Ishii Yoichiro , Miyamoto Takashi , Nakajima Kimiko , Tanaka Kensuke , Ikeda Kentaro , Inamura Noboru , Takagi Takeshi , Kobayashi Tomio , Arakawa Hirokazu
Published: November 2015

Left pulmonary artery sling (LPAS) is a rare vascular anomaly. The left pulmonary artery arises distally from the right pulmonary artery on the right side of the trachea and passes between the trachea and esophagus towards the left lung, compressing the lower trachea. LPAS is associated with congenital tracheal stenosis, which frequently requires early surgical intervention and has a poor prognosis due to severe airway obstruction after birth. Therefore, LPAS should be prenatally diagnosed to prepare for surgical intervention for tracheal stenosis. To the best of our knowledge, there are few reports on prenatal echocardiographic findings in LPAS. We report three prenatal cases of LPAS, which resulted in respiratory symptoms. We discuss fetal ultrasound findings and highlight the abnormal rotation of the fetal cardiac axis to the right as a useful sign in the prenatal screening of LPAS.
Can absence of pyuria exclude urinary tract infection in febrile infants? About 2011 AAP guidelines on UTI
Authors: Kim Seong Heon , Lyu Soo Young , Kim Hye Young , Park Su Eun , Kim Su Young
Published: November 2015

Background

The aim of this study was to describe clinical and laboratory characteristics of urinary tract infection (UTI) without significant pyuria in young children aged 2–24 months.

Methods

The subjects consisted of infants and young children with febrile UTI treated at Pusan National University Children's Hospital, Korea. Group A included 283 patients with definite UTI who fulfilled the revised American Academy of Pediatrics diagnostic criteria, and group B included 19 patients with presumed UTI who had significant culture of uropathogens without pyuria, bacteriuria or other focus of infection.

Results

Duration of fever before hospital visit in group B was significantly shorter than in group A (17.7 ± 14.0 vs 34.5 ± 30.7 h). Most patients in group B (17/19, 89.5%) came to the hospital within 24 h of onset of fever. Acute scintigraphic lesions were found in 47.8% of patients in group A and 50% in group B. Underlying urological abnormalities such as vesicoureteral reflux and obstructive uropathy were found in 24.5% of patients in group A and in 33.3% of patients in group B (P = 0.74).

Conclusions

Clinicians cannot exclude UTI on the absence of pyuria in young children aged 2–24 months.
Comparison of innate and Th1‐type host immune responses in Oesophagostomum dentatum and Trichuris suis infections in pigs
Authors: Andreasen A. , Skovgaard K. , Klaver E. J. , van Die I. , Mejer H. , Thamsborg S. M. , Kringel H.
Published: November 2015

This study investigated the details of the innate and Th1/Treg‐type‐associated host immune responses in Trichuris suis and Oesophagostomum dentatum mono‐ and co‐infected pigs and in vitro in stimulated porcine dendritic cell cultures. Forty‐eight pigs were allocated into a 2‐factorial design with two groups trickle‐inoculated with 10 T. suis eggs/kg/day (Group T) or 20 O. dentatum L3/kg/day (O). Another group (OT) was infected with both parasites. Group C remained uninfected. Expression of innate and Th1/Treg‐cell‐associated genes in gut mucosa and associated lymph nodes was determined by qPCR at necropsy day 35 and 71. Gene expression showed suppressed/inhibited Th1 and Treg‐type immune reactions, in accordance with previous findings of a predominant Th2‐type immune response to both nematodes. The in vitro part examined the production of TNF‐α in porcine dendritic cells (DC) exposed to T. suis and/or O. dentatum excretory/secretory (E/S) products. Further, binding capacity and structure of E/S products were characterized. Glycan and lectin‐binding capacity were generally lower in O. dentatum E/S products compared to T. suis which may explain the earlier found weaker Th2 response to the former. Surprisingly, O. dentatum E/S products induced a significant (P < 0·0001) increase in TNF‐α DC production, potentially indicating a new mode of helminth–host immune response interaction.
Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice
Authors: Shimono Hiroyuki , Abe Akira , Aoki Naohiro , Koumoto Takemasa , Sato Masahiro , Yokoi Shuji , Kuroda Eiki , Endo Takashi , Saeki Ken‐ich , Nagano Kuniaki
Published: November 2015

Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quantitative trait loci (QTLs), we modeled genotypic variation in the physiological processes involved in low temperature spikelet sterility on the basis of anther length (AL), a proxy for microspore and pollen grain number per anther. The model accounted for 83% of the genotypic variation in potential AL at normal temperature and the ability to maintain AL at LT. We tested the model on 208 recombinant inbred lines of cold‐tolerant ‘Tohoku‐PL3’ (PL3) × cold‐sensitive ‘Akihikari’ (AH) for 2 years. QTLs for spikelet fertility (FRT) at LT were detected on chromosomes 5 (QTL for Cold Tolerance at Reproductive stage, qCTR5) and 12 (qCTR12). qCTR12 was annotated with the ability to maintain AL under LTs. qCTR5 was in a region shared with QTLs for culm length and heading date. Genome‐wide expression analysis showed 798 genes differentially expressed in the spikelets between the parents at LTs. Of these, 12 were near qCTR5 and 23 were near qCTR12. Gene expression analysis confirmed two candidate genes for qCTR5 (O‐methyltransferase ZRP4, Os05g0515600; beta‐1,3‐glucanase‐like protein, Os05g0535100) and one for qCTR12 (conserved hypothetical protein, Os12g0550600). Nucleotide polymorphisms (21 deletions, 2 insertions and 10 single nucleotide polymorphisms) in PL3 were found near the candidate conserved hypothetical protein (Os12g0550600) and upstream in PL3, but not in AH. Haplotype analysis revealed that this gene came from ‘Kuchum’. The combination of mapping physiological QTLs with gene expression analysis can be extended to identify other genes for abiotic stress response in cereals.
Real Effective Exchange Rate Misalignment in the Euro Area: A Counterfactual Analysis
Authors: El‐Shagi Makram , Lindner Axel , von Schweinitz Gregor
Published: November 2015

The European debt crisis has revealed severe imbalances within the Euro area, sparking a debate about the magnitude of those imbalances, in particular concerning real effective exchange rate misalignments. We use synthetic matching to construct a counterfactual economy for each member state in order to identify the degree of these misalignments. We find that crisis countries are best described as a combination of advanced and emerging economies. Comparing the actual real effective exchange rate with those of the counterfactuals gives evidence of misalignments before the outbreak of the crisis: all peripheral countries appear strongly and significantly overvalued.
Modeling Urban Land Use Changes Using Support Vector Machines
Authors: Samardžić‐Petrović Mileva , Dragićević Suzana , Kovačević Miloš , Bajat Branislav
Published: November 2015

Support Vector Machines (SVM) is a machine learning (ML) algorithm commonly applied to the classification of remotely sensing data and more recently for modeling land use changes. However, in most geospatial applications the current literature does not elaborate on specifications of the SVM method with respect to data sampling, attribute selection and optimal parameters choices. Therefore the main objective of this study is to present and investigate the SVM technique for modeling urban land use change. The SVM model building procedure is presented together with the detailed evaluation of the output results with respect to the choice of datasets, attributes and the change of SVM parameters. Geospatial datasets containing nine land use classes and spatial attributes for the Municipality of Zemun, Republic of Serbia were used for years 2001, 2003, 2007 and 2011. The Correlation‐based Feature Subset method, kappa coefficient, Area Under Receiver Operating Characteristic Curve (AUC) and kappa simulation were used to perform the model evaluation and compare the model outputs with the real land use datasets. The obtained results indicate that the SVM‐based models perform better when implementing balanced data sampling, reduced data sets to informative subsets of attributes and properly identify the optimal learning parameters.
Are Acts of Supererogation Always Praiseworthy?
Authors: Archer Alfred
Published: November 2015

It is commonly assumed that praiseworthiness should form part of the analysis of supererogation. I will argue that this view should be rejected. I will start by arguing that, at least on some views of the connection between moral value and praiseworthiness, it does not follow from the fact that acts of supererogation go beyond what is required by duty that they will always be praiseworthy to perform. I will then consider and dismiss what I will call the Argument from Stipulation in favour of holding that acts of supererogation are always praiseworthy. Next, I will examine what I will call the Necessary Connection Argument, which posits a necessary connection between supererogation and praiseworthiness. I will argue that the intuitions used to motivate this argument are best explained by a debunking explanation.
Dendritic cells modulate burn wound healing by enhancing early proliferation
Authors: Vinish Monika , Cui Weihua , Stafford Eboni , Bae Leon , Hawkins Hal , Cox Robert , Toliver‐Kinsky Tracy
Published: November 2015

Adequate wound healing is vital for burn patients to reduce the risk of infections and prolonged hospitalization. Dendritic cells (DCs) are antigen presenting cells that release cytokines and are central for the activation of innate and acquired immune responses. Studies have showed their presence in human burn wounds; however, their role in burn wound healing remains to be determined. This study investigated the role of DCs in modulating healing responses within the burn wound. A murine model of full‐thickness contact burns was used to study wound healing in the absence of DCs (CD11c promoter‐driven diphtheria toxin receptor transgenic mice) and in a DC‐rich environment (using fms‐like tyrosine kinase‐3 ligand, FL‐ a DC growth factor). Wound closure was significantly delayed in DC‐deficient mice and was associated with significant suppression of early cellular proliferation, granulation tissue formation, wound levels of TGFβ1 and formation of CD31+ vessels in healing wounds. In contrast, DC enhancement significantly accelerated early wound closure, associated with increased and accelerated cellular proliferation, granulation tissue formation, and increased TGFβ1 levels and CD31+ vessels in healing wounds. We conclude that DCs play an important role in the acceleration of early wound healing events, likely by secreting factors that trigger the proliferation of cells that mediate wound healing. Therefore, pharmacological enhancement of DCs may provide a therapeutic intervention to facilitate healing of burn wounds.
Subcutaneous perfusion before and during surgery in obese and nonobese patients
Authors: Kaiser Heiko A. , Kaiser Dagmar J. , Krejci Vladimir , Saager Leif , Erdoes Gabor , Hiltebrand Luzius B.
Published: November 2015

Hypoxia at the surgical site impairs wound healing and oxidative killing of microbes. Surgical site infections are more common in obese patients. We hypothesized that subcutaneous oxygen tension (PsqO2) would decrease substantially in both obese and non‐obese patients following induction of anesthesia and after surgical incision. We performed a prospective observational study that enrolled obese and non‐obese surgical patients and measured serial PsqO2 before and during surgery. Seven morbidly obese and seven non‐obese patients were enrolled. At baseline breathing room air, PsqO2 values were not significantly different (p = 0.66) between obese (6.8 kPa) and non‐obese (6.5 kPa) patients. The targeted arterial oxygen tension (40 kPa) was successfully achieved in both groups with an expected significant increase in PsqO2 (obese 16.1 kPa and non‐obese 13.4 kPa; p = 0.001). After induction of anesthesia and endotracheal intubation, PsqO2 did not change significantly in either cohort in comparison to levels right before induction (obese 15.5, non‐obese 13.5 kPa; p = 0.95), but decreased significantly during surgery (obese 10.1, non‐obese 9.3 kPa; p = 0.01). In both morbidly obese and non‐obese patients, PsqO2 does not decrease appreciably following induction of anesthesia, but decreases markedly (∼33%) after commencement of surgery. Given the theoretical risks associated with low PsqO2, future research should investigate how PsqO2 can be maintained after surgical incision.
Economic Assessment of Zoonoses Surveillance in a ‘One Health’ Context: A Conceptual Framework
Authors: Babo Martins S. , Rushton J. , Stärk K. D. C.
Published: November 2015

Collaboration between animal and public health sectors has been highlighted as a means to improve the management of zoonotic threats. This includes surveillance systems for zoonoses, where enhanced cross‐sectoral integration and sharing of information are seen as key to improved public health outcomes. Yet, there is a lack of evidence on the economic returns of such collaboration, particularly in the development and implementation of surveillance programmes. The economic assessment of surveillance in this context needs to be underpinned by the understanding of the links between zoonotic disease surveillance in animal populations and the wider public health disease mitigation process and how these relations impact on the costs and benefits of the surveillance activities. This study presents a conceptual framework of these links as a basis for the economic assessment of cross‐sectoral zoonoses surveillance with the aim of supporting the prioritization of resource allocation to surveillance. In the proposed framework, monetary, non‐monetary and intermediate or intangible cost components and benefit streams of three conceptually distinct stages of zoonotic disease mitigation are identified. In each stage, as the final disease mitigation objective varies so does the use of surveillance information generated in the animal populations for public health decision‐making. Consequently, the associated cost components and benefit streams also change. Building on the proposed framework and taking into account these links, practical steps for its application are presented and future challenges are discussed.
On Berman–Gibbs stability and K-stability of -Fano varieties
Authors: Fujita Kento
Published: November 2015

The notion of Berman–Gibbs stability was originally introduced by Berman for$\mathbb{Q}$-Fano varieties$X$. We show that the pair$(X,-K_{X})$is K-stable (respectively K-semistable) provided that$X$is Berman–Gibbs stable (respectively semistable).
Integral points of bounded degree on affine curves
Authors: Levin Aaron
Published: November 2015

We generalize Siegel’s theorem on integral points on affine curves to integral points of bounded degree, giving a complete characterization of affine curves with infinitely many integral points of degree $d$ or less over some number field. Generalizing Picard’s theorem, we prove an analogous result characterizing complex affine curves admitting a nonconstant holomorphic map from a degree $d$ (or less) analytic cover of $\mathbb{C}$.
Functional properties of in vitro excitatory cortical neurons derived from human pluripotent stem cells
Authors: Livesey Matthew R. , Magnani Dario , Hardingham Giles E. , Chandran Siddharthan , Wyllie David J. A.
Published: November 2015

The in vitro derivation of regionally defined human neuron types from patient‐derived stem cells is now established as a resource to investigate human development and disease. Characterization of such neurons initially focused on the expression of developmentally regulated transcription factors and neural markers, in conjunction with the development of protocols to direct and chart the fate of differentiated neurons. However, crucial to the understanding and exploitation of this technology is to determine the degree to which neurons recapitulate the key functional features exhibited by their native counterparts, essential for determining their usefulness in modelling human physiology and disease in vitro. Here, we review the emerging data concerning functional properties of human pluripotent stem cell‐derived excitatory cortical neurons, in the context of both maturation and regional specificity.

image
Satellite cell response to erythropoietin treatment and endurance training in healthy young men
Authors: Hoedt Andrea , Christensen Britt , Nellemann Birgitte , Mikkelsen Ulla Ramer , Hansen Mette , Schjerling Peter , Farup Jean
Published: November 2015

Key point

Erythropoietin (Epo) treatment may induce myogenic differentiation factor (MyoD) expression and prevent apoptosis in satellite cells (SCs) in murine and in vitro models.

Endurance training stimulates SC proliferation in vivo in murine and human skeletal muscle.

In the present study, we show, in human skeletal muscle, that treatment with an Epo‐stimulating agent (darbepoetin‐α) in vivo increases the content of MyoD+ SCs in healthy young men. Moreover, we report that Epo receptor mRNA is expressed in adult human SCs, suggesting that Epo may directly target SCs through ligand‐receptor interaction.

Moreover, endurance training, but not Epo treatment, increases the SC content in type II myofibres, as well as the content of MyoD+ SCs.

Collectively, our results suggest that Epo treatment can regulate human SCs in vivo, supported by Epo receptor mRNA expression in human SCs. In effect, long‐term Epo treatment during disease conditions involving anaemia may impact SCs and warrants further investigation.

Satellite cell (SC) proliferation is observed following erythropoitin treatment in vitro in murine myoblasts and endurance training in vivo in human skeletal muscle. The present study aimed to investigate the effects of prolonged erythropoiesis‐stimulating agent (ESA; darbepoetin‐α) treatment and endurance training, separately and combined, on SC quantity and commitment in human skeletal muscle. Thirty‐five healthy, untrained men were randomized into four groups: sedentary‐placebo (SP, n = 9), sedentary‐ESA (SE, n = 9), training‐placebo (TP, n = 9) or training‐ESA (TE, n = 8). ESA/placebo was injected once weekly and training consisted of ergometer cycling three times a week for 10 weeks. Prior to and following the intervention period, blood samples and muscle biopsies were obtained and maximal oxygen uptake () was measured. Immunohistochemical analyses were used to quantify fibre type specific SCs (Pax7+), myonuclei and active SCs (Pax7+/MyoD+). ESA treatment led to elevated haematocrit, whereas endurance training increased . Endurance training led to an increase in SCs associated with type II fibres (P < 0.05), whereas type I fibres showed no changes. Both ESA treatment and endurance training increased Pax7+/MyoD+ cells, whereas only ESA treatment increased the total content of MyoD+ cells. Epo‐R mRNA presence in adult SC was tested with real‐time RT‐PCR using fluorescence‐activated cell sorting (CD56+/CD45−/CD31−) to isolate cells from a human rectus abdominis muscle and was found to be considerably higher than in whole muscle. In conclusion, endurance training and ESA treatment may separately stimulate SC commitment to the myogenic program. Furthermore, ESA‐treatment may alter SC activity by direct interaction with the Epo‐R expressed on SCs.
The roles of c‐Jun NH2‐terminal kinases (JNKs) in obesity and insulin resistance
Authors: Pal Martin , Febbraio Mark A. , Lancaster Graeme I.
Published: November 2015

Obesity is currently at epidemic levels worldwide and is associated with a wide range of diseases such as type 2 diabetes, cardiovascular disease, fatty liver disease and certain forms of cancer. Obesity‐induced chronic inflammation is central to the disrupted metabolic homeostasis which underlies many of these conditions. While research over the past decade has identified many of the cells and signalling molecules that contribute to obesity‐induced inflammation, perhaps the best characterised are the stress‐activated c‐Jun NH2‐terminal kinases (JNKs). JNKs are activated in obesity in numerous metabolically important cells and tissues such as adipose tissue, macrophages, liver, skeletal muscle and regions of the brain and pituitary. Elegant in vivo mouse studies using Cre‐LoxP‐mediated recombination of the JNK1 and JNK2 genes have revealed the remarkably diverse roles that JNKs play in the development of obesity‐induced inflammation, impaired glucose homeostasis and hepatic steatosis. While JNK activation in classical metabolically active tissues such as skeletal muscle and adipose tissue only appears to play a minor role on the induction of the above‐mentioned pathologies, recent studies have clearly established the important roles JNK signalling fulfils in macrophages, the liver and cells of the anterior pituitary. Collectively, these studies place JNKs as important mediators of obesity and obesity‐associated disruptions to metabolic homeostasis.

image
Robust Full-Order and Reduced-Order Observers for a Class of Uncertain Switched Systems
Authors: Yang Junqi , Zhu Fanglai , Tan Xingguo , Wang Yunjian
Published: November 2015

This paper deals with the problem of robust state estimation for a class of switched linear systems with unknown inputs under average dwell time (ADT) switching, where the switching of the observers is synchronous with that of the estimated system. First, based on the feasibility of an optimization problem with linear matrix inequality (LMI) constraint, a robust sliding-mode switched observer is developed such that the asymptotic state reconstruction is guaranteed even if the switched system is with unknown inputs. Second, a reduced-order switched system which avoids the influence of unknown inputs is constructed by the technique of state transformation, and a reduced-order switched observer is proposed to estimate the continuous states of the original switched system. Next, the conditions under which a full-order switched observer exists also guarantee the existence of a reduced-order switched observer. The convergence of the state estimate is proved to be exponential by appropriate Lyapunov analysis. Finally, the simulation results confirm the predicted performance and applicability by a simplified three-tank system.
After Paris: The rocky road ahead
Authors: Kintisch Eli
Published: November 2015

Officials call the Paris talks a beginning, but what's the destination? Below are three possible future paths for annual global greenhouse gas emissions. Models suggest each would produce very different ranges of atmospheric greenhouse gas levels and warming in 2100. And all would cause the seas to rise for centuries after 2100.
Vibrational spectroscopic imaging of living systems: An emerging platform for biology and medicine
Authors: Cheng Ji-Xin , Xie X. Sunney
Published: November 2015

Imaging with molecular vibrations

The vibrational spectra of biomolecules could in principle image cells and tissue without added markers. Practically, several technical problems need to be overcome to achieve sufficient imaging depths, resolution, and data acquisition speed. Cheng and Xie review emerging bioimaging methods for use in the lab and the clinic.

Science
, this issue p.
10.1126/science.aaa8870
A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids
Authors: McGee Matthew D. , Borstein Samuel R. , Neches Russell Y. , Buescher Heinz H. , Seehausen Ole , Wainwright Peter C.
Published: November 2015

The downside of innovation

Evolutionary innovation allows a species to invade a new niche or environment. Generally, the emergence of adaptive traits is thought to lead to diversification. Support for this process in nature, however, is mixed. McGeeet al.show that the evolution of secondary jaws in fish may be an example of how innovation can reduce diversification (see the Perspective by Vermeij). Fish with secondary jaws are less able to rapidly ingest fish prey, which puts them at a competitive disadvantage to regularly jawed fish. Such competition could lead to reduced variation and the extinction of lineages with the trait.

Science, this issue p.1077; see also p.1038
Predicting poverty and wealth from mobile phone metadata
Authors: Blumenstock Joshua , Cadamuro Gabriel , On Robert
Published: November 2015

Predicting unmeasurable wealth

In developing countries, collecting data on basic economic quantities, such as wealth and income, is costly, time-consuming, and unreliable. Taking advantage of the ubiquity of mobile phones in Rwanda, Blumenstocket al.mapped mobile phone metadata inputs to individual phone subscriber wealth. They applied the model to predict wealth throughout Rwanda and show that the predictions matched well with those from detailed boots-on-the-ground surveys of the population.

Science, this issue p.1073
A continent-wide assessment of the form and intensity of large mammal herbivory in Africa
Authors: Hempson Gareth P. , Archibald Sally , Bond William J.
Published: November 2015

How herbivores affect ecosystems

Abiotic forces, such as fire and water, have powerful effects on ecosystem structure and function. Animals that eat plants also have strong effects in natural systems, but their impacts are harder to assess. Hempson
et al.
measured how herbivores affect vegetation across Africa (see the Perspective by Gill). Four distinct herbivory regimes emerge from the analysis, characterized by forest antelopes, arid-region gazelles, high-diversity savannah fauna, and bulk feeders (such as elephants), which have had equivalent impact to those of fire and water on shaping ecosystems.

Science
, this issue p.
1056
; see also p.
1036
Deformation-assisted fluid percolation in rock salt
Authors: Ghanbarzadeh Soheil , Hesse Marc A. , Prodanović Maša , Gardner James E.
Published: November 2015

Salted away no longer?

Rock salt deposits are thought to be impermeable to fluid flow and so are candidates for nuclear waste repositories. Ghanbarzadeh
et al.
found that some salt deposits in the Gulf of Mexico are infiltrated by oil and other hydrocarbons. If these salt domes are not completely isolated from the surrounding environment, they will not be suitable for deep geological waste storage sites.

Science
, this issue p.
1069
Principles of connectivity among morphologically defined cell types in adult neocortex
Authors: Jiang Xiaolong , Shen Shan , Cadwell Cathryn R. , Berens Philipp , Sinz Fabian , Ecker Alexander S. , Patel Saumil , Tolias Andreas S.
Published: November 2015

A census of neocortical neurons

Despite the importance of the brain's neocortex, we still do not completely understand the diversity and functional connections of its cell types. Jiang
et al.
recorded, labeled, and classified over 1200 interneurons and more than 400 pyramidal neurons in the mature mouse visual cortex. Fifteen major classes of interneurons fell into three types: some connect to all neurons, some connect to other interneurons, and some form synapses with pyramidal neurons.

Science
, this issue p.
10.1126/science.aac9462
Intimate details
Database of Dreams: The Lost Quest to Catalog Humanity
Rebecca Lemov
Yale University Press, 2015. 377 pp.
Authors: Stark Laura
Published: November 2015

A long-forgotten social science archive offers a lesson in responsible data management
A quick look at how photoelectrodes work
Authors: Hansen Ole , Seger Brian , Vesborg Peter C. K. , Chorkendorff Ib
Published: November 2015

Transient photoreflectance spectroscopy reveals charge carrier dynamics in water splitting

[Also see Report by

Yang
et al.

]
Learning from Africa's herbivores
Authors: Gill Jacquelyn L.
Published: November 2015

Herbivore diversity plays a key role in grassland ecosystems

[Also see Research Article by

Hempson
et al.

]
The indispensable genome
Authors: Boone Charles , Andrews Brenda J.
Published: November 2015

The core genes essential for life in human cells are defined

[Also see Reports by

Blomen
et al.

and

Wang
et al.

]
Standardization of Assays That Detect Anti-Rubella Virus IgG Antibodies
Authors: Dimech Wayne , Grangeot-Keros Liliane , Vauloup-Fellous Christelle
Published: November 2015

Rubella virus usually causes a mild infection in humans but can cause congenital rubella syndrome (CRS). Vaccination programs have significantly decreased primary rubella virus infection and CRS; however, vaccinated individuals usually have lower levels of rubella virus IgG than those with natural infections. Rubella virus IgG is quantified with enzyme immunoassays that have been calibrated against the World Health Organization (WHO) international standard and report results in international units per milliliter. It is recognized that the results reported by these assays are not standardized. This investigation into the reasons for the lack of standardization found that the current WHO international standard (RUB-1-94) fails by three key metrological principles. The standard is not a pure analyte but is composed of pooled human immunoglobulin. It was not calibrated by certified reference methods; rather, superseded tests were used. Finally, no measurement uncertainty estimations have been provided. There is an analytical and clinical consequence to the lack of standardization of rubella virus IgG assays, which leads to misinterpretation of results. The current approach to standardization of rubella virus IgG assays has not achieved the desired results. A new approach is required.
Evaluation of a Fiber-Modified Adenovirus Vector Vaccine against Foot-and-Mouth Disease in Cattle
Authors: Medina Gisselle N. , Montiel Nestor , Diaz-San Segundo Fayna , Sturza Diego , Ramirez-Medina Elizabeth , Grubman Marvin J. , de los Santos Teresa
Published: November 2015

Novel vaccination approaches against foot-and-mouth disease (FMD) include the use of replication-defective human adenovirus type 5 (Ad5) vectors that contain the capsid-encoding regions of FMD virus (FMDV). Ad5 containing serotype A24 capsid sequences (Ad5.A24) has proved to be effective as a vaccine against FMD in livestock species. However, Ad5-vectored FMDV serotype O1 Campos vaccine (Ad5.O1C.2B) provides only partial protection of cattle against homologous challenge. It has been reported that a fiber-modified Ad5 vector expressing Arg-Gly-Asp (RGD) enhances transduction of antigen-presenting cells (APC) in mice. In the current study, we assessed the efficacy of a fiber-modified Ad5 (Adt.O1C.2B.RGD) in cattle. Expression of FMDV capsid proteins was superior in cultured cells infected with the RGD-modified vector. Furthermore, transgene expression of Adt.O1C.2B.RGD was enhanced in cell lines that constitutively express integrin α
v
β6, a known receptor for FMDV. In contrast, capsid expression in cattle-derived enriched APC populations was not enhanced by infection with this vector. Our data showed that vaccination with the two vectors yielded similar levels of protection against FMD in cattle. Although none of the vaccinated animals had detectable viremia, FMDV RNA was detected in serum samples from animals with clinical signs. Interestingly, CD4
+
and CD8
+
gamma interferon (IFN-γ)
+
cell responses were detected at significantly higher levels in animals vaccinated with Adt.O1C.2B.RGD than in animals vaccinated with Ad5.O1C.2B. Our results suggest that inclusion of an RGD motif in the fiber of Ad5-vectored FMD vaccine improves transgene delivery and cell-mediated immunity but does not significantly enhance vaccine performance in cattle.
Draft Genome Sequence of the Ant-Associated Fungus
Phialophora attae
(CBS 131958)
Authors: Moreno Leandro F. , Stielow J. Benjamin , de Vries Michel , Weiss Vinicius A. , Vicente Vania A. , de Hoog Sybren
Published: November 2015

The black yeast
Phialophora attae
was isolated from the cuticle of tropical ant gynes. The ant-fungus association is sustained due to symbiotic evolutionary adaptations that allow fungal assimilation and tolerance of toxic compounds produced by the ant. The genome sequence of the first ant-associated fungus,
P. attae
, is presented here.
Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India
Authors: Saxena Rituja , Chaudhary Nikhil , Dhakan Darshan B. , Sharma Vineet K.
Published: November 2015

This paper reports the draft genome sequence of the proteobacterium
Gulbenkiania mobilis
strain MB1, a sulfur-metabolizing thermophile isolated from a hot spring located in Pachmarhi, India. This study reports the first draft genome sequence of any species from the genus
Gulbenkiania
.
Genome Sequence of Streptococcus phocae subsp.
phocae
Strain ATCC 51973
T
Isolated from a Harbor Seal (
Phoca vitulina
)
Authors: Avendaño-Herrera Ruben , Poblete-Morales Matías
Published: November 2015

Streptococcus phocae
subsp.
phocae
is a pathogen that affects different pinniped and mammalian species. This announcement reports the genome sequence of the type strain ATCC 51973 isolated in Norway from clinical specimens of harbor seal (
Phoca vitulina
), revealing interesting genes related to possible virulence factors.
Draft Genome Sequences of Two South African Bacillus anthracis Strains
Authors: Lekota Kgaugelo E. , Mafofo Joseph , Madoroba Evelyn , Rees Jasper , van Heerden Henriette , Muchadeyi Farai C.
Published: November 2015

Bacillus anthracis
is a Gram-positive bacterium that causes anthrax, mainly in herbivores through exotoxins and capsule produced on plasmids, pXO1 and pXO2. This paper compares the whole-genome sequences of two
B. anthracis
strains from an endemic region and a sporadic outbreak in South Africa. Sequencing was done using next-generation sequencing technologies.
Draft Genome Sequence of the Serratia rubidaea CIP 103234
T
Reference Strain, a Human-Opportunistic Pathogen
Authors: Bonnin Rémy A. , Girlich Delphine , Imanci Dilek , Dortet Laurent , Naas Thierry
Published: November 2015

We provide here the first genome sequence of a
Serratia rubidaea
isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the
Serratia
genus.
Draft Genome Sequences of Two Isolates of the Plant-Pathogenic Fungus
Neonectria ditissima
That Differ in Virulence
Authors: Deng Cecilia H. , Scheper Reiny W. A. , Thrimawithana Amali H. , Bowen Joanna K.
Published: November 2015

Neonectria ditissima
is the causal agent of apple canker. Here, we present the draft genome sequences of two isolates of
N. ditissima
that differ in virulence. Comparative genomics will enable pathogenicity determinants to be identified in this plant-pathogenic fungus.
Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the
Chloroflexi
Class
Anaerolineae
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W.
Published: November 2015

We report the draft genome sequence of
Ornatilinea apprima
P3M-1, a strictly anaerobic member of the
Chloroflexi
class
Anaerolineae
. This genome provides insight into the diversity of metabolism within the
Anaerolineae
, and the evolution of respiration within the
Chloroflexi
.
Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the
Chloroflexi
Class
Anaerolineae
Authors: Ward Lewis M. , Hemp James , Pace Laura A. , Fischer Woodward W.
Published: November 2015

We present the draft genome sequence of
Leptolinea tardivitalis
YMTK-2, a member of the
Chloroflexi
phylum. This organism was initially characterized as a strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates that it encodes for a flagella and might be capable of aerobic respiration.
Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the
Chloroflexi
Class
Anaerolineae
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W.
Published: November 2015

We report the draft genome sequence of
Levilinea saccharolytica
KIBI-1
,
a facultative anaerobic member of the
Chloroflexi
class
Anaerolineae
. While
L. saccharolytica
was characterized as an obligate anaerobe, genome analysis provides evidence for the presence of both aerobic respiration and partial denitrification pathways.
Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft
Authors: Coil David A. , Benardini James N. , Eisen Jonathan A.
Published: November 2015

Here, we present the draft genome of
Bacillus safensis
JPL-MERTA-8-2, a strain found in a spacecraft assembly cleanroom before launch of the Mars Exploration Rovers. The assembly contains 3,671,133 bp in 14 contigs.
Draft Genome Sequence of Amikacin- and Kanamycin-Resistant Mycobacterium tuberculosis MT433 without
rrs
and
eis
Mutations
Authors: Sowajassatakul Angkanang , Coker Olabisi O. , Prammananan Therdsak , Chaiprasert Angkana , Phunpruch Saranya
Published: November 2015

We announce the draft genome sequence of amikacin- and kanamycin-resistant
Mycobacterium tuberculosis
MT433, which has been previously described as the strain carrying an unknown resistance mechanism.
First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327)
Authors: Ehsani Elham , Jauregui Ruy , Geffers Robert , Jarek Michael , Boon Nico , Pieper Dietmar H. , Vilchez-Vargas Ramiro
Published: November 2015

We report the draft genome sequence of the
Acidovorax caeni
type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to
Acidovorax caeni
strain R-24608 is
Acidovorax
sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.
Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile
Authors: Cavalcante Ana Lídia Q. , Dias Larissa M. , Alves Jorianne T. C. , Veras Adonney A. O. , Guimarães Luis C. , Rocha Flávia S. , Gala-García Alfonso , Retamal Patricio , Ramos Rommel T. J. , Azevedo Vasco , Silva Artur , Carneiro Adriana R.
Published: November 2015

Corynebacterium pseudotuberculosis
is related to several diseases infecting horses and small ruminants, causing economic losses to agribusiness. Here, we present the genome sequence of
C. pseudotuberculosis
strain E19. The genome includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112 genes predicted, 12 rRNAs, and 48 tRNAs.
Genome Sequence of the Atypical Symbiotic
Frankia
R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium
Authors: Pujic Petar , Bolotin Alexander , Fournier Pascale , Sorokin Alexei , Lapidus Alla , Richau Kerstin H. , Briolay Jerome , Mebarki Farida , Normand Philippe , Sellstedt Anita
Published: November 2015

Frankia
strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that was isolated from nodules of
Casuarina cunninghamiana
but infects only
Elaeagnaceae
. This communication reports the genome of the strain R43 and provides insights into the microbe genomics and physiological potentials.
Complete Genome Sequences of Three Laboratory Strains of Dengue Virus (Serotypes 2, 3, and 4) Available in South Korea
Authors: Go Yun Young , Jung Eunhye , Balasuriya Udeni B. R.
Published: November 2015

Here, we report the complete genome sequences of three laboratory strains of dengue virus serotype-2 (DENV-2/KBPV-VR-29), -3 (DENV-3/KBPV-VR-30), and -4 (DENV-4/KBPV-VR-31) obtained from the Korea Bank for Pathogenic Viruses (
http://kbpv.knrrc.or.kr
). The complete genetic information presented in this study on commonly used DENV laboratory strains provides valuable information for future studies.
Performance of the Cryptococcal Antigen Lateral Flow Assay in Non-HIV-Related Cryptococcosis
Authors: Jitmuang Anupop , Panackal Anil A. , Williamson Peter R. , Bennett John E. , Dekker John P. , Zelazny Adrian M.
Published: November 2015

The cryptococcal antigen lateral flow assay (CrAg LFA) was evaluated for the diagnosis of cryptococcosis in HIV-negative patients. The sensitivity was excellent, suggesting that this assay can replace conventional testing based on latex agglutination (LA). CrAg LFA and LA titers were correlated but were not directly comparable, with implications for conversion between assays.
Epidemiologic and Genotypic Review of Carbapenemase-Producing Organisms in British Columbia, Canada, between 2008 and 2014
Authors: Sekirov Inna , Croxen Matthew A. , Ng Corrinne , Azana Robert , Chang Yin , Mataseje Laura , Boyd David , Mangat Chand , Mack Benjamin , Tadros Manal , Brodkin Elizabeth , Kibsey Pamela , Stefanovic Aleksandra , Champagne Sylvie , Mulvey Michael R. , Hoang Linda M. N.
Published: November 2015

Carbapenemase-producing organisms (CPOs) are a serious emerging problem for health care facilities worldwide. Owing to their resistance to most antimicrobial therapies, CPOs are difficult to treat and pose a challenge for infection prevention and control. Since 2010, lab-based surveillance for CPOs and PCR-based testing were implemented in British Columbia (BC), Canada. A review of CPOs in BC from 2008 to March 2014 was done to characterize the resistance mechanisms and possible clonal strain transmission and to compare pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and plasmid restriction fragment length polymorphism (RFLP) as molecular typing tools. During this study period, a total of 177 CPO cases were identified. Patient demographics and travel history were reviewed, and a descriptive analysis was carried out. PFGE profiles, MLST, and plasmid RFLP analysis for a subset of
Escherichia coli
,
Klebsiella pneumoniae
, and
Enterobacter
species isolates were obtained and analyzed. Our findings demonstrate that CPOs have been increasing in number in BC over time, from 1 isolate/year retrospectively identified in 2008 and 2009 to 82 isolates in 2013 and 30 isolates in the first quarter of 2014. Overall,
K. pneumoniae
isolates lack clonality, although some seemingly related clusters have been found. Plasmid analysis showed evidence of the spread of plasmids carrying carbapenemase-encoding genes between the examined isolates. Analysis of
Enterobacter cloacae
isolates revealed a more clonal nature of these CPOs in BC. The presence of related clusters provides evidence of interpatient organism transmission both within and between institutions. Although in our study, NDM-harboring
E. cloacae
isolates appeared to spread clonally, the spread of carbapenem resistance in
K. pneumoniae
seems to be plasmid mediated.
Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes
Authors: Kwong Jason C. , Mercoulia Karolina , Tomita Takehiro , Easton Marion , Li Hua Y. , Bulach Dieter M. , Stinear Timothy P. , Seemann Torsten , Howden Benjamin P.
Published: November 2015

Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of
Listeria monocytogenes
has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423
L. monocytogenes
isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred
in silico
from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97
L. monocytogenes
isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective
L. monocytogenes
surveillance and investigated for other pathogens relevant to public health.