bluuebunny/crossref_metadata_2025 huggingface dataset:
The Elasticity of Poverty with respect to Sectoral Growth inAfrica
Authors: Berardi Nicoletta , Marzo Federica
Published: May 2015

TheAfrican continent has grown by more than 4 percent yearly on average during the past decade. However, the link between this remarkable growth rate and poverty reduction is neither obvious nor simple. This paper focuses on the elasticity of poverty with respect toGDPgrowth at the sectoral level and takes into account the fact that economic growth may affect poverty directly as well as indirectly through sectoral labor share intensity. It develops a methodology that sheds light on the contribution of sectoral growth to poverty reduction country‐by‐country in Africa, guiding policy recommendations. As the composition of growth matters at least as much as its overall intensity, it is key to identify the sectors that have the strongest impact on poverty reduction and unleash their potential; if growth happens to concentrate in sectors with scarce pro‐poor potential, like commodity‐driven growth, redistributive strategies are necessary to compensate the weak effect on poverty.
Wages, Productivity and Labour's Declining Income Share in Post‐Apartheid South Africa
Authors: Burger Philippe
Published: May 2015

The Marikana incident in 2012, as well as the protracted strikes by platinum miners, metal and postal workers in 2014 suggest that not all is well in the South African labour market. Even though those in employment are better off than the unemployed poor, macroeconomic data indicate that labour's share in gross value added has declined significantly during the first two decades following the first democratic election in 1994. A falling share of labour in income also means, by definition, that average labour productivity growth outstrips real wages growth. Data for South Africa suggest that productivity has indeed increased faster than wages in South Africa. This article argues that financialisation and more aggressive returns‐oriented investment strategies applied by for instance large investment institutions translated into higher required rates of return on capital, which in turn caused an increased implementation of capital‐augmenting labour‐saving technology that reduces labour's share in income.
Breakdown of the Whitham Modulation Theory and the Emergence of Dispersion
Authors: Bridges Thomas J.
Published: May 2015

The Whitham modulation theory for periodic traveling waves of PDEs generated by a Lagrangian produces first‐order dispersionless PDEs that are, generically, either hyperbolic or elliptic. In this paper, degeneracy of the Whitham equations is considered where one of the characteristic speeds is zero. In this case, the Whitham equations are no longer valid. Reformulation and rescaling show that conservation of wave action morphs into the Korteweg–de Vries (KdV) equation on a longer time scale thereby generating dispersion in the Whitham modulation equations even for finite amplitude waves.
Treatment of platelets with riboflavin and ultraviolet light mediates complement activation and suppresses monocyte interleukin‐12 production in whole blood
Authors: Loh Y. S. , Dean M. M. , Johnson L. , Marks D. C.
Published: May 2015

Background and Objectives

Pathogen inactivation (PI) and storage may alter the immunomodulatory capacity of platelets (PLTs). The aim of this study was to examine the effect of PI (Riboflavin and ultraviolet light treatment) and storage on the capacity of PLTs to induce cytokine responses in recipient inflammatory cells.

Materials and Methods

A pool and split design was used to prepare untreated and PI‐treated buffy coat‐derived platelet concentrates (PCs). Samples were taken on days 2 and 7 postcollection and incubated with ABO/RhD‐matched fresh whole blood for 6 h with or without lipopolysaccharide (LPS). The intracellular production of IP‐10, MCP‐1, MIP‐1α, IL‐8, IL‐6, IL‐10, IL‐12, TNF‐α and MIP‐1β in monocytes and neutrophils was assessed using flow cytometry. Complement proteins in PLT supernatants were measured using a cytometric bead array.

Results

PLTs and PLT supernatant (both untreated and PI‐treated) resulted in modulation of intracellular MIP‐1β and IL‐12 production in monocytes. Compared to untreated PLTs, PI‐treated PLTs resulted in significantly lower LPS‐induced monocyte IL‐12 production (day 7). The concentration of C3a and C5a (and their desArg forms) was significantly increased in PLT supernatants following PI.

Conclusion

PI results in decreased LPS‐induced monocyte IL‐12 production and increased complement activation. The association between platelet‐induced complement activation and IL‐12 production warrants further investigation.
Quality control on mononuclear cells collected for extracorporeal photochemotherapy: comparison between two UV‐A irradiation devices
Authors: Cervio M. , Scudeller L. , Viarengo G. , Del Fante C. , Perotti C.
Published: May 2015

Recently, MacoPharma released a new UV‐A cell irradiator device (Macogenic G2) for extracorporeal photopheresis (ECP), smaller and lighter than the Macogenic G1 but with no integrated cooling system. We compared the two devices at different working temperatures (G1 at standard irradiation temperature – 21°C – and G2 set by purpose at 34°C) in patients affected with chronic graft‐versus‐host disease and chronic lung allograft dysfunction treated by ECP. We demonstrate that both G1 and G2 devices are efficient in inducing the inhibition of lymphocytic proliferation and mononuclear cells apoptosis after 48 h even when G2 is set at higher‐than‐standard temperature.
Impaired CO2 sensitivity of astrocytes in a mouse model of Rett syndrome
Authors: Turovsky Egor , Karagiannis Anastassios , Abdala Ana Paula , Gourine Alexander V.
Published: May 2015

Key points

Rett syndrome is a prototypical neurological disorder characterised by abnormal breathing pattern and reduced ventilatory CO2 sensitivity. Medullary astrocytes are a crucial component of central CO2/pH chemosensitivity.

This study tested the hypotheses that methyl‐CpG‐binding protein 2 (MeCP2) deficient medullary astrocytes are (i) unable to produce/release appropriate amounts of lactate, and/or (ii) unable to sense changes in /[H+].

We found no differences in tonic or hypoxia‐induced release of lactate from the ventral surface of the medulla oblongata or cerebral cortex between MeCP2‐knockout and wild‐type mice.

Respiratory acidosis triggered robust [Ca2+]i responses in wild‐type astrocytes residing near the ventral surface of the medulla oblongata. CO2‐induced [Ca2+]i responses in astrocytes were dramatically reduced in conditions of MeCP2 deficiency.

These data suggest that (i) ‘metabolic’ function of astrocytes in releasing lactate into the extracellular space is not affected by MeCP2 deficiency, and (ii) MeCP2 deficiency impairs the ability of medullary astrocytes to sense changes in /[H+].

Rett syndrome, a prototypical neurological disorder caused by loss of function of the transcriptional regulator methyl‐CpG‐binding protein 2 (MeCP2) gene, is associated with a severely disordered breathing pattern and reduced ventilatory CO2 sensitivity. In a mouse model of Rett syndrome (MeCP2 knockout), re‐introduction of the MeCP2 gene selectively in astrocytes rescues normal respiratory phenotype. In the present study we determined whether the metabolic and/or signalling functions of astrocytes are affected by testing the hypotheses that in conditions of MeCP2 deficiency, medullary astrocytes are unable to produce/release appropriate amounts of lactate or detect changes in /[H+], or both. No differences in tonic or hypoxia‐induced release of lactate from the ventral surface of the medulla oblongata or cerebral cortex in brain slices of MeCP2‐knockout and wild‐type mice were found. In brainstem slices of wild‐type mice, respiratory acidosis triggered robust elevations in [Ca2+]i in astrocytes residing near the ventral surface of the medulla oblongata. The magnitude of CO2‐induced [Ca2+]i responses in medullary astrocytes was markedly reduced in conditions of MeCP2 deficiency, whereas [Ca2+]i responses to ATP were unaffected. These data suggest that (i) metabolic function of astrocytes in releasing lactate into the extracellular space is not affected by MeCP2 deficiency, and (ii) MeCP2 deficiency impairs the ability of medullary astrocytes to sense changes in /[H+]. Taken together with the evidence of severely blunted ventilatory sensitivity to CO2 in mice with conditional MeCP2 deletion in astroglia, these data support the hypothesis of an important role played by astrocytes in central respiratory CO2/pH chemosensitivity.
Drag Forces on, and Deformation of, Closed Flexible Bags
Authors: Lader Pål , Fredriksson David W. , Volent Zsolt , DeCew Jud , Rosten Trond , Strand Ida M.
Published: May 2015

The use of closed flexible bags is among the suggestions considered as a potential way to expand the salmon production in Norway. Few ocean structures exist with large, heavily compliant submerged components, and there is presently limited existing knowledge about how aquaculture systems with flexible closed cages will respond to external sea loads. The flexibility and deformation of the bag are coupled to the hydrodynamic forces, and the forces and deformation will be dependent on the filling level of the bag. In order to get a better understanding of the drag forces on, and deformation of, such bags, experiments were conducted with a series of closed flexible bags. The bags were towed in a towing tank in order to simulate uniform current. Four different geometries were investigated, cylindrical, cubical, conical, and pyramidal, and the filling levels were varied between 70% and 120%. The main findings from the experiments were that the drag force was highly dependent on the filling level, and that the drag force increases with decreasing filling level. Comparing the drag force on a deflated bag with an inflated one showed an increase of up to 2.5 times.
Ultrasonic Measurement of Cylindrical Roller Bearing Lubrication Using High Pulse Repletion Rates
Authors: Li Meng , Liu Heng , Xu Cong , Jing Minqing , Xin Wenhui
Published: May 2015

This paper describes a measurement of lubricant-film thickness in a roller bearing using a new ultrasonic pulser-receiver, which has a maximum pulse repetition rate (PRR) of 100 kHz. The experimental results show that a higher PRR can help to get more measurement points and more details of the oil-film thickness distribution. Furthermore, the influence of rotor vibration response for the oil-film thickness is discussed, which is in keeping with the simulation result. Finally, the limits of the PRR are discussed in detail and the effect of the transducer focal zone size is also observed.
Acquisition, preprocessing, and reconstruction of ultralow dose volumetric CT scout for organ‐based CT scan planning
Authors: Yin Zhye , Yao Yangyang , Montillo Albert , Wu Mingye , Edic Peter M. , Kalra Mannudeep , De Man Bruno
Published: May 2015

Purpose:

Traditionally, 2D radiographic preparatory scan images (scout scans) are used to plan diagnostic CT scans. However, a 3D CT volume with a full 3D organ segmentation map could provide superior information for customized scan planning and other purposes. A practical challenge is to design the volumetric scout acquisition and processing steps to provide good image quality (at least good enough to enable 3D organ segmentation) while delivering a radiation dose similar to that of the conventional 2D scout.

Methods:

The authors explored various acquisition methods, scan parameters, postprocessing methods, and reconstruction methods through simulation and cadaver data studies to achieve an ultralow dose 3D scout while simultaneously reducing the noise and maintaining the edge strength around the target organ.

Results:

In a simulation study, the 3D scout with the proposed acquisition, preprocessing, and reconstruction strategy provided a similar level of organ segmentation capability as a traditional 240 mAs diagnostic scan, based on noise and normalized edge strength metrics. At the same time, the proposed approach delivers only 1.25% of the dose of a traditional scan. In a cadaver study, the authors’ pictorial‐structures based organ localization algorithm successfully located the major abdominal‐thoracic organs from the ultralow dose 3D scout obtained with the proposed strategy.

Conclusions:

The authors demonstrated that images with a similar degree of segmentation capability (interpretability) as conventional dose CT scans can be achieved with an ultralow dose 3D scout acquisition and suitable postprocessing. Furthermore, the authors applied these techniques to real cadaver CT scans with a CTDI dose level of less than 0.1 mGy and successfully generated a 3D organ localization map.
Determination of Technopedagogical Content Knowledge Competencies of Preservice Physical Education Teachers: A Turkish Sample
Authors: Arslan Yunus
Published: May 2015

This study examined preservice physical education teachers’ (PPETs’) technopedagogical content knowledge (TPCK) competencies. The participants were 1028 PPETs from 26 major universities representing all seven geographical regions of Turkey. The Technological Pedagogical Content Knowledge Deep- Scale developed by Kabakci Yurdakul et al. (2012) was used to measure TPCK competencies of PPETs. Descriptive statistics, an independent samples t test, and multivariate analysis of variance were used to analyze the data. The results showed that PPETs rated themselves at a high level in self-reported TPCK competencies in terms of the entire scale and its factors (design, exertion, ethics and proficiency). There was no significant main effect for gender (p < .05). Computer/internet-based background (p > .05) and PPETs’ interest in keeping up with the latest PE-related technological developments (p > .05) were significant variables in PPETs’ TPCK competencies. Overall, this study offers some evidence that the use of information and communication technology (ICT) is an important factor affecting PPETs’ TPCK competencies.
Genomic signatures of evolutionary transitions from solitary to group living
Authors: Kapheim Karen M. , Pan Hailin , Li Cai , Salzberg Steven L. , Puiu Daniela , Magoc Tanja , Robertson Hugh M. , Hudson Matthew E. , Venkat Aarti , Fischman Brielle J. , Hernandez Alvaro , Yandell Mark , Ence Daniel , Holt Carson , Yocum George D. , Kemp William P. , Bosch Jordi , Waterhouse Robert M. , Zdobnov Evgeny M. , Stolle Eckart , Kraus F. Bernhard , Helbing Sophie , Moritz Robin F. A. , Glastad Karl M. , Hunt Brendan G. , Goodisman Michael A. D. , Hauser Frank , Grimmelikhuijzen Cornelis J. P. , Pinheiro Daniel Guariz , Nunes Francis Morais Franco , Soares Michelle Prioli Miranda , Tanaka Érica Donato , Simões Zilá Luz Paulino , Hartfelder Klaus , Evans Jay D. , Barribeau Seth M. , Johnson Reed M. , Massey Jonathan H. , Southey Bruce R. , Hasselmann Martin , Hamacher Daniel , Biewer Matthias , Kent Clement F. , Zayed Amro , Blatti Charles , Sinha Saurabh , Johnston J. Spencer , Hanrahan Shawn J. , Kocher Sarah D. , Wang Jun , Robinson Gene E. , Zhang Guojie
Published: May 2015

For bees, many roads lead to social harmony

Eusociality, where workers sacrifice their reproductive rights to support the colony, has evolved repeatedly and represents the most evolved form of social evolution in insects. Kapheim
et al.
looked across the genomes of 10 bee species with varying degrees of sociality to determine the underlying genomic contributions. No one genomic path led to eusociality, but similarities across genomes were seen in features such as increases in gene regulation and methylation. It also seems that selection pressures relaxed after the emergence of complex sociality.

Science
, this issue p.
1139
Pioneers of the final frontier
We Could Not Fail The First African Americans in the Space Program
Richard Paul and Steven Moss
University of Texas Press, 2015. 312 pp.
Authors: Alexander Claudia
Published: May 2015

African Americans and the early days of the space program.
The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
Authors: Bell Robert J. A. , Rube H. Tomas , Kreig Alex , Mancini Andrew , Fouse Shaun D. , Nagarajan Raman P. , Choi Serah , Hong Chibo , He Daniel , Pekmezci Melike , Wiencke John K. , Wrensch Margaret R. , Chang Susan M. , Walsh Kyle M. , Myong Sua , Song Jun S. , Costello Joseph F.
Published: May 2015

A mutant promoter's partner in crime

Telomerase is an enzyme that maintains the ends of chromosomes.
TERT
, the gene coding for the enzyme's catalytic subunit, is not expressed in healthy somatic cells, but its expression is reactivated in the majority of human cancers. The resultant high levels of telomerase help cancer cells survive and multiply. Recurrent mutations in the promoter region of
TERT
are associated with high telomerase levels in multiple cancer types. Bell
et al.
show that a specific transcription factor called GABP is selectively recruited to the mutant form of the
TERT
promoter, which activates
TERT
gene expression

Science
, this issue p.
1036
Cross-Reactive Epitopes in Borrelia burgdorferi p66
Authors: Arnaboldi Paul M. , Dattwyler Raymond J.
Published: May 2015

Epitope mapping of the p66 outer membrane protein ofBorrelia burgdorferirevealed that the protein contains numerous cross-reactive linear epitopes recognized by serum antibody in the majority of individuals tested, regardless of Lyme disease history, limiting the usefulness of this antigen in Lyme disease serodiagnostic assays.
Seroepidemiology of Human Papillomavirus 16 (HPV16) L2 and Generation of L2-Specific Human Chimeric Monoclonal Antibodies
Authors: Wang Joshua W. , Jagu Subhashini , Wu Wai-Hong , Viscidi Raphael P. , Macgregor-Das Anne , Fogel Jessica M. , Kwak Kihyuck , Daayana Sai , Kitchener Henry , Stern Peter L. , Gravitt Patti E. , Trimble Cornelia L. , Roden Richard B. S.
Published: May 2015

Presently, the seroprevalence of human papillomavirus (HPV) minor capsid antigen L2-reactive antibody is not well understood, and no serologic standard exists for L2-specific neutralizing antibodies. Therefore, we screened a total of 1,078 serum samples for HPV16 L2 reactivity, and these were obtained from four prior clinical studies: a population-based (n= 880) surveillance study with a high-risk HPV DNA prevalence of 10.8%, a cohort study of women (n= 160) with high-grade cervical intraepithelial neoplasia (CIN), and two phase II trials in women with high-grade vulvar intraepithelial neoplasia (VIN) receiving imiquimod therapy combined with either photodynamic therapy (PDT) (n= 19) or vaccination with a fusion protein comprising HPV16 L2, E7, and E6 (TA-CIN) (n= 19). Sera were screened sequentially by HPV16 L2 enzyme-linked immunosorbent assay (ELISA) and then Western blot. Seven of the 1,078 serum samples tested had L2-specific antibodies, but none were detectably neutralizing for HPV16. To develop a standard, we substituted human IgG1 sequences into conserved regions of two rodent monoclonal antibodies (MAbs) specific for neutralizing epitopes at HPV16 L2 residues 17 to 36 and 58 to 64, creating JWW-1 and JWW-2, respectively. These chimeric MAbs retained neutralizing activity and together reacted with 33/34 clinically relevant HPV types tested. In conclusion, our inability to identify an HPV16 L2-specific neutralizing antibody response even in the sera of patients with active genital HPV disease suggests the subdominance of L2 protective epitopes and the value of the chimeric MAbs JWW-1 and JWW-2 as standards for immunoassays to measure L2-specific human antibodies.
Draft Genome Sequence of Norvancomycin-Producing Strain Amycolatopsis orientalis CPCC200066
Authors: Lei Xuan , Yuan Fang , Shi Yuanyuan , Li Xingxing , Wang Lifei , Hong Bin
Published: May 2015

Amycolatopsis orientalis
CPCC200066 is an actinomycete that can produce the glycopeptide antibiotic norvancomycin, which has significant inhibitory activity against Gram-positive cocci and bacilli. Here, we report the draft genome sequence of
A. orientalis
CPCC200066 and identified the genes involved in norvancomycin biosynthesis.
Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site
Authors: Ray Jayashree , Waters R. Jordan , Skerker Jeffrey M. , Kuehl Jennifer V. , Price Morgan N. , Huang Jiawen , Chakraborty Romy , Arkin Adam P. , Deutschbauer Adam
Published: May 2015

Cupriavidus basilensis
4G11 was isolated from groundwater at the Oak Ridge Field Research Center (FRC) site. Here, we report the complete genome sequence and annotation of
Cupriavidus basilensis
4G11. The genome contains 8,421,483 bp, 7,661 predicted protein-coding genes, and a total GC content of 64.4%.
Draft Genome Sequence of
Alicycliphilus
sp. B1, an
N
-Acylhomoserine Lactone-Producing Bacterium, Isolated from Activated Sludge
Authors: Okutsu Noriya , Morohoshi Tomohiro , Ikeda Tsukasa
Published: May 2015

We report here the draft genome sequence of
Alicycliphilus
sp. B1, isolated from activated sludge in a wastewater treatment plant of an electronic component factory as an
N
-acylhomoserine lactone-producing strain. The draft genome is 7,465,959 bp in length, with 59 large contigs. About 7,391 protein-coding genes, 82 tRNAs, and 13 rRNAs are predicted from this assembly.
Draft Genome Sequence of Burkholderia andropogonis Type Strain ICMP2807, Isolated from Sorghum bicolor
Authors: Lopes-Santos Lucilene , Castro Daniel Bedo Assumpção , Ottoboni Laura Maria Mariscal , Park Duckchul , Weir Bevan Simon , Destéfano Suzete Aparecida Lanza
Published: May 2015

Here, we report the draft genome sequence of
Burkholderia andropogonis
ICMP2807, a phytopathogenic bacterium isolated from
Sorghum bicolor
plants in the United States.
Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344
Authors: Eng Wilhelm Wei Han , Gan Han Ming , Gan Huan You , Hudson André O. , Savka Michael A.
Published: May 2015

Here, we report the whole-genome sequence and annotation of
Pseudomonas kilonensis
1855-344 (previously known as
P. fluorescens
1855-344). The genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. A biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antiSMASH server.
Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients
Authors: Kairov Ulykbek , Kozhamkulov Ulan , Molkenov Askhat , Rakhimova Saule , Askapuli Ayken , Zhabagin Maxat , Akhmetova Ainur , Yerezhepov Dauren , Abilova Zhannur , Abilmazhinova Aliya , Bismilda Venera , Chingisova Leila , Zhumadilov Zhaxybay , Akilzhanova Ainur
Published: May 2015

Here, we report the draft genome sequences of two clinical isolates ofMycobacterium tuberculosis(MTB-476 and MTB-489) isolated from sputum of Kazakh patients.
Draft Genome Sequence of the Nonmarine Agarolytic Bacterium
Cellvibrio
sp. OA-2007
Authors: Syazni  , Yanagisawa Mitsunori , Kasuu Masahiro , Nakasaki Kiyohiko , Ariga Osamu
Published: May 2015

Cellvibrio
sp. OA-2007 is a Gram-negative, aerobic, and agarolytic bacterium isolated from activated sludge. We present the draft genome sequence of strain OA-2007, composed of 97 contigs, totaling 4,595,379 bp in size, and containing 4,094 open reading frames, with a G+C content of 47.71%.
Draft Genome Sequence of Methylobacterium radiotolerans,a DDE-Degrading and Plant Growth-Promoting Strain Isolated from
Cucurbita pepo
Authors: Eevers Nele , Van Hamme Jonathan D. , Bottos Eric M. , Weyens Nele , Vangronsveld Jaco
Published: May 2015

We announce the draft genome of
Methylobacterium radiotolerans
, a Gram-negative bacterium isolated from
Cucurbita pepo
roots. This strain shows 2,2-bis(
p
-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant growth-promoting capacities. Analyses of its 6.8-Mb genome will improve our understanding of DDE-degradation pathways and aid in the deployment of phytoremediation technologies to remediate DDE-contaminated soils.
Rapid and EasyIn SilicoSerotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data
Authors: Joensen Katrine G. , Tetzschner Anna M. M. , Iguchi Atsushi , Aarestrup Frank M. , Scheutz Flemming
Published: May 2015

Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping ofEscherichia coliis a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-basedin silicoserotyping ofE. coliapplicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). AllE. coliisolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682E. coligenomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen geneswzx,wzy,wzm, andwztand the flagellin genesfliC,flkA,fllA,flmA, andflnAwere detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools,E. coliserotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies.
Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples
Authors: Fischer Nicole , Indenbirken Daniela , Meyer Thomas , Lütgehetmann Marc , Lellek Heinrich , Spohn Michael , Aepfelbacher Martin , Alawi Malik , Grundhoff Adam
Published: May 2015

Unbiased nontargeted metagenomic RNA sequencing (UMERS) has the advantage to detect known as well as unknown pathogens and, thus, can significantly improve the detection of viral, bacterial, parasitic, and fungal sequences in public health settings. In particular, conventional diagnostic methods successfully identify the putative pathogenic agent in only 30% to 40% of respiratory specimens from patients with acute respiratory illness. Here, we applied UMERS to 24 diagnostic respiratory specimens (bronchoalveolar lavage [BAL] fluid, sputum samples, and a swab) from patients with seasonal influenza infection and 5 BAL fluid samples from patients with pneumonia that tested negative for influenza to validate RNA sequencing as an unbiased diagnostic tool in comparison to conventional diagnostic methods. In addition to our comparison to PCR, we evaluated the potential to retrieve comprehensive influenza virus genomic information and the capability to detect known superinfecting pathogens. Compared to quantitative real-time PCR for influenza viral sequences, UMERS detected influenza viral sequences in 18 of 24 samples. Complete influenza virus genomes could be assembled from 8 samples. Furthermore, in 3 of 24 influenza-positive samples, additional viral pathogens could be detected, and 2 of 24 samples showed a significantly increased abundance of individual bacterial species known to cause superinfections during an influenza virus infection. Thus, analysis of respiratory samples from known or suspected influenza patients by UMERS provides valuable information that is relevant for clinical investigation.
Arenavirus Genome Rearrangement for the Development of Live Attenuated Vaccines
Authors: Cheng Benson Yee Hin , Ortiz-Riaño Emilio , de la Torre Juan Carlos , Martínez-Sobrido Luis
Published: May 2015

Several members of the
Arenaviridae
family cause hemorrhagic fever disease in humans and pose serious public health problems in their geographic regions of endemicity as well as a credible biodefense threat. To date, there have been no FDA-approved arenavirus vaccines, and current antiarenaviral therapy is limited to an off-label use of ribavirin that is only partially effective. Arenaviruses are enveloped viruses with a bisegmented negative-stranded RNA genome. Each genome segment uses an ambisense coding strategy to direct the synthesis of two viral polypeptides in opposite orientations, separated by a noncoding intergenic region. Here we have used minigenome-based approaches to evaluate expression levels of reporter genes from the nucleoprotein (NP) and glycoprotein precursor (GPC) loci within the S segment of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). We found that reporter genes are expressed to higher levels from the NP than from the GPC locus. Differences in reporter gene expression levels from the NP and GPC loci were confirmed with recombinant trisegmented LCM viruses. We then used reverse genetics to rescue a recombinant LCMV (rLCMV) containing a translocated viral S segment (rLCMV/TransS), where the viral NP and GPC open reading frames replaced one another. The rLCMV/TransS showed slower growth kinetics in cultured cells and was highly attenuated
in vivo
in a mouse model of lethal LCMV infection, but immunization with rLCMV/TransS conferred complete protection against a lethal challenge with wild-type LCMV. Attenuation of rLCMV/TransS was associated with reduced NP expression levels. These results open a new avenue for the development of arenavirus live attenuated vaccines based on rearrangement of their viral genome.

IMPORTANCE
Several arenaviruses cause severe hemorrhagic fever in humans and also pose a credible bioterrorism threat. Currently, no FDA-licensed vaccines are available to combat arenavirus infections and antiarenaviral therapy is limited to the off-label use of ribavirin, which is only partially effective and associated with side effects. Here we describe, for the first time, the generation of a recombinant LCMV where the viral protein products encoded by the S RNA segment (NP and GPC) were swapped to generate rLCMV/TransS. rLCMV/TransS exhibited reduced viral multiplication in cultured cells and was highly attenuated
in vivo
while conferring protection, upon a single immunization dose, against a lethal challenge with wild-type LCMV. Our studies provide a proof of concept for the rational development of safe and protective live attenuated vaccine candidates based on genome reorganization for the treatment of pathogenic arenavirus infections in humans.
Two-Year Follow-Up of Macaques Developing Intermittent Control of the Human Immunodeficiency Virus Homolog Simian Immunodeficiency Virus SIVmac251 in the Chronic Phase of Infection
Authors: Shytaj Iart Luca , Nickel Gabrielle , Arts Eric , Farrell Nicholas , Biffoni Mauro , Pal Ranajit , Chung Hye Kyung , LaBranche Celia , Montefiori David , Vargas-Inchaustegui Diego , Robert-Guroff Marjorie , Lewis Mark G. , Sacha Jonah B. , Palamara Anna Teresa , Savarino Andrea
Published: May 2015

Off-therapy control of viremia by HIV-infected individuals has been associated with two likely players: a restricted viral reservoir and an efficient cell-mediated immune response. We previously showed that a combination of highly suppressive antiretroviral therapy and two experimental drugs, i.e., auranofin and buthionine sulfoximine, was able to reduce the viral reservoir, elicit efficient cell-mediated antiviral responses, and induce intermittent posttherapy viral load control in chronically SIVmac251-infected macaques. We here show that the macaques that had received this drug combination and then stopped antiretroviral therapy were also able to maintain low numbers of activated CD4
+
T cells at viral rebound. Moreover, these macaques consistently displayed low-level simian immunodeficiency virus (SIV) diversity, which was in line with the strong and broadly reactive cell-mediated immune responses against conserved Gag antigens. Extended follow-up showed that the two macaques that had received the complete drug combination remained healthy and did not develop AIDS in 2 years of follow-up after therapy suspension. This disease-free survival is longer than twice the average time of progression to AIDS in SIVmac251-infected rhesus macaques. These results suggest that limited numbers of activated T cells at viral rebound and subsequent development of broadly reactive cell-mediated responses may be interrelated in reducing the viral reservoir.

IMPORTANCE
The HIV reservoir in CD4
+
T cells represents one main obstacle to HIV eradication. Recent studies, however, show that a drastic reduction of this reservoir is insufficient for inducing a functional cure of AIDS. In the present work, we thoroughly studied and subjected to long-term follow-up two macaques showing intermittent control of the virus following suspension of antiretroviral therapy plus an experimental antireservoir treatment, i.e., the gold salt auranofin and the investigational chemotherapeutic agent buthionione sulfoximine (BSO). We found that these drugs were able to decrease the number of activated CD4
+
T cells, which are preferential targets for HIV infection. Then, efficient immune responses against the virus were developed in the macaques, which remained healthy during 2 years of follow-up. This result may furnish another building block for future attempts to cure HIV/AIDS.
Regulation of DNA Damage Signaling and Cell Death Responses by Epstein-Barr Virus Latent Membrane Protein 1 (LMP1) and LMP2A in Nasopharyngeal Carcinoma Cells
Authors: Wasil Laura R. , Wei Leizhen , Chang Christopher , Lan Li , Shair Kathy H. Y.
Published: May 2015

Nasopharyngeal carcinoma (NPC) is closely associated with latent Epstein-Barr virus (EBV) infection. Although EBV infection of preneoplastic epithelial cells is not immortalizing, EBV can modulate oncogenic and cell death mechanisms. The viral latent membrane proteins 1 (LMP1) and LMP2A are consistently expressed in NPC and can cooperate in bitransgenic mice expressed from the keratin-14 promoter to enhance carcinoma development in an epithelial chemical carcinogenesis model. In this study, LMP1 and LMP2A were coexpressed in the EBV-negative NPC cell line HK1 and examined for combined effects in response to genotoxic treatments. In response to DNA damage activation, LMP1 and LMP2A coexpression reduced γH2AX (S139) phosphorylation and caspase cleavage induced by a lower dose (5 μM) of the topoisomerase II inhibitor etoposide. Regulation of γH2AX occurred before the onset of caspase activation without modulation of other DNA damage signaling mediators, including ATM, Chk1, or Chk2, and additionally was suppressed by inducers of DNA single-strand breaks (SSBs) and replication stress. Despite reduced DNA damage repair signaling, LMP1-2A coexpressing cells recovered from cytotoxic doses of etoposide; however, LMP1 expression was sufficient for this effect. LMP1 and LMP2A coexpression did not enhance cell growth, with a moderate increase of cell motility to fibronectin. This study supports that LMP1 and LMP2A jointly regulate DNA repair signaling and cell death activation with no further enhancement in the growth properties of neoplastic cells.

IMPORTANCE
NPC is characterized by clonal EBV infection and accounts for >78,000 annual cancer cases with increased incidence in regions where EBV is endemic, such as southeast Asia. The latent proteins LMP1 and LMP2A coexpressed in NPC can individually enhance growth or survival properties in epithelial cells, but their combined effects and potential regulation of DNA repair and checkpoint mechanisms are relatively undetermined. In this study, LMP1-2A coexpression suppressed activation of the DNA damage response (DDR) protein γH2AX induced by selective genotoxins that promote DNA replication stress or SSBs. Expression of LMP1 was sufficient to recover cells, resulting in outgrowth of LMP1 and LMP1-2A-coexpressing cells and indicating distinct LMP1-dependent effects in the restoration of replicative potential. These findings demonstrate novel properties for LMP1 and LMP2A in the cooperative modulation of DDR and apoptotic signaling pathways, further implicating both proteins in the progression of NPC and epithelial malignancies.
Conservation of the STING-Mediated Cytosolic DNA Sensing Pathway in Zebrafish
Authors: Ge Rui , Zhou Yi , Peng Rui , Wang Rui , Li Mi , Zhang Yunbin , Zheng Chunfu , Wang Chen
Published: May 2015

Zebrafish (
Danio rerio
) is a unique potential model animal for dissecting innate immune signaling. Here we demonstrate that herpes simplex virus 1 (HSV-1) could infect zebrafish at its different developmental stages and trigger the expression of type I interferons (IFNs) as well as interferon-stimulated genes (ISGs) in zebrafish larvae. Silencing of zSTING, but not zMAVS, markedly attenuates the DNA virus-induced antiviral responses. Notably, a conserved serine residue (S373) is essential for the action of zSTING. Unexpectedly, zebrafish cyclic GMP-AMP synthase (cGAS) is dispensable for the STING signaling, whereas zDHX9 and zDDX41 are potential sensors for HSV-1 infection
in vivo
. Taken together, this proof-of-concept study establishes the zebrafish larva as a feasible model for investigating the cytosolic DNA sensing mechanism, shedding light on the conservation of the STING antiviral signaling pathway.

IMPORTANCE
The zebrafish larva provides technical advantages for understanding host-pathogen interactions. In this study, we established the zebrafish larva as a useful model for studying HSV-1 infection. HSV-1 infection triggers strong type I interferon production, which depends on STING expression. In addition, STING-mediated antiviral signaling is conserved in zebrafish. Interestingly, zDHX9 and zDDX41 are indispensable for detecting HSV-1, while cGAS is dispensable. This proof-of-concept study indicates that the zebrafish represents an amenable model for the investigation of cytosolic DNA sensing mechanisms.
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
Authors: Wetmore Kelly M. , Price Morgan N. , Waters Robert J. , Lamson Jacob S. , He Jennifer , Hoover Cindi A. , Blow Matthew J. , Bristow James , Butland Gareth , Arkin Adam P. , Deutschbauer Adam
Published: May 2015

Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn
5
and
mariner
transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with
Escherichia coli
,
Phaeobacter inhibens
,
Pseudomonas stutzeri
,
Shewanella amazonensis
, and
Shewanella oneidensis
. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In
P. inhibens
, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative
d
-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling.

IMPORTANCE
A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data.
Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors
Authors: Smith Mark B. , Rocha Andrea M. , Smillie Chris S. , Olesen Scott W. , Paradis Charles , Wu Liyou , Campbell James H. , Fortney Julian L. , Mehlhorn Tonia L. , Lowe Kenneth A. , Earles Jennifer E. , Phillips Jana , Techtmann Steve M. , Joyner Dominique C. , Elias Dwayne A. , Bailey Kathryn L. , Hurt Richard A. , Preheim Sarah P. , Sanders Matthew C. , Yang Joy , Mueller Marcella A. , Brooks Scott , Watson David B. , Zhang Ping , He Zhili , Dubinsky Eric A. , Adams Paul D. , Arkin Adam P. , Fields Matthew W. , Zhou Jizhong , Alm Eric J. , Hazen Terry C.
Published: May 2015

Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as
in situ
environmental sensors that respond to and capture perturbations caused by human impacts. These
in situ
biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive.

IMPORTANCE
Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.
Can we change a genetically determined future?
Authors: Fernandes Lígia Rodrigues , Rodrigues Luis Vaz , Costa Filipa , Martins Yvette
Published: May 2015

We describe the clinical evolution of the first patient diagnosed with a severe α-1 antitrypsin (AAT) deficiency caused by a rare null allele (Q0Ourém), over the past 18 years. We highlight the clinical course of the disease as well as the evolution of the pulmonary function tests from initial diagnosis and the benefits of augmentation therapy for this specific condition. We report the case of a 43-year-old man with exertion dyspnoea who was observed in our pulmonology unit. The unexpected findings in the complementary examinations led us to diagnose AAT deficiency and to the discovery of a new mutation with the SERPIN A1 gene (hence named Q0Ourém) responsible for the disease. Augmentation therapy was initiated, as is the protocol in this condition. Eighteen years after the diagnosis, the patient is clinically stable, fully autonomous and maintaining an acceptable quality of life, despite severe obstructive lung disease.
Exploring risk of experiencing intimate partner violence after HIV infection: a qualitative study among women with HIV attending postnatal services in Swaziland
Authors: Mulrenan Claire , Colombini Manuela , Howard Natasha , Kikuvi Joshua , Mayhew Susannah H
Published: May 2015

Objective

To explore risks of experiencing intimate partner violence (IPV) after HIV infection among women with HIV in a postnatal care setting in Swaziland.

Design

A qualitative semistructured in-depth interview study, using thematic analysis with deductive and inductive coding, of IPV experiences after HIV infection extracted from service-integration interview transcripts.

Setting

Swaziland.

Participants

19 women with HIV, aged 18–44, were purposively sampled for an in-depth interview about their experiences of services, HIV and IPV from a quantitative postnatal cohort participating in an evaluation of HIV and reproductive health services integration in Swaziland.

Results

Results indicated that women were at risk of experiencing IPV after HIV infection, with 9 of 19 disclosing experiences of physical violence and/or coercive control post-HIV. IPV was initiated through two key pathways: (1) acute interpersonal triggers (eg, status disclosure, mother-to-child transmission of HIV) and (2) chronic normative tensions (eg, fertility intentions, initiating contraceptives).

Conclusions

The results highlight a need to mitigate the risk of IPV for women with HIV in shorter and longer terms in Swaziland. While broader changes are needed to resolve gender disparities, practical steps can be institutionalised within health facilities to reduce, or avoid increasing, IPV pathways for women with HIV. These might include mutual disclosure between partners, greater engagement of Swazi males with HIV services, and promoting positive masculinities that support and protect women.

Trial registration number

NCT01694862.