bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome sequencing of different narrow‐leafed lupin tissue types provides a comprehensive uni‐gene assembly and extensive gene‐based molecular markers
Authors: Kamphuis Lars G. , Hane James K. , Nelson Matthew N. , Gao Lingling , Atkins Craig A. , Singh Karam B.
Published: July 2014

Narrow‐leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome‐derived gene‐based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome‐derived markers and 66 BAC‐end sequence‐derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.
Maternal Life Course Socio‐Economic Position and Offspring Body Composition at Birth in a Multi‐Ethnic Population
Authors: Sletner Line , Jenum Anne Karen , Mørkrid Kjersti , Vangen Siri , Holme Ingar M. , Birkeland Kåre I. , Nakstad Britt
Published: July 2014

Background

Size and body composition at birth may affect long‐term health. Mean birthweight and body composition differ between ethnic groups living in Europe. We wanted to explore if this relates to differences in socio‐economic conditions in country of origin and over the maternal life course.

Methods

This is a population‐based cohort study of healthy pregnant women living in Oslo, Norway. Data on maternal early life and present socio‐economic position (SEP) were collected in early gestation, and SEP scores were extracted through two separate principal components analyses. The associations between maternal present SEP and four different offspring anthropometric measures at birth were assessed separately, stratified by maternal early life SEP (dichotomised score) and Human Development Index (HDI, a country‐level socio‐economic indicator) in the country of origin [high HDI (Reference), n = 287 and low HDI, n = 250].

Results

A strong positive association between maternal present SEP and offspring birthweight was observed if maternal early life SEP was high, but not if maternal early life SEP was low (P < 0.001 for the interaction term). This interactional effect was observed in both HDI groups. Maternal life course SEP affected offspring birthweight mainly through an effect on length and sum of skin folds. Offspring of mothers with origin from low HDI countries had smaller abdominal circumference, possibly indicating less fat‐free mass, regardless of maternal life course SEP.

Conclusion

Our results suggest that there are transgenerational effects of maternal past socio‐economic conditions on offspring size and body composition at birth that modify the associations with present socio‐economic factors.
Multiple-Change-Point Detection for High Dimensional Time Series via Sparsified Binary Segmentation
Authors: Cho Haeran , Fryzlewicz Piotr
Published: July 2014

Time series segmentation, which is also known as multiple-change-point detection, is a well-established problem. However, few solutions have been designed specifically for high dimensional situations. Our interest is in segmenting the second-order structure of a high dimensional time series. In a generic step of a binary segmentation algorithm for multivariate time series, one natural solution is to combine cumulative sum statistics obtained from local periodograms and cross-periodograms of the components of the input time series. However, the standard ‘maximum’ and ‘average’ methods for doing so often fail in high dimensions when, for example, the change points are sparse across the panel or the cumulative sum statistics are spuriously large. We propose the sparsified binary segmentation algorithm which aggregates the cumulative sum statistics by adding only those that pass a certain threshold. This ‘sparsifying’ step reduces the influence of irrelevant noisy contributions, which is particularly beneficial in high dimensions. To show the consistency of sparsified binary segmentation, we introduce the multivariate locally stationary wavelet model for time series, which is a separate contribution of this work.
Psychiatric and Self‐Injury Profiles of Adolescent Suicide Attempters versus Adolescents Engaged in Nonsuicidal Self‐Injury
Authors: Kim Kerri L. , Galvan Thania , Puzia Megan E. , Cushman Grace K. , Seymour Karen E. , Vanmali Roshani , Jones Richard N. , Spirito Anthony , Dickstein Daniel P.
Published: July 2014

To better delineate the unique correlates of self‐injurious behaviors (SIB), psychiatric profiles of mutually exclusive groups of adolescents who made a suicide attempt (SA) versus those engaged in nonsuicidal self‐injury (NSSI) were examined. Contrary to hypotheses, the NSSI group endorsed earlier onsets of SIB and suicidal ideation (SI), as well as higher rates of depression and anxiety compared with their SA counterparts. Future work is warranted to understand the role of SI, including duration of SI and anxiety in the development of NSSI, and to identify risk and resiliency factors useful in predicting an adolescent's SIB status.
The Arabidopsis nitrate transporter NRT2.5 plays a role in nitrate acquisition and remobilization in nitrogen‐starved plants
Authors: Lezhneva Lina , Kiba Takatoshi , Feria‐Bourrellier Ana‐Belen , Lafouge Florence , Boutet‐Mercey Stéphanie , Zoufan Parzhak , Sakakibara Hitoshi , Daniel‐Vedele Françoise , Krapp Anne
Published: July 2014

Nitrogen is a key mineral nutrient playing a crucial role in plant growth and development. Understanding the mechanisms of nitrate uptake from the soil and distribution through the plant in response to nitrogen starvation is an important step on the way to improve nitrogen uptake and utilization efficiency for better growth and productivity of plants, and to prevent negative effects of nitrogen fertilizers on the environment and human health. In this study, we show that Arabidopsis NITRATE TRANSPORTER 2.5 (NRT2.5) is a plasma membrane‐localized high‐affinity nitrate transporter playing an essential role in adult plants under severe nitrogen starvation. NRT2.5 expression is induced under nitrogen starvation and NRT2.5 becomes the most abundant transcript amongst the seven NRT2 family members in shoots and roots of adult plants after long‐term starvation. GUS reporter analyses showed that NRT2.5 is expressed in the epidermis and the cortex of roots at the root hair zone and in minor veins of mature leaves. Reduction of NRT2.5 expression resulted in a decrease in high‐affinity nitrate uptake without impacting low‐affinity uptake. In the background of the high‐affinity nitrate transporter mutant nrt2.4, an nrt2.5 mutation reduced nitrate levels in the phloem of N‐starved plants further than in the single nrt2.4 mutants. Growth analyses of multiple mutants between NRT2.1, NRT2.2, NRT2.4, and NRT2.5 revealed that NRT2.5 is required to support growth of nitrogen‐starved adult plants by ensuring the efficient uptake of nitrate collectively with NRT2.1, NRT2.2 and NRT2.4 and by taking part in nitrate loading into the phloem during nitrate remobilization.
A new background distribution‐based active contour model for three‐dimensional lesion segmentation in breast DCE‐MRI
Authors: Liu Hui , Liu Yiping , Zhao Zuowei , Zhang Lina , Qiu Tianshuang
Published: July 2014

Purpose:

To develop and evaluate a computerized semiautomatic segmentation method for accurate extraction of three‐dimensional lesions from dynamic contrast‐enhanced magnetic resonance images (DCE‐MRIs) of the breast.

Methods:

The authors propose a new background distribution‐based active contour model using level set (BDACMLS) to segment lesions in breast DCE‐MRIs. The method starts with manual selection of a region of interest (ROI) that contains the entire lesion in a single slice where the lesion is enhanced. Then the lesion volume from the volume data of interest, which is captured automatically, is separated. The core idea of BDACMLS is a new signed pressure function which is based solely on the intensity distribution combined with pathophysiological basis. To compare the algorithm results, two experienced radiologists delineated all lesions jointly to obtain the ground truth. In addition, results generated by other different methods based on level set (LS) are also compared with the authors’ method. Finally, the performance of the proposed method is evaluated by several region‐based metrics such as the overlap ratio.

Results:

Forty‐two studies with 46 lesions that contain 29 benign and 17 malignant lesions are evaluated. The dataset includes various typical pathologies of the breast such as invasive ductal carcinoma, ductal carcinomain situ, scar carcinoma, phyllodes tumor, breast cysts, fibroadenoma, etc. The overlap ratio for BDACMLS with respect to manual segmentation is 79.55% ± 12.60% (mean ± s.d.).

Conclusions:

A new active contour model method has been developed and shown to successfully segment breast DCE‐MRI three‐dimensional lesions. The results from this model correspond more closely to manual segmentation, solve the weak‐edge‐passed problem, and improve the robustness in segmenting different lesions.
An initial study on the estimation of time‐varying volumetric treatment images and 3D tumor localization from single MV cine EPID images
Authors: Mishra Pankaj , Li Ruijiang , Mak Raymond H. , Rottmann Joerg , Bryant Jonathan H. , Williams Christopher L. , Berbeco Ross I. , Lewis John H.
Published: July 2014

Purpose:

In this work the authors develop and investigate the feasibility of a method to estimate time‐varying volumetric images from individual MV cine electronic portal image device (EPID) images.

Methods:

The authors adopt a two‐step approach to time‐varying volumetric image estimation from a single cine EPID image. In the first step, a patient‐specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient‐specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculated through deformable image registration (DIR) of a reference 4DCT phase image (typically peak‐exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen‐coefficients. To generate a new volumetric image, the eigen‐coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen‐coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image.

Results:

The algorithm was tested on (1) Eight digital eXtended CArdiac‐Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root‐mean‐squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data.

Conclusions:

The authors introduced a novel method of estimating volumetric time‐varying images from single cine EPID images and a PCA‐based lung motion model. This is the first method to estimate volumetric time‐varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient.
Sub-wavelength energy trapping of elastic waves in a metamaterial
Authors: Colombi Andrea , Roux Philippe , Rupin Matthieu
Published: July 2014

Deep sub-wavelength focusing has been demonstrated for locally resonant metamaterials using electromagnetic and acoustic waves. The elastic equivalents of such objects are made of sub-wavelength resonating beams fixed to a two-dimensional plate, as presented here. Independent of a random or regular arrangement of the resonators, the metamaterial shows large bandgaps that are independent of the incident wave direction. Numerical simulations demonstrate that the insertion of a defect in the layout, as a shorter resonator, creates strong amplification of the wave-field on the defect. This energy trapping, which is localized on a spatial scale that is much smaller than the wavelength in the two-dimensional plate, leads to a >1 factor in terms of the local density of energy.
Fisher information and entanglement of non-Gaussian spin states
Authors: Strobel Helmut , Muessel Wolfgang , Linnemann Daniel , Zibold Tilman , Hume David B. , Pezzè Luca , Smerzi Augusto , Oberthaler Markus K.
Published: July 2014

Subtle entanglement in an atomic cloud

In the quantum world, atoms can be correlated with each other—“entangled”—which reduces the uncertainty in the knowledge of some of their properties. Physicists then use this reduced uncertainty to perform precision measurements. Strobel
et al.
made an unusual type of entangled state consisting of hundreds of ultracold Rb atoms. These methods may in the future be able to generate states that will be more useful in precision measurement.

Science
, this issue p.
424
Synchronization of North Pacific and Greenland climates preceded abrupt deglacial warming
Authors: Praetorius Summer K. , Mix Alan C.
Published: July 2014

Climates conspire together to make big changes

The regional climates of the North Pacific and North Atlantic fluttered between synchrony and asynchrony during the last deglaciation, with correspondingly more and less intense effects on the rest of the world, researchers have found. The climate system can be highly nonlinear, meaning that small changes in one part can lead to much larger changes elsewhere. This type of behavior is especially evident during transitions from glacial to interglacial conditions, when climate is affected by a wide variety of time-varying influences and is relatively unstable. Praetorius and Mix present a record of North Pacific climate over the past 18,000 years. When the climates of the more local high-latitude Pacific and Atlantic sectors varied in parallel, large, abrupt climate fluctuations occurred on a more global scale.

Science
, this issue p.
444
A cloaking coating for murky media
Authors: Smith David R.
Published: July 2014

Objects shrouded in fog disappear entirely with simple coating

[Also see Report by

Schittny
et al.

]
Ribosome rescue and neurodegeneration
Authors: Darnell Jennifer C.
Published: July 2014

A mutation in a brain-specific tRNA reveals the link between ribosome maintenance and neuronal cell death

[Also see Report by

Ishimura
et al.

]
Oil sands fight heats up in U.S.
Authors: Malakoff David
Published: July 2014

Environmentalists oppose federal lease in Utah.
Fusion's restless pioneers
Authors: Clery Daniel
Published: July 2014

Startups with novel technologies are taking on fusion's Goliaths.
A Novel Live Vector Group A StreptococcalemmType 9 Vaccine Delivered Intranasally Protects Mice against Challenge Infection withemmType 9 Group A Streptococci
Authors: Wozniak Aniela , García Patricia , Geoffroy Enrique A. , Aguirre Daniel B. , González Samantha A. , Sarno Victoria A. , Dale James B. , Salazar-Echegarai Francisco J. , Vera Andrea , Bueno Susan M. , Kalergis Alexis M.
Published: July 2014

The availability of a protective vaccine againstStreptococcus pyogenes(group AStreptococcus[GAS]) is a priority for public health worldwide. Here, we have generated six live vaccine strains, each engineered to express an N-terminal M protein peptide from one of six of the most prevalentemmtypes of GAS (M1, M2, M4, M9, M12, and M28). The vaccine strains are based on a food-gradeLactococcus lactisstrain and do not bear any antibiotic resistance. Mice immunized with the vaccine strain expressing the M9 peptide (termed here theL. lactisM9 strain) showed high titers of serum antibodies when delivered intranasally. Mice immunized with theL. lactisM9 strain were protected against infection after intranasal challenge with type 9 streptococci. Several parameters of disease, such as weight loss, body temperature, colony counts in mouth washes, and lung histology, were significantly improved in immunized mice compared to naive control mice. Our results indicate that intranasal delivery of theL. lactisM9 strain live bacterial vaccine induced GAS-specific IgG titers, prevented pharyngeal colonization of GAS, and protected mice from disease upon challenge. The design of this vaccine prototype may provide a lower cost alternative to vaccines comprised of purified recombinant proteins.
Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere
Authors: Wang Yinghuan , Wang Xiaoyi , Greenfield Paul , Jin Decai , Bai Zhihui
Published: July 2014

Bacillus amyloliquefaciens
strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs).
Detection of Mycobacterium leprae by PCR Testing of Sputa from a Patient with Pulmonary Cryptococcus Coinfection in Northern Australia
Authors: Edwards Laura J. , Price Ric N. , Krause Vicki L. , Huffam Sarah E. , Globan Maria , Fyfe Janet , Hajkowicz Krispin M.
Published: July 2014

A case of fever, sepsis, and chest lesions evident on a computed tomography scan of an indigenous man in northern Australia following burns to the feet is described. Sputum PCR testing revealed
Mycobacterium leprae
, and a fine-needle aspirate of the chest lesions demonstrated
Cryptococcus
coinfection.
Using Crude Whole-Genome Assemblies of Neisseria gonorrhoeae as a Platform for Strain Analysis: Clonal Spread of Gonorrhea Infection in Saskatchewan, Canada
Authors: Vidovic Sinisa , Caron Carolyn , Taheri Ali , Thakur Sidharath D. , Read Timothy D. , Kusalik Anthony , Dillon Jo-Anne R.
Published: July 2014

Using crude whole-genome assemblies, we analyzed 25 isolates of
Neisseria gonorrhoeae
by using a high-resolution single nucleotide polymorphism (SNP) approach for nine housekeeping genes, characterizing
penA
alleles, and antimicrobial susceptibility phenotypes coupled with population structure analysis. Two clonal complexes, characterized by their spatial and geographical persistence, were identified. In addition, the clonal spread of penicillin-resistant/intermediate phenotypes and a novel introduction of the azithromycin resistance phenotype in Saskatchewan, Canada, were ascertained using this method.
Microbial Typing by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Do We Need Guidance for Data Interpretation?
Authors: Spinali Sébastien , van Belkum Alex , Goering Richard V. , Girard Victoria , Welker Martin , Van Nuenen Marc , Pincus David H. , Arsac Maud , Durand Géraldine
Published: July 2014

The integration of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has revolutionized species identification of bacteria, yeasts, and molds. However, beyond straightforward identification, the method has also been suggested to have the potential for subspecies-level or even type-level epidemiological analyses. This minireview explores MALDI-TOF MS-based typing, which has already been performed on many clinically relevant species. We discuss the limits of the method's resolution and we suggest interpretative criteria allowing valid comparison of strain-specific data. We conclude that guidelines for MALDI-TOF MS-based typing can be developed along the same lines as those used for the interpretation of data from pulsed-field gel electrophoresis (PFGE).
False-Positive Results for Rapid Diagnostic Tests for Malaria in Patients with Rheumatoid Factor
Authors: Lee Jong-Han , Jang Jin Woo , Cho Chi Hun , Kim Ju Yeon , Han Eun Taek , Yun Seung Gyu , Lim Chae Seung
Published: July 2014

Four different rapid diagnostic tests (RDTs) for malaria were evaluated by testing 82 healthy control patients, 89
Plasmodium vivax
-infected patients, and 92 rheumatoid factor (RF)-positive nonmalaria patients. The false-positive rate ranged from 2.2% to 13% in RF-positive patients. High RF levels are associated with malaria RDT false positivity.
Comparison of Two Commercial Real-Time PCR Assays for Detection of Dengue Virus in Patient Serum Samples
Authors: Saengsawang J. , Nathalang O. , Kamonsil M. , Watanaveeradej V.
Published: July 2014

This study evaluated and compared the performance of two real-time PCR assays using nested reverse transcription (RT)-PCR as the reference method. Among 117 nested RT-PCR-positive cases, the
ab
TES DEN 5 qPCR kit detected 97.4% of dengue virus (DENV) infections, while the innuDETECT Dengue TwoStep assay did so for 44.4%. Sensitivity varied by infecting serotype and the stage of infection. The
ab
TES kit has the potential to replace nested RT-PCR for the rapid diagnosis of DENV infection.
Kaposi's Sarcoma-Associated Herpesvirus ORF18 and ORF30 Are Essential for Late Gene Expression during Lytic Replication
Authors: Gong Danyang , Wu Nicholas C. , Xie Yafang , Feng Jun , Tong Leming , Brulois Kevin F. , Luan Harding , Du Yushen , Jung Jae U. , Wang Cun-yu , Kang Mo Kwan , Park No-Hee , Sun Ren , Wu Ting-Ting
Published: July 2014

Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with several human malignances. As saliva is likely the major vehicle for KSHV transmission, we studied
in vitro
KSHV infection of oral epithelial cells. Through infection of two types of oral epithelial cells, normal human oral keratinocytes (NHOKs) and papilloma-immortalized human oral keratinocyte (HOK16B) cells, we found that KSHV can undergo robust lytic replication in oral epithelial cells. By employing
de novo
lytic infection of HOK16B cells, we studied the functions of two previously uncharacterized genes, ORF18 and ORF30, during the KSHV lytic cycle. For this purpose, an ORF18-deficient virus and an ORF30-deficient virus were generated using a mutagenesis strategy based on bacterial artificial chromosome (BAC) technology. We found that neither ORF18 nor ORF30 is required for immediately early or early gene expression or viral DNA replication, but each is essential for late gene expression during both
de novo
lytic replication and reactivation. This critical role of ORF18 and ORF30 in late gene expression was also observed during KSHV reactivation. In addition, global analysis of viral transcripts by RNA sequencing indicated that ORF18 and ORF30 control the same set of viral genes. Therefore, we suggest that these two viral ORFs are involved in the same mechanism or pathway that coregulates the viral late genes as a group.

IMPORTANCE
While KSHV can infect multiple cell types
in vitro
, only a few can support a full lytic replication cycle with progeny virions produced. Consequently, KSHV lytic replication is mostly studied through reactivation, which requires chemicals to induce the lytic cycle or overexpression of the viral transcriptional activator, RTA. In this study, we present a robust
de novo
lytic infection system based on oral epithelial cells. Using this system, we demonstrate the role of two viral ORFs, ORF18 and ORF30, in regulating viral gene expression during KSHV lytic replication. As the major route of KSHV transmission is thought to be via saliva, this new KSHV lytic replication system will have important utility in the field.
New Insights into the Nonconserved Noncoding Region of the Subtype-Determinant Hemagglutinin and Neuraminidase Segments of Influenza A Viruses
Authors: Zhao Lili , Peng Yousong , Zhou Kai , Cao Mengmeng , Wang Jingfeng , Wang Xue , Jiang Taijiao , Deng Tao
Published: July 2014

The noncoding regions (NCRs) of the eight-segmented viral RNAs (vRNAs) of influenza A virus consist of the highly conserved promoter region and the nonconserved segment-specific NCRs at both the 3′ and 5′ ends. The roles of the segment-specific NCRs of the eight segments have been extensively studied. However, the diversities in the same region of the two subtype-determinant hemagglutinin (HA) and neuraminidase (NA) segments have received little attention. In this study, we bioinformatically analyzed all available NCRs of HA and NA vRNAs of influenza A viruses and found that nucleotides in the segment-specific NCRs of HA and NA vRNAs are subtype specific and vary significantly in sequence and length at both the 3′ and 5′ ends among different subtypes. We then systematically studied the biological significance of the HA subtype-specific NCRs (HA ssNCRs) of the common HA subtypes (H1 to H7 and H9) in the context of the WSN (H1N1) reverse genetics system. We found that the HA ssNCRs play a critical role in HA vRNA virion incorporation. Upon HA vRNA incorporation, the 3′-end HA ssNCR plays a more critical role than the 5′-end HA ssNCR, and no stringent compatibility between the two ends is required. Furthermore, our data imply that, in addition to a particular nucleotide(s), the length of the HA ssNCR is involved in regulating HA vRNA incorporation efficiency. These results provide new insights into the HA segment virion incorporation that is critical for the emergence of epidemic and pandemic influenza A virus strains.

IMPORTANCE
The nonconserved noncoding regions (NCRs) of the vRNAs of influenza A virus have been extensively studied, whereas the diversities in the nonconserved NCRs of the two subtype-determinant segments hemagglutinin (HA) and neuraminidase (NA) have received little attention. In this study, we bioinformatically analyzed all available NCRs of HA and NA vRNAs and discovered that the HA and NA vRNAs contain key subtype signatures in the NCRs. Our functional studies of the HA subtype-specific NCRs (HA ssNCRs) of the common HA subtypes in the context of WSN virus (H1N1) demonstrated that the HA ssNCR modulates virus replication efficiency by influencing HA segment virion incorporation. Moreover, we revealed important features of the HA ssNCR in determining HA vRNA incorporation efficiency. These data not only show new genetic characteristics of influenza A viruses, but also provide further evidence for understanding the selective genome packaging of influenza virus required for the emergence of epidemic and pandemic influenza virus strains.
Downregulation of MicroRNA miR-526a by Enterovirus Inhibits RIG-I-Dependent Innate Immune Response
Authors: Xu Changzhi , He Xiang , Zheng Zirui , Zhang Zhe , Wei Congwen , Guan Kai , Hou Lihua , Zhang Buchang , Zhu Lin , Cao Yuan , Zhang Yanhong , Cao Ye , Ma Shengli , Wang Penghao , Zhang Pingping , Xu Quanbin , Ling Youguo , Yang Xiao , Zhong Hui
Published: July 2014

Retinoic acid-inducible gene I (RIG-I) is an intracellular RNA virus sensor that induces type I interferon-mediated host-protective innate immunity against viral infection. Although cylindromatosis (CYLD) has been shown to negatively regulate innate antiviral response by removing K-63-linked polyubiquitin from RIG-I, the regulation of its expression and the underlying regulatory mechanisms are still incompletely understood. Here we show that RIG-I activity is regulated by inhibition of CYLD expression mediated by the microRNA miR-526a. We found that viral infection specifically upregulates miR-526a expression in macrophages via interferon regulatory factor (IRF)-dependent mechanisms. In turn, miR-526a positively regulates virus-triggered type I interferon (IFN-I) production, thus suppressing viral replication, the underlying mechanism of which is the enhancement of RIG-I K63-linked ubiquitination by miR-526a via suppression of the expression of CYLD. Remarkably, virus-induced miR-526a upregulation and CYLD downregulation are blocked by enterovirus 71 (EV71) 3C protein, while ectopic miR-526a expression inhibits the replication of EV71 virus. The collective results of this study suggest a novel mechanism of the regulation of RIG-I activity during RNA virus infection by miR-526a and suggest a novel mechanism for the evasion of the innate immune response controlled by EV71.

IMPORTANCE
RNA virus infection upregulates the expression of miR-526a in macrophages through IRF-dependent pathways. In turn, miR-526a positively regulates virus-triggered type I IFN production and inhibits viral replication, the underlying mechanism of which is the enhancement of RIG-I K-63 ubiquitination by miR-526a via suppression of the expression of CYLD. Remarkably, virus-induced miR-526a upregulation and CYLD downregulation are blocked by enterovirus 71 (EV71) 3C protein; cells with overexpressed miR-526a were highly resistant to EV71 infection. The collective results of this study suggest a novel mechanism of the regulation of RIG-I activity during RNA virus infection by miR-526a and propose a novel mechanism for the evasion of the innate immune response controlled by EV71.
Antiviral Regulation in Porcine Monocytic Cells at Different Activation States
Authors: Sang Yongming , Rowland Raymond R. R. , Blecha Frank
Published: July 2014

Monocytic cells, including macrophages and dendritic cells, exist in different activation states that are critical to the regulation of antimicrobial immunity. Many pandemic viruses are monocytotropic, including porcine reproductive and respiratory syndrome virus (PRRSV), which directly infects subsets of monocytic cells and interferes with antiviral responses. To study antiviral responses in PRRSV-infected monocytic cells, we characterized inflammatory cytokine responses and genome-wide profiled signature genes to investigate response pathways in uninfected and PRRSV-infected monocytic cells at different activation states. Our findings showed suppressed interferon (IFN) production in macrophages in non-antiviral states and an arrest of lipid metabolic pathways in macrophages at antiviral states. Importantly, porcine monocytic cells at different activation states were susceptible to PRRSV and responded differently to viral infection. Based on Gene Ontology (GO) analysis, two approaches were used to potentiate antiviral activity: (i) pharmaceutical modulation of cellular lipid metabolism and (ii)
in situ
PRRSV replication-competent expression of interferon alpha (IFN-α). Both approaches significantly suppressed exogenous viral infection in monocytic cells. In particular, the engineered IFN-expressing PRRSV strain eliminated exogenous virus infection and sustained cell viability at 4 days postinfection in macrophages. These findings suggest an intricate interaction of viral infection with the activation status of porcine monocytic cells. An understanding and integration of antiviral infection with activation status of monocytic cells may provide a means of potentiating antiviral immunity.

IMPORTANCE
Activation statuses of monocytic cells, including monocytes, macrophages (Mϕs), and dendritic cells (DCs), are critically important for antiviral immunity. Unfortunately, the activation status of porcine monocytic cells or how cell activation status functionally interacts with antiviral immunity remains largely unknown. This is a significant omission because many economically important porcine viruses are monocytotropic, including our focus, PRRSV, which alone causes nearly $800 million economic loss annually in the U.S. swine industries. PRRSV is ideal for deciphering how monocytic cell activation statuses interact with antiviral immunity, because it directly infects subsets of monocytic cells and subverts overall immune responses. In this study, we systematically investigate the activation status of porcine monocytic cells to determine the intricate interaction of viral infection with activation statuses and functionally regulate antiviral immunity within the framework of the activation paradigm. Our findings may provide a means of potentiating antiviral immunity and leading to novel vaccines for PRRS prevention.
Characterization of the Mode of Action of a Potent Dengue Virus Capsid Inhibitor
Authors: Scaturro Pietro , Trist Iuni Margaret Laura , Paul David , Kumar Anil , Acosta Eliana G. , Byrd Chelsea M. , Jordan Robert , Brancale Andrea , Bartenschlager Ralf
Published: July 2014

Dengue viruses (DV) represent a significant global health burden, with up to 400 million infections every year and around 500,000 infected individuals developing life-threatening disease. In spite of attempts to develop vaccine candidates and antiviral drugs, there is a lack of approved therapeutics for the treatment of DV infection. We have previously reported the identification of ST-148, a small-molecule inhibitor exhibiting broad and potent antiviral activity against DV
in vitro
and
in vivo
(C. M. Byrd et al., Antimicrob. Agents Chemother. 57:15–25, 2013, doi:10
.1128/AAC.01429-12). In the present study, we investigated the mode of action of this promising compound by using a combination of biochemical, virological, and imaging-based techniques. We confirmed that ST-148 targets the capsid protein and obtained evidence of bimodal antiviral activity affecting both assembly/release and entry of infectious DV particles. Importantly, by using a robust bioluminescence resonance energy transfer-based assay, we observed an ST-148-dependent increase of capsid self-interaction. These results were corroborated by molecular modeling studies that also revealed a plausible model for compound binding to capsid protein and inhibition by a distinct resistance mutation. These results suggest that ST-148-enhanced capsid protein self-interaction perturbs assembly and disassembly of DV nucleocapsids, probably by inducing structural rigidity. Thus, as previously reported for other enveloped viruses, stabilization of capsid protein structure is an attractive therapeutic concept that also is applicable to flaviviruses.

IMPORTANCE
Dengue viruses are arthropod-borne viruses representing a significant global health burden. They infect up to 400 million people and are endemic to subtropical and tropical areas of the world. Currently, there are neither vaccines nor approved therapeutics for the prophylaxis or treatment of DV infections, respectively. This study reports the characterization of the mode of action of ST-148, a small-molecule capsid inhibitor with potent antiviral activity against all DV serotypes. Our results demonstrate that ST-148 stabilizes capsid protein self-interaction, thereby likely perturbing assembly and disassembly of viral nucleocapsids by inducing structural rigidity. This, in turn, might interfere with the release of viral RNA from incoming nucleocapsids (uncoating) as well as assembly of progeny virus particles. As previously reported for other enveloped viruses, we propose the capsid as a novel tractable target for flavivirus inhibitors.
Comparison of Genotypes I and III in Japanese Encephalitis Virus Reveals Distinct Differences in Their Genetic and Host Diversity
Authors: Han Na , Adams James , Chen Ping , Guo Zhen-yang , Zhong Xiang-fu , Fang Wei , Li Na , Wen Lei , Tao Xiao-yan , Yuan Zhi-ming , Rayner Simon
Published: July 2014

Japanese encephalitis (JE) is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been phylogenetically divided into five genotypes. Recent surveillance data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. To investigate the mechanism behind the genotype shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination, we collected (i) all full-length and partial JEV molecular sequences and (ii) associated genotype and host information comprising a data set of 873 sequences. We then examined differences between the two genotypes at the genetic and epidemiological level by investigating amino acid mutations, positive selection, and host range.

IMPORTANCEWe found that although GI is dominant, it has fewer sites predicted to be under positive selection, a narrower host range, and significantly fewer human isolates. For the E protein, the sites under positive selection define a haplotype set for each genotype that shows striking differences in their composition and diversity, with GIII showing significantly more variety than GI. Our results suggest that GI has displaced GIII by achieving a replication cycle that is more efficient but is also more restricted in its host range.

Japanese encephalitis is an arthropod-borne disease associated with the majority of viral encephalitis cases in the Asia-Pacific region. The causative agent, Japanese encephalitis virus (JEV), has been divided into five genotypes based on sequence similarity. Recent data indicate that genotype I (GI) is gradually replacing genotype III (GIII) as the dominant genotype. Understanding the reasons behind this shift and the potential consequences in terms of vaccine efficacy, human cases, and virus dissemination is important for controlling the spread of the virus and reducing human fatalities. We collected all available full-length and partial JEV molecular sequences and associated genotype and host information. We then examined differences between the two genotypes at the genetic and epidemiological levels by investigating amino acid mutations, positive selection, and host range. Our results suggest that GI has displaced GIII by achieving a replication cycle that is more efficient but more restricted in host range.
Undiagnosed diabetes from cross-sectional GP practice data: an approach to identify communities with high likelihood of undiagnosed diabetes
Authors: Bagheri Nasser , McRae Ian , Konings Paul , Butler Danielle , Douglas Kirsty , Del Fante Peter , Adams Robert
Published: July 2014

Objectives

To estimate undiagnosed diabetes prevalence from general practitioner (GP) practice data and identify areas with high levels of undiagnosed and diagnosed diabetes.

Design

Data from the North-West Adelaide Health Survey (NWAHS) were used to develop a model which predicts total diabetes at a small area. This model was then applied to cross-sectional data from general practices to predict the total level of expected diabetes. The difference between total expected and already diagnosed diabetes was defined as undiagnosed diabetes prevalence and was estimated for each small area. The patterns of diagnosed and undiagnosed diabetes were mapped to highlight the areas of high prevalence.

Setting

North-West Adelaide, Australia.

Participants

This study used two population samples—one from the de-identified GP practice data (n=9327 active patients, aged 18 years and over) and another from NWAHS (n=4056, aged 18 years and over).

Main outcome measures

Total diabetes prevalence, diagnosed and undiagnosed diabetes prevalence at GP practice and Statistical Area Level 1.

Results

Overall, it was estimated that there was one case of undiagnosed diabetes for every 3–4 diagnosed cases among the 9327 active patients analysed. The highest prevalence of diagnosed diabetes was seen in areas of lower socioeconomic status. However, the prevalence of undiagnosed diabetes was substantially higher in the least disadvantaged areas.

Conclusions

The method can be used to estimate population prevalence of diabetes from general practices wherever these data are available. This approach both flags the possibility that undiagnosed diabetes may be a problem of less disadvantaged social groups, and provides a tool to identify areas with high levels of unmet need for diabetes care which would enable policy makers to apply geographic targeting of effective interventions.
‘I'm not a druggie, I'm just a diabetic’: a qualitative study of stigma from the perspective of adults with type 1 diabetes
Authors: Browne Jessica L , Ventura Adriana , Mosely Kylie , Speight Jane
Published: July 2014

Objectives

While health-related stigma has been the subject of considerable research in other conditions (eg, HIV/AIDS, obesity), it has not received substantial attention in diabetes. Our aim was to explore perceptions and experiences of diabetes-related stigma from the perspective of adults with type 1 diabetes mellitus (T1DM).

Design

A qualitative study using semistructured interviews, which were audio recorded, transcribed and subject to thematic analysis.

Setting

All interviews were conducted in non-clinical settings in metropolitan areas of Victoria, Australia.

Participants

Adults aged ≥18 years with T1DM living in Victoria were eligible to take part. Participants were recruited primarily through the state consumer organisation representing people with diabetes. A total of 27 adults with T1DM took part: 15 (56%) were women; median IQR age was 42 (23) years and diabetes duration was 15 (20) years).

Results

Australian adults with T1DM perceive and experience T1DM-specific stigma as well as stigma-by-association with type 2 diabetes. Such stigma is characterised by blame, negative social judgement, stereotyping, exclusion, rejection and discrimination. Participants identified the media, family and friends, healthcare professionals and school teachers as sources of stigma. The negative consequences of this stigma span numerous life domains, including impact on relationships and social identity, emotional well-being and behavioural management of T1DM. This stigma also led to reluctance to disclose the condition in various environments. Adults with T1DM can be both the target and the source of diabetes-related stigma.

Conclusions

Stigmatisation is part of the social experience of living with T1DM for Australian adults. Strategies and interventions to address and mitigate this diabetes-related stigma need to be developed and evaluated.
Disseminated aspergillosis causing intestinal failure following colectomy for perforated colitis
Authors: McElvanna Kevin , Loughrey Maurice B , Gillespie Scott , Gardiner Keith R
Published: July 2014

Disseminated aspergillosis is a rare, invasive, opportunistic, fungal infection associated with a high mortality. We report a non-fatal case diagnosed following extensive enterectomy for intestinal infarction in a patient recovering from emergency abdominal colectomy for perforated ulcerative colitis. This resulted in intestinal failure necessitating life-long parenteral nutrition and prolonged antifungal therapy.
Increases in aboveground biomass and leaf area 85 years after drainage in a bog
Authors: Talbot Julie , Roulet Nigel T. , Sonnentag Oliver , Moore Tim R.
Published: July 2014

Climate change scenarios suggest that northern peatlands could become drier. To address the type and magnitude of vegetation change associated with persistent drying, we studied changes in biomass and leaf area index following drainage 85 years previously of a bog, using destructive sampling, allometric relationships, and optical measurements. Our results show a 10-fold increase in aboveground biomass between the reference site and the most severely drained site, resulting from the growth of a tree layer. The total leaf biomass increased slightly as a result of drainage, thus an increase in woody biomass was the main cause of the increase in aboveground biomass. Leaf area index approximately tripled in sites where trees grew. Sphagnum L. moss biomass decreased from 120 g·m−2 at the reference site (20% of all aboveground biomass) to 8 g·m−2 under the tree canopy (<1% of all aboveground biomass). The percentage of deciduous shrubs increased from 3% of the total shrub biomass in the reference site to 72% in the most severely drained site. Our results show that lowering the water table of a bog can have a profound effect on vegetation but the net effect of these changes on the role of the peatland as a carbon sink remains difficult to assess.
Correlations between low energy leptonic CP violation and leptogenesis in the light of recent experiments
Authors: Zeen Devi H.
Published: July 2014

Leptogenesis is the most favorable mechanism for generating the observed baryon asymmetry of the universe (BAU) which implies CP violation in the high energy scale. The low energy leptonic CP violation is expected to be observed in the neutrino oscillations and 0ν2β decay experiments. Generally, it is not possible to connect both the CP violations. Here we revisit the issue of connecting the two in flavored leptogenesis scenario within the Type I seesaw in the light of recent neutrino oscillation and Planck data. With the recent precise measurements of θ13 and BAU, we are able to find new correlations between the low and high energy CP violating phases when leptogenesis occurs at temperature between 109 to 1012 GeV and there is no contribution to CP violation from the heavy neutrino sector.
A Strategy to Formalize Specification and Its Application to an Advanced Railway System
Authors: Xie Guo , Hei Xinhong , Takahashi Sei , Nakamura Hideo
Published: July 2014

This paper proposes a novel strategy for formally analyzing functional requirements specification (FRS) and applies it to the Automatic Train Protection and Block (ATPB) system, which is proposed to reconstruct conventional rail lines in Japan. Based on the FRS in natural language, firstly, dynamic state transitions are extracted to express the operational mechanisms and determine the system parameters. A complete model of the ATPB system is then established using Unified Modeling Language (UML) to express the system structure graphically and explicitly. After achieving a common understanding, a VDM++ model is established formally to redescribe the original FRS of the ATPB system which is written in natural language (i.e. Japanese). Following that, in order to ensure internal consistency of the specification, proof obligations of the VDM++ model are discharged. Furthermore, a comprehensive testing is implemented to ensure that the FRS meets actual requirements. Finally, the system is simulated strictly in accordance with the formal specification. Without any runtime errors, collisions or derailments, the results of the simulation demonstrate the high quality and safety of the specification.
Stiffness and Transfer Matrix Analysis in Global Coordinates of a 3D Curved Beam
Authors: Gonzaga Pedro , Gimena Faustino N. , Gimena Lazaro
Published: July 2014

This article presents the differential equation in the global coordinates governing the structural behavior of 3D curved beams existing in building structures and civil works. This differential equation presented is of the lower-triangular form, which allows us to obtain the transfer matrix, also of lower-triangular form and with unit diagonal, through simple integrals. The stiffness matrix is determined from the transfer matrix expression, only by reordering operations, without employing additional structural methods, energy theorems or other. This rearrangement can be more easily done under the global system, compared with the natural reference system, since the order of the matrices involved has been reduced. The examples presented show the process to apply this general procedure to derivation of the stiffness matrix of a member from its transfer expression, through reordering operations.