bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Control of HIV-1 by Cytotoxic T Cells Specific for Multiple Conserved Epitopes
Authors: Murakoshi Hayato , Akahoshi Tomohiro , Koyanagi Madoka , Chikata Takayuki , Naruto Takuya , Maruyama Rie , Tamura Yoshiko , Ishizuka Naoki , Gatanaga Hiroyuki , Oka Shinichi , Takiguchi Masafumi
Published: March 2015

Identification and characterization of CD8
+
T cells effectively controlling HIV-1 variants are necessary for the development of AIDS vaccines and for studies of AIDS pathogenesis, although such CD8
+
T cells have been only partially identified. In this study, we sought to identify CD8
+
T cells controlling HIV-1 variants in 401 Japanese individuals chronically infected with HIV-1 subtype B, in which protective alleles HLA-B*57 and HLA-B*27 are very rare, by using comprehensive and exhaustive methods. We identified 13 epitope-specific CD8
+
T cells controlling HIV-1 in Japanese individuals, though 9 of these epitopes were not previously reported. The breadths of the T cell responses to the 13 epitopes were inversely associated with plasma viral load (
P
= 2.2 × 10
−11
) and positively associated with CD4 count (
P
= 1.2 × 10
−11
), indicating strong synergistic effects of these T cells on HIV-1 control
in vivo
. Nine of these epitopes were conserved among HIV-1 subtype B-infected individuals, whereas three out of four nonconserved epitopes were cross-recognized by the specific T cells. These findings indicate that these 12 epitopes are strong candidates for antigens for an AIDS vaccine. The present study highlighted a strategy to identify CD8
+
T cells controlling HIV-1 and demonstrated effective control of HIV-1 by those specific for 12 conserved or cross-reactive epitopes.

IMPORTANCE
HLA-B*27-restricted and HLA-B*57-restricted cytotoxic T lymphocytes (CTLs) play a key role in controlling HIV-1 in Caucasians and Africans, whereas it is unclear which CTLs control HIV-1 in Asian countries, where HLA-B*57 and HLA-B*27 are very rare. A recent study showed that HLA-B*67:01 and HLA-B*52:01-C*12:02 haplotypes were protective alleles in Japanese individuals, but it is unknown whether CTLs restricted by these alleles control HIV-1. In this study, we identified 13 CTLs controlling HIV-1 in Japan by using comprehensive and exhaustive methods. They included 5 HLA-B*52:01-restricted and 3 HLA-B*67:01-restricted CTLs, suggesting that these CTLs play a predominant role in HIV-1 control. The 13 CTLs showed synergistic effects on HIV-1 control. Twelve out of these 13 epitopes were recognized as conserved or cross-recognized ones. These findings strongly suggest that these 12 epitopes are candidates for antigens for AIDS vaccines.
Viral Bcl-2 Encoded by the Kaposi's Sarcoma-Associated Herpesvirus Is Vital for Virus Reactivation
Authors: Gelgor Anastasia , Kalt Inna , Bergson Shir , Brulois Kevin F. , Jung Jae U. , Sarid Ronit
Published: March 2015

The Kaposi's sarcoma-associated herpesvirus (KSHV) open reading frame 16 (
orf16
) encodes a viral Bcl-2 (vBcl-2) protein which shares sequence and functional homology with the Bcl-2 family. Like its cellular homologs, vBcl-2 protects various cell types from apoptosis and can also negatively regulate autophagy. vBcl-2 is transcribed during lytic infection; however, its exact function has not been determined to date. By using bacterial artificial chromosome 16 (BAC16) clone carrying the full-length KSHV genome, we have generated recombinant KSHV mutants that fail to express vBcl-2 or express mCherry-tagged vBcl-2. We show that the vBcl-2 protein is expressed at relatively low levels during lytic induction and that a lack of vBcl-2 largely reduces the efficiency of KSHV reactivation in terms of lytic gene expression, viral DNA replication, and production of infectious particles. In contrast, the establishment of latency was not affected by the absence of vBcl-2. Our findings suggest an important role for vBcl-2 during initial phases of lytic reactivation and/or during subsequent viral propagation. Given the known functions of vBcl-2 in regulating apoptosis and autophagy, which involve its direct interaction with cellular proteins and thus require high levels of protein expression, it appears that vBcl-2 may have additional regulatory functions that do not depend on high levels of protein expression.

IMPORTANCE
The present study shows for the first time the expression of endogenous vBcl-2 protein in KSHV-infected cell lines and demonstrates the importance of vBcl-2 during the initial phases of lytic reactivation and/or during its subsequent propagation. It is suggested that vBcl-2 has additional regulatory functions beyond apoptosis and autophagy repression that do not depend on high levels of protein expression.
Identification of the Essential Role of Viral Bcl-2 for Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication
Authors: Liang Qiming , Chang Brian , Lee Patrick , Brulois Kevin F. , Ge Jianning , Shi Mude , Rodgers Mary A. , Feng Pinghui , Oh Byung-Ha , Liang Chengyu , Jung Jae U.
Published: March 2015

Kaposi's sarcoma-associated herpesvirus (KSHV) evades host defenses through tight suppression of autophagy by targeting each step of its signal transduction: by viral Bcl-2 (vBcl-2) in vesicle nucleation, by viral FLIP (vFLIP) in vesicle elongation, and by K7 in vesicle maturation. By exploring the roles of KSHV autophagy-modulating genes, we found, surprisingly, that vBcl-2 is essential for KSHV lytic replication, whereas vFLIP and K7 are dispensable. Knocking out vBcl-2 from the KSHV genome resulted in decreased lytic gene expression at the mRNA and protein levels, a lower viral DNA copy number, and, consequently, a dramatic reduction in the amount of progeny infectious viruses, as also described in the accompanying article (
A. Gelgor, I. Kalt, S. Bergson, K. F. Brulois, J. U. Jung, and R. Sarid
, J Virol 89:5298–5307, 2015). More importantly, the antiapoptotic and antiautophagic functions of vBcl-2 were not required for KSHV lytic replication. Using a comprehensive mutagenesis analysis, we identified that glutamic acid 14 (E
14
) of vBcl-2 is critical for KSHV lytic replication. Mutating E
14
to alanine totally blocked KSHV lytic replication but showed little or no effect on the antiapoptotic and antiautophagic functions of vBcl-2. Our study indicates that vBcl-2 harbors at least three important and genetically separable functions to modulate both cellular signaling and the virus life cycle.

IMPORTANCE
The present study shows for the first time that vBcl-2 is essential for KSHV lytic replication. Removal of the vBcl-2 gene results in a lower level of KSHV lytic gene expression, impaired viral DNA replication, and consequently, a dramatic reduction in the level of progeny production. More importantly, the role of vBcl-2 in KSHV lytic replication is genetically separated from its antiapoptotic and antiautophagic functions, suggesting that the KSHV Bcl-2 carries a novel function in viral lytic replication.
Characterization of Two Novel Linear B-Cell Epitopes in the Capsid Protein of Avian Hepatitis E Virus (HEV) That Are Common to Avian, Swine, and Human HEVs
Authors: Wang Xinjie , Zhao Qin , Dang Lu , Sun Yani , Gao Jiming , Liu Baoyuan , Syed Shahid Faraz , Tao Hu , Zhang Gaiping , Luo Jianxun , Zhou En-Min
Published: March 2015

Antisera raised against the avian hepatitis E virus (HEV) capsid protein are cross-reactive with human and swine HEV capsid proteins. In this study, two monoclonal antibodies (MAbs) against the avian HEV capsid protein, namely, 3E8 and 1B5, were shown to cross-react with the swine HEV capsid protein. The motifs involved in binding both MAbs were identified and characterized using phage display biopanning, peptide synthesis, and truncated or mutated protein expression, along with indirect enzyme-linked immunosorbent assay (ELISA) and Western blotting. The results showed that the I/VPHD motif is a necessary core sequence and that P and H are two key amino acids for recognition by MAb 3E8. The VKLYM/TS motif is the minimal amino acid sequence necessary for recognition by MAb 1B5. Cross-reactivity between the two epitopes and antibodies against avian, swine, and human HEVs in sera showed that both epitopes are common to avian, swine, and human HEVs. In addition, amino acid sequence alignment of the capsid proteins revealed that the key motifs of both novel epitopes are the same in HEVs from different animal species, predicting that they may be common to HEV isolates from boars, rabbits, rats, ferrets, mongooses, deer, and camels as well. Protein modeling analysis showed that both epitopes are at least partially exposed on the surface of the HEV capsid protein. Protective capacity analysis demonstrated that the two epitopes are nonprotective against avian HEV infection in chickens. Collectively, these studies characterize two novel linear B-cell epitopes common to avian, swine, and human HEVs, which furthers the understanding of HEV capsid protein antigenic structure.

IMPORTANCE
More and more evidence indicates that the host range diversity of hepatitis E virus (HEV) is a global public health concern. A better understanding of the antigenic structure of the HEV capsid protein may improve disease diagnosis and prevention. In this study, binding site mapping and localization as well as the antigenic biology of two novel linear B-cell epitopes common to several different species of HEV were characterized. These findings partially reveal the antigenic structure of the HEV capsid protein and provide potential applications for the development of diagnostics and interventions for HEV infection.
BH3 Profiling Reveals Selectivity by Herpesviruses for Specific Bcl-2 Proteins To Mediate Survival of Latently Infected Cells
Authors: Cojohari Olesea , Burrer Christine M. , Peppenelli Megan A. , Abulwerdi Fardokht A. , Nikolovska-Coleska Zaneta , Chan Gary C.
Published: March 2015

Herpesviruses, including human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), and Kaposi’s sarcoma-associated herpesvirus, establish latency by modulating or mimicking antiapoptotic Bcl-2 proteins to promote survival of carrier cells. BH3 profiling, which assesses the contribution of Bcl-2 proteins towards cellular survival, was able to globally determine the level of dependence on individual cellular and viral Bcl-2 proteins within latently infected cells. Moreover, BH3 profiling predicted the sensitivity of infected cells to small-molecule inhibitors of Bcl-2 proteins.
Role of Hydrogen Sulfide in Paramyxovirus Infections
Authors: Li Hui , Ma Yinghong , Escaffre Oliver , Ivanciuc Teodora , Komaravelli Narayana , Kelley John P. , Coletta Ciro , Szabo Csaba , Rockx Barry , Garofalo Roberto P. , Casola Antonella
Published: March 2015

Hydrogen sulfide (H
2
S) is an endogenous gaseous mediator that has gained increasing recognition as an important player in modulating acute and chronic inflammatory diseases. However, its role in virus-induced lung inflammation is currently unknown. Respiratory syncytial virus (RSV) is a major cause of upper and lower respiratory tract infections in children for which no vaccine or effective treatment is available. Using the slow-releasing H
2
S donor GYY4137 and propargylglycin (PAG), an inhibitor of cystathionine-γ-lyase (CSE), a key enzyme that produces intracellular H
2
S, we found that RSV infection led to a reduced ability to generate and maintain intracellular H
2
S levels in airway epithelial cells (AECs). Inhibition of CSE with PAG resulted in increased viral replication and chemokine secretion. On the other hand, treatment of AECs with the H
2
S donor GYY4137 reduced proinflammatory mediator production and significantly reduced viral replication, even when administered several hours after viral absorption. GYY4137 also significantly reduced replication and inflammatory chemokine production induced by human metapneumovirus (hMPV) and Nipah virus (NiV), suggesting a broad inhibitory effect of H
2
S on paramyxovirus infections. GYY4137 treatment had no effect on RSV genome replication or viral mRNA and protein synthesis, but it inhibited syncytium formation and virus assembly/release. GYY4137 inhibition of proinflammatory gene expression occurred by modulation of the activation of the key transcription factors nuclear factor κB (NF-κB) and interferon regulatory factor 3 (IRF-3) at a step subsequent to their nuclear translocation. H
2
S antiviral and immunoregulatory properties could represent a novel treatment strategy for paramyxovirus infections.

IMPORTANCE
RSV is a global health concern, causing significant morbidity and economic losses as well as mortality in developing countries. After decades of intensive research, no vaccine or effective treatment, with the exception of immunoprophylaxis, is available for this infection as well as for other important respiratory mucosal viruses. This study identifies hydrogen sulfide as a novel cellular mediator that can modulate viral replication and proinflammatory gene expression, both important determinants of lung injury in respiratory viral infections, with potential for rapid translation of such findings into novel therapeutic approaches for viral bronchiolitis and pneumonia.
Characterization of the Influence of Semen-Derived Enhancer of Virus Infection on the Interaction of HIV-1 with Female Reproductive Tract Tissues
Authors: Allen Shannon A. , Carias Ann M. , Anderson Meegan R. , Okocha Eneniziaogochukwu A. , Benning Lorie , McRaven Michael D. , Kelley Z L. , Lurain John , Veazey Ronald S. , Hope Thomas J.
Published: March 2015

The majority of human immunodeficiency virus type 1 (HIV-1) transmission events occur in women when semen harboring infectious virus is deposited onto the mucosal barriers of the vaginal, ectocervical, and endocervical epithelia. Seminal factors such as semen-derived enhancer of virus infection (SEVI) fibrils were previously shown to greatly enhance the infectivity of HIV-1 in cell culture systems. However, when SEVI is intravaginally applied to living animals, there is no effect on vaginal transmission. To define how SEVI might function in the context of sexual transmission, we applied HIV-1 and SEVI to intact human and rhesus macaque reproductive tract tissues to determine how it influences virus interactions with these barriers. We show that SEVI binds HIV-1 and sequesters most virions to the luminal surface of the stratified squamous epithelium, significantly reducing the number of virions that penetrated the tissue. In the simple columnar epithelium, SEVI was no longer fibrillar in structure and was detached from virions but allowed significantly deeper epithelial virus penetration. These observations reveal that the action of SEVI in intact tissues is very different in the anatomical context of sexual transmission and begin to explain the lack of stimulation of infection observed in the highly relevant mucosal transmission model.

IMPORTANCE
The most common mode of HIV-1 transmission in women occurs via genital exposure to the semen of HIV-infected men. A productive infection requires the virus to penetrate female reproductive tract epithelial barriers to infect underlying target cells. Certain factors identified within semen, termed semen-derived enhancers of virus infection (SEVI), have been shown to significantly enhance HIV-1 infectivity in cell culture. However, when applied to the genital tracts of living female macaques, SEVI did not enhance virus transmission. Here we show that SEVI functions very differently in the context of intact mucosal tissues. SEVI decreases HIV-1 penetration of squamous epithelial barriers in humans and macaques. At the mucus-coated columnar epithelial barrier, the HIV-1/SEVI interaction is disrupted. These observations suggest that SEVI may not play a significant stimulatory role in the efficiency of male-to-female sexual transmission of HIV.
Efficiently Editing the Vaccinia Virus Genome by Using the CRISPR-Cas9 System
Authors: Yuan Ming , Zhang Wensheng , Wang Jun , Al Yaghchi Chadwan , Ahmed Jahangir , Chard Louisa , Lemoine Nick R. , Wang Yaohe
Published: March 2015

Vaccinia virus (VACV) continues to be used in immunotherapy for the prevention of infectious diseases and treatment of cancer since its use for the eradication of smallpox. However, the current method of editing the VACV genome is not efficient. Here, we demonstrate that the CRISPR-Cas9 system can be used to edit the VACV genome rapidly and efficiently. Additionally, a set of 8,964 computationally designed unique guide RNAs (gRNAs) targeting all VACV genes will be valuable for the study of VACV gene functions.
Viral Sensing of the Subcellular Environment Regulates the Assembly of New Viral Replicase Complexes during the Course of Infection
Authors: Nagy Peter D.
Published: March 2015

Replication of plus-stranded RNA [(+)RNA] viruses depends on the availability of coopted host proteins and lipids. But, how could viruses sense the accessibility of cellular resources? An emerging concept based on tombusviruses, small plant viruses, is that viruses might regulate viral replication at several steps depending on what cellular factors are available at a given time point. I discuss the role of phospholipids, sterols, and cellular WW domain proteins and eukaryotic elongation factor 1A (eEF1A) in control of activation of the viral RNA-dependent RNA polymerase (RdRp) and regulation of the assembly of viral replicase complexes (VRCs). These regulatory mechanisms might explain how tombusviruses could adjust the efficiency of RNA replication and new VRC assembly to the limiting resources of the host cells during infections.
Alterations in Hemagglutinin Receptor-Binding Specificity Accompany the Emergence of Highly Pathogenic Avian Influenza Viruses
Authors: Heider Alla , Mochalova Larisa , Harder Timm , Tuzikov Alexander , Bovin Nicolai , Wolff Thorsten , Matrosovich Mikhail , Schweiger Brunhilde
Published: March 2015

Highly pathogenic avian influenza viruses (HPAIVs) of hemagglutinin H5 and H7 subtypes emerge after introduction of low-pathogenic avian influenza viruses (LPAIVs) from wild birds into poultry flocks, followed by subsequent circulation and evolution. The acquisition of multiple basic amino acids at the endoproteolytical cleavage site of the hemagglutinin (HA) is a molecular indicator for high pathogenicity, at least for infections of gallinaceous poultry. Apart from the well-studied significance of the multibasic HA cleavage site, there is only limited knowledge on other alterations in the HA and neuraminidase (NA) molecules associated with changes in tropism during the emergence of HPAIVs from LPAIVs. We hypothesized that changes in tropism may require alterations of the sialyloligosaccharide specificities of HA and NA. To test this hypothesis, we compared a number of LPAIVs and HPAIVs for their HA-mediated binding and NA-mediated desialylation of a set of synthetic receptor analogs, namely, α2-3-sialylated oligosaccharides. NA substrate specificity correlated with structural groups of NAs and did not correlate with pathogenic potential of the virus. In contrast, all HPAIVs differed from LPAIVs by a higher HA receptor-binding affinity toward the trisaccharides Neu5Acα2-3Galβ1-4GlcNAcβ (3′SLN) and Neu5Acα2-3Galβ1-3GlcNAcβ (SiaLe
c
) and by the ability to discriminate between the nonfucosylated and fucosylated sialyloligosaccharides 3′SLN and Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ (SiaLe
x
), respectively. These results suggest that alteration of the receptor-binding specificity accompanies emergence of the HPAIVs from their low-pathogenic precursors.

IMPORTANCE
Here, we have found for the first time correlations of receptor-binding properties of the HA with a highly pathogenic phenotype of poultry viruses. Our study suggests that enhanced receptor-binding affinity of HPAIVs for a typical “poultry-like” receptor, 3′SLN, is provided by substitutions in the receptor-binding site of HA which appeared in HA of LPAIVs in the course of transmission of LPAIVs from wild waterfowl into poultry flocks, with subsequent adaptation in poultry. The identification of LPAIVs with receptor characteristics of HPAIVs argues that the sialic acid-binding specificity of the HA may be used as a novel phenotypic marker of HPAIVs.
Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus
Authors: Zhu Henan , Hughes Joseph , Murcia Pablo R.
Published: March 2015

Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼700 million.

IMPORTANCE
Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating the mechanisms underpinning viral emergence. An avian-origin canine influenza virus (CIV) has recently emerged in dogs and is spreading in Asia. We reconstructed the evolutionary history of CIV and show that it originated from both Eurasian and North American avian lineages. We also identified the mutations that might have been responsible for the cross-species jump. Finally, we provide evidence of multiple reassortment events between CIV and other influenza viruses (including an H5N1 avian virus). This is a cause for concern, as there is a large global dog population to which humans are highly exposed.
Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env
Authors: Georgiev Ivelin S. , Joyce M. Gordon , Yang Yongping , Sastry Mallika , Zhang Baoshan , Baxa Ulrich , Chen Rita E. , Druz Aliaksandr , Lees Christopher R. , Narpala Sandeep , Schön Arne , Van Galen Joseph , Chuang Gwo-Yu , Gorman Jason , Harned Adam , Pancera Marie , Stewart-Jones Guillaume B. E. , Cheng Cheng , Freire Ernesto , McDermott Adrian B. , Mascola John R. , Kwong Peter D.
Published: March 2015

Similar to other type I fusion machines, the HIV-1 envelope glycoprotein (Env) requires proteolytic activation; specifically, cleavage of a gp160 precursor into gp120 and gp41 subunits creates an N-terminal gp41 fusion peptide and permits folding from an immature uncleaved state to a mature closed state. While the atomic-level consequences of cleavage for HIV-1 Env are still being determined, the uncleaved state is antigenically distinct from the mature closed state, and cleavage has been reported to be essential for mimicry of the mature viral spike by soluble versions of Env. Here we report the redesign of a current state-of-the-art soluble Env mimic, BG505.SOSIP, to make it cleavage independent. Specifically, we replaced the furin cleavage site between gp120 and gp41 with Gly-Ser linkers of various lengths. The resultant linked gp120-gp41 constructs, termed single-chain gp140 (sc-gp140), exhibited different levels of structural and antigenic mimicry of the parent cleaved BG505.SOSIP. When constructs were subjected to negative selection to remove subspecies recognized by poorly neutralizing antibodies, trimers of high antigenic mimicry of BG505.SOSIP could be obtained; negative-stain electron microscopy indicated these to resemble the mature closed state. Higher proportions of BG505.SOSIP-trimer mimicry were observed in sc-gp140s with linkers of 6 or more residues, with a linker length of 15 residues exhibiting especially promising traits. Overall, flexible linkages between gp120 and gp41 in BG505.SOSIP can thus substitute for cleavage, and sc-gp140s that closely mimicked the vaccine-preferred mature closed state of Env could be obtained.

IMPORTANCE
The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41, to achieve structural and antigenic mimicry of mature Env spikes on virions. Here we show that replacement of the cleavage site between gp120 and gp41 in a lead soluble gp140 construct, BG505.SOSIP, with flexible linkers can result in molecules that do not require cleavage to fold efficiently into the mature closed state. Our results provide insights into the impact of cleavage on HIV-1 Env folding. In some contexts such as genetic immunization, optimized cleavage-independent soluble gp140 constructs may have utility over the parental BG505.SOSIP, as they would not require furin cleavage to achieve mimicry of mature Env spikes on virions.
Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans
Authors: Lee Alexandra J. , Das Suman R. , Wang Wei , Fitzgerald Theresa , Pickett Brett E. , Aevermann Brian D. , Topham David J. , Falsey Ann R. , Scheuermann Richard H.
Published: March 2015

Although a large number of immune epitopes have been identified in the influenza A virus (IAV) hemagglutinin (HA) protein using various experimental systems, it is unclear which are involved in protective immunity to natural infection in humans. We developed a data mining approach analyzing natural H1N1 human isolates to identify HA protein regions that may be targeted by the human immune system and can predict the evolution of IAV. We identified 16 amino acid sites experiencing diversifying selection during the evolution of prepandemic seasonal H1N1 strains and found that 11 sites were located in experimentally determined B-cell/antibody (Ab) epitopes, including three distinct neutralizing Caton epitopes: Sa, Sb, and Ca2 [A. J. Caton, G. G. Brownlee, J. W. Yewdell, and W. Gerhard, Cell 31:417–427, 1982,
http://dx.doi.org/10.1016/0092-8674(82)90135-0
]. We predicted that these diversified epitope regions would be the targets of mutation as the 2009 H1N1 pandemic (pH1N1) lineage evolves in response to the development of population-level protective immunity in humans. Using a chi-squared goodness-of-fit test, we identified 10 amino acid sites that significantly differed between the pH1N1 isolates and isolates from the recent 2012-2013 and 2013-2014 influenza seasons. Three of these sites were located in the same diversified B-cell/Ab epitope regions as identified in the analysis of prepandemic sequences, including Sa and Sb. As predicted, hemagglutination inhibition (HI) assays using human sera from subjects vaccinated with the initial pH1N1 isolate demonstrated reduced reactivity against 2013-2014 isolates. Taken together, these results suggest that diversifying selection analysis can identify key immune epitopes responsible for protective immunity to influenza virus in humans and thereby predict virus evolution.

IMPORTANCE
The WHO estimates that approximately 5 to 10% of adults and 20 to 30% of children in the world are infected by influenza virus each year. While an adaptive immune response helps eliminate the virus following acute infection, the virus rapidly evolves to evade the established protective memory immune response, thus allowing for the regular seasonal cycles of influenza virus infection. The analytical approach described here, which combines an analysis of diversifying selection with an integration of immune epitope data, has allowed us to identify antigenic regions that contribute to protective immunity and are therefore the key targets of immune evasion by the virus. This information can be used to determine when sequence variations in seasonal influenza virus strains have affected regions responsible for protective immunity in order to decide when new vaccine formulations are warranted.
Profiling of Virus-Encoded MicroRNAs in Epstein-Barr Virus-Associated Gastric Carcinoma and Their Roles in Gastric Carcinogenesis
Authors: Shinozaki-Ushiku Aya , Kunita Akiko , Isogai Maya , Hibiya Takashi , Ushiku Tetsuo , Takada Kenzo , Fukayama Masashi
Published: March 2015

Epstein-Barr virus (EBV) is one of the major oncogenic viruses and is found in nearly 10% of gastric carcinomas. EBV is known to encode its own microRNAs (miRNAs); however, their roles have not been fully investigated. The present report is the largest series to comprehensively profile the expression of 44 known EBV miRNAs in tissue samples from patients with EBV-associated gastric carcinoma. Several miRNAs were highly expressed in EBV-associated gastric carcinoma, and
in silico
analysis revealed that the target genes of these EBV miRNAs had functions associated with cancer-related pathways, especially the regulation of apoptosis. Apoptosis was reduced in EBV-associated gastric carcinoma tissue samples, and gastric carcinoma cell lines infected with EBV exhibited downregulation of the proapoptotic protein Bid (the BH3-interacting domain death agonist), a member of the Bcl-2 family. The luciferase activity of the reporter vector containing the 3′ untranslated region of BID was inhibited by an ebv-miR-BART4-5p mimic in gastric cancer cell lines. Transfection of an ebv-miR-BART4-5p mimic reduced Bid expression in EBV-negative cell lines, leading to reduced apoptosis under serum deprivation. The inhibition of ebv-miR-BART4-5p expression was associated with partial recovery of Bid levels in EBV-positive cell lines. The results demonstrated the antiapoptotic role of EBV miRNA via regulation of Bid expression in EBV-associated gastric carcinoma. These findings provide novel insights in the roles of EBV miRNAs in gastric carcinogenesis, which would be a potential therapeutic target.

IMPORTANCE
This report is the largest series to comprehensively profile the expression of 44 known EBV miRNAs in clinical samples from EBV-associated gastric carcinoma patients. Of the EBV miRNAs, ebv-miR-BART4-5p plays an important role in gastric carcinogenesis via regulation of apoptosis.
Major ischaemic stroke caused by an air embolism from a ruptured giant pulmonary bulla
Authors: Gudmundsdottir Johanna F , Geirsson Arnar , Hannesson Petur , Gudbjartsson Tomas
Published: March 2015

We report an extremely rare complication of a major ischaemic cerebral event caused by an air embolism due to spontaneous rupture of a giant pulmonary bulla that occurred during an airline flight. Shortly after take-off, the patient experienced sudden right-sided hemiplegia and dyspnoea. Following an emergency landing in Reykjavik, a CT scan of the brain showed minute air bubbles consistent with air emboli within the left-sided intracerebral arteries, and MRI showed signs of acute ischaemic cerebral infarction in the left hemisphere. The patient later underwent a pulmonary lobectomy and survived this life-threatening complication with relatively mild neurological sequelae.
Neuropsychiatric systemic lupus erythematosus: a diagnostic challenge
Authors: Sommerlad Andrew , Duncan John , Lunn Michael P T , Foong Jacqueline
Published: March 2015

A 58-year-old woman presented to neuropsychiatric services with increased frequency of confusional episodes and intermittent psychotic symptoms. She had a 19-year history of atypical epileptic seizures and cognitive decline. Detailed review of history and clinical investigations revealed that she had accumulated sufficient features to meet diagnostic criteria for systemic lupus erythematosus (SLE). She had previously had lymphopenia and a malar rash; she had positive antinuclear, anti-Ro (anti-Sjögren's-syndrome-related antigen A) and anti-SM (anti-Smith Antibody) antibodies, and elevated erythrocyte sedimentation rate. The seizures, cognitive impairment and psychosis were attributable to neuropsychiatric SLE. Treatment with immune-modulating therapy, cyclophosphamide, resulted in significant improvement in subjective and objective clinical presentation. Neuropsychiatric SLE should be considered a potential differential diagnosis for patients presenting with seizures, psychotic symptoms or cognitive decline. A detailed clinical evaluation with review of the medical history and appropriate laboratory analyses allows this diagnosis to be made, and appropriate treatment to be initiated.
Implantable collamer lens in a case of corneal scar with anisometropic amblyopia in an adult: an expanded indication
Authors: Prakash Gaurav , Avadhani Kavitha , Kalliath Jay , Srivastava Dhruv
Published: March 2015

A 35-year-old man, a unilateral high myope with corneal scarring, presented for evaluation. He had a stromal scar that started temporally, traversed along the pupillary zone partially and extended across the horizontal diameter of the cornea. The Descemet's membrane appeared intact even though the scar was extending into deep stroma towards the nasal end, as seen in the optical coherence tomography image. The patient had an uncorrected distance visual acuity (UDVA) of 4/60 OD, which improved with a refraction of −9.0 DS/−1.50 DC at 15 to 6/18p and 6/6p OS. He underwent an uneventful toric implantable collamer lens (ICL) implantation of −15.0 D/−2.0 D at 102 after preoperative yttrium–aluminium–garnet (YAG) laser iridotomy in the right eye. The postoperative UDVA and corrected distance visual acuity for the right eye were 6/12 and 6/9p (with a refraction of +0.50 D/−0.50 D at 85), respectively. The corneal scar and topography were stable. This case reports an expanded indication for toric ICL in cases with corneal scar/opacity but good spectacle corrected visual acuity.
Work and non-work stressors, psychological distress and obesity: evidence from a 14-year study on Canadian workers
Authors: Marchand Alain , Beauregard Nancy , Blanc Marie-Eve
Published: March 2015

Objective

This study aimed to evaluate the contribution of work, non-work and individual factors to obesity with regard to gender-related differences, and to clarify the mediating role that psychological distress plays in these dynamics in Canada from 1994 to 2008 using the Canadian National Population Health Survey (NPHS).

Design

Longitudinal.

Settings

The NPHS is a randomised longitudinal cohort study with biennial interviews of the Canadian adult population from 18 to 64.

Participants

5925 non-obese workers in cycle 1 (49% were women).

Measurements

Obesity was measured using the body mass index (BMI), with a threshold of BMI >30 kg/m2. BMI was corrected in accordance with the recommendations of Connor Gorberet alto adjust for gender bias in responses.

Results

Of the work characteristics evaluated, only decision authority was associated with obesity for women but not for men. Living as a couple, child-related strains, psychotropic drug use, hypertension, being physically inactive and low psychological distress were obesity risk factors but were not moderated by gender. Overall, psychological distress did not mediate the associations that work factors have on obesity.

Conclusions

Our study suggests that men and women differ little in the extent to which work, non-work and individual factors predict obesity. However, for women, the level of decision authority is associated with a lower obesity risk. In addition, psychological distress did not mediate the contribution of work factors and actually seems, contrary to expectations, to decrease the obesity risk when work, non-work and individual factors are taken into account.
Diagnosis of Horner's syndrome in dogs and cats
Authors: Penderis Jacques
Published: March 2015

Horner's syndrome is a common condition in veterinary patients, particularly in dogs and cats, presenting with the typical features of miosis, enophthalmos, protrusion of the third eyelid and ptosis. It results from lesions affecting the sympathetic supply to the head and orbit. This article discusses what causes Horner's syndrome and how to diagnose the condition.
Always tell the truth?
Authors: Rees Gwen
Published: March 2015

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved.

In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Always tell the truth?’, was submitted by Richard Brown and is discussed by Gwen Rees. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘Emergency exsanguination of working equids’, which was published in the February issue of In Practice, appears on page 151.

The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
Five steps to a successful consultation
Authors: Faulkner Brian
Published: March 2015

Every veterinary practice must consistently deliver on four outcomes – clinical resolution, client satisfaction, financial resolution and team harmony and happiness – in order to be effective and sustainable, says Brian Faulkner. Here he describes how his Colourful Consultation model can facilitate these four outcomes in the consulting room.
Preliminary test of the LFA rapid evaluation of activity in lupus (LFA-REAL): an efficient outcome measure correlates with validated instruments
Authors: Askanase Anca , Li Xiaoqing , Pong Avery , Shum Katrina , Kamp Stan , Carthen Fredonna , Aberle Teresa , Hanrahan Leslie , Daly Paola , Giles Jon , Merrill Joan T
Published: March 2015

Objective

Current disease activity measures for systemic lupus erythematosus (SLE) are difficult to score or interpret and problematic for use in clinical practice. Lupus Foundation of America (LFA)-Rapid Evaluation of Activity in Lupus (REAL) is a pilot application composed of anchored visual analogue scores (0–100 mm each) for each organ affected by lupus. This study evaluated the use of LFA-REAL in capturing SLE disease activity.

Methods

In a preliminary test of LFA-REAL, this simplified, organ-based system was compared with the most widely used outcome measures in clinical trials, the British Isles Lupus Assessment Group 2004 Index (BILAG), the SLE Disease Activity Index (SLEDAI) and the Safety of Estrogens in Lupus Erythematosus National Assessment (SELENA) SLEDAI Physician's Global Assessment (SS-PGA). The level of agreement was analysed using Spearman rank correlations.

Results

91 patients with SLE with mild to severe disease activity were evaluated, their median SLEDAI score was 4.0 (range 0–28) and BILAG score 8.0 (0–32). The median SS-PGA was 38 mm (4–92) versus the total REAL 50 mm (0–268), which expands in range by additive organ scores. Thirty-three patients had moderate to severe disease activity (≥1.5 on SS-PGA landmarks). The median SS-PGA score of this group was 66 mm (50–92) versus median REAL score of 100 mm (59–268), confirming ability to detect a wider distribution of scores at higher disease activity. Total REAL correlated with SLEDAI, BILAG and SS-PGA (correlation coefficient=0.816, 0.933 and 0.903, respectively; p<0.001 for all). Individual LFA-REAL organ scores for musculoskeletal and mucocutaneous also correlated with corresponding BILAG domain scores (correlation coefficient=0.925 and 0.934, p<0.001).

Conclusions

In this preliminary exercise, there were strong correlations between LFA-REAL and validated lupus disease activity indices. Further development may be valuable for consistent scoring in clinical trials, grading optimal assessment of change in disease activity and reliable monitoring of patients in practice.
Reading Digital Video Clocks
Authors: Yu Xinguo , Ding Wan , Zeng Zhizhong , Leong Hon Wai
Published: March 2015

This paper presents an algorithm for reading digital video clocks reliably and quickly. Reading digital clocks from videos is difficult due to the challenges such as color variety, font diversity, noise, and low resolution. The proposed algorithm overcomes these challenges by using the novel methods derived from the domain knowledge. This algorithm first localizes the digits of a digital video clock and then recognizes the digits representing the time of digital video clock. It is a robust three-step algorithm. The first step is an efficient procedure that directly identifies the region of the second digit at a very low computational cost, which replaces the traditional tedious image processing procedure of identifying the second digit region. The success of the first step mainly leverages on the novel second-pixel periodicity method. Using the acquired second digit region as input, the second step is a clock digit localization procedure. It first acquires the colors of the digits of the digital video clock and performs the color conversion. Then it localizes the remaining clock digits. Finally, the last step is a clock digit recognition procedure. It first employs an enhanced digit-sequence recognition method to robustly recognize the digits on the second; it then adopts a deep learning procedure to recognize the remaining digits. The proposed algorithm is tested on a prepared benchmark of 1000 videos that is publicly available and the experimental results show that it can read digital video clocks with a 100% accuracy at a low computational cost.
Coclass of ${\rm Gal}({\mathbb K}_2^{(2)}/{\mathbb K})$ for some fields ${\mathbb K} = {\mathbb Q}(\sqrt{p_1p_2q}, \sqrt{-1})$ with 2-class groups of types (2, 2, 2)
Authors: Azizi Abdelmalek , Zekhnini Abdelkader , Taous Mohammed
Published: March 2015

Let p1 ≡ p2 ≡ -q ≡ 1 ( mod 4) be primes such that [Formula: see text] and [Formula: see text]. Put [Formula: see text] and d = p1p2q, then the bicyclic biquadratic field [Formula: see text] has an elementary Abelian 2-class group of rank 3. In this paper we determine the nilpotency class, the coclass, the generators and the structure of the non-Abelian Galois group [Formula: see text] of the second Hilbert 2-class field [Formula: see text] of 𝕂, we study the 2-class field tower of 𝕂, and we study the capitulation problem of the 2-classes of 𝕂 in its fourteen abelian unramified extensions of relative degrees two and four.
Urban land use and geohazards in Itanagar, Arunachal Pradesh, India: the need for geotechnical intervention and geoethical policies in urban disaster resilience programmes in a changing climate
Authors: Acharjee Swapna
Published: March 2015

The capital city, Itanagar in Arunachal Pradesh, India, is exposed to multiple geohazards as it is located both in a region which experiences extreme physical phenomena due to changing climate, and in the tectonically active Eastern Himalaya. The geohazards in Itanagar include landslides, flash floods, soil erosion and earthquakes. Due to rapid and haphazard growth in urban land use, the city’ residents have been increasingly exposed to these geohazards over the past two decades. The high decadal growth rate of just over 111% shown in the 1991–2001 censuses has introduced many challenges with respect to the capital city's development planning, and geoscientists are warning of land suitability and stability in terms of rock types, soil, slope, geomorphology and groundwater conditions in their scientific communications. The present condition of the city has raised issues of immediate concern related to effective hazard management. The vulnerability of existing urban land use to landslides, flash floods and soil erosion is increasing steadily, and Itanagar needs to become a disaster-resilient hill city. Experts agree there is therefore a need for appropriate engineering geology intervention as well as the development of geoethical policies in sustainable development planning of the city, which could be achieved by using a strategic urban plan through community participation and awareness generation under the Itanagar Urban Disaster Risk Reduction (UDRR) programme.
Interleukin-22 in kidney injury and regeneration
Authors: Weidenbusch Marc , Rodler Severin , Anders Hans-Joachim
Published: March 2015

Interleukins have become well-known regulators of innate and adaptive immunity-related tissue inflammation. Recently, IL-22 has gained a lot of interest for its unique functions in maintaining and regaining epithelial integrity. IL-22 is exclusively secreted by different immune cell subsets, while IL-22 receptors are mainly expressed by epithelial cells. As the kidney is largely an epithelial organ, the functional role of IL-22 in the kidney deserves to be explored in detail. Here, we briefly summarize the key features of IL-22 biology and review the available data on its expression and functional roles in kidney injury and kidney regeneration. Furthermore, we provide suggestions on how to explore this evolving field in the future.
Microcircuitry of agranular frontal cortex: contrasting laminar connectivity between occipital and frontal areas
Authors: Ninomiya Taihei , Dougherty Kacie , Godlove David C. , Schall Jeffrey D. , Maier Alexander
Published: March 2015

Neocortex is striking in its laminar architecture. Tracer studies have uncovered anatomical connectivity among laminae, but the functional connectivity between laminar compartments is still largely unknown. Such functional connectivity can be discerned through spontaneous neural correlations during rest. Previous work demonstrated a robust pattern of mesoscopic resting-state connectivity in macaque primary visual cortex (V1) through interlaminar cross-frequency coupling. Here we investigated whether this pattern generalizes to other cortical areas by comparing resting-state laminar connectivity between V1 and the supplementary eye field (SEF), a frontal area lacking a granular layer 4 (L4). Local field potentials (LFPs) were recorded with linear microelectrode arrays from all laminae of granular V1 and agranular SEF while monkeys rested in darkness. We found substantial differences in the relationship between the amplitude of gamma-band (>30 Hz) LFP and the phase of alpha-band (7–14 Hz) LFP between these areas. In V1, gamma amplitudes in L2/3 and L5 were coupled with alpha-band LFP phase in L5, as previously described. In contrast, in SEF phase-amplitude coupling was prominent within L3 and much weaker across layers. These results suggest that laminar interactions in agranular SEF are unlike those in granular V1. Thus the intrinsic functional connectivity of the cortical microcircuit does not seem to generalize across cortical areas.