bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Enrichment of Cryptosporidium DNA and Verification of DNA Purity for Whole-Genome Sequencing
Authors: Guo Yaqiong , Li Na , Lysén Colleen , Frace Michael , Tang Kevin , Sammons Scott , Roellig Dawn M. , Feng Yaoyu , Xiao Lihua
Published: December 2014

Whole-genome sequencing of
Cryptosporidium
spp. is hampered by difficulties in obtaining sufficient, highly pure genomic DNA from clinical specimens. In this study, we developed procedures for the isolation and enrichment of
Cryptosporidium
genomic DNA from fecal specimens and verification of DNA purity for whole-genome sequencing. The isolation and enrichment of genomic DNA were achieved by a combination of three oocyst purification steps and whole-genome amplification (WGA) of DNA from purified oocysts. Quantitative PCR (qPCR) analysis of WGA products was used as an initial quality assessment of amplified genomic DNA. The purity of WGA products was assessed by Sanger sequencing of cloned products. Next-generation sequencing tools were used in final evaluations of genome coverage and of the extent of contamination. Altogether, 24 fecal specimens of
Cryptosporidium parvum
,
C. hominis
,
C. andersoni
,
C. ubiquitum
,
C. tyzzeri
, and
Cryptosporidium
chipmunk genotype I were processed with the procedures. As expected, WGA products with low (<16.0) threshold cycle (

C
T

) values yielded mostly
Cryptosporidium
sequences in Sanger sequencing. The cloning-sequencing analysis, however, showed significant contamination in 5 WGA products (proportion of positive colonies derived from
Cryptosporidium
genomic DNA, ≤25%). Following this strategy, 20 WGA products from six
Cryptosporidium
species or genotypes with low (mostly <14.0)

C
T

values were submitted to whole-genome sequencing, generating sequence data covering 94.5% to 99.7% of
Cryptosporidium
genomes, with mostly minor contamination from bacterial, fungal, and host DNA. These results suggest that the described strategy can be used effectively for the isolation and enrichment of
Cryptosporidium
DNA from fecal specimens for whole-genome sequencing.
Performance of the 47-Kilodalton Membrane Protein versus DNA Polymerase I Genes for Detection of Treponema pallidum by PCR in Ulcers
Authors: Gayet-Ageron Angèle , Laurent Frédéric , Schrenzel Jacques , Charton Béatrice , Jimenez-Getaz Gisela , Tangomo Manuela , Ferry Tristan , Sednaoui Patrice , Lautenschlager Stephan , Toutous-Trellu Laurence , Martinez de Tejada Begoña , Cavassini Matthias , Emonet Stéphane , Perneger Thomas , Salord Hélène
Published: December 2014

Treponema pallidum
PCR (
Tp
-PCR) is a direct diagnostic method for primary and secondary syphilis, but there is no recommendation regarding the best choice of target gene. In this study, we sequentially tested 272 specimens from patients with sexually transmitted ulcers using
Tp
-PCR targeting the
tpp47
and then
polA
genes. The two methods showed similar accuracies and an almost-perfect agreement.
Delayed Inflammatory and Cell Death Responses Are Associated with Reduced Pathogenicity in Lujo Virus-Infected Cynomolgus Macaques
Authors: Rasmussen Angela L. , Tchitchek Nicolas , Safronetz David , Carter Victoria S. , Williams Christopher M. , Haddock Elaine , Korth Marcus J. , Feldmann Heinz , Katze Michael G.
Published: December 2014

To identify host factors associated with arenavirus virulence, we used a cynomolgus macaque model to evaluate the pathogenesis of Lujo virus (LUJV), a recently emerged arenavirus that caused an outbreak of severe viral hemorrhagic fever in southern Africa. In contrast to human cases, LUJV caused mild, nonlethal illness in macaques. We then compared this to contrasting clinical outcomes during arenavirus infection, specifically to samples obtained from macaques infected with three highly pathogenic lines of Lassa virus (LASV), the causative agent of Lassa fever (LF). We assessed gene expression in peripheral blood mononuclear cells (PBMC) and determined genes that significantly changed expression relative to that in uninfected animals over the course of infection. We detected a 72-h delay in the induction of host responses to infection during LUJV infection compared to that of the animals infected with LASV. This included genes associated with inflammatory and antiviral responses and was particularly apparent among groups of genes promoting cell death. We also observed early differential expression of a subset of genes specific to LUJV infection that accounts for the delayed inflammatory response. Cell type enrichment analysis suggested that host response induction delay and an LUJV-specific profile are due to a different proportion of natural killer cells responding in LUJV infection than that in the LASV-infected animals. Together, these data indicate that delayed proinflammatory and proapoptotic host responses to arenavirus infection could ameliorate disease severity. This conclusion provides insight into the cellular and molecular mechanisms of arenaviral hemorrhagic fever and suggests potential strategies for therapeutic development.

IMPORTANCEOld World arenaviruses are significant human pathogens that often are associated with high mortality. However, mechanisms underlying disease severity and virulence in arenavirus hemorrhagic fever are largely unknown, particularly regarding host responses that contribute to pathogenicity. This study describes a comparison between Lujo and Lassa virus infection in cynomolgus macaques. Lujo virus-infected macaques developed only mild illness, while Lassa virus-infected macaques developed severe illness consistent with Lassa fever. We determined that mild disease is associated with a delay in host expression of genes linked to virulence, such as those causing inflammation and cell death, and with distinct cell types that may mediate this delay. This is the first study to associate the timing and directionality of gene expression with arenaviral pathogenicity and disease outcome and evokes new potential approaches for developing effective therapeutics for treating these deadly emerging pathogens.
Ataxia Telangiectasia Mutated Kinase Mediates NF-κB Serine 276 Phosphorylation and Interferon Expression via the IRF7-RIG-I Amplification Loop in Paramyxovirus Infection
Authors: Fang Ling , Choudhary Sanjeev , Tian Bing , Boldogh Istvan , Yang Chunying , Ivanciuc Teodora , Ma Yinghong , Garofalo Roberto P. , Brasier Allan R.
Published: December 2014

Respiratory syncytial virus (RSV) is a primary etiological agent of childhood lower respiratory tract disease. Molecular patterns induced by active infection trigger a coordinated retinoic acid-inducible gene I (RIG-I)-Toll-like receptor (TLR) signaling response to induce inflammatory cytokines and antiviral mucosal interferons. Recently, we discovered a nuclear oxidative stress-sensitive pathway mediated by the DNA damage response protein, ataxia telangiectasia mutated (ATM), in cytokine-induced NF-κB/RelA Ser 276 phosphorylation. Here we observe that ATM silencing results in enhanced single-strand RNA (ssRNA) replication of RSVand Sendai virus, due to decreased expression and secretion of type I and III interferons (IFNs), despite maintenance of IFN regulatory factor 3 (IRF3)-dependent IFN-stimulated genes (ISGs). In addition to enhanced oxidative stress, RSV replication enhances foci of phosphorylated histone 2AX variant (γH2AX), Ser 1981 phosphorylation of ATM, and IKKγ/NEMO-dependent ATM nuclear export, indicating activation of the DNA damage response. ATM-deficient cells show defective RSV-induced mitogen and stress-activated kinase 1 (MSK-1) Ser 376 phosphorylation and reduced RelA Ser 276 phosphorylation, whose formation is required for IRF7 expression. We observe that RelA inducibly binds the native IFN regulatory factor 7 (IRF7) promoter in an ATM-dependent manner, and IRF7 inducibly binds to the endogenous retinoic acid-inducible gene I (RIG-I) promoter. Ectopic IRF7 expression restores RIG-I expression and type I/III IFN expression in ATM-silenced cells. We conclude that paramyxoviruses trigger the DNA damage response, a pathway required for MSK1 activation of phospho Ser 276 RelA formation to trigger the IRF7-RIG-I amplification loop necessary for mucosal IFN production. These data provide the molecular pathogenesis for defects in the cellular innate immunity of patients with homozygous ATM mutations.

IMPORTANCE
RNA virus infections trigger cellular response pathways to limit spread to adjacent tissues. This “innate immune response” is mediated by germ line-encoded pattern recognition receptors that trigger activation of two, largely independent, intracellular NF-κB and IRF3 transcription factors. Downstream, expression of protective antiviral interferons is amplified by positive-feedback loops mediated by inducible interferon regulatory factors (IRFs) and retinoic acid inducible gene (RIG-I). Our results indicate that a nuclear oxidative stress- and DNA damage-sensing factor, ATM, is required to mediate a cross talk pathway between NF-κB and IRF7 through mediating phosphorylation of NF-κB. Our studies provide further information about the defects in cellular and innate immunity in patients with inherited ATM mutations.
The Stress Granule Protein G3BP1 Recruits Protein Kinase R To Promote Multiple Innate Immune Antiviral Responses
Authors: Reineke Lucas C. , Lloyd Richard E.
Published: December 2014

Stress granules (SGs) are cytoplasmic storage sites containing translationally silenced mRNPs that can be released to resume translation after stress subsides. We previously showed that poliovirus 3C proteinase cleaves the SG-nucleating protein G3BP1, blocking the ability of cells to form SGs late in infection. Many other viruses also target G3BP1 and inhibit SG formation, but the reasons why these functions evolved are unclear. Previously, we also showed a link between G3BP1-induced SGs and protein kinase R (PKR)-mediated translational control, but the mechanism of PKR interplay with SG and the antiviral consequences are unknown. Here, we show that G3BP1 exhibits antiviral activity against several enteroviruses, whereas truncated G3BP1 that cannot form SGs does not. G3BP1-induced SGs are linked to activation of innate immune transcriptional responses through NF-κB and JNK. The G3BP1-induced SGs also recruit PKR and other antiviral proteins. We show that the PXXP domain within G3BP1 is essential for the recruitment of PKR to SGs, for eIF2α phosphorylation driven by PKR, and for nucleating SGs of normal composition. We also show that deletion of the PXXP domain in G3BP1 compromises its antiviral activity. These findings tie PKR activation to its recruitment to SGs by G3BP1 and indicate that G3BP1 promotes innate immune responses at both the transcriptional and translational levels and integrates cellular stress responses and innate immunity.

IMPORTANCE
Stress granules appear during virus infection, and their importance is not well understood. Previously, it was assumed that they were nonfunctional artifacts associated with cellular stress. PKR is a well-known antiviral protein; however, its regulation in cells is not well understood. Our work links cellular stress granules with activation of PKR and other innate immune pathways through the activity of G3BP1, a critical stress granule component. The ability of stress granules and G3BP1 to activate PKR and other innate immune transcriptional responses indicates that G3BP1 is an antiviral protein. This work helps to refine a longstanding paradigm indicating stress granules are inert structures and explains why G3BP1 is subverted by many viruses to promote a productive infection.
Severe Acute Respiratory Syndrome-Associated Coronavirus Vaccines Formulated with Delta Inulin Adjuvants Provide Enhanced Protection while Ameliorating Lung Eosinophilic Immunopathology
Authors: Honda-Okubo Yoshikazu , Barnard Dale , Ong Chun Hao , Peng Bi-Hung , Tseng Chien-Te Kent , Petrovsky Nikolai
Published: December 2014

Although the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) epidemic was controlled by nonvaccine measures, coronaviruses remain a major threat to human health. The design of optimal coronavirus vaccines therefore remains a priority. Such vaccines present major challenges: coronavirus immunity often wanes rapidly, individuals needing to be protected include the elderly, and vaccines may exacerbate rather than prevent coronavirus lung immunopathology. To address these issues, we compared in a murine model a range of recombinant spike protein or inactivated whole-virus vaccine candidates alone or adjuvanted with either alum, CpG, or Advax, a new delta inulin-based polysaccharide adjuvant. While all vaccines protected against lethal infection, addition of adjuvant significantly increased serum neutralizing-antibody titers and reduced lung virus titers on day 3 postchallenge. Whereas unadjuvanted or alum-formulated vaccines were associated with significantly increased lung eosinophilic immunopathology on day 6 postchallenge, this was not seen in mice immunized with vaccines formulated with delta inulin adjuvant. Protection against eosinophilic immunopathology by vaccines containing delta inulin adjuvants correlated better with enhanced T-cell gamma interferon (IFN-γ) recall responses rather than reduced interleukin-4 (IL-4) responses, suggesting that immunopathology predominantly reflects an inadequate vaccine-induced Th1 response. This study highlights the critical importance for development of effective and safe coronavirus vaccines of selection of adjuvants based on the ability to induce durable IFN-γ responses.

IMPORTANCE
Coronaviruses such as SARS-CoV and Middle East respiratory syndrome-associated coronavirus (MERS-CoV) cause high case fatality rates and remain major human public health threats, creating a need for effective vaccines. While coronavirus antigens that induce protective neutralizing antibodies have been identified, coronavirus vaccines present a unique problem in that immunized individuals when infected by virus can develop lung eosinophilic pathology, a problem that is further exacerbated by the formulation of SARS-CoV vaccines with alum adjuvants. This study shows that formulation of SARS-CoV spike protein or inactivated whole-virus vaccines with novel delta inulin-based polysaccharide adjuvants enhances neutralizing-antibody titers and protection against clinical disease but at the same time also protects against development of lung eosinophilic immunopathology. It also shows that immunity achieved with delta inulin adjuvants is long-lived, thereby overcoming the natural tendency for rapidly waning coronavirus immunity. Thus, delta inulin adjuvants may offer a unique ability to develop safer and more effective coronavirus vaccines.
COMMD1/Murr1 Reinforces HIV-1 Latent Infection through IκB-α Stabilization
Authors: Taura Manabu , Kudo Eriko , Kariya Ryusho , Goto Hiroki , Matsuda Kouki , Hattori Shinichiro , Vaeteewoottacharn Kulthida , McDonald Fiona , Suico Mary Ann , Shuto Tsuyoshi , Kai Hirofumi , Okada Seiji
Published: December 2014

The transcription factor NF-κB is important for HIV-1 transcription initiation in primary HIV-1 infection and reactivation in latently HIV-1-infected cells. However, comparative analysis of the regulation and function of NF-κB in latently HIV-1-infected cells has not been done. Here we show that the expression of IκB-α, an endogenous inhibitor of NF-κB, is enhanced by latent HIV-1 infection via induction of the host-derived factor COMMD1/Murr1 in myeloid cells but not in lymphoid cells by using four sets of latently HIV-1-infected cells and the respective parental cells. IκB-α protein was stabilized by COMMD1, which attenuated NF-κB signaling during Toll-like receptor ligand and tumor necrosis factor alpha treatment and enhanced HIV-1 latency in latently HIV-1-infected cells. Activation of the phosphoinositol 3-kinase (PI3K)–JAK pathway is involved in COMMD1 induction in latently HIV-1-infected cells. Our findings indicate that COMMD1 induction is the NF-κB inhibition mechanism in latently HIV-1-infected cells that contributes to innate immune deficiency and reinforces HIV-1 latency. Thus, COMMD1 might be a double-edged sword that is beneficial in primary infection but not beneficial in latent infection when HIV-1 eradication is considered.

IMPORTANCE
HIV-1 latency is a major barrier to viral eradication in the era of combination antiretroviral therapy. In this study, we found that COMMD1/Murr1, previously identified as an HIV-1 restriction factor, inhibits the proteasomal degradation of IκB-α by increasing the interaction with IκB-α in latently HIV-1-infected myeloid cells. IκB-α protein was stabilized by COMMD1, which attenuated NF-κB signaling during the innate immune response and enhanced HIV-1 latency in latently HIV-1-infected cells. Activation of the PI3K-JAK pathway is involved in COMMD1 induction in latently HIV-1-infected cells. Thus, the host-derived factor COMMD1 is beneficial in suppressing primary infection but enhances latent infection, indicating that it may be a double-edged sword in HIV-1 eradication.
Nanobody Binding to a Conserved Epitope Promotes Norovirus Particle Disassembly
Authors: Koromyslova Anna D. , Hansman Grant S.
Published: December 2014

Human noroviruses are icosahedral single-stranded RNA viruses. The capsid protein is divided into shell (S) and protruding (P) domains, which are connected by a flexible hinge region. There are numerous genetically and antigenically distinct noroviruses, and the dominant strains evolve every other year. Vaccine and antiviral development is hampered by the difficulties in growing human norovirus in cell culture and the continually evolving strains. Here, we show the X-ray crystal structures of human norovirus P domains in complex with two different nanobodies. One nanobody, Nano-85, was broadly reactive, while the other, Nano-25, was strain specific. We showed that both nanobodies bound to the lower region on the P domain and had nanomolar affinities. The Nano-85 binding site mainly comprised highly conserved amino acids among the genetically distinct genogroup II noroviruses. Several of the conserved residues also were recognized by a broadly reactive monoclonal antibody, which suggested this region contained a dominant epitope. Superposition of the P domain nanobody complex structures into a cryoelectron microscopy particle structure revealed that both nanobodies bound at occluded sites on the particles. The flexible hinge region, which contained ∼10 to 12 amino acids, likely permitted a certain degree of P domain movement on the particles in order to accommodate the nanobodies. Interestingly, the Nano-85 binding interaction with intact particles caused the particles to disassemble
in vitro
. Altogether, these results suggested that the highly conserved Nano-85 binding epitope contained a trigger mechanism for particle disassembly. Principally, this epitope represents a potential site of norovirus vulnerability.

IMPORTANCE
We characterized two different nanobodies (Nano-85 and Nano-25) that bind to human noroviruses. Both nanobodies bound with high affinities to the lower region of the P domain, which was occluded on intact particles. Nano-25 was specific for GII.10, whereas Nano-85 bound several different GII genotypes, including GII.4, GII.10, and GII.12. We showed that Nano-85 was able to detect norovirus virions in clinical stool specimens using a sandwich enzyme-linked immunosorbent assay. Importantly, we found that Nano-85 binding to intact particles caused the particles to disassemble. We believe that with further testing, Nano-85 not only will work as a diagnostic reagent in norovirus detection systems but also could function as a broadly reactive GII norovirus antiviral.
Acanthamoeba polyphaga Mimivirus Prevents Amoebal Encystment-Mediating Serine Proteinase Expression and Circumvents Cell Encystment
Authors: Boratto Paulo , Albarnaz Jonas Dutra , Almeida Gabriel Magno de Freitas , Botelho Lucas , Fontes Alide Caroline Lima , Costa Adriana Oliveira , Santos Daniel de Assis , Bonjardim Cláudio Antônio , La Scola Bernard , Kroon Erna Geessien , Abrahão Jônatas Santos
Published: December 2014

Acanthamoeba
is a genus of free-living amoebas distributed worldwide. Few studies have explored the interactions between these protozoa and their infecting giant virus,
Acanthamoeba polyphaga
mimivirus (APMV). Here we show that, once the amoebal encystment is triggered, trophozoites become significantly resistant to APMV. Otherwise, upon infection, APMV is able to interfere with the expression of a serine proteinase related to amoebal encystment and the encystment can no longer be triggered.
Clustered MicroRNAs of the Epstein-Barr Virus Cooperatively Downregulate an Epithelial Cell-Specific Metastasis Suppressor
Authors: Kanda Teru , Miyata Mamiko , Kano Makoto , Kondo Satoru , Yoshizaki Tomokazu , Iizasa Hisashi
Published: December 2014

The Epstein-Barr virus (EBV) encodes its own microRNAs (miRNAs); however, their biological roles remain elusive. The commonly used EBV B95-8 strain lacks a 12-kb genomic region, known as BamHI A rightward transcripts (BART) locus, where a number of BART miRNAs are encoded. Here, bacterial artificial chromosome (BAC) technology was used to generate an EBV B95-8 strain in which the 12-kb region was fully restored at its native locus [BART(+) virus]. Epithelial cells were stably infected with either the parental B95-8 virus or the BART(+) virus, and BART miRNA expression was successfully reconstituted in the BART(+) virus-infected cells. Microarray analyses of cellular gene expression identified N-myc downstream regulated gene 1 (
NDRG1
) as a putative target of BART miRNAs. The NDRG1 protein was barely expressed in B cells, highly expressed in epithelial cells, including primary epithelial cells, and strongly downregulated in the BART(+) virus-infected epithelial cells of various origins. Although
in vitro
reporter assays identified BART22 as being responsible for the NDRG1 downregulation, EBV genetic analyses revealed that BART22 was not solely responsible; rather, the entire BART miRNA cluster 2 was responsible for the downregulation. Immunohistochemical analyses revealed that the expression level of the NDRG1 protein was downregulated significantly in EBV-positive nasopharyngeal carcinoma specimens. Considering that
NDRG1
encodes an epithelial differentiation marker and a suppressor of metastasis, these data implicate a causative relationship between BART miRNA expression and epithelial carcinogenesis
in vivo
.

IMPORTANCE
EBV-related epithelial cancers, such as nasopharyngeal carcinomas and EBV-positive gastric cancers, encompass more than 80% of EBV-related malignancies. Although it is known that they express high levels of virally encoded BART miRNAs, how these miRNAs contribute to EBV-mediated epithelial carcinogenesis remains unknown. Although a number of screenings have been performed to identify targets of viral miRNAs, many targets likely have not been identified, especially in case of epithelial cell infection. This is the first study to use EBV genetics to perform unbiased screens of cellular genes that are differentially expressed in viral miRNA-positive and -negative epithelial cells. The result indicates that multiple EBV-encoded miRNAs cooperatively downregulate NDRG1, an epithelial differentiation marker and suppressor of metastasis. The experimental system described in this study should be useful for further clarifying the mechanism of EBV-mediated epithelial carcinogenesis.
Modified Vaccinia Virus Ankara-Infected Dendritic Cells Present CD4
+
T-Cell Epitopes by Endogenous Major Histocompatibility Complex Class II Presentation Pathways
Authors: Thiele Frank , Tao Sha , Zhang Yi , Muschaweckh Andreas , Zollmann Tina , Protzer Ulrike , Abele Rubert , Drexler Ingo
Published: December 2014

CD4
+
T lymphocytes play a central role in the immune system and mediate their function after recognition of their respective antigens presented on major histocompatibility complex II (MHCII) molecules on antigen-presenting cells (APCs). Conventionally, phagocytosed antigens are loaded on MHCII for stimulation of CD4
+
T cells. Certain epitopes, however, can be processed directly from intracellular antigens and are presented on MHCII (endogenous MHCII presentation). Here we characterized the MHCII antigen presentation pathways that are possibly involved in the immune response upon vaccination with modified vaccinia virus Ankara (MVA), a promising live viral vaccine vector. We established CD4
+
T-cell lines specific for MVA-derived epitopes as tools for
in vitro
analysis of MHCII antigen processing and presentation in MVA-infected APCs. We provide evidence that infected APCs are able to directly transfer endogenous viral proteins into the MHCII pathway to efficiently activate CD4
+
T cells. By using knockout mice and chemical inhibitory compounds, we further elucidated the molecular basis, showing that among the various subcellular pathways investigated, proteasomes and autophagy are key players in the endogenous MHCII presentation during MVA infection. Interestingly, although proteasomal processing plays an important role, neither TAP nor LAMP-2 was found to be involved in the peptide transport. Defining the molecular mechanism of MHCII presentation during MVA infection provides a basis for improving MVA-based vaccination strategies by aiming for enhanced CD4
+
T-cell activation by directing antigens into the responsible pathways.

IMPORTANCE
This work contributes significantly to our understanding of the immunogenic properties of pathogens by deciphering antigen processing pathways contributing to efficient activation of antigen-specific CD4
+
T cells. We identified autophagosome formation, proteasomal activity, and lysosomal integrity as being crucial for endogenous CD4
+
T-cell activation. Since poxvirus vectors such as MVA are already used in clinical trials as recombinant vaccines, the data provide important information for the future design of optimized poxviral vaccines for the study of advanced immunotherapy options.
Impact of Bilateral St36 and Pc6 Electroacupuncture on the Depth of Sedation in General Anaesthesia
Authors: Chen Yiding , Zhang Hongwei , Tang Yumin , Shu Jingjun
Published: December 2014

Objective

To investigate the impact of electroacupuncture (EA) at bilateral acupuncture points ST36 and PC6 on the level of sedation in general anaesthesia.

Methods

40 patients undergoing abdominal surgery were randomly divided into two groups: EA combined with general anaesthesia (EA group, n=20) and general anaesthesia control group (n=20). The bilateral acupuncture points ST36 and PC6 were selected in both groups. Target-controlled infusion (TCI) of propofol was used for the induction and maintenance of general anaesthesia to reach an equilibrium state of Narcotrend Index (NT index). In the EA group, EA was performed with a Hans EA device. In the control group, general anaesthesia was performed without EA stimulation. In both groups, heart rate (HR), mean blood pressure (MAP) and NT index were recorded at corresponding time points up to 30 min after the end of acupuncture.

Results

The NT indices of the EA group showed a downward trend after EA stimulation (p=0.01). From 15 min after the start of EA stimulation the NT indices of the EA group were significantly lower than those of the control group (p<0.05). HR and MAP of the two groups showed no significant differences at any time points (p≥0.05).

Conclusions

EA stimulation at bilateral ST36 and PC6 significantly deepens the sedation level of general anaesthesia in patients with propofol TCI, has little impact on haemodynamics and provides significant delayed sedation effects.
The REFORM study protocol: a cohort randomised controlled trial of a multifaceted podiatry intervention for the prevention of falls in older people
Authors: Cockayne Sarah , Adamson Joy , Corbacho Martin Belen , Fairhurst Caroline , Hewitt Catherine , Hicks Kate , Hull Robin , Keenan Anne Maree , Lamb Sarah E , Loughrey Lorraine , McIntosh Caroline , Menz Hylton B , Redmond Anthony C , Rodgers Sara , Vernon Wesley , Watson Judith , Torgerson David
Published: December 2014

Introduction

Falls and fall-related injuries are a serious cause of morbidity and cost to society. Foot problems and inappropriate footwear may increase the risk of falls; therefore podiatric interventions may play a role in reducing falls. Two Cochrane systematic reviews identified only one study of a podiatry intervention aimed to reduce falls, which was undertaken in Australia. The REFORM trial aims to evaluate the clinical and cost-effectiveness of a multifaceted podiatry intervention in reducing falls in people aged 65 years and over in a UK and Irish setting.

Methods and analysis

This multicentre, cohort randomised controlled trial will recruit 2600 participants from routine podiatry clinics in the UK and Ireland to the REFORM cohort. In order to detect a 10% point reduction in falls from 50% to 40%, with 80% power 890 participants will be randomised to receive routine podiatry care and a falls prevention leaflet or routine podiatry care, a falls prevention leaflet and a multifaceted podiatry intervention. The primary outcome is rate of falls (falls/person/time) over 12 months assessed by patient self-report falls diary. Secondary self-report outcome measures include: the proportion of single and multiple fallers and time to first fall over a 12-month period; Short Falls Efficacy Scale—International; fear of falling in the past 4 weeks; Frenchay Activities Index; fracture rate; Geriatric Depression Scale; EuroQoL-five dimensional scale 3-L; health service utilisation at 6 and 12 months. A qualitative study will examine the acceptability of the package of care to participants and podiatrists.

Ethics and dissemination

The trial has received a favourable opinion from the East of England—Cambridge East Research Ethics Committee and Galway Research Ethics Committee. The trial results will be published in peer-reviewed journals and at conference presentations.

Trial registration number

Current Controlled Trials ISRCTN68240461assigned 01/07/2011.
Improving the recognition of post-operative acute kidney injury
Authors: Trotter Nicola , Doherty Cal , Tully Vicki , Davey Peter , Bell Samira
Published: December 2014

The National Institute for Health and Care Excellence (NICE) state that acute kidney injury (AKI) is seen in 13-18% of all people being admitted to hospital and that other patients will further go on to develop AKI during their time in hospital, with around 30-40% being in the operative setting. AKI has an estimated inpatient mortality of 20-30% in the UK and can lead to long-term morbidities like chronic kidney disease.[2]

AKI is under-recognised and badly managed despite its prevalence and seriousness, with NCEPOD report stating that only 50% of patients with AKI received good care, that there was poor assessment of risk factors for AKI, and there was an unacceptable delay in recognising post-admission AKI in 43% of patients.[4]

Baseline data collected on the urology ward in Ninewells Hospital, showed that only five of 22 (23%) patients undergoing urological surgery had post-operative creatinine measured on the ward within 48 hours (the primary method for detecting AKI). Excluding patients who were discharged the same day 5/16 (31%) received the blood test.

The aim of the project was to increase the number of patients returning to ward 9 post-surgery who receive a serum creatinine measurement within two days of their urological surgery, excluding daycases. Specifically, we wanted the reliability of this measurement to be 95% or over in ward 9 by 30 July 2014.

This was to be done by raising awareness around AKI on ward 9 and changing protocol so that every patient staying on ward 9 beyond their day of surgery should receive a post-operative creatinine. This would be tested for a set amount of time to see if patients with AKI were being missed.

Despite not being able to implement a set protocol, the percentage of patients receiving post-operative creatinine measurements on ward 9 after a urological surgery still increased significantly. By interacting with the urology team and presenting our data, the knowledge and comprehension of the problem was altered. This lead to a change in culture and a significant increase in the number of post-operative creatinine measurements being taken. Through building relationships on the ward and sharing our data and knowledge there was an increase from 27% of patients receiving post-op creatinine in our first week of collecting data, to 87% in our last week on ward 9. However, without a set tool or change in protocol this change appears to have not been sustainable as the percentage dropped to 42% two weeks later.
Switched on to business
Authors: Lambert Alison
Published: December 2014

Alison Lambert describes her career path as being unusual; however, she says, since all vets know that there's no such thing as an average day, why should there be an average way to get the best out of the valuable and varied skills that the veterinary qualification offers?
A Longitudinal EEG Study of Alzheimer's Disease Progression Based on A Complex Network Approach
Authors: Morabito Francesco Carlo , Campolo Maurizio , Labate Domenico , Morabito Giuseppe , Bonanno Lilla , Bramanti Alessia , de Salvo Simona , Marra Angela , Bramanti Placido
Published: December 2014

A complex network approach is combined with time dynamics in order to conduct a space–time analysis applicable to longitudinal studies aimed to characterize the progression of Alzheimer's disease (AD) in individual patients. The network analysis reveals how patient-specific patterns are associated with disease progression, also capturing the widespread effect of local disruptions. This longitudinal study is carried out on resting electroence phalography (EEGs) of seven AD patients. The test is repeated after a three months' period. The proposed methodology allows to extract some averaged information and regularities on the patients' cohort and to quantify concisely the disease evolution. From the functional viewpoint, the progression of AD is shown to be characterized by a loss of connected areas here measured in terms of network parameters (characteristic path length, clustering coefficient, global efficiency, degree of connectivity and connectivity density). The differences found between baseline and at follow-up are statistically significant. Finally, an original topographic multiscale approach is proposed that yields additional results.
Hodge polynomials of the SL(2, ℂ)-character variety of an elliptic curve with two marked points
Authors: Logares Marina , Muñoz Vicente
Published: December 2014

We compute the Hodge polynomials for the moduli space of representations of an elliptic curve with two marked points into SL(2, ℂ). When we fix the conjugacy classes of the representations around the marked points to be diagonal and of modulus one, the character variety is diffeomorphic to the moduli space of strongly parabolic Higgs bundles, whose Betti numbers are known. In that case we can recover some of the Hodge numbers of the character variety. We extend this result to the moduli space of doubly periodic instantons.
Dirac equation with complex potentials
Authors: Ho C.-L. , Roy P.
Published: December 2014

We study (2+1)-dimensional Dirac equation with complex scalar and Lorentz scalar potentials. It is shown that the Dirac equation admits exact analytical solutions with real eigenvalues for certain complex potentials while for another class of potentials zero energy solutions can be obtained analytically. For the scalar potential cases, it has also been shown that the effective Schrödinger-like equations resulting from decoupling the spinor components can be interpreted as exactly solvable energy-dependent Schrödinger equations.
Mimetic F(R) gravity: Inflation, dark energy and bounce
Authors: Nojiri Shin'ichi , Odintsov Sergei D.
Published: December 2014

We propose the mimetic F(R) theory and investigate the early-time and late-time acceleration in such theory. It is demonstrated that inflation consistent with observable data may be realized in such theory. The reconstruction of realistic ΛCDM era is also possible as well as the unification of early-time inflation with late-time acceleration or bounce universe. It is stressed that specific universe evolution is governed by mimetic F(R) theory which is different from convenient F(R) gravity. The corresponding examples are presented. Mimetic F(R) gravity is generalized by the addition of the scalar potential in the formulation of convenient F(R) gravity with specific Lagrange multiplier constraint. It is demonstrated that such theory may admit the arbitrary universe evolution via the corresponding choice of the scalar potential and/or function F(R).
A search for decay η′ → 4 π0 with GAMS-4π setup
Authors: Donskov Sergey V. , Kolosov Vladimir N. , Lednev Anatoly A. , Mikhailov Yury V. , Polyakov Vladimir A. , Samoylenko Vladimir D. , Khaustov Guennady V.
Published: December 2014

A search for rare decay η′ → 4 π0 has been performed with GAMS-4π setup. The new upper limit is BR (η′ → 4 π0) < 3.2 ⋅10-4 at 90% confidence level. The π- p charge-exchange reaction at 32.5 GeV /c was used as a source of 1.3⋅106η′ mesons. Experiment was carried out at the IHEP U-70 accelerator.
A phenomenological solution small x to the longitudinal structure function dynamical behavior
Authors: Boroun G. R. , Rezaei B. , Sarma J. K.
Published: December 2014

In this paper, the evolutions of longitudinal proton structure function have been obtained at small x up to next-to-next-to-leading order using a hard Pomeron behavior. In our paper, evolutions of gluonic as well as heavy longitudinal structure functions have been obtained separately and the total contributions have been calculated. The total longitudinal structure functions have been compared with results of Donnachie–Landshoff (DL) model, Color Dipole (CD) model, kT factorization and H1 data.
New Similarity Measures Between Generalized Trapezoidal Fuzzy Numbers Using the Jaccard Index
Authors: Hwang Chao-Ming , Yang Miin-Shen
Published: December 2014

Similarity measures between generalized trapezoidal fuzzy numbers (GTFNs) are employed to indicate the degrees of similarity between GTFNs. Although several similarity measures of GTFNs have been proposed in the literature, none has considered using the Jaccard index. In general, the Jaccard index is a statistic used for comparing the similarity and diversity of sample sets. This paper presents a new similarity measure between GTFNs, which involves the Jaccard index. The proposed similarity measure is found to have better properties. Several examples are employed to compare the proposed measure with some existing methods. An experiment is performed using 15 sets of GTFNs to compare the proposed similarity measure with existing ones. Numerical results show that the proposed measure is more reasonable than those existing methods.
Advertisement Policy, Reliability Dependent Imperfect Production and Environmental Pollution Control Problem in Fuzzy-Rough Environment
Authors: Maity K.
Published: December 2014

In this study, a problem for advertising policy to avoid the depreciation rate of sale, an imperfect production rate and environmental pollution control is formulated with reliability and rework over a finite time horizon. The advertisement and production rates are function of time which are taken as control variables. Also, recent studies indicate that industrial solid waste (ISW) in production period has been an important contributor to greenhouse gas (GHG) emissions. The company has agreed to invest a large amount of money to manage the ISW through technological up gradation, etc that reduce the GHG in environment. The unit production cost is a function of production rate and also dependent on raw material cost, development cost due to technological up gradation and reliability and wear-tear cost. The total profit which consists of the sales proceeds, marginal selling price, production cost, operating cost, pollution cost, inventory holding cost and advertisement cost is formulated as an optimal control problem. The selling price and all inventory costs are fuzzy rough in nature and using expectation of fuzzy rough technique, the problem is converted into equivalent crisp problem and solved using Pontryagin's Maximum Principle and Generalized Reduced Gradient Method (GRG). Finally numerical experiment, sensitivity analysis for marginal selling price, defective parameter, rework and depreciation rate of sale and graphical representation are provided to illustrate the model.
Cross-Correlations and Structures of Aero-Engine Gas Path System Based on DCCA Coefficient and Rooted Tree
Authors: Dong Keqiang , Fan Jie , Gao You
Published: December 2014

Identifying the mutual interaction is a crucial problem that facilitates the understanding of emerging structures in complex system. We here focus on aero-engine dynamic as an example of complex system. By applying the detrended cross-correlation analysis (DCCA) coefficient method to aero-engine gas path system, we find that the low-spool rotor speed (N1) and high-spool rotor speed (N2) fluctuation series exhibit cross-correlation characteristic. Further, we employ detrended cross-correlation coefficient matrix and rooted tree to investigate the mutual interactions of other gas path variables. The results can infer that the exhaust gas temperature (EGT), N1, N2, fuel flow (WF) and engine pressure ratio (EPR) are main gas path parameters.
Memory efficient assembly of human genome
Authors: Hormozdiari Farhad , Eskin Eleazar
Published: December 2014

The ability to detect the genetic variations between two individuals is an essential component for genetic studies. In these studies, obtaining the genome sequence of both individuals is the first step toward variation detection problem. The emergence of high-throughput sequencing (HTS) technology has made DNA sequencing practical, and is widely used by diagnosticians to increase their knowledge about the casual factor in genetic related diseases. As HTS advances, more data are generated every day than the amount that scientists can process. Genome assembly is one of the existing methods to tackle the variation detection problem. The de Bruijn graph formulation of the assembly problem is widely used in the field. Furthermore, it is the only method which can assemble any genome in linear time. However, it requires an enormous amount of memory in order to assemble any mammalian size genome. The high demands of sequencing more individuals and the urge to assemble them are the driving forces for a memory efficient assembler. In this work, we propose a novel method which builds the de Bruijn graph while consuming lower memory. Moreover, our proposed method can reduce the memory usage by 37% compared to the existing methods. In addition, we used a real data set (chromosome 17 of A/J strain) to illustrate the performance of our method.
Simultaneous effects of Hall current and thermal deposition in peristaltic transport of Eyring–Powell fluid
Authors: Hayat T. , Tanveer Anum , Yasmin Humaira , Alsaadi Fuad
Published: December 2014

Peristaltic flow by a sinusoidal traveling wave in the walls of two-dimensional channel with wall properties is investigated. The channel is filled with incompressible Eyring–Powell fluid. Mathematical modeling is developed through aspects of Hall current, thermal deposition and convection. Long wavelength and low Reynolds number considerations are adopted. Perturbation solutions to the resulting problem for small material parameter of fluid are obtained. Expressions of velocity, temperature, concentration and stream function are derived. Variations of pertinent parameters on the physical quantities of interest are explored in detail. The present analysis is especially important to predict the rheological characteristics in engineering applications by peristalsis.
MEASUREMENT OF THE HADRONIC CROSS SECTION AT KLOE/KLOE-2
Authors: PALLADINO ANTHONY ,   for the KLOE-2 Collaboration
Published: December 2014

The KLOE experiment at the DAΦNE ϕ-factory in Frascati was the first to use Initial State Radiation to precisely determine the e+e− → π+π−(γ) cross section below 1 GeV. This measurement is particularly important to test the Standard Model calculation for the anomalous magnetic moment of the muon, (g-2), where a long standing 3σ discrepancy between measurement and theory is observed. In 2005 and 2008 KLOE published two measurements of the π+π− cross section with the photon emitted at small angle. In 2011 an independent measurement of the π+π− cross section with the photon emitted at large angle was published using data at a collision energy of 1 GeV, 20 MeV below the ϕ-peak. A new analysis, published in 2013, derives the pion form factor directly from the bin-by-bin π+π−γ/μ+μ−γ ratio significantly reducing the systematic uncertainty, while the previous measurements were normalized to the DAΦNE luminosity using large angle Bhabha scattering. We present the final result of this measurement, as well as a preliminary value for the combined result of all KLOE hadronic cross section measurements, and evaluate the hadronic contribution to the muon anomaly.
RECENT KLOE RESULTS ON THE SEARCH FOR DARK FORCES
Authors: GRAZIANI ENRICO ,   on behalf of the KLOE Collaboration
Published: December 2014

The existence of a light dark force mediator has been tested with the KLOE detector at DAΦNE. This particle, the dark photon U, has been searched for in three different processes and four different final states: a) Φ → ηU, with U → e+e−, η → π+π−π0 and η → π0π0π0; b) e+e− → Uγ with U → μ+μ−; c) e+e− → Uh′ (dark Higgsstrahlung), U → μ+μ−, where h′ is a Higgs-like particle responsible for the breaking of the hidden symmetry.

We did not find any evidence of the processes above and set upper limits on the parameters of the model, for different MU (and Mh′) mass ranges, depending on the considered final state.
THE ANOMALOUS PROCESS γπ → ππ AND ITS IMPACT ON THE π0 TRANSITION FORM FACTOR
Authors: KUBIS BASTIAN
Published: December 2014

The process γπ → ππ, in the limit of vanishing photon and pion energies, is determined by the chiral anomaly. This reaction can be investigated experimentally using Primakoff reactions, as currently done at COMPASS. We derive a dispersive representation that allows one to extract the chiral anomaly from cross-section measurements up to 1 GeV, where effects of the ρ resonance are included model-independently via the ππ P-wave phase shift. We discuss how this amplitude serves as an important input to a dispersion-theoretical analysis of the π0 transition form factor, which in turn is a vital ingredient to the hadronic light-by-light contribution to the anomalous magnetic moment of the muon.
A RATIONAL APPROACH TO η AND η′ TRANSITION FORM FACTORS
Authors: ESCRIBANO RAFEL
Published: December 2014

The η and η′ transition form factors in the space-like region are analyzed at low and intermediate energies in a model-independent way through the use of rational approximants. The slope and curvature parameters of the form factors as well as their values at infinity are extracted from experimental data. The impact of these results on the mixing parameters of the η-η′ system are also discussed.
VIRTUAL PHOTON–PHOTON SCATTERING
Authors: HOFERICHTER MARTIN , COLANGELO GILBERTO , PROCURA MASSIMILIANO , STOFFER PETER
Published: December 2014

Based on analyticity, unitarity, and Lorentz invariance the contribution from hadronic vacuum polarization to the anomalous magnetic moment of the muon is directly related to the cross section of e+e− → hadrons . We review the main difficulties that impede such an approach for light-by-light scattering and identify the required ingredients from experiment. Amongst those, the most critical one is the scattering of two virtual photons into meson pairs. We analyze the analytic structure of the process γ*γ* → ππ and show that the usual Muskhelishvili–Omnès representation can be amended in such a way as to remain valid even in the presence of anomalous thresholds.
g - 2 AT FNAL
Authors: MAXFIELD STEPHEN J.
Published: December 2014

The g - 2 experiment at Fermi National Laboratory is planned to refine previous measurements of the anomalous magnetic moment of the muon, reducing systematic errors and generate constraints on possible physics beyond the standard model. This paper describes some of the ways in which a four-fold reduction in systematic errors will be achieved.