bluuebunny/crossref_metadata_2025 huggingface dataset:
Using a radial ultrasound probe's virtual origin to compute midsagittal smoothing splines in polar coordinates
Authors: Heyne Matthias , Derrick Donald
Published: December 2015

Tongue surface measurements from midsagittal ultrasound scans are effectively arcs with deviations representing tongue shape, but smoothing-spline analysis of variances (SSANOVAs) assume variance around a horizontal line. Therefore, calculating SSANOVA average curves of tongue traces in Cartesian Coordinates [Davidson, J. Acoust. Soc. Am. 120(1), 407–415 (2006)] creates errors that are compounded at tongue tip and root where average tongue shape deviates most from a horizontal line. This paper introduces a method for transforming data into polar coordinates similar to the technique by Mielke [J. Acoust. Soc. Am. 137(5), 2858–2869 (2015)], but using the virtual origin of a radial ultrasound transducer as the polar origin—allowing data conversion in a manner that is robust against between-subject and between-session variability.
Knowledge in Action: Fitness Lesson Segments That Teach Health-Related Fitness in Elementary Physical Education
Authors: Hodges Michael G. , Kulinna Pamela Hodges , van der Mars Hans , Lee Chong
Published: December 2015

The purpose of this study was to determine students’ health-related fitness knowledge (HRFK) and physical activity levels after the implementation of a series of fitness lessons segments called Knowledge in Action (KIA). KIA aims to teach health-related fitness knowledge (HRFK) during short episodes of the physical education lesson. Teacher participants from one district (N = 10) were randomly assigned into either the intervention or comparison group. Intervention teachers used the KIA fitness lessons during fifth grade students’ physical education classes. These teachers received training sessions, teaching materials, and YouTube videos that modeled the KIA fitness lessons. Intervention fidelity was assessed through observations and a fidelity checklist. Students’ physical activity levels were measured using accelerometers and HRFK was examined by PE Metrics 28-question pencil and paper test. General linear models (GLM) and Hierarchical linear models (HLM) were used to examine group differences. Intervention students had a 3.4 (20%) greater unit improvement in HRFK scores when compared with their comparison counterparts (p < .001), at the school level. Student activity levels of moderate-vigorous physical activity (MVPA) time were similar in both groups (p = .64). Teachers can use the KIA fitness lesson segments or similar strategies to effectively teach HRFK in elementary physical education classes.
RANKL blockade prevents and treats aggressive osteosarcomas
Authors: Chen Yan , Di Grappa Marco A. , Molyneux Sam D. , McKee Trevor D. , Waterhouse Paul , Penninger Josef M. , Khokha Rama
Published: December 2015

Denosumab, an antibody targeting RANKL, is effective against osteosarcoma in mouse models.
Recruitment of classical monocytes can be inhibited by disturbing heteromers of neutrophil HNP1 and platelet CCL5
Authors: Alard Jean-Eric , Ortega-Gomez Almudena , Wichapong Kanin , Bongiovanni Dario , Horckmans Michael , Megens Remco T. A. , Leoni Giovanna , Ferraro Bartolo , Rossaint Jan , Paulin Nicole , Ng Judy , Ippel Hans , Suylen Dennis , Hinkel Rabea , Blanchet Xavier , Gaillard Fanny , D’Amico Michele , von Hundelshausen Phillipp , Zarbock Alexander , Scheiermann Christoph , Hackeng Tilman M. , Steffens Sabine , Kupatt Christian , Nicolaes Gerry A. F. , Weber Christian , Soehnlein Oliver
Published: December 2015

Disrupting the HNP1 and CCL5 heteromer between neutrophils and platelets blocks monocyte recruitment to inflammatory sites.
CREBBP-mutated cancers HAT-tricked
Authors: Thomas Anish
Published: December 2015

CREBBP-deficient cancer cells are profoundly addicted to
EP300
, and MYC plays a key role in this interaction.
Role of Serologic and Molecular Diagnostic Assays in Identification and Management of Hepatitis C Virus Infection
Authors: Cloherty Gavin , Talal Andrew , Coller Kelly , Steinhart Corklin , Hackett John , Dawson George , Rockstroh Juergen , Feld Jordan
Published: December 2015

The drugs available for the treatment of hepatitis C virus (HCV) have evolved to provide shorter treatment duration and higher rates of sustained virologic response (SVR), and the role of HCV infection diagnostic tests has had to evolve in order to meet changing clinical needs. This review gives an overview on the role of HCV infection diagnostic testing (molecular and serological tools) used in the diagnosis and management of HCV infection. All of this critical information guides physician decisions to optimize patient clinical outcomes. Also discussed is the future direction of diagnostic testing in the context of further advances in drug development.
Clinical Laboratory Assessment of Mycoplasma genitalium Transcription-Mediated Amplification Using Primary Female Urogenital Specimens
Authors: Munson Erik , Bykowski Holly , Munson Kimber L. , Napierala Maureen , Reiss Pamela J. , Schell Ronald F. , Hryciuk Jeanne E.
Published: December 2015

Following analysis of primary cervix, vagina, and first-void female urine specimens for
Chlamydia trachomatis
,
Neisseria gonorrhoeae
, and
Trichomonas vaginalis
via commercial transcription-mediated amplification (TMA), residual material was subjected to
Mycoplasma genitalium
research-use-only TMA. Representation within a 2,478-specimen retrospective study set was established by comparison to a 6-month audit of clinical
C. trachomatis
TMA (12,999 specimens) on the basis of the
C. trachomatis
detection rate, specimen source distribution, clinic location, and age.
M. genitalium
was detected in 282 (11.4%) patients. This rate was higher than those seen with
T. vaginalis
(9.0%;
P
= 0.005),
C. trachomatis
(6.2%), and
N. gonorrhoeae
(1.4%). Positive
M. genitalium
results were confirmed by repeat testing or alternative-target TMA at a rate of 98.7%. The mean age of the
M. genitalium
-infected females (24.7 years) was lower than that of the
T. vaginalis
-infected females (mean, 30.1 years;
P
< 0.0001) and higher than that of the
C. trachomatis
-infected females (mean, 23.8 years;
P
= 0.003). Of 566 patient encounters positive for at least one sexually transmitted infection (STI), 35.9% exhibited sole detection of
M. genitalium
(
P
≤ 0.0004 versus sole detection of other STI agents) and 26.1% were solely positive for
T. vaginalis
(
P
< 0.0002 versus
C. trachomatis
). The
M. genitalium
and
T. vaginalis
detection rates among 755 patients at urban emergency departments were 14.6% and 13.0%, respectively (
P
= 0.37). A 10.0%
M. genitalium
detection rate from other facilities exceeded that of
T. vaginalis
(7.2%;
P
= 0.004). Incorporation of
M. genitalium
TMA into comprehensive testing programs would detect
M. genitalium
in a significant proportion of females, particularly those in outpatient obstetrics and gynecology (OB/GYN) settings.
Evaluation of the Bruker MALDI Biotyper for Identification of Fastidious Gram-Negative Rods
Authors: Schulthess Bettina , Bloemberg Guido V. , Zbinden Andrea , Mouttet Forouhar , Zbinden Reinhard , Böttger Erik C. , Hombach Michael
Published: December 2015

Matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as theEnterobacteriaceae. In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.
Laboratory Evaluation of a Dual-Path Platform Assay for Rapid Point-of-Care HIV and Syphilis Testing
Authors: Leon S. R. , Ramos L. B. , Vargas S. K. , Kojima N. , Perez D. G. , Caceres C. F. , Klausner J. D.
Published: December 2015

We assessed the laboratory performance of the Chembio dual-path platform HIV-syphilis rapid immunodiagnostic test and electronic reader for detection of HIV and
Treponema pallidum
antibodies in 450 previously characterized serum specimens. For visual or electronic reader HIV antibody detection, the sensitivity was 100% and the specificity was 98.7%. For visual
T. pallidum
antibody detection, the test sensitivity was 94.7% and the specificity was 100.0%; with the electronic reader, the sensitivity was 94.7% and the specificity was 99.7%.
Crystal Structure of Marburg Virus VP40 Reveals a Broad, Basic Patch for Matrix Assembly and a Requirement of the N-Terminal Domain for Immunosuppression
Authors: Oda Shun-ichiro , Noda Takeshi , Wijesinghe Kaveesha J. , Halfmann Peter , Bornholdt Zachary A. , Abelson Dafna M. , Armbrust Tammy , Stahelin Robert V. , Kawaoka Yoshihiro , Saphire Erica Ollmann
Published: December 2015

Marburg virus (MARV), a member of the filovirus family, causes severe hemorrhagic fever with up to 90% lethality. MARV matrix protein VP40 is essential for assembly and release of newly copied viruses and also suppresses immune signaling in the infected cell. Here we report the crystal structure of MARV VP40. We found that MARV VP40 forms a dimer in solution, mediated by N-terminal domains, and that formation of this dimer is essential for budding of virus-like particles. We also found the N-terminal domain to be necessary and sufficient for immune antagonism. The C-terminal domains of MARV VP40 are dispensable for immunosuppression but are required for virus assembly. The C-terminal domains are only 16% identical to those of Ebola virus, differ in structure from those of Ebola virus, and form a distinct broad and flat cationic surface that likely interacts with the cell membrane during virus assembly.

IMPORTANCE
Marburg virus, a cousin of Ebola virus, causes severe hemorrhagic fever, with up to 90% lethality seen in recent outbreaks. Molecular structures and visual images of the proteins of Marburg virus are essential for the development of antiviral drugs. One key protein in the Marburg virus life cycle is VP40, which both assembles the virus and suppresses the immune system. Here we provide the molecular structure of Marburg virus VP40, illustrate differences from VP40 of Ebola virus, and reveal surfaces by which Marburg VP40 assembles progeny and suppresses immune function.
Bovine Herpesvirus 4 Modulates Its β-1,6-
N
-Acetylglucosaminyltransferase Activity through Alternative Splicing
Authors: Lété Céline , Markine-Goriaynoff Nicolas , Machiels Bénédicte , Pang Poh-Choo , Xiao Xue , Canis Kevin , Suzuki Masami , Fukuda Minoru , Dell Anne , Haslam Stuart M. , Vanderplasschen Alain , Gillet Laurent
Published: December 2015

Carbohydrates play major roles in host-virus interactions. It is therefore not surprising that, during coevolution with their hosts, viruses have developed sophisticated mechanisms to hijack for their profit different pathways of glycan synthesis. Thus, the Bo17 gene of Bovine herpesvirus 4 (BoHV-4) encodes a homologue of the cellular core 2 protein β-1,6-
N
-acetylglucosaminyltransferase-mucin type (C2GnT-M), which is a key player for the synthesis of complex
O
-glycans. Surprisingly, we show in this study that, as opposed to what is observed for the cellular enzyme, two different mRNAs are encoded by the Bo17 gene of all available BoHV-4 strains. While the first one corresponds to the entire coding sequence of the Bo17 gene, the second results from the splicing of a 138-bp intron encoding critical residues of the enzyme. Antibodies generated against the Bo17 C terminus showed that the two forms of Bo17 are expressed in BoHV-4 infected cells, but enzymatic assays revealed that the spliced form is not active. In order to reveal the function of these two forms, we then generated recombinant strains expressing only the long or the short form of Bo17. Although we did not highlight replication differences between these strains, glycomic analyses and lectin neutralization assays confirmed that the splicing of the Bo17 gene gives the potential to BoHV-4 to fine-tune the global level of core 2 branching activity in the infected cell. Altogether, these results suggest the existence of new mechanisms to regulate the activity of glycosyltransferases from the Golgi apparatus.

IMPORTANCE
Viruses are masters of adaptation that hijack cellular pathways to allow their growth. Glycans play a central role in many biological processes, and several studies have highlighted mechanisms by which viruses can affect glycosylation. Glycan synthesis is a nontemplate process regulated by the availability of key glycosyltransferases. Interestingly, bovine herpesvirus 4 encodes one such enzyme which is a key enzyme for the synthesis of complex
O
-glycans. In this study, we show that, in contrast to cellular homologues, this virus has evolved to alternatively express two proteins from this gene. While the first one is enzymatically active, the second results from the alternative splicing of the region encoding the catalytic site of the enzyme. We postulate that this regulatory mechanism could allow the virus to modulate the synthesis of some particular glycans for function at the location and/or the moment of infection.
Pan-genotypic Hepatitis C Virus Inhibition by Natural Products Derived from the Wild Egyptian Artichoke
Authors: Elsebai Mahmoud Fahmi , Koutsoudakis George , Saludes Verónica , Pérez-Vilaró Gemma , Turpeinen Ari , Mattila Sampo , Pirttilä Anna Maria , Fontaine-Vive Fabien , Mehiri Mohamed , Meyerhans Andreas , Diez Juana
Published: December 2015

Hepatitis C virus (HCV) infection is the leading cause of chronic liver diseases. Water extracts of the leaves of the wild Egyptian artichoke (WEA) [
Cynara cardunculus
L. var.
sylvestris
(Lam.) Fiori] have been used for centuries in the Sinai Peninsula to treat hepatitis symptoms. Here we isolated and characterized six compounds from the water extracts of WEA and evaluated their HCV inhibition capacities
in vitro
. Importantly, two of these compounds, grosheimol and cynaropicrin, inhibited HCV with half-maximal effective concentrations (EC
50
s) in the low micromolar range. They inhibited HCV entry into target cells and were active against both cell-free infection as well as cell-cell transmission. Furthermore, the antiviral activity of both compounds was pan-genotypic as HCV genotypes 1a, 1b, 2b, 3a, 4a, 5a, 6a, and 7a were inhibited. Thus, grosheimol and cynaropicrin are promising candidates for the development of new pan-genotypic entry inhibitors of HCV infection.

IMPORTANCE
Because there is no preventive HCV vaccine available today, the discovery of novel anti-HCV cell entry inhibitors could help develop preventive measures against infection. The present study describes two compounds isolated from the wild Egyptian artichoke (WEA) with respect to their structural elucidation, absolute configuration, and quantitative determination. Importantly, both compounds inhibited HCV infection
in vitro
. The first compound was an unknown molecule, and it was designated “grosheimol,” while the second compound is the known molecule cynaropicrin. Both compounds belong to the group of sesquiterpene lactones. The mode of action of these compounds occurred during the early steps of the HCV life cycle, including cell-free and cell-cell infection inhibition. These natural compounds present promising candidates for further development into anti-HCV therapeutics.
Interaction of Human Parainfluenza Virus Type 3 Nucleoprotein with Matrix Protein Mediates Internal Viral Protein Assembly
Authors: Zhang Guangyuan , Zhong Yi , Qin Yali , Chen Mingzhou
Published: December 2015

Human parainfluenza virus type 3 (HPIV3) belongs to the
Paramyxoviridae
family. Its three internal viral proteins, the nucleoprotein (N), the phosphoprotein (P), and the polymerase (L), form the ribonucleoprotein (RNP) complex, which encapsidates the viral genome and associates with the matrix protein (M) for virion assembly. We previously showed that the M protein expressed alone is sufficient to assemble and release virus-like particles (VLPs) and a mutant with the L305A point mutation in the M protein (M
L305A
) has a VLP formation ability similar to that of wild-type M protein. In addition, recombinant HPIV3 (rHPIV3) containing the M
L305A
mutation (rHPIV3-M
L305A
) could be successfully recovered. In the present study, we found that the titer of rHPIV3-M
L305A
was at least 10-fold lower than the titer of rHPIV3. Using VLP incorporation and coimmunoprecipitation assays, we found that VLPs expressing the M protein (M-VLPs) can efficiently incorporate N and P via an N-M or P-M interaction and M
L305A
-VLPs had an ability to incorporate P via a P-M interaction similar to that of M-VLPs but were unable to incorporate N and no longer interacted with N. Furthermore, we found that the incorporation of P into M
L305A
-VLPs but not M-VLPs was inhibited in the presence of N. In addition, we provide evidence that the C-terminal region of P is involved in its interaction with both N and M and N binding to the C-terminal region of P inhibits the incorporation of P into M
L305A
-VLPs. Our findings provide new molecular details to support the idea that the N-M interaction and not the P-M interaction is critical for packaging N and P into infectious viral particles.

IMPORTANCE
Human parainfluenza virus type 3 (HPIV3) is a nonsegmented, negative-sense, single-stranded RNA virus that belongs to the
Paramyxoviridae
family and can cause lower respiratory tract infections in infants and young children as well as elderly or immunocompromised individuals. However, no effective vaccine has been developed or licensed. We used virus-like particle (VLP) incorporation and coimmunoprecipitation assays to determine how the M protein assembles internal viral proteins. We demonstrate that both nucleoprotein (N) and phosphoprotein (P) can incorporate into M-VLPs and N inhibits the M-P interaction via the binding of N to the C terminus of P. We also provide additional evidence that the N-M interaction but not the P-M interaction is critical for the regulation of HPIV3 assembly. Our studies provide a more complete characterization of HPIV3 virion assembly and substantiation that N interaction with M regulates internal viral organization.
Transcriptional Regulation in Ebola Virus: Effects of Gene Border Structure and Regulatory Elements on Gene Expression and Polymerase Scanning Behavior
Authors: Brauburger Kristina , Boehmann Yannik , Krähling Verena , Mühlberger Elke
Published: December 2015

The highly pathogenic Ebola virus (EBOV) has a nonsegmented negative-strand (NNS) RNA genome containing seven genes. The viral genes either are separated by intergenic regions (IRs) of variable length or overlap. The structure of the EBOV gene overlaps is conserved throughout all filovirus genomes and is distinct from that of the overlaps found in other NNS RNA viruses. Here, we analyzed how diverse gene borders and noncoding regions surrounding the gene borders influence transcript levels and govern polymerase behavior during viral transcription. Transcription of overlapping genes in EBOV bicistronic minigenomes followed the stop-start mechanism, similar to that followed by IR-containing gene borders. When the gene overlaps were extended, the EBOV polymerase was able to scan the template in an upstream direction. This polymerase feature seems to be generally conserved among NNS RNA virus polymerases. Analysis of IR-containing gene borders showed that the IR sequence plays only a minor role in transcription regulation. Changes in IR length were generally well tolerated, but specific IR lengths led to a strong decrease in downstream gene expression. Correlation analysis revealed that these effects were largely independent of the surrounding gene borders. Each EBOV gene contains exceptionally long untranslated regions (UTRs) flanking the open reading frame. Our data suggest that the UTRs adjacent to the gene borders are the main regulators of transcript levels. A highly complex interplay between the different
cis
-acting elements to modulate transcription was revealed for specific combinations of IRs and UTRs, emphasizing the importance of the noncoding regions in EBOV gene expression control.

IMPORTANCE
Our data extend those from previous analyses investigating the implication of noncoding regions at the EBOV gene borders for gene expression control. We show that EBOV transcription is regulated in a highly complex yet not easily predictable manner by a set of interacting
cis
-active elements. These findings are important not only for the design of recombinant filoviruses but also for the design of other replicon systems widely used as surrogate systems to study the filovirus replication cycle under low biosafety levels. Insights into the complex regulation of EBOV transcription conveyed by noncoding sequences will also help to interpret the importance of mutations that have been detected within these regions, including in isolates of the current outbreak.
Type I Interferon Response Limits Astrovirus Replication and Protects against Increased Barrier Permeability
In Vitro
and
In Vivo
Authors: Marvin Shauna A. , Huerta C. Theodore , Sharp Bridgett , Freiden Pamela , Cline Troy D. , Schultz-Cherry Stacey
Published: December 2015

Little is known about intrinsic epithelial cell responses against astrovirus infection. Here we show that human astrovirus type 1 (HAstV-1) infection induces type I interferon (beta interferon [IFN-β]) production in differentiated Caco2 cells, which not only inhibits viral replication by blocking positive-strand viral RNA and capsid protein synthesis but also protects against HAstV-1-increased barrier permeability. Excitingly, we found similar results
in vivo
using a murine astrovirus (MuAstV) model, providing new evidence that virus-induced type I IFNs may protect against astrovirus replication and pathogenesis
in vivo
.

IMPORTANCE
Human astroviruses are a major cause of pediatric diarrhea, yet little is known about the immune response. Here we show that type I interferon limits astrovirus infection and preserves barrier permeability both
in vitro
and
in vivo
. Importantly, we characterized a new mouse model for studying astrovirus replication and pathogenesis.
Crystal Structure of Feline Infectious Peritonitis Virus Main Protease in Complex with Synergetic Dual Inhibitors
Authors: Wang Fenghua , Chen Cheng , Liu Xuemeng , Yang Kailin , Xu Xiaoling , Yang Haitao
Published: December 2015

Coronaviruses (CoVs) can cause highly prevalent diseases in humans and animals. Feline infectious peritonitis virus (FIPV) belongs to the genus
Alphacoronavirus
, resulting in a lethal systemic granulomatous disease called feline infectious peritonitis (FIP), which is one of the most important fatal infectious diseases of cats worldwide. No specific vaccines or drugs have been approved to treat FIP. CoV main proteases (M
pro
s) play a pivotal role in viral transcription and replication, making them an ideal target for drug development. Here, we report the crystal structure of FIPV M
pro
in complex with dual inhibitors, a zinc ion and a Michael acceptor. The complex structure elaborates a unique mechanism of two distinct inhibitors synergizing to inactivate the protease, providing a structural basis to design novel antivirals and suggesting the potential to take advantage of zinc as an adjunct therapy against CoV-associated diseases.

IMPORTANCE
Coronaviruses (CoVs) have the largest genome size among all RNA viruses. CoV infection causes various diseases in humans and animals, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). No approved specific drugs or vaccinations are available to treat their infections. Here, we report a novel dual inhibition mechanism targeting CoV main protease (M
pro
) from feline infectious peritonitis virus (FIPV), which leads to lethal systemic granulomatous disease in cats. M
pro
, conserved across all CoV genomes, is essential for viral replication and transcription. We demonstrated that zinc ion and a Michael acceptor-based peptidomimetic inhibitor synergistically inactivate FIPV M
pro
. We also solved the structure of FIPV M
pro
complexed with two inhibitors, delineating the structural view of a dual inhibition mechanism. Our study provides new insight into the pharmaceutical strategy against CoV M
pro
through using zinc as an adjuvant therapy to enhance the efficacy of an irreversible peptidomimetic inhibitor.
Sensing of HIV-1 Infection in Tzm-bl Cells with Reconstituted Expression of STING
Authors: Trotard Maud , Tsopoulidis Nikolaos , Tibroni Nadine , Willemsen Joschka , Binder Marco , Ruggieri Alessia , Fackler Oliver T.
Published: December 2015

Production of proinflammatory cytokines indicative of potent recognition by the host innate immune system has long been recognized as a hallmark of the acute phase of HIV-1 infection. The first components of the machinery by which primary HIV target cells sense infection have recently been described; however, the mechanistic dissection of innate immune recognition and viral evasion would be facilitated by an easily accessible cell line model. Here we describe that reconstituted expression of the innate signaling adaptor STING enhanced the ability of the well-established HIV reporter cell line Tzm-bl to sense HIV infection and to convert this information into nuclear translocation of IRF3 as well as expression of cytokine mRNA. STING-dependent immune sensing of HIV-1 required virus entry and reverse transcription but not genome integration. Particularly efficient recognition was observed for an HIV-1 variant lacking expression of the accessory protein Vpr, suggesting a role of the viral protein in circumventing STING-mediated immune signaling. Vpr as well as STING significantly impacted the magnitude and breadth of the cytokine mRNA expression profile induced upon HIV-1 infection. However, cytoplasmic DNA sensing did not result in detectable cytokine secretion in this cell system, and innate immune recognition did not affect infection rates. Despite these deficits in eliciting antiviral effector functions, these results establish Tzm-bl STING and Tzm-bl STING IRF3.GFP cells as useful tools for studies aimed at dissecting mechanisms and regulation of early innate immune recognition of HIV infection.

IMPORTANCE
Cell-autonomous immune recognition of HIV infection was recently established as an important aspect by which the host immune system attempts to fend off HIV-1 infection. Mechanistic studies on host cell recognition and viral evasion are hampered by the resistance of many primary HIV target cells to detailed experimental manipulation. We describe here that expression of the signaling adaptor STING renders the well-established HIV reporter cell line Tzm-bl competent for innate recognition of HIV infection. Key characteristics reflected in this cell model include nuclear translocation of IRF3, expression of a broad range of cytokine mRNAs, and an antagonistic activity of the HIV-1 protein Vpr. These results establish Tzm-bl STING and Tzm-bl STING IRF3.GFP cells as a useful tool for studies of innate recognition of HIV infection.
The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice
Authors: Forero Adriana , Tisoncik-Go Jennifer , Watanabe Tokiko , Zhong Gongxun , Hatta Masato , Tchitchek Nicolas , Selinger Christian , Chang Jean , Barker Kristi , Morrison Juliet , Berndt Jason D. , Moon Randall T. , Josset Laurence , Kawaoka Yoshihiro , Katze Michael G.
Published: December 2015

The 1918-1919 influenza pandemic remains the single greatest infectious disease outbreak in the past century. Mouse and nonhuman primate infection models have shown that the 1918 virus induces overly aggressive innate and proinflammatory responses. To understand the response to viral infection and the role of individual 1918 genes on the host response to the 1918 virus, we examined reassortant avian viruses nearly identical to the pandemic 1918 virus (1918-like avian virus) carrying either the 1918 hemagglutinin (HA) or PB2 gene. In mice, both genes enhanced 1918-like avian virus replication, but only the mammalian host adaptation of the 1918-like avian virus through reassortment of the 1918 PB2 led to increased lethality. Through the combination of viral genetics and host transcriptional profiling, we provide a multidimensional view of the molecular mechanisms by which the 1918 PB2 gene drives viral pathogenicity. We demonstrate that 1918 PB2 enhances immune and inflammatory responses concomitant with increased cellular infiltration in the lung. We also show for the first time, that 1918 PB2 expression results in the repression of both canonical and noncanonical Wnt signaling pathways, which are crucial for inflammation-mediated lung regeneration and repair. Finally, we utilize regulatory enrichment and network analysis to define the molecular regulators of inflammation, epithelial regeneration, and lung immunopathology that are dysregulated during influenza virus infection. Taken together, our data suggest that while both HA and PB2 are important for viral replication, only 1918 PB2 exacerbates lung damage in mice infected with a reassortant 1918-like avian virus.

IMPORTANCE
As viral pathogenesis is determined in part by the host response, understanding the key host molecular driver(s) of virus-mediated disease, in relation to individual viral genes, is a promising approach to host-oriented drug efforts in preventing disease. Previous studies have demonstrated the importance of host adaptive genes, HA and PB2, in mediating disease although the mechanisms by which they do so are still poorly understood. Here, we combine viral genetics and host transcriptional profiling to show that although both 1918 HA and 1918 PB2 are important mediators of efficient viral replication, only 1918 PB2 impacts the pathogenicity of an avian influenza virus sharing high homology to the 1918 pandemic influenza virus. We demonstrate that 1918 PB2 enhances deleterious inflammatory responses and the inhibition of regeneration and repair functions coordinated by Wnt signaling in the lungs of infected mice, thereby promoting virus-associated disease.
Molecular Basis of the Divergent Immunogenicity of Two Pediatric Tick-Borne Encephalitis Virus Vaccines
Authors: Beck Yvonne , Fritz Richard , Orlinger Klaus , Kiermayr Stefan , Ilk Reinhard , Portsmouth Daniel , Pöllabauer Eva-Maria , Löw-Baselli Alexandra , Hessel Annett , Kölch Doris , Howard M. Keith , Barrett P. Noel , Kreil Thomas R.
Published: December 2015

Studies evaluating the immunogenicity of two pediatric tick-borne encephalitis virus (TBEV) vaccines have reported contradictory results. These vaccines are based on two different strains of the European TBEV subtype: FSME-Immun Junior is based on the Neudörfl (Nd) strain, whereas Encepur Children is based on the Karlsruhe (K23) strain. The antibody (Ab) response induced by these two vaccines might be influenced by antigenic differences in the envelope (E) protein, which is the major target of neutralizing antibodies. We used an established hybrid virus assay platform to compare the levels of induction of neutralizing antibodies against the two vaccine virus strains in children aged 1 to 11 years who received two immunizations with FSME-Immun Junior or Encepur Children. The influence of amino acid differences between the E proteins of the Nd and K23 vaccine strains was investigated by mutational analyses and three-dimensional computer modeling. FSME-Immun Junior induced 100% seropositivity and similar neutralizing antibody titers against hybrid viruses containing the TBEV E protein of the two vaccine strains. Encepur Children induced 100% seropositivity only against the hybrid virus containing the E protein of the homologous K23 vaccine strain. Antibody responses induced by Encepur Children to the hybrid virus containing the E protein of the heterologous Nd strain were substantially and significantly (
P
< 0.001) lower than those to the K23 vaccine strain hybrid virus. Structure-based mutational analyses of the TBEV E protein indicated that this is due to a mutation in the DI-DII hinge region of the K23 vaccine strain E protein which may have occurred during production of the vaccine seed virus and which is not present in any wild-type TBE viruses.

IMPORTANCE
Our data suggest that there are major differences in the abilities of two European subtype pediatric TBEV vaccines to induce antibodies capable of neutralizing heterologous TBEV strains. This is a result of a mutation in the DI-DII hinge region of the E protein of the K23 vaccine virus strain used to manufacture Encepur Children which is not present in the Nd strain used to manufacture FSME-Immun Junior or in any other known naturally occurring TBEVs.
The Basic Domain of Herpes Simplex Virus 1 pUS9 Recruits Kinesin-1 To Facilitate Egress from Neurons
Authors: Diefenbach Russell J. , Davis April , Miranda-Saksena Monica , Fernandez Marian A. , Kelly Barbara J. , Jones Cheryl A. , LaVail Jennifer H. , Xue Jing , Lai Joey , Cunningham Anthony L.
Published: December 2015

The alphaherpesviral envelope protein pUS9 has been shown to play a role in the anterograde axonal transport of herpes simplex virus 1 (HSV-1), yet the molecular mechanism is unknown. To address this, we used an
in vitro
pulldown assay to define a series of five arginine residues within the conserved pUS9 basic domain that were essential for binding the molecular motor kinesin-1. The mutation of these pUS9 arginine residues to asparagine blocked the binding of both recombinant and native kinesin-1. We next generated HSV-1 with the same pUS9 arginine residues mutated to asparagine (HSV-1pUS9KBDM) and then restored them being to arginine (HSV-1pUS9KBDR). The two mutated viruses were analyzed initially in a zosteriform model of recurrent cutaneous infection. The primary skin lesion scores were identical in severity and kinetics, and there were no differences in viral load at dorsal root ganglionic (DRG) neurons at day 4 postinfection (p.i.) for both viruses. In contrast, HSV-1pUS9KBDM showed a partial reduction in secondary skin lesions at day 8 p.i. compared to the level for HSV-1pUS9KBDR. The use of rat DRG neuronal cultures in a microfluidic chamber system showed both a reduction in anterograde axonal transport and spread from axons to nonneuronal cells for HSV-1pUS9KBDM. Therefore, the basic domain of pUS9 contributes to anterograde axonal transport and spread of HSV-1 from neurons to the skin through recruitment of kinesin-1.

IMPORTANCE
Herpes simplex virus 1 and 2 cause genital herpes, blindness, encephalitis, and occasionally neonatal deaths. There is also increasing evidence that sexually transmitted genital herpes increases HIV acquisition, and the reactivation of HSV increases HIV replication and transmission. New antiviral strategies are required to control resistant viruses and to block HSV spread, thereby reducing HIV acquisition and transmission. These aims will be facilitated through understanding how HSV is transported down nerves and into skin. In this study, we have defined how a key viral protein plays a role in both axonal transport and spread of the virus from nerve cells to the skin.
Risk and protective factors for falls on stairs in young children: multicentre case–control study
Authors: Kendrick D , Zou K , Ablewhite J , Watson M , Coupland C , Kay B , Hawkins A , Reading R
Published: December 2015

Aim

To investigate risk and protective factors for stair falls in children aged <5 years.

Methods

Multicentre case–control study at hospitals, minor injury units and general practices in and around four UK study centres. Cases were children with medically attended stair fall injuries. Controls were matched on age, sex, calendar time and study centre. A total of 610 cases and 2658 controls participated.

Results

Cases’ most common injuries were bangs on the head (66%), cuts/grazes not requiring stitches (14%) and fractures (12%). Parents of cases were significantly more likely not to have stair gates (adjusted OR (AOR) 2.50, 95% CI 1.90 to 3.29; population attributable fraction (PAF) 21%) or to leave stair gates open (AOR 3.09, 95% CI 2.39 to 4.00; PAF 24%) both compared with having closed stair gates. They were more likely not to have carpeted stairs (AOR 1.52, 95% CI 1.09 to 2.10; PAF 5%) and not to have a landing part-way up their stairs (AOR 1.34, 95% CI 1.08 to 1.65; PAF 18%). They were more likely to consider their stairs unsafe to use (AOR 1.46, 95% CI 1.07 to 1.99; PAF 5%) or to be in need of repair (AOR 1.71, 95% CI 1.16 to 2.50; PAF 5%).

Conclusion

Structural factors including having landings part-way up the stairs and keeping stairs in good repair were associated with reduced stair fall injury risk. Family factors including having stair gates, not leaving gates open and having stair carpets were associated with reduced injury risk. If these associations are causal, addressing these factors in housing policy and routine child health promotion could reduce stair fall injuries.
Characteristics of admissions and variations in the use of basic investigations, treatments and outcomes in Kenyan hospitals within a new Clinical Information Network
Authors: Ayieko Philip , Ogero Morris , Makone Boniface , Julius Thomas , Mbevi George , Nyachiro Wycliffe , Nyamai Rachel , Were Fred , Githanga David , Irimu Grace , English Mike
Published: December 2015

Background

Lack of detailed information about hospital activities, processes and outcomes hampers planning, performance monitoring and improvement in low-income countries (LIC). Clinical networks offer one means to advance methods for data collection and use, informing wider health system development in time, but are rare in LIC. We report baseline data from a new Clinical Information Network (CIN) in Kenya seeking to promote data-informed improvement and learning.

Methods

Data from 13 hospitals engaged in the Kenyan CIN between April 2014 and March 2015 were captured from medical and laboratory records. We use these data to characterise clinical care and outcomes of hospital admission.

Results

Data were available for a total of 30 042 children aged between 2 months and 15 years. Malaria (in five hospitals), pneumonia and diarrhoea/dehydration (all hospitals) accounted for the majority of diagnoses and comorbidity was found in 17 710 (59%) patients. Overall, 1808 deaths (6%) occurred (range per hospital 2.5%–11.1%) with 1037 deaths (57.4%) occurring by day 2 of admission (range 41%–67.8%). While malaria investigations are commonly done, clinical health workers rarely investigate for other possible causes of fever, test for blood glucose in severe illness or ascertain HIV status of admissions. Adherence to clinical guideline-recommended treatment for malaria, pneumonia, meningitis and acute severe malnutrition varied widely across hospitals.

Conclusion

Developing clinical networks is feasible with appropriate support. Early data demonstrate that hospital mortality remains high in Kenya, that resources to investigate severe illness are limited, that care provided and outcomes vary widely and that adoption of effective interventions remains slow. Findings suggest considerable scope for improving care within and across sites.
Water-only fasting and an exclusively plant foods diet in the management of stage IIIa, low-grade follicular lymphoma
Authors: Goldhamer Alan C , Klaper Michael , Foorohar Afsoon , Myers Toshia R
Published: December 2015

Follicular lymphoma (FL), the second most common non-Hodgkin's lymphoma (NHL), is well characterised by a classic histological appearance and an indolent course. Current treatment protocols for FL range from close observation to immunotherapy, chemotherapy and/or radiotherapies. We report the case of a 42-year-old woman diagnosed by excisional biopsy with stage IIIa, grade 1 FL. In addition to close observation, the patient underwent a medically supervised, 21-day water-only fast after which enlarged lymph nodes were substantially reduced in size. The patient then consumed a diet of minimally processed plant foods free of added sugar, oil and salt (SOS), and has remained on the diet since leaving the residential facility. At 6 and 9-month follow-up visits, the patient's lymph nodes were non-palpable and she remained asymptomatic. This case establishes a basis for further studies evaluating water-only fasting and a plant foods, SOS-free diet as a treatment protocol for FL.
Application of an autoregressive integrated moving average model for predicting injury mortality in Xiamen, China
Authors: Lin Yilan , Chen Min , Chen Guowei , Wu Xiaoqing , Lin Tianquan
Published: December 2015

Objective

Injury is currently an increasing public health problem in China. Reducing the loss due to injuries has become a main priority of public health policies. Early warning of injury mortality based on surveillance information is essential for reducing or controlling the disease burden of injuries. We conducted this study to find the possibility of applying autoregressive integrated moving average (ARIMA) models to predict mortality from injuries in Xiamen.

Method

The monthly mortality data on injuries in Xiamen (1 January 2002 to 31 December 2013) were used to fit the ARIMA model with the conditional least-squares method. The values p, q and d in the ARIMA (p, d, q) model refer to the numbers of autoregressive lags, moving average lags and differences, respectively. The Ljung–Box test was used to measure the ‘white noise’ and residuals. The mean absolute percentage error (MAPE) between observed and fitted values was used to evaluate the predicted accuracy of the constructed models.

Results

A total of 8274 injury-related deaths in Xiamen were identified during the study period; the average annual mortality rate was 40.99/100 000 persons. Three models, ARIMA (0, 1, 1), ARIMA (4, 1, 0) and ARIMA (1, 1, (2)), passed the parameter (p<0.01) and residual (p>0.05) tests, with MAPE 11.91%, 11.96% and 11.90%, respectively. We chose ARIMA (0, 1, 1) as the optimum model, the MAPE value for which was similar to that of other models but with the fewest parameters. According to the model, there would be 54 persons dying from injuries each month in Xiamen in 2014.

Conclusion

The ARIMA (0, 1, 1) model could be applied to predict mortality from injuries in Xiamen.
Diagnostic accuracy of the Whooley questions for the identification of depression: a diagnostic meta-analysis
Authors: Bosanquet Katharine , Bailey Della , Gilbody Simon , Harden Melissa , Manea Laura , Nutbrown Sarah , McMillan Dean
Published: December 2015

Objectives

To determine the diagnostic accuracy of the Whooley questions in the identification of depression; and, to examine the effect of an additional ‘help’ question.

Design

Systematic review with random effects bivariate diagnostic meta-analysis. Search strategies included electronic databases, examination of reference lists, and forward citation searches.

Inclusion criteria

Studies were included that provided sufficient data to calculate the diagnostic accuracy of the Whooley questions against a gold standard diagnosis of major depression.

Data extraction

Descriptive information, methodological quality criteria, and 2×2 contingency tables were extracted.

Results

Ten studies met inclusion criteria. Pooled sensitivity was 0.95 (95% CI 0.88 to 0.97) and pooled specificity was 0.65 (95% CI 0.56 to 0.74). Heterogeneity was low (I2=24.1%). Primary care subgroup analysis gave broadly similar results. Four of the ten studies provided information on the effect of an additional help question. The addition of this question did not consistently improve specificity while retaining high sensitivity as reported in the original validation study.

Conclusions

The two-item Whooley questions have high sensitivity and modest specificity in the detection of depression. The current evidence for the use of an additional help question is not consistent and there is, as yet, insufficient data to recommend its use for screening or case finding.

Trial registration number

CRD42014009695.
Does the engagement of clinicians and organisations in research improve healthcare performance: a three-stage review
Authors: Boaz Annette , Hanney Stephen , Jones Teresa , Soper Bryony
Published: December 2015

Objective

There is a widely held assumption that engagement by clinicians and healthcare organisations in research improves healthcare performance at various levels, but little direct empirical evidence has previously been collated. The objective of this study was to address the question: Does research engagement (by clinicians and organisations) improve healthcare performance?

Methods

An hourglass-shaped review was developed, consisting of three stages: (1) a planning and mapping stage; (2) a focused review concentrating on the core question of whether or not research engagement improves healthcare performance; and (3) a wider (but less systematic) review of papers identified during the two earlier stages, focusing on mechanisms.

Results

Of the 33 papers included in the focused review, 28 identified improvements in health services performance. Seven out of these papers reported some improvement in health outcomes, with others reporting improved processes of care. The wider review demonstrated that mechanisms such as collaborative and action research can encourage some progress along the pathway from research engagement towards improved healthcare performance. Organisations that have deliberately integrated the research function into organisational structures demonstrate how research engagement can, among other factors, contribute to improved healthcare performance.

Conclusions

Current evidence suggests that there is an association between the engagement of individuals and healthcare organisations in research and improvements in healthcare performance. The mechanisms through which research engagement might improve healthcare performance overlap and rarely act in isolation, and their effectiveness often depends on the context in which they operate.