bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen silsesquioxane on SOI proximity and microloading effects correction from a single 1D characterization sample
Authors: Bickford Justin R. , Lopez Gerald , Belic Nikola , Hofmann Ulrich
Published: November 2014

Designs patterned by electron beam lithography without applying process effect correction exhibit overexposed dense features and underexposed sparse features for most practical exposure scenarios. This is typified by the limited exposure latitude of hydrogen silsesquioxane resist on silicon-on-insulator substrates used for silicon photonics, which commonly display very high density features (vertical grating couplers, ring resonators) mixed with very sparse features (inverse tapered waveguides, lone waveguides) in a single pattern. The authors have optimized a proximity effect correction (PEC) based on our analysis of a single 1D process control monitor characterization sample. Our PEC verification sample, which includes electron backscatter and process-related microloading effects, achieved linewidths with an RMS error of ±5.0 nm for features with pattern densities spanning 1%–67%. Ignoring the pattern density-dependent microloading effect limits the resolvable pattern density span to a smaller range and degrades the linewidth error.
Three‐dimensional texture analysis of contrast enhanced CT images for treatment response assessment in Hodgkin lymphoma: Comparison with F‐18‐FDG PET
Authors: Knogler Thomas , El‐Rabadi Karem , Weber Michael , Karanikas Georgios , Mayerhoefer Marius E.
Published: November 2014

Purpose:

To determine the diagnostic performance of three‐dimensional (3D) texture analysis (TA) of contrast‐enhanced computed tomography (CE‐CT) images for treatment response assessment in patients with Hodgkin lymphoma (HL), compared with F‐18‐fludeoxyglucose (FDG) positron emission tomography/CT.

Methods:

3D TA of 48 lymph nodes in 29 patients was performed on venous‐phase CE‐CT images before and after chemotherapy. All lymph nodes showed pathologically elevated FDG uptake at baseline. A stepwise logistic regression with forward selection was performed to identify classic CT parameters and texture features (TF) that enable the separation of complete response (CR) and persistent disease.

Results:

The TF fraction of image in runs, calculated for the 45° direction, was able to correctly identify CR with an accuracy of 75%, a sensitivity of 79.3%, and a specificity of 68.4%. Classical CT features achieved an accuracy of 75%, a sensitivity of 86.2%, and a specificity of 57.9%, whereas the combination of TF and CT imaging achieved an accuracy of 83.3%, a sensitivity of 86.2%, and a specificity of 78.9%.

Conclusions:

3D TA of CE‐CT images is potentially useful to identify nodal residual disease in HL, with a performance comparable to that of classical CT parameters. Best results are achieved when TA and classical CT features are combined.
Effects of Regular Away Travel on Training Loads, Recovery, and Injury Rates in Professional Australian Soccer Players
Authors: Fowler Peter , Duffield Rob , Waterson Adam , Vaile Joanna
Published: November 2014

The current study examined the acute and longitudinal effects of regular away travel on training load (TL), player wellness, and injury surrounding competitive football (soccer) matches. Eighteen male professional football players, representing a team competing in the highest national competition in Australia, volunteered to participate in the study. Training loads, player wellness and injury incidence, rate, severity, and type, together with the activity at the time of injury, were recorded on the day before, the day of, and for 4 d after each of the 27 matches of the 2012−13 season. This included 14 home and 13 away matches, further subdivided based on the midpoint of the season into early (1−13) and late competition (14−27) phases. While TLs were significantly greater on day 3 at home compared with away during the early competition phase (P = .03), no other significant effects of match location were identified (P > .05). Total TL and mean wellness over the 6 d surrounding matches and TL on day 3 were significantly reduced during the late compared with the early competition phase at home and away (P < .05). Although not significantly (P > .05), training missed due to injury was 60% and 50% greater during the late than during the early competition phase at home and away, respectively. In conclusion, no significant interactions between match location and competition phase were evident during the late competition phase, which suggests that away travel had negligible cumulative effects on the reduction in player wellness in the latter half of the season.
Force-Production Asymmetry in Male and Female Athletes of Differing Strength Levels
Authors: Bailey Christopher A. , Sato Kimitake , Burnett Angus , Stone Michael H.
Published: November 2014

The purpose of this investigation was to determine the existence of bilateral strength and force-production asymmetry and evaluate possible differences based on sex, as well as strength level. Asymmetry was assessed during weight-distribution (WtD) testing, unloaded and lightly loaded static- (SJ) and countermovement-jump (CMJ) testing, and isometric midthigh-pull (IMTP) strength testing. Subjects included 63 athletes (31 male, 32 female) for WtD, SJ, and CMJ tests, while 129 athletes (64 male, 65 female) participated in IMTP testing. Independent-samples t tests were used to determine possible differences in asymmetry magnitude between males and females, as well as between strong and weak athletes. Cohen d effect-size (ES) estimates were also used to estimate difference magnitudes. Statistically different asymmetry levels with moderate to strong ESs were seen between males and females in WtD, 0-kg SJ (peak force [PF]), 20-kg SJ (peak power [PP]), 0-kg CMJ (PF, PP, net impulse), and 20-kg CMJ (PF), but no statistical differences were observed in IMTP variables. Dividing the sample into strong and weak groups produced statistically significant differences with strong ES estimates in IMTP PF and rate of force development, and many ESs in jump symmetry variables increased. The results of this investigation indicate that females may be more prone to producing forces asymmetrically than males during WtD and jumping tasks. Similarly, weaker athletes displayed more asymmetry than stronger athletes. This may indicate that absolute strength may play a larger role in influencing asymmetry magnitude than sex.
Changes in Physical Activity and Sedentary Behavior During the Transition From Elementary to Secondary School
Authors: Rutten Cindy , Boen Filip , Seghers Jan
Published: November 2014

Background:

The purpose of this study was to identify longitudinal changes in physical activity (PA) and sedentary behavior (SB) and to analyze its association with gender and weight status during the transition from elementary to secondary school.

Methods:

Flemish children were recruited in 6th grade of elementary school (age = 10.97 ± 0.41) and reassessed 2 years later (age = 12.96 ± .40). Children completed a questionnaire on moderate-to-vigorous PA and SB and wore pedometers to monitor habitual PA. Longitudinal data from 472 children were analyzed.

Results:

A significant decrease was observed in self-reported moderate to vigorous PA (-12.2%), but not in pedometer-determined PA. With respect to SB, a pronounced increase in recreational computer use was found (+3.22 hours/week), particularly in overweight boys (+8.18 hours/week). Finally, a significant increase in time spent on homework was observed in girls (+3.57 hours/week) and normal weight children (+2.83 hours/week).

Conclusions:

No longitudinal change in pedometer-determined PA was observed. Nevertheless, the decline in self-reported moderate-to-vigorous PA suggests that the transition to secondary school induced a change in the contribution of different types of PA. Finally, time spent on homework and recreational computer use increased during the school transition.
Adult Physical Activity Counseling by Health Professionals in Brazil: A National Urban Population Survey
Authors: Duro Suele Manjourany Silva , Tomasi Elaine , Siqueira Fernando Vinholes , Silveira Denise Silva , Thumé Elaine , Facchini Luiz Augusto
Published: November 2014

Background:

Physical activity counseling is an attribution of health professionals. As such, this paper aims to analyze the receipt of this form of counseling.

Methods:

Cross-sectional national study interviewing 12,402 adults living in the urban area of 100 Brazilian municipalities.

Results:

Overall counseling prevalence was 30%, falling to 20% when considering only counseling provided by health professionals. Counseling was significantly more frequent among women and among individuals who were older, married, had higher socioeconomic status, were former smokers, physically active, and reporting hypertension, diabetes, and excess weight.

Conclusions:

Little counseling was found to be done, this being a missed opportunity for health promotion. Health services and professionals therefore need to be trained and encouraged to provide adequate information to all health service users on the benefits of leading healthy lifestyles.
Accounting for Sitting and Moving: An Analysis of Sedentary Behavior in Mass Media Campaigns
Authors: Knox Emily , Biddle Stuart , Esliger Dale W. , Piggin Joe , Sherar Lauren
Published: November 2014

Background:

Mass media campaigns are an important tool for promoting health-related physical activity. The relevance of sedentary behavior to public health has propelled it to feature prominently in health campaigns across the world. This study explored the use of messages regarding sedentary behavior in health campaigns within the context of current debates surrounding the association between sedentary behavior and health, and messaging strategies to promote moderate-to-vigorous physical activity (MVPA).

Methods:

A web-based search of major campaigns in the United Kingdom, United States, Canada, and Australia was performed to identify the main campaign from each country. A directed content analysis was then conducted to analyze the inclusion of messages regarding sedentary behavior in health campaigns and to elucidate key themes. Important areas for future research were illustrated.

Results:

Four key themes from the campaigns emerged: clinging to sedentary behavior guidelines, advocating reducing sedentary behavior as a first step on the activity continuum and the importance of light activity, confusing the promotion of MVPA, and the demonization of sedentary behavior.

Conclusions:

Strategies for managing sedentary behavior as an additional complicating factor in health promotion are urgently required. Lessons learned from previous health communication campaigns should stimulate research to inform future messaging strategies.
Prevention and cure of rotavirus infection via TLR5/NLRC4–mediated production of IL-22 and IL-18
Authors: Zhang Benyue , Chassaing Benoit , Shi Zhenda , Uchiyama Robin , Zhang Zhan , Denning Timothy L. , Crawford Sue E. , Pruijssers Andrea J. , Iskarpatyoti Jason A. , Estes Mary K. , Dermody Terence S. , Ouyang Wenjun , Williams Ifor R. , Vijay-Kumar Matam , Gewirtz Andrew T.
Published: November 2014

Activators of innate immunity may have the potential to combat a broad range of infectious agents. We report that treatment with bacterial flagellin prevented rotavirus (RV) infection in mice and cured chronically RV-infected mice. Protection was independent of adaptive immunity and interferon (IFN, type I and II) and required flagellin receptors Toll-like receptor 5 (TLR5) and NOD-like receptor C4 (NLRC4). Flagellin-induced activation of TLR5 on dendritic cells elicited production of the cytokine interleukin-22 (IL-22), which induced a protective gene expression program in intestinal epithelial cells. Flagellin also induced NLRC4-dependent production of IL-18 and immediate elimination of RV-infected cells. Administration of IL-22 and IL-18 to mice fully recapitulated the capacity of flagellin to prevent or eliminate RV infection and thus holds promise as a broad-spectrum antiviral agent.
Defining a mesenchymal progenitor niche at single-cell resolution
Authors: Kumar Maya E. , Bogard Patrick E. , Espinoza F. Hernán , Menke Douglas B. , Kingsley David M. , Krasnow Mark A.
Published: November 2014

Most vertebrate organs are composed of epithelium surrounded by support and stromal tissues formed from mesenchyme cells, which are not generally thought to form organized progenitor pools. Here, we use clonal cell labeling with multicolor reporters to characterize individual mesenchymal progenitors in the developing mouse lung. We observe a diversity of mesenchymal progenitor populations with different locations, movements, and lineage boundaries. Airway smooth muscle (ASM) progenitors map exclusively to mesenchyme ahead of budding airways. Progenitors recruited from these tip pools differentiate into ASM around airway stalks; flanking stalk mesenchyme can be induced to form an ASM niche by a lateral bud or by an airway tip plus focal Wnt signal. Thus, mesenchymal progenitors can be organized into localized and carefully controlled domains that rival epithelial progenitor niches in regulatory sophistication.
A molecular ruler determines the repeat length in eukaryotic cilia and flagella
Authors: Oda Toshiyuki , Yanagisawa Haruaki , Kamiya Ritsu , Kikkawa Masahide
Published: November 2014

Existence of cellular structures with specific size raises a fundamental question in biology: How do cells measure length? One conceptual answer to this question is by a molecular ruler, but examples of such rulers in eukaryotes are lacking. In this work, we identified a molecular ruler in eukaryotic cilia and flagella. Using cryo-electron tomography, we found that FAP59 and FAP172 form a 96–nanometer (nm)–long complex in
Chlamydomonas
flagella and that the absence of the complex disrupted 96-nm repeats of axonemes. Furthermore, lengthening of the FAP59/172 complex by domain duplication resulted in extension of the repeats up to 128 nm, as well as duplication of specific axonemal components. Thus, the FAP59/172 complex is the molecular ruler that determines the 96-nm repeat length and arrangements of components in cilia and flagella.
Differential Mycobacterium bovis BCG Vaccine-Derived Efficacy in C3Heb/FeJ and C3H/HeOuJ Mice Exposed to a Clinical Strain of Mycobacterium tuberculosis
Authors: Henao-Tamayo Marcela , Obregón-Henao Andrés , Creissen Elizabeth , Shanley Crystal , Orme Ian , Ordway Diane J.
Published: November 2014

The global epidemic caused by the bacterial pathogenMycobacterium tuberculosiscontinues unabated. Moreover, the only available vaccine against tuberculosis,Mycobacterium bovisbacillus Calmette-Guérin (BCG), demonstrates variable efficacy. To respond to this global threat, new animal models that mimic the pathological disease process in humans are required for vaccine testing. One new model, susceptible C3Heb/FeJ mice, is similar to human tuberculosis in that these animals are capable of forming necrotic tubercle granulomas, in contrast to resistant C3H/HeOuJ mice. In this study, we evaluated the impact of prior BCG vaccination of C3Heb/FeJ and C3H/HeOuJ mice on exposure to a low-dose aerosol ofMycobacterium tuberculosisW-Beijing strain SA161. Both BCG-vaccinated murine strains demonstrated reduced bacterial loads 25 days after infection compared to controls, indicating vaccine efficacy. However, during chronic infection, vaccine efficacy waned in C3H/HeOuJ but not in C3Heb/FeJ mice. Protection in vaccinated C3Heb/FeJ mice was associated with reduced numbers of CD11b+Gr1+cells, increased numbers of effector and memory T cells, and an absence of necrotic granulomas. BCG vaccine efficacy waned in C3H/HeOuJ mice, as indicated by reduced expression of gamma interferon (IFN-γ) and increased expressions of interleukin-17 (IL-17), IL-10, and Foxp3 by T cells compared to C3Heb/FeJ mice. This is the first murine vaccine model system described to date that can be utilized to dissect differential vaccine-derived immune efficacy.
Supplementary Testing Is Not Required in the cobas 4800 CT/NG Test for Neisseria gonorrhoeae Weak-Positive Urogenital Samples
Authors: Bromhead Collette , Liyanarachchy Nadika , Mayes Julia , Upton Arlo , Balm Michelle
Published: November 2014

Weak-positive
Neisseria gonorrhoeae
nucleic acid amplification test results are difficult to interpret. We show that the frequency of unconfirmed
N. gonorrhoeae
results from the cobas 4800 test rises exponentially after 38.0 cycles, where the likelihood of an unconfirmed result exceeds 29%. Supplementary testing of such samples should be avoided; instead, treatment should be based on clinical pretest probability.
Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses
Authors: Pavšič Jernej , Devonshire Alison S. , Parkes Helen , Schimmel Heinz , Foy Carole A. , Karczmarczyk Maria , Gutiérrez-Aguirre Ion , Honeyborne Isobella , Huggett Jim F. , McHugh Timothy D. , Milavec Mojca , Zeichhardt Heinz , Žel Jana
Published: November 2014

Nucleic acid-based tests for infectious diseases currently used in the clinical laboratory and in point-of-care devices are diverse. Measurement challenges associated with standardization of quantitative viral load testing are discussed in relation to human cytomegalovirus, BK virus, and Epstein-Barr virus, while the importance of defining the performance of qualitative methods is illustrated with
Mycobacterium tuberculosis
and influenza virus. The development of certified reference materials whose values are traceable to higher-order standards and reference measurement procedures, using, for instance, digital PCR, will further contribute to the understanding of analytical performance characteristics and promote clinical data comparability.
Evaluation of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Vibrio cholerae
Authors: Rychert Jenna , Creely David , Mayo-Smith Leslie M. , Calderwood Stephen B. , Ivers Louise C. , Ryan Edward T. , Boncy Jacques , Qadri Firdausi , Ahmed Dilruba , Ferraro Mary Jane , Harris Jason B.
Published: November 2014

We evaluated the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MS) for the identification ofVibrio cholerae. MS identified all 42 isolates ofV. choleraeO1 and O139 and 7 of 9 non-O1/O139 isolates. MS correctly discriminated between allAeromonasandV. choleraeisolates. Overall, MS performed as well as or better than biochemical methods.
Evaluation of an Online Program To Teach Microbiology to Internal Medicine Residents
Authors: Guarner Jeannette , Burd Eileen M. , Kraft Colleen S. , Armstrong Wendy S. , Lenorr Kenya , Spicer Jennifer O. , Martin Donna , del Rio Carlos
Published: November 2014

Microbiology rounds are an integral part of infectious disease consultation service. During microbiology rounds, we highlight microbiology principles using vignettes. We created case-based, interactive, microbiology online modules similar to the vignettes presented during microbiology rounds. Since internal medicine residents rotating on our infectious disease elective have limited time to participate in rounds and learn microbiology, our objective was to evaluate the use of the microbiology online modules by internal medicine residents. We asked residents to complete 10 of 25 online modules during their infectious disease elective. We evaluated which modules they chose and the change in their knowledge level. Forty-six internal medicine residents completed assessments given before and after accessing the modules with an average of 11/20 (range, 6 to 19) and 16/20 (range, 9 to 20) correct questions, respectively (average improvement, 5 questions;
P
= 0.0001). The modules accessed by more than 30 residents included those related to
Clostridium difficile
, anaerobes,
Candida
spp.,
Streptococcus pneumoniae
, influenza,
Mycobacterium tuberculosis
, and
Neisseria meningitidis
. We demonstrated improved microbiology knowledge after completion of the online modules. This improvement may not be solely attributed to completing the online modules, as fellows and faculty may have provided additional microbiology education during the rotation.
The Nature of the N-Terminal Amino Acid Residue of HIV-1 RNase H Is Critical for the Stability of Reverse Transcriptase in Viral Particles
Authors: Boso Guney , Örvell Claes , Somia Nikunj V.
Published: November 2014

Reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) is synthesized and packaged into the virion as a part of the GagPol polyprotein. Mature RT is released by the action of viral protease. However, unlike other viral proteins, RT is subject to an internal cleavage event leading to the formation of two subunits in the virion: a p66 subunit and a p51 subunit that lacks the RNase H domain. We have previously identified RNase H to be an HIV-1 protein that has the potential to be a substrate for the N-end rule pathway, which is an ubiquitin-dependent proteolytic system in which the identity of the N-terminal amino acid determines the half-life of a protein. Here we examined the importance of the N-terminal amino acid residue of RNase H in the early life cycle of HIV-1. We show that changing this residue to an amino acid structurally different from the conserved residue leads to the degradation of RT and, in some cases, integrase in the virus particle and this abolishes infectivity. Using intravirion complementation and
in vitro
protease cleavage assays, we show that degradation of RT in RNase H N-terminal mutants occurs in the absence of active viral protease in the virion. Our results also indicate the importance of the RNase H N-terminal residue in the dimerization of RT subunits.

IMPORTANCE
HIV-1 proteins are initially made as part of a polyprotein that is cleaved by the viral protease into the proteins that form the virus particle. We were interested in one particular protein, RNase H, that is cleaved from reverse transcriptase. In particular, we found that the first amino acid of RNase H never varied in over 1,850 isolates of HIV-1 that we compared. When we changed the first amino acid, we found that the reverse transcriptase in the virus was degraded. While other studies have implied that the viral protease can degrade mutant RT proteins, we show here that this may not be the case for our mutants. Our results suggest that the presence of active viral protease is not required for the degradation of RT in RNase H N-terminal mutants, suggesting a role for a cellular protease in this process.
The Murine Norovirus Core Subgenomic RNA Promoter Consists of a Stable Stem-Loop That Can Direct Accurate Initiation of RNA Synthesis
Authors: Yunus Muhammad Amir , Lin Xiaoyan , Bailey Dalan , Karakasiliotis Ioannis , Chaudhry Yasmin , Vashist Surender , Zhang Guo , Thorne Lucy , Kao C. Cheng , Goodfellow Ian
Published: November 2014

All members of the
Caliciviridae
family of viruses produce a subgenomic RNA during infection. The subgenomic RNA typically encodes only the major and minor capsid proteins, but in murine norovirus (MNV), the subgenomic RNA also encodes the VF1 protein, which functions to suppress host innate immune responses. To date, the mechanism of norovirus subgenomic RNA synthesis has not been characterized. We have previously described the presence of an evolutionarily conserved RNA stem-loop structure on the negative-sense RNA, the complementary sequence of which codes for the viral RNA-dependent RNA polymerase (NS7). The conserved stem-loop is positioned 6 nucleotides 3′ of the start site of the subgenomic RNA in all caliciviruses. We demonstrate that the conserved stem-loop is essential for MNV viability. Mutant MNV RNAs with substitutions in the stem-loop replicated poorly until they accumulated mutations that revert to restore the stem-loop sequence and/or structure. The stem-loop sequence functions in a noncoding context, as it was possible to restore the replication of an MNV mutant by introducing an additional copy of the stem-loop between the NS7- and VP1-coding regions. Finally,
in vitro
biochemical data suggest that the stem-loop sequence is sufficient for the initiation of viral RNA synthesis by the recombinant MNV RNA-dependent RNA polymerase, confirming that the stem-loop forms the core of the norovirus subgenomic promoter.

IMPORTANCE
Noroviruses are a significant cause of viral gastroenteritis, and it is important to understand the mechanism of norovirus RNA synthesis. Here we describe the identification of an RNA stem-loop structure that functions as the core of the norovirus subgenomic RNA promoter in cells and
in vitro
. This work provides new insights into the molecular mechanisms of norovirus RNA synthesis and the sequences that determine the recognition of viral RNA by the RNA-dependent RNA polymerase.
Tulane Virus Recognizes the A Type 3 and B Histo-Blood Group Antigens
Authors: Zhang Dongsheng , Huang Pengwei , Zou Lu , Lowary Todd L. , Tan Ming , Jiang Xi
Published: November 2014

Tulane virus (TV), the prototype of the
Recovirus
genus in the calicivirus family, was isolated from the stools of rhesus monkeys and can be cultivated
in vitro
in monkey kidney cells. TV is genetically closely related to the genus
Norovirus
and recognizes the histo-blood group antigens (HBGAs), similarly to human noroviruses (NoVs), making it a valuable surrogate for human NoVs. However, the precise structures of HBGAs recognized by TV remain elusive. In this study, we performed binding and blocking experiments on TV with extended HBGA types and showed that, while TV binds all four types (types 1 to 4) of the B antigens, it recognizes only the A type 3 antigen among four types of A antigens tested. The requirements for HBGAs in TV replication were demonstrated by blocking of TV replication in cell culture using the A type 3/4 and B saliva samples. Similar results were also observed in oligosaccharide-based blocking assays. Importantly, the previously reported, unexplained increase in TV replication by oligosaccharide in cell-based blocking assays has been clarified, which will facilitate the application of TV as a surrogate for human NoVs.

IMPORTANCE
Our understanding of the role of HBGAs in NoV infection has been significantly advanced in the past decade, but direct evidence for HBGAs as receptors for human NoVs remains lacking due to a lack of a cell culture method. TV recognizes HBGAs and can replicate
in vitro
, providing a valuable surrogate for human NoVs. However, TV binds to some but not all saliva samples from A-positive individuals, and an unexplained observation of synthetic oligosaccharide blocking of TV binding has been reported. These issues have been resolved in this study.
Measles Virus Glycoprotein Complexes Preassemble Intracellularly and Relax during Transport to the Cell Surface in Preparation for Fusion
Authors: Brindley Melinda A. , Chaudhury Sukanya , Plemper Richard K.
Published: November 2014

Measles virus (MeV), a morbillivirus within the paramyxovirus family, expresses two envelope glycoproteins. The attachment (H) protein mediates receptor binding, followed by triggering of the fusion (F) protein, which leads to merger of the viral envelope with target cell membranes. Receptor binding by members of related paramyxovirus genera rearranges the head domains of the attachment proteins, liberating an F-contact domain within the attachment protein helical stalk. However, morbillivirus glycoproteins first assemble intracellularly prior to receptor binding, raising the question of whether alternative protein-protein interfaces are involved or whether an entirely distinct triggering principle is employed. To test these possibilities, we generated headless H stem mutants of progressively shorter length. Conformationally restricted H stems remained capable of intracellular assembly with a standard F protein and a soluble MeV F mutant. Proteolytic maturation of F, but not the altered biochemical conditions at the cell surface, reduces the strength of glycoprotein interaction, readying the complexes for triggering. F mutants stabilized in the prefusion conformation interact with H intracellularly and at the cell surface, while destabilized F mutants interact only intracellularly, prior to F maturation. These results showcase an MeV entry machinery that functionally varies conserved motifs of the proposed paramyxovirus infection pathway. Intracellular and plasma membrane-resident MeV glycoprotein complexes employ the same protein-protein interface. F maturation prepares for complex separation after triggering, and the H head domains in prereceptor-bound conformation prevent premature stalk rearrangements and F activation. Intracellular preassembly affects MeV fusion profiles and may contribute to the high cell-to-cell fusion activity characteristic of the morbillivirus genus.

IMPORTANCE
Paramyxoviruses of the morbillivirus genus, such as measles, are highly contagious, major human and animal pathogens. MeV envelope glycoproteins preassemble intracellularly into tightly associated hetero-oligomers. To address whether preassembly reflects a unique measles virus entry strategy, we characterized the protein-protein interface of intracellular and surface-exposed fusion complexes and investigated the effect of the attachment protein head domains, glycoprotein maturation, and altered biochemical conditions at the cell surface on measles virus fusion complexes. Our results demonstrate that measles virus functionally varies conserved elements of the paramyxovirus entry pathway, providing a possible explanation for the high cell-to-cell fusion activity of morbilliviruses. Insight gained from these data affects the design of effective broad-spectrum paramyxovirus entry inhibitors.
Structure-Based Functional Analyses of Domains II and III of Pseudorabies Virus Glycoprotein H
Authors: Böhm Sebastian W. , Eckroth Elisa , Backovic Marija , Klupp Barbara G. , Rey Felix A. , Mettenleiter Thomas C. , Fuchs Walter
Published: November 2014

Enveloped viruses utilize membrane fusion for entry into, and release from, host cells. For entry, members of the
Herpesviridae
require at least three envelope glycoproteins: the homotrimeric gB and a heterodimer of gH and gL. The crystal structures of three gH homologues, including pseudorabies virus (PrV) gH, revealed four conserved domains. Domain II contains a planar β-sheet (“fence”) and a syntaxin-like bundle of three α-helices (SLB), similar to those found in eukaryotic fusion proteins, potentially executing an important role in gH function. To test this hypothesis, we introduced targeted mutations into the PrV gH gene, which either disrupt the helices of the SLB by introduction of proline residues or covalently join them by artificial intramolecular disulfide bonds between themselves, to the adjacent fence region, or to domain III. Disruption of either of the three α-helices of the SLB (A250P, V275P, V298P) severely affected gH function in
in vitro
fusion assays and replication of corresponding PrV mutants. Considerable defects in fusion activity of gH, as well as in penetration kinetics and cell-to-cell spread of PrV mutants, were also observed after disulfide linkage of two α-helices within the SLB (A284C-S291C) or between SLB and domain III (H251C-L432C), as well as by insertions of additional cysteine pairs linking fence, SLB, and domain III.
In vitro
fusion activity of mutated gH could be partly restored by reduction of the artificial disulfide bonds. Our results indicate that the structure and flexibility of the SLB are relevant for the function of PrV gH in membrane fusion.

IMPORTANCE
Mutational analysis based on crystal structures of proteins is a powerful tool to understand protein function. Here, we continued our study of pseudorabies virus gH, a part of the core fusion machinery of herpesviruses. We previously showed that the “flap” region in domain IV of PrV gH is important for its function. We now demonstrate that mutations within domain II that interfere with integrity or flexibility of a syntaxin-like three-helix bundle also significantly impair gH function during fusion. These studies provide important insights into the structural requirements of gH for function in fusion.
Ebola Virus Transmission in Guinea Pigs
Authors: Wong Gary , Qiu Xiangguo , Richardson Jason S. , Cutts Todd , Collignon Brad , Gren Jason , Aviles Jenna , Embury-Hyatt Carissa , Kobinger Gary P.
Published: November 2014

Ebola virus (EBOV) transmission is currently poorly characterized and is thought to occur primarily by direct contact with infectious material; however transmission from swine to nonhuman primates via the respiratory tract has been documented. To establish an EBOV transmission model for performing studies with statistical significance, groups of six guinea pigs (gps) were challenged intranasally (i.n.) or intraperitoneally (i.p.) with 10,000 times the 50% lethal dose (LD
50
) of gp-adapted EBOV, and naive gps were then introduced as cage mates for contact exposure at 1 day postinfection (p.i.). The animals were monitored for survival and clinical signs of disease and quantitated for virus shedding postexposure. Changes in the duration of contact of naive gps with infected animals were evaluated for their impact on transmission efficiency. Transmission was more efficient from i.n.- than from i.p.-challenged gps, with 17% versus 83% of naive gps surviving exposure, respectively. Virus shedding was detected beginning at 3 days p.i. from both i.n.- and i.p.-challenged animals. Contact duration positively correlated with transmission efficiency, and the abrogation of direct contact between infected and naive animals through the erection of a steel mesh was effective at stopping virus spread, provided that infectious animal bedding was absent from the cages. Histopathological and immunohistochemical findings show that i.n.-infected gps display enhanced lung pathology and EBOV antigen in the trachea, which supports increased virus transmission from these animals. The results suggest that i.n.-challenged gps are more infectious to naive animals than their systemically infected counterparts and that transmission occurs through direct contact with infectious materials, including those transported through air movement over short distances.

IMPORTANCE
Ebola is generally thought to be spread between humans though infectious bodily fluids. However, a study has shown that Ebola can be spread from pigs to monkeys without direct contact. Further studies have been hampered, because an economical animal model for Ebola transmission is not available. To address this, we established a transmission model in guinea pigs and determined the mechanisms behind virus spread. The survival data, in addition to microscopic examination of lung and trachea sections, show that mucosal infection of guinea pigs is an efficient model for Ebola transmission. Virus spread is increased with longer contact times with an infected animal and is possible without direct contact between an infected and a naive host but can be stopped if infectious materials are absent. These results warrant consideration for the development of future strategies against Ebola transmission and for a better understanding of the parameters involved in virus spread.
A Cryo-Electron Microscopy Study Identifies the Complete H16.V5 Epitope and Reveals Global Conformational Changes Initiated by Binding of the Neutralizing Antibody Fragment
Authors: Lee Hyunwook , Brendle Sarah A. , Bywaters Stephanie M. , Guan Jian , Ashley Robert E. , Yoder Joshua D. , Makhov Alexander M. , Conway James F. , Christensen Neil D. , Hafenstein Susan
Published: November 2014

Human papillomavirus 16 (HPV16) is a worldwide health threat and an etiologic agent of cervical cancer. To understand the antigenic properties of HPV16, we pursued a structural study to elucidate HPV capsids and antibody interactions. The cryo-electron microscopy (cryo-EM) structures of a mature HPV16 particle and an altered capsid particle were solved individually and as complexes with fragment of antibody (Fab) from the neutralizing antibody H16.V5. Fitted crystal structures provided a pseudoatomic model of the virus-Fab complex, which identified a precise footprint of H16.V5, including previously unrecognized residues. The altered-capsid–Fab complex map showed that binding of the Fab induced significant conformational changes that were not seen in the altered-capsid structure alone. These changes included more ordered surface loops, consolidated so-called “invading-arm” structures, and tighter intercapsomeric connections at the capsid floor. The H16.V5 Fab preferentially bound hexavalent capsomers likely with a stabilizing effect that directly correlated with the number of bound Fabs. Additional cryo-EM reconstructions of the virus-Fab complex for different incubation times and structural analysis provide a model for a hyperstabilization of the capsomer by H16.V5 Fab and showed that the Fab distinguishes subtle differences between antigenic sites.

IMPORTANCE
Our analysis of the cryo-EM reconstructions of the HPV16 capsids and virus-Fab complexes has identified the entire HPV.V5 conformational epitope and demonstrated a detailed neutralization mechanism of this clinically important monoclonal antibody against HPV16. The Fab bound and ordered the apical loops of HPV16. This conformational change was transmitted to the lower region of the capsomer, resulting in enhanced intercapsomeric interactions evidenced by the more ordered capsid floor and “invading-arm” structures. This study advances the understanding of the neutralization mechanism used by H16.V5.
Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes
Authors: Zhou Jinglie , Sun Dawei , Childers Alyson , McDermott Timothy R. , Wang Yongjie , Liles Mark R.
Published: November 2014

Virophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.

IMPORTANCE
This study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photic-zone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.
Extrauterine fibroids: a diagnostic challenge and a long-term battle
Authors: Chin Hsuan , Ong Xiaohui H , Yam Philip Kwai Lam , Chern Bernard Su Min
Published: November 2014

Extrauterine fibroids often present a diagnostic challenge due to the unusual locations they arise from. We present a series of rare extrauterine fibroids. In recent years, these fibroids have been associated with previous morcellated hysterectomies or myomectomies. Our series of six patients were found to have extrauterine fibroids (confirmed through histology) and underwent open hysterectomy and open or laparoscopic myomectomy. Four had undergone previous laparoscopic myomectomies while the other two had no previous intra-abdominal surgeries. Postsurgical occurrence may be caused by incomplete removal of morcellated fibroid tissue. Spontaneous occurrence can be associated with congenital Müllerian system defects. Extrapolating from this hypothesis, we recommend physicians to make sure that counselling for extrauterine seeding and dissemination of unexpected malignancy is undertaken in cases of minimally invasive surgeries where morcellation is expected. Long-term tumour surveillance is thus essential in such instances.
Steroid-induced scleroderma renal crisis in an at-risk patient
Authors: Toescu Sebastian Miguel , Mansell Alex , Dinneen Eoin , Persey Malcolm
Published: November 2014

Scleroderma renal crisis (SRC) is a major complication of systemic sclerosis (SSc). We present a case of a patient who died of complications attributable to SRC in the context of recently diagnosed SSc. We review the typical clinical and laboratory features of SSc present in our patient and highlight those that identify greater risk of progression to SRC. Particular risk factors for SRC include cutaneous involvement, positive anti-RNA polymerase III antibodies and use of corticosteroids (CS). The authors emphasise the importance of risk evaluation when choosing to use CS in patients with SSc.
Acupuncture for postherpetic neuralgia: a systematic review protocol
Authors: Li Wang , Peng Weina , Zhou Jing , Liu Zhishun
Published: November 2014

Introduction

Postherpetic neuralgia (PHN) is one of the most common complications following herpes zoster. Clinical trials indicate that acupuncture could reduce pain and discomfort among patients with PHN. This protocol aims to describe how to accumulate the current evidence on the efficacy and safety of acupuncture for treating PHN.

Methods and analysis

This systematic review will electronically search multiple databases including the Cochrane Skin Group Trials Register, MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese Biomedical Literature Database (CBM), the Chinese Medical Current Content (CMCC) and the China National Knowledge Infrastructure (CNKI), and will hand search a list of medical journals as a supplement. Any clinical randomised controlled trials related to acupuncture for treating PHN will be included. Outcomes will include pain intensity, global impression, quality of life, safety and costs. By screening the titles, abstracts and full texts, two reviewers will independently select studies, extract data, and assess study quality. Meta-analysis of randomised controlled trials will be conducted using Revman 5.1 software. The results will be presented as risk ratio for dichotomous data, and standardised or weighted mean difference for continuous data.

Ethics and dissemination

This systematic review does not need ethical approval because there are no data used in our study that are linked to individual patient data. Also, the findings will be disseminated through a peer-review publication or conference presentation.

Trial registration number

PROSPERO registration number: CRD42014009555.
Development and validation of a new disease severity index: the Inflammatory Bowel Disease Index (IBDEX)
Authors: Alrubaiy Laith , Dodds Phedra , Hutchings Hayley Anne , Russell Ian Trevor , Watkins Alan , Williams John Gordon
Published: November 2014

Objective

To develop, validate and apply a generic clinical severity index applicable to all adult patients with inflammatory bowel disease (IBD).

Design

A review of the literature and an expert focus group consultation were carried out in order to draw out relevant items from existing literature. The new index was called the IBD Index (IBDEX). Standard psychometric analysis was carried out. The construct validity was assessed against biochemical markers, clinical and endoscopic indices. The new index was completed again within 6 weeks to check responsiveness and reproducibility.

Results

IBDEX was used to assess 255 adult patients with IBD (125 with Crohn’s disease and 130 with ulcerative colitis), and 64 patients were re-evaluated within 6 weeks. It had good internal consistency (Cronbach's α=0.79) and correlated very well with the Harvey Bradshaw Index (r=0.94), the Simple Clinical Colitis Activity Index (r=0.92), the Mayo Clinic Index (r=0.87) and the Simple Endoscopic Score (r=0.76), all with p values <0.05. IBDEX had a moderate but positive correlation with C reactive protein (r=0.51) and erythrocyte sedimentation rate (r=0.36) p values both <0.05. The test–retest reliability was good (intraclass correlation coefficient 0.97) and responsiveness ratio was 2.27.

Conclusions

IBDEX is the first properly validated Clinical Disease Severity Index in IBD. Our results showed that it is valid, reliable and reproducible and has the potential to be used in clinical practice.
Diagnosis and treatment of generalised tetanus in dogs
Authors: Fawcett Anne , Irwin Peter
Published: November 2014

Generalised tetanus in the canine patient, well described in numerous case reports, is a life‐threatening disorder. The causative organism, Clostridium tetani, produces a potent neurotoxin that causes dramatic clinical signs, including spastic paralysis.

The prognosis for patients receiving treatment is good but, as recovery is prolonged, many dogs are euthanased because of estimated costs of hospitalisation. This article discusses the diagnosis and treatment of generalised tetanus in the dog and the potential complications.
Studying the lepton number and lepton flavor violating $D^0\to e^\pm\mu^\mp$ and $D^+_{d/s}\to \pi(K)^+e^\pm\mu^\mp$ decays
Authors: Wang Ru-Min , Sheng Jin-Huan , Zhu Jie , Fan Ying-Ying , Gao Yang
Published: November 2014

The rare D decays are sensitive to new physics involving the up quark sector such as certain R-parity violating supersymmetric models. We study the lepton number and lepton flavor violating [Formula: see text] and [Formula: see text] decays in the supersymmetry without R-parity. From the best experimental upper limits of these decay branching ratios, we derive constraints on the relevant coupling products for the first time, and examine their contributions to relevant branching ratios and dileptonic invariant mass spectra. We find that all branching ratios are very sensitive to moduli of the squark exchange coupling products. Accurate measurements of these decay branching ratios in the future experiments at LHC and BESIII could give very strong bounds on relevant lepton number and lepton flavor violating coupling products.
Influence of the deformable substrate potential on Shapiro steps in the incommensurate structure
Authors: Shao Zhi-Gang , Li Jia-Yu , Wang Cang-Long , Yang Lei
Published: November 2014

Influence of the deformable substrate potential on Shapiro steps is investigated in the overdamped Frenkel–Kontorova model with incommensurate structure. Both the number and size of Shapiro steps are strongly affected by the deformation of substrate potential. As substrate potential gets deformed, the oscillation of Shapiro steps reduces and the periodicity of oscillation significantly changes. For some value of shape parameter r, the odd and even maxima oscillation forms of harmonic steps still maintain the Bessel-like form. Compared with those in standard potential, the amplitude dependence of harmonic step exhibits obvious difference. The dynamical DC threshold force correspondingly increases with rising the value of r.