bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of p38 MAPK activation attenuates esophageal mucosal damage in a chronic model of reflux esophagitis
Authors: Zhang L. , Liu G. , Han X. , Liu J. , Li G.‐X. , Zou D.‐W. , Li Z.‐S.
Published: September 2015

Background

Reflux esophagitis (RE) is one of the common gastrointestinal diseases that are increasingly recognized as a significant health problem. This study was designed to investigate the role of p38 mitogen‐activated protein kinase (MAPK) in experimental chronic RE model of rats.

Methods

Chronic acid RE rats were induced by fundus ligation and partial obstruction of the pylorus and treated with SB203580 (a p38 MAPK inhibitor, i.p., 1 mg/kg/day) for 14 days.

Key Results

Immunohistochemical staining and Western blotting results revealed the activation of p38 MAPK signaling in the esophagus mucosa 14 days post injury. Through gross and histological assessment, we found that inhibition of p38 MAPK activation by SB203580 attenuated esophageal mucosal damage in RE rats. Inhibition of p38 MAPK activation in RE rats attenuated esophageal barrier dysfunction, through enhancing the expression of tight junction proteins and reducing the expression of matrix matalloproteinases‐3 and ‐9. Inhibition of p38 MAPK activation in RE rats reduced CD68‐positive cells in esophagus mucosa and mRNA levels of tumor necrosis factor (TNF)‐α, interleukin (IL)‐6, and IL‐1β in esophagus and protein levels of TNF‐α, IL‐6, and IL‐1β in serum. In addition, we found that inhibition of p38 MAPK activation in RE rats suppressed protein expression of inducible nitric oxide synthase and reduced formation of nitric oxide (NO), 3‐nitrotyrosin, and malondialdehyde in esophagus.

Conclusions & Inferences

Inhibition of p38 MAPK activation attenuated esophageal mucosal damage in acid RE rats, possibly by modulating esophageal barrier function and regulating inflammatory cell recruitment, and the subsequent formation of cytokines, NO, and reactive oxygen species.
Ubiquitin‐conjugated degradation of golden 2‐like transcription factor is mediated by CUL4‐DDB1‐based E3 ligase complex in tomato
Authors: Tang Xiaofeng , Miao Min , Niu Xiangli , Zhang Danfeng , Cao Xulv , Jin Xichen , Zhu Yunye , Fan Youhong , Wang Hongtao , Liu Ying , Sui Yuan , Wang Wenjie , Wang Anquan , Xiao Fangming , Giovannoni Jim , Liu Yongsheng
Published: September 2015

CULLIN4‐RING ubiquitin ligases (CRL4s) as well as their targets are fundamental regulators functioning in many key developmental and stress responses in eukaryotes. In tomato (Solanum lycopersicum), molecular cloning has revealed that the underlying genes of natural spontaneous mutations high pigment 1 (hp1), high pigment 2 (hp2) and uniform ripening (u) encode UV‐DAMAGED DNA BINDING PROTEIN 1 (DDB1), DE‐ETIOLATED 1 (DET1) and GOLDEN 2‐LIKE (GLK2), respectively. However, the molecular basis of the opposite actions of tomato GLK2 vs CUL4‐DDB1‐DET1 complex on regulating plastid level and fruit quality remains unknown.

Here, we provide molecular evidence showing that the tomato GLK2 protein is a substrate of the CUL4‐DDB1‐DET1 ubiquitin ligase complex for the proteasome degradation.

SlGLK2 is degraded by the ubiquitin‐proteasome system, which is mainly determined by two lysine residues (K11 and K253). SlGLK2 associates with the CUL4‐DDB1‐DET1 E3 complex in plant cells. Genetically impairing CUL4, DDB1 or DET1 results in a retardation of SlGLK2 degradation by the 26S proteasome.

These findings are relevant to the potential of nutrient accumulation in tomato fruit by mediating the plastid level and contribute to a deeper understanding of an important regulatory loop, linking protein turnover to gene regulation.
Interaction of obesity and infections
Authors: Dhurandhar N. V. , Bailey D. , Thomas D.
Published: September 2015

There is evidence that certain infections may induce obesity. Obese persons may also have more severe infections and have compromised response to therapies. The objective of this study is to review the available literature identifying infections that potentially contribute to greater body mass index (BMI) and differential responses of overweight and obese persons to infections. A systematic literature review of human studies examining associations between infections and weight gain, differential susceptibility, severity, and response to prevention and treatment of infection according to BMI status (January 1980–July 2014) was conducted. Three hundred and forty‐three studies were eligible for inclusion. Evidence indicated that viral infection by human adenovirus Ad36 and antibiotic eradication of Helicobacter pylori were followed by weight gain. People who were overweight or obese had higher susceptibility to developing post‐surgical infections, H1N1 influenza and periodontal disease. More severe infections tended to be present in people with a larger BMI. People with a higher BMI had a reduced response to vaccinations and antimicrobial drugs. Higher doses of antibiotics were more effective in obese patients. Infections may influence BMI, and BMI status may influence response to certain infections, as well as to preventive and treatment measures. These observations have potential clinical implications.
A corneal elastic dynamic model derived from Scheimpflug imaging technology
Authors: Shih Po‐Jen , Cao Huei‐Jyun , Huang Chun‐Ju , Wang I‐Jong , Shih Wen‐Pin , Yen Jia‐Yush
Published: September 2015

Purpose

To simultaneously extract the corneal Young's modulus and the damping ratio from Scheimpflug imaging data.

Methods

A spherical diaphragm model can better represent the geometry and physics of an eyeball than the popular mass‐spring‐damper model. This research derived the dynamic model of a water‐filled spherical diaphragm based on the hydrodynamics and wave propagation theories. By applying modal analysis on the model, one can decouple the cornea vibration into individual modes and reconstruct the air puff vibration from the decoupled responses. By matching this response with the Scheimpflug imaging data from the Corvis® ST, it was then possible to extract multiple physiological properties as desired.

Results

The dynamic modal analysis was employed to extract the corneal physiological properties of 25 Taiwanese normal subjects. Specifically, the corneal Young's moduli and damping ratios were estimated. In fact the model is dependent on the physiological parameters such as cornea thickness, densities, and intraocular pressure. It is thus also possible to extract these parameters through multi‐goal minimisation processes.

Conclusions

The spherical diaphragm model was able to better describe the dynamic response of the eyeball. The model analysis also provides additional corneal physiological properties that were not available through other means.
Age and the amplitude of accommodation measured using dynamic retinoscopy
Authors: León Alejandro , Estrada Jorge M. , Rosenfield Mark
Published: September 2015

Purpose

Dynamic retinoscopy (DR) is a procedure for assessing the accommodative response using a standard clinical instrument. The present study compared measurements of the amplitude of accommodation (AA) obtained using this technique with two subjective methods (modified push‐down and minus lens). Additionally, the expected ranges for AA when measured by DR were determined.

Method

AA was measured in 1298 subjects between 5 and 60 years of age using the three techniques described above. Subjects were grouped into 5‐year bins, and a descriptive univariate analysis of the data performed. Goodness‐of fit plots were constructed to examine the overall model fit. Centile curves were calculated from the final model.

Results

Mean values of AA obtained using DR were significantly lower than for the two subjective techniques. For the DR findings, no significant change was observed between 5 and 19 years of age (mean AA = 8.3 D) and between 45 and 60 years of age (mean AA = 0.6 D). AA values as a function of age were best fit by the polynomial regression equation: logAA = 1.93 + 0.49(age) − 0.19(age)2.

Conclusion

Measurements of AA determined using DR are significantly lower than the normative subjective findings published previously. This difference is at least partly due to the depth‐of‐field of the eye. These norms markedly overestimate accommodative responsivity. DR provides a simple technique for quantifying accommodation in the clinical setting.
A Cholesterol‐Dependent Endocytic Mechanism Generates Midbody Tubules During Cytokinesis
Authors: Kettle Emma , Page Scott L. , Morgan Garry P. , Malladi Chandra S. , Wong Chin L. , Boadle Ross A. , Marsh Brad J. , Robinson Phillip J. , Chircop Megan
Published: September 2015

Cytokinesis is the final stage of cell division and produces two independent daughter cells. Vesicles derived from internal membrane stores, such as the Golgi, lysosomes, and early and recycling endosomes accumulate at the intracellular bridge (ICB) during cytokinesis. Here, we use electron tomography to show that many ICB vesicles are not independent but connected, forming a newly described ICB vesicular structure – narrow tubules that are often branched. These ‘midbody tubules’ labelled with horseradish peroxidase (HRP) within 10 min after addition to the surrounding medium demonstrating that they are derived from endocytosis. HRP‐labelled vesicles and tubules were observed at the rim of the ICB after only 1 min, suggesting that midbody tubules are likely to be generated by local endocytosis occurring at the ICB rim. Indeed, at least one tubule was open to the extracellular space, indicative of a local origin within the ICB. Inhibition of cholesterol‐dependent endocytosis by exposure to methyl‐β‐cyclodextrin and filipin reduced formation of HRP‐labelled midbody tubules, and induced multinucleation following ICB formation. In contrast, dynamin inhibitors, which block clathrin‐mediated endocytosis, induced multinucleation but had no effect on the formation of HRP‐labelled midbody tubules. Therefore, our data reveal the existence of a cholesterol‐dependent endocytic pathway occurring locally at the ICB, which contributes to the accumulation of vesicles and tubules that contribute to the completion of cytokinesis.
Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia
Authors: Shen Xin , Sun Song , Zhao Fang Qing , Zhang Guang Tao , Tian Mei , Tsang Ling Ming , Wang Jin Feng , Chu Ka Hou
Published: September 2015

The phylum Chaetognatha (arrow worms) comprises a group of small marine predators that constitute a critical component of the zooplankton community throughout the world's oceans. Various phylogenetic affiliations have been proposed for the Chaetognatha, for which there are at least nine possible phylogenetic positions. Resolving the phylogenetic position of the chaetognaths is a key in understanding the fundamental developmental features of bilaterians. In comparison with the typical gene content of metazoan mitogenomes, two protein‐coding genes (atp6 and atp8) are absent from all chaetognaths. The two mitogenomes sequenced from Sagitta crassa and Zonosagitta nagae in this study nevertheless contain two and four tRNA genes, respectively, in contrast to those of the other five chaetognaths reported where only one tRNA gene (trnMet) is present, thus invalidating the view that all chaetognath mitogenomes have a single tRNA gene. A conserved major gene order shared by all chaetognaths could be partially identified in many protostome mitogenomes, but not in any ancestral mitogenome gene arrangement of the four deuterostome groups. Phylogenetic analysis of the deduced amino acid sequences of protein‐coding genes from 85 mitogenomes of 19 groups suggests the Chaetognatha to be a sister group to the protostomes, a result consistent with evidences from the developmental pattern and other molecular analyses.
On the Propagation and Attenuation of Turbulent Fluid Transients in Circular Pipes
Authors: Wahba E. M.
Published: September 2015

The attenuation of turbulent fluid transients in pipes is numerically investigated in the present study using one-dimensional (1D) and two-dimensional (2D) water hammer models. The method of characteristics (MOC) is used for the integration of the 1D model, while the semidiscretization approach and the fourth-order accurate Runge–Kutta method are used for the integration of the 2D model. The present results for a reservoir–pipe–valve system indicate that the damping of the transient is governed by a nondimensional parameter representing the ratio of the steady-state frictional head to the Joukowsky pressure head. Based on this parameter, the attenuation of the transient could be classified into three main categories. The first category is for values of the nondimensional parameter much smaller than unity, where attenuation of the transient is insignificant and line packing effects are negligible. The second category is for values of the parameter approaching unity, where the attenuation of the transient is significant and line packing results in a pressure rise at the valve that is slightly higher than the Joukowsky pressure rise. The third category is for values of the parameter much greater than unity, such as in long cross-country pipelines, where the transient is damped out within a few cycles and excessive line packing effects would result in a pressure rise at the valve that is significantly larger the Joukowsky pressure rise.
Numerical Investigation of Contrasting Flow Physics in Different Zones of a High-Lift Low-Pressure Turbine Blade
Authors: Cui Jiahuan , Nagabhushana Rao V. , Tucker Paul
Published: September 2015

Using a range of high-fidelity large eddy simulations (LES), the contrasting flow physics on the suction surface, pressure surface, and endwalls of a low-pressure turbine (LPT) blade (T106A) was studied. The current paper attempts to provide an improved understanding of the flow physics over these three zones under the influence of different inflow boundary conditions. These include: (a) the effect of wakes at low and high turbulence intensity on the flow at midspan and (b) the impact of the state of the incoming boundary layer on endwall flow features. On the suction surface, the pressure fluctuations on the aft portion significantly reduced at high freestream turbulence (FST). The instantaneous flow features revealed that this reduction at high FST (HF) is due to the dominance of “streak-based” transition over the “Kelvin–Helmholtz” (KH) based transition. Also, the transition mechanisms observed over the turbine blade were largely similar to those on a flat plate subjected to pressure gradients. On pressure surface, elongated vortices were observed at low FST (LF). The possibility of the coexistence of both the Görtler instability and the severe straining of the wakes in the formation of these elongated vortices was suggested. While this was true for the cases under low turbulence levels, the elongated vortices vanished at higher levels of background turbulence. At endwalls, the effect of the state of the incoming boundary layer on flow features has been demonstrated. The loss cores corresponding to the passage vortex and trailing shed vortex were moved farther from the endwall with a turbulent boundary layer (TBL) when compared to an incoming laminar boundary layer (LBL). Multiple horse-shoe vortices, which constantly moved toward the leading edge due to a low-frequency unstable mechanism, were captured.
Thin-Shell Thickness of Two-Dimensional Materials
Authors: Gao Enlai , Xu Zhiping
Published: September 2015

In applying the elastic shell models to monolayer or few-layer two-dimensional (2D) materials, an effective thickness has to be defined to capture their tensile and out-of-plane mechanical behaviors. This thin-shell thickness differs from the interlayer distance of their layer-by-layer assembly in the bulk and is directly related to the Föppl–von Karman number that characterizes the mechanism of nonlinear structural deformation. In this work, we assess such a definition for a wide spectrum of 2D crystals of current interest. Based on first-principles calculations, we report that the discrepancy between the thin-shell thickness and interlayer distance is weakened for 2D materials with lower tensile stiffness, higher bending stiffness, or more number of atomic layers. For multilayer assembly of 2D materials, the tensile and bending stiffness have different scaling relations with the number of layers, and the thin-shell thickness per layer approaches the interlayer distance as the number of layers increases. These findings lay the ground for constructing continuum models of 2D materials with both tensile and bending deformation.
Assessment of Dimensional Integrity and Spatial Defect Localization in Additive Manufacturing Using Spectral Graph Theory
Authors: Rao Prahalad K. , Kong Zhenyu , Duty Chad E. , Smith Rachel J. , Kunc Vlastimil , Love Lonnie J.
Published: September 2015

The ability of additive manufacturing (AM) processes to produce components with virtually any geometry presents a unique challenge in terms of quantifying the dimensional quality of the part. In this paper, a novel spectral graph theory (SGT) approach is proposed for resolving the following critical quality assurance concern in the AM: how to quantify the relative deviation in dimensional integrity of complex AM components. Here, the SGT approach is demonstrated for classifying the dimensional integrity of standardized test components. The SGT-based topological invariant Fiedler number (λ2) was calculated from 3D point cloud coordinate measurements and used to quantify the dimensional integrity of test components. The Fiedler number was found to differ significantly for parts originating from different AM processes (statistical significance p-value <1%). By comparison, prevalent dimensional integrity assessment techniques, such as traditional statistical quantifiers (e.g., mean and standard deviation) and examination of specific facets/landmarks failed to capture part-to-part variations, proved incapable of ranking the quality of test AM components in a consistent manner. In contrast, the SGT approach was able to consistently rank the quality of the AM components with a high degree of statistical confidence independent of sampling technique used. Consequently, from a practical standpoint, the SGT approach can be a powerful tool for assessing the dimensional integrity of the AM components, and thus encourage wider adoption of the AM capabilities.
Control of Magnetic Bearings for Rotor Unbalance With Plug-In Time-Varying Resonators
Authors: Kang Christopher , Tsao Tsu-Chin
Published: September 2015

Rotor unbalance, common phenomenon of rotational systems, manifests itself as a periodic disturbance synchronized with the rotor's angular velocity. In active magnetic bearing (AMB) systems, feedback control is required to stabilize the open-loop unstable electromagnetic levitation. Further, feedback action can be added to suppress the repeatable runout but maintain closed-loop stability. In this paper, a plug-in time-varying resonator is designed by inverting cascaded notch filters. This formulation allows flexibility in designing the internal model for appropriate disturbance rejection. The plug-in structure ensures that stability can be maintained for varying rotor speeds. Experimental results of an AMB–rotor system are presented.
Mixed Uncertainty Analysis of Pole Placement and H∞ Controllers for Directional Drilling Attitude Tracking
Authors: Bayliss Martin T. , Whidborne James F.
Published: September 2015

This paper describes the design of attitude-hold controllers and their subsequent stability and performance analysis for directional drilling tools as typically used in the oil industry. Based on an input transformation developed in earlier work that partially linearizes and decouples the plant dynamics of the drilling tool, the resulting plant model is used as the basis for both pole placement and optimal H∞ controller designs. A mixed uncertainty stability and performance analysis is then performed on each of the controller designs. Results for a transient simulation of the proposed controller are also presented.
ZrC epitaxy on Si(111)
Authors: Aizawa Takashi , Otani Shigeki , Ohkubo Isao , Mori Takao
Published: September 2015

ZrC epitaxy was examined on ZrC(111) (homoepitaxy) and on several reconstructed Si(111) surfaces using physical vapor deposition: clean 7 × 7, 3×3-Al, 3×3-Ga, and 3×3-Ag. Layer-by-layer homoepitaxy was realized at a temperature as low as 400 °C on clean ZrC(111). Even at room temperature, it grew epitaxially although the surface became rough. On a Si(111) substrate at 400–600 °C, ZrC grew epitaxially but with a rough surface. Above 800 °C, ZrC and Si reacted to produce other silicide phases. The epitaxial relation was (111)ZrC∥(111)Si and [11¯0]ZrC∥[11¯0]Si, cube-on-cube, which was not influenced by the substrate reconstruction. Actually, Si was detected on all film surfaces grown at temperatures above 400 °C, which was probably diffused from the substrate onto the surface. The authors clarified an important problem: surface-segregated Si disturbs the layer-by-layer epitaxy of ZrC.
A theoretical relation between the celerity and trace velocity of infrasonic phases
Authors: Lonzaga Joel B.
Published: September 2015

This paper presents a relationship between the celerity and trace velocity of infrasound signals propagating in a stratified, windy atmosphere. Despite their importance, known celerity values have only been determined empirically. An infrasonic phase (I-phase) diagram is developed which is useful in identifying different I-phases. Such an I-phase diagram allows for the prediction of the range of values of the celerity and trace velocity for each I-phase. The phase diagram can easily be extended to underwater acoustic and acoustic-gravity waves. An I-phase diagram is compared with data obtained from a ground-truth event where qualitative agreement is obtained.
Assignment of Weight-Based Antibody Units for Seven Additional Serotypes to a Human Pneumococcal Standard Reference Serum, 007sp
Authors: Goldblatt D. , Tan C. Y. , Burbidge P. , McElhiney S. , McLaughlin L. , Tucker R. , Rauh M. , Sidhu M. , Giardina P. C.
Published: September 2015

The pneumococcal enzyme-linked immunosorbent assay (ELISA) reference standard serum, lot 89SF, has been in use since 1990 and was replaced in 2013 with a new reference standard, 007sp, that is projected to be available for the next 25 years. 007sp was generated under an FDA-approved clinical protocol; 278 adult volunteers were immunized with the 23-valent unconjugated polysaccharide vaccine Pneumovax II, and a unit of blood was obtained twice from each immunized subject within 120 days following immunization. Pooled serum was prepared from the plasma of 262 subjects, filled at 6 ml per vial, and lyophilized. Five independent laboratories participated in bridging the serotype-specific IgG assignments for 89SF to the new reference standard, 007sp, to establish equivalent reference values for 13 pneumococcal capsular serotypes (1,3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F) by using the WHO reference ELISA. In a second study involving three laboratories, a similar protocol was used to assign weight-based IgG concentrations in micrograms per ml to 007sp of seven serotypes (8, 10A, 11A, 12F, 15B, 22F, and 33F) also present in the 23-valent pneumococcal unconjugated polysaccharide vaccine. In addition, the IgG assignments for a 12-member WHO quality control (QC) serum panel were also extended to cover these seven serotypes. Agreement was excellent, with a concordance correlation coefficient (
r
c
) of >0.996 when each laboratory was compared to the assigned values for the 12 WHO QC serum samples. There are four remaining pneumococcal serotypes (2, 9N, 17F, and 20) found in Pneumovax II for which IgG assignments exist for 89SF and remain to be bridged.
Molecular Characterization of a Catalase-Negative Staphylococcus aureus Blood Culture Isolate
Authors: Teo Jeanette W. P. , Kum Steven , Jureen Roland , Lin Raymond T. P.
Published: September 2015

Here we report a catalase-negative methicillin-sensitive
Staphylococcus aureus
isolate collected from a blood culture. Sequencing through the gene encoding catalase,
katA
, demonstrated a 2-bp insertion. The resulting frameshift mutation generates a protein that has lost 26 amino acids (aa) at its C-terminal domain.
Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses
Authors: Kerr Scott A. , Jackson Eleisha L. , Lungu Oana I. , Meyer Austin G. , Demogines Ann , Ellington Andrew D. , Georgiou George , Wilke Claus O. , Sawyer Sara L.
Published: September 2015

Animal viruses frequently cause zoonotic disease in humans. As these viruses are highly diverse, evaluating the threat that they pose remains a major challenge, and efficient approaches are needed to rapidly predict virus-host compatibility. Here, we develop a combined computational and experimental approach to assess the compatibility of New World arenaviruses, endemic in rodents, with the host TfR1 entry receptors of different potential new host species. Using signatures of positive selection, we identify a small motif on rodent TfR1 that conveys species specificity to the entry of viruses into cells. However, we show that mutations in this region affect the entry of each arenavirus differently. For example, a human single nucleotide polymorphism (SNP) in this region, L212V, makes human TfR1 a weaker receptor for one arenavirus, Machupo virus, but a stronger receptor for two other arenaviruses, Junin and Sabia viruses. Collectively, these findings set the stage for potential evolutionary trade-offs, where natural selection for resistance to one virus may make humans or rodents susceptible to other arenavirus species. Given the complexity of this host-virus interplay, we propose a computational method to predict these interactions, based on homology modeling and computational docking of the virus-receptor protein-protein interaction. We demonstrate the utility of this model for Machupo virus, for which a suitable cocrystal structural template exists. Our model effectively predicts whether the TfR1 receptors of different species will be functional receptors for Machupo virus entry. Approaches such at this could provide a first step toward computationally predicting the “host jumping” potential of a virus into a new host species.

IMPORTANCE
We demonstrate how evolutionary trade-offs may exist in the dynamic evolutionary interplay between viruses and their hosts, where natural selection for resistance to one virus could make humans or rodents susceptible to other virus species. We present an algorithm that predicts which species have cell surface receptors that make them susceptible to Machupo virus, based on computational docking of protein structures. Few molecular models exist for predicting the risk of spillover of a particular animal virus into humans or new animal populations. Our results suggest that a combination of evolutionary analysis, structural modeling, and experimental verification may provide an efficient approach for screening and assessing the potential spillover risks of viruses circulating in animal populations.
Requirement for Host RNA-Silencing Components and the Virus-Silencing Suppressor when Second-Site Mutations Compensate for Structural Defects in the 3′ Untranslated Region
Authors: Chattopadhyay Maitreyi , Stupina Vera A. , Gao Feng , Szarko Christine R. , Kuhlmann Micki M. , Yuan Xuefeng , Shi Kerong , Simon Anne E.
Published: September 2015

Turnip crinkle virus (TCV) contains a structured 3′ region with hairpins and pseudoknots that form a complex network of noncanonical RNA:RNA interactions supporting higher-order structure critical for translation and replication. We investigated several second-site mutations in the p38 coat protein open reading frame (ORF) that arose in response to a mutation in the asymmetric loop of a critical 3′ untranslated region (UTR) hairpin that disrupts local higher-order structure. All tested second-site mutations improved accumulation of TCV in conjunction with a partial reversion of the primary mutation (TCV-rev1) but had neutral or a negative effect on wild-type (wt) TCV or TCV with the primary mutation. SHAPE (
s
elective 2′-
h
ydroxyl
a
cylation analyzed by
p
rimer
e
xtension) structure probing indicated that these second-site mutations reside in an RNA domain that includes most of p38 (domain 2), and evidence for RNA:RNA interactions between domain 2 and 3′UTR-containing domain 1 was found. However, second-site mutations were not compensatory in the absence of p38, which is also the TCV silencing suppressor, or in
dcl-2/dcl4
or
ago1/ago2
backgrounds. One second-site mutation reduced silencing suppressor activity of p38 by altering one of two GW motifs that are required for p38 binding to double-stranded RNAs (dsRNAs) and interaction with RNA-induced silencing complex (RISC)-associated AGO1/AGO2. Another second-site mutation substantially reduced accumulation of TCV-rev1 in the absence of p38 or DCL2/DCL4. We suggest that the second-site mutations in the p38 ORF exert positive effects through a similar downstream mechanism, either by enhancing accumulation of beneficial DCL-produced viral small RNAs that positively regulate the accumulation of TCV-rev1 or by affecting the susceptibility of TCV-rev1 to RISC loaded with viral small RNAs.

IMPORTANCE
Genomes of positive-strand RNA viruses fold into high-order RNA structures. Viruses with mutations in regions critical for translation and replication often acquire second-site mutations that exert a positive compensatory effect through reestablishment of canonical base pairing with the altered region. In this study, two distal second-site mutations that individually arose in response to a primary mutation in a critical 3′ UTR hairpin in the genomic RNA of turnip crinkle virus did not directly interact with the primary mutation. Although different second-site changes had different attributes, compensation was dependent on the production of the viral p38 silencing suppressor and on the presence of silencing-required DCL and AGO proteins. Our results provide an unexpected connection between a 3′ UTR primary-site mutation proposed to disrupt higher-order structure and the RNA-silencing machinery.
Characterization of the Determinants of NS2-3-Independent Virion Morphogenesis of Pestiviruses
Authors: Klemens O. , Dubrau D. , Tautz N.
Published: September 2015

A peculiarity of theFlaviviridaeis the critical function of nonstructural (NS) proteins for virus particle formation. For pestiviruses, like bovine viral diarrhea virus (BVDV), uncleaved NS2-3 represents an essential factor for virion morphogenesis, while NS3 is an essential component of the viral replicase. Accordingly, in natural pestivirus isolates, processing at the NS2-3 cleavage site is not complete, to allow for virion morphogenesis. Virion morphogenesis of the related hepatitis C virus (HCV) shows a major deviation from that of pestiviruses: while RNA replication also requires free NS3, virion formation does not depend on uncleaved NS2-NS3. Recently, we described a BVDV-1 chimera based on strain NCP7 encompassing the NS2-4B*-coding region of strain Osloss (E. Lattwein, O. Klemens, S. Schwindt, P. Becher, and N. Tautz, J Virol 86:427–437, 2012, doi:10.1128/JVI.06133-11). This chimera allowed for the production of infectious virus particles in the absence of uncleaved NS2-3. The Osloss sequence deviates in the NS2-4B* part from NCP7 in 48 amino acids and also has a ubiquitin insertion between NS2 and NS3. The present study demonstrates that in the NCP7 backbone, only two amino acid exchanges in NS2 (E1576V) and NS3 (V1721A) are sufficient and necessary to allow for efficient NS2-3-independent virion morphogenesis. The adaptation of a bicistronic virus encompassing an internal ribosomal entry site element between the NS2 and NS3 coding sequences to efficient virion morphogenesis led to the identification of additional amino acids in E2, NS2, and NS5B that are critically involved in this process. The surprisingly small requirements for approximating the packaging schemes of pestiviruses and HCV with respect to the NS2-3 region is in favor of a common mechanism in an ancestral virus.

IMPORTANCEFor positive-strand RNA viruses, the processing products of the viral polyprotein serve in RNA replication as well as virion morphogenesis. For bovine viral diarrhea virus, nonstructural protein NS2-3 is of critical importance to switch between these processes. While free NS3 is essential for RNA replication, uncleaved NS2-3, which accumulates over time in the infected cell, is required for virion morphogenesis. In contrast, the virion morphogenesis of the related hepatitis C virus is independent from uncleaved NS2-NS3. Here, we demonstrate that pestiviruses can adapt to virion morphogenesis in the absence of uncleaved NS2-3 by just two amino acid exchanges. While the mechanism behind this gain of function remains elusive, the fact that it can be achieved by such minor changes is in line with the assumption that an ancestral virus already used this mechanism but lost it in the course of adapting to a new host/infection strategy.
Virus Multiplicity of Infection Affects Type I Interferon Subtype Induction Profiles and Interferon-Stimulated Genes
Authors: Zaritsky Luna A. , Bedsaul Jacquelyn R. , Zoon Kathryn C.
Published: September 2015

Type I interferons (IFNs) are induced upon viral infection and important mediators of innate immunity. While there is 1 beta interferon (IFN-β) protein, there are 12 different IFN-α subtypes. It has been reported extensively that different viruses induce distinct patterns of IFN subtypes, but it has not been previously shown how the viral multiplicity of infection (MOI) can affect IFN induction. In this study, we discovered the novel finding that human U937 cells infected with 2 different concentrations of Sendai virus (SeV) induce 2 distinct type I IFN subtype profiles. Cells infected at the lower MOI induced more subtypes than cells infected at the higher MOI. We found that this was due to the extent of signaling through the IFN receptor (IFNAR). The cells infected at the lower viral MOI induced the IFNAR2-dependent IFN-α subtypes 4, 6, 7, 10, and 17, which were not induced in cells infected at higher virus concentrations. IFN-β and IFN-α1, -2, and -8 were induced in an IFNAR-independent manner in cells infected at both virus concentrations. IFN-α5, -14, -16, and -21 were induced in an IFNAR-dependent manner in cells infected at lower virus concentrations and in an IFNAR-independent manner in cells infected at higher virus concentrations. These differences in IFN subtype profiles in the 2 virus concentrations also resulted in distinct interferon-stimulated gene induction. These results present the novel finding that different viral MOIs differentially activate JAK/STAT signaling through the IFNAR, which greatly affects the profile of IFN subtypes that are induced.

IMPORTANCE
Type I IFNs are pleiotropic cytokines that are instrumental in combating viral diseases. Understanding how the individual subtypes are induced is important in developing strategies to block viral replication. Many studies have reported that different viruses induce distinct type I IFN subtype profiles due to differences in the way viruses are sensed in different cell types. However, we report in our study the novel finding that the amount of virus used to infect a system can also affect which type I IFN subtypes are induced due to the extent of activation of certain signaling pathways. These distinct IFN subtype profiles in cells infected at different MOIs are correlated with differences in interferon-stimulated gene induction, indicating that the same virus can induce distinct antiviral responses depending on the MOI. Because type I IFNs are used as therapeutic agents to treat viral diseases, understanding their antiviral mechanisms can enhance clinical treatments.
Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids
Authors: Quemin Emmanuelle R. J. , Pietilä Maija K. , Oksanen Hanna M. , Forterre Patrick , Rijpstra W. Irene C. , Schouten Stefan , Bamford Dennis H. , Prangishvili David , Krupovic Mart
Published: September 2015

Geothermal and hypersaline environments are rich in virus-like particles, among which spindle-shaped morphotypes dominate. Currently, viruses with spindle- or lemon-shaped virions are exclusive to
Archaea
and belong to two distinct viral families. The larger of the two families, the
Fuselloviridae
, comprises tail-less, spindle-shaped viruses, which infect hosts from phylogenetically distant archaeal lineages.
Sulfolobus
spindle-shaped virus 1 (SSV1) is the best known member of the family and was one of the first hyperthermophilic archaeal viruses to be isolated. SSV1 is an attractive model for understanding virus-host interactions in
Archaea
; however, the constituents and architecture of SSV1 particles remain only partially characterized. Here, we have conducted an extensive biochemical characterization of highly purified SSV1 virions and identified four virus-encoded structural proteins, VP1 to VP4, as well as one DNA-binding protein of cellular origin. The virion proteins VP1, VP3, and VP4 undergo posttranslational modification by glycosylation, seemingly at multiple sites. VP1 is also proteolytically processed. In addition to the viral DNA-binding protein VP2, we show that viral particles contain the
Sulfolobus solfataricus
chromatin protein Sso7d. Finally, we provide evidence indicating that SSV1 virions contain glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, resolving a long-standing debate on the presence of lipids within SSV1 virions. A comparison of the contents of lipids isolated from the virus and its host cell suggests that GDGTs are acquired by the virus in a selective manner from the host cytoplasmic membrane, likely during progeny egress.

IMPORTANCE
Although spindle-shaped viruses represent one of the most prominent viral groups in
Archaea
, structural data on their virion constituents and architecture still are scarce. The comprehensive biochemical characterization of the hyperthermophilic virus SSV1 presented here brings novel and significant insights into the organization and architecture of spindle-shaped virions. The obtained data permit the comparison between spindle-shaped viruses residing in widely different ecological niches, improving our understanding of the adaptation of viruses with unusual morphotypes to extreme environmental conditions.
Recent advances in the understanding and management of delayed puberty
Authors: Wei Christina , Crowne Elizabeth Clare
Published: September 2015

Delayed puberty, especially in boys, is a common presentation in paediatrics. Recent advances have improved our understanding of the neuroendocrine, genetic and environmental factors controlling pubertal development, and hence inform the pathophysiology of delayed puberty. The discovery of kisspeptin signalling through its receptor identified neuroendocrine mechanisms controlling the gonadotrophin-releasing hormone (GnRH) pulse generator at the onset of puberty. Genetic mechanisms from single gene mutations to single nucleotide polymorphism associated with delayed puberty are being identified. Environmental factors, including nutritional factors and endocrine disruptors, have also been implicated in changes in secular trends and abnormal timing of puberty. Despite these advances, the key clinical question is to distinguish delayed puberty associated with an underlying pathology or hypogonadism from constitutional delay in growth and puberty, which remains challenging as biochemical tests are not always discriminatory. The diagnostic accuracies of newer investigations, including 36-hour luteinising hormone releasing hormone (LHRH) tests, GnRH-agonist tests, antimullerian hormone and inhibin-B, require further evaluation. Sex hormone replacement remains the main available treatment for delayed puberty, the choice of which is largely dictated by clinical practice and availability of the various sex steroid preparations. Spontaneous reversal of hypogonadism has been reported in boys with idiopathic hypogonadotrophic hypogonadism after a period of sex steroid treatment, highlighting the importance of reassessment at the end of pubertal induction. Novel therapies with a more physiological basis such as gonadotrophins or kisspeptin-agonist are being investigated for the management of hypogonadotrophic hypogonadism. Careful clinical assessment and appreciation of the normal physiology remain the key approach to patients with delayed puberty.
Technical efficiency and productivity of Chinese county hospitals: an exploratory study in Henan province, China
Authors: Cheng Zhaohui , Tao Hongbing , Cai Miao , Lin Haifeng , Lin Xiaojun , Shu Qin , Zhang Ru-ning
Published: September 2015

Objectives

Chinese county hospitals have been excessively enlarging their scale during the healthcare reform since 2009. The purpose of this paper is to examine the technical efficiency and productivity of county hospitals during the reform process, and to determine whether, and how, efficiency is affected by various factors.

Setting and participants

114 sample county hospitals were selected from Henan province, China, from 2010 to 2012.

Outcome measures

Data envelopment analysis was employed to estimate the technical and scale efficiency of sample hospitals. The Malmquist index was used to calculate productivity changes over time. Tobit regression was used to regress against 4 environmental factors and 5 institutional factors that affected the technical efficiency.

Results

(1) 112 (98.2%), 112 (98.2%) and 104 (91.2%) of the 114 sample hospitals ran inefficiently in 2010, 2011 and 2012, with average technical efficiency of 0.697, 0.748 and 0.790, respectively. (2) On average, during 2010–2012, productivity of sample county hospitals increased by 7.8%, which was produced by the progress in technical efficiency changes and technological changes of 0.9% and 6.8%, respectively. (3) Tobit regression analysis indicated that government subsidy, hospital size with above 618 beds and average length of stay assumed a negative sign with technical efficiency; bed occupancy rate, ratio of beds to nurses and ratio of nurses to physicians assumed a positive sign with technical efficiency.

Conclusions

There was considerable space for technical efﬁciency improvement in Henan county hospitals. During 2010–2012, sample hospitals experienced productivity progress; however, the adverse change in pure technical efficiency should be emphasised. Moreover, according to the Tobit results, policy interventions that strictly supervise hospital bed scale, shorten the average length of stay and coordinate the proportion among physicians, nurses and beds, would benefit hospital efficiency.
Clinical and economic characteristics of emergency department visits due to acetaminophen toxicity in the USA
Authors: Altyar Ahmed , Kordi Lama , Skrepnek Grant
Published: September 2015

Objectives

To estimate the number of acetaminophen (APAP) toxicity-related emergency department (ED) visits, and to assess their associated clinical and economic burden in the USA from 2006 to 2010.

Design

Cross-sectional, retrospective, large-scale database study.

Setting

Non-federal, non-rehabilitation, community EDs in the USA.

Participants

Inclusion criteria included any listed diagnosis identifying poisoning by aromatic analgesics paracetamol/APAP or associated supplementary code. Generalised linear models were used to investigate the association between outcomes of inpatient admission, mortality, requirement of invasive mechanical ventilation, charges and inpatient lengths of stay based on patient, hospital and clinical characteristics.

Results

Across the 625.2 million ED visits in the USA from 2006 to 2010, 411 811 APAP-related toxicity ED visits were observed, with 45.5% resulting in inpatient admission, 4.7% requiring invasive mechanical ventilation and 0.6% involving death. Overall, the incidence proportion was 27.10 per 100 000 US population, exceeding 70 per 100 000 at age 2 years and ages 16–18 years. The total national bill was $1.06 billion per year (US$ 2014), and predominantly involved females (65.5%) and intentional self-harm (58.4%), which were notably higher within the 12–20 years age category (female12–20 years=74.8%, intentional self-harm12–20 years=71.4%). Behavioural and mental health comorbidities were relatively common and associated with an increased relative risk of admission and likelihood of charges almost entirely across all age categories of ≥12 years within the multivariable analyses. The number of ED visits did not appreciably change over time, decreasing by <2% from 2006 to 2010 (n=1351). Multivariable results also suggested no consistent change in outcomes across the study's time horizon.

Conclusions

A substantial public health impact of APAP toxicity-related cases was observed in the US from 2006 to 2010, with incidence proportions peaking at age 2 years and ages 16–18 years. After controlling for numerous factors, no consistent change was observed over the 5-year time horizon concerning outcomes of admission, mortality, invasive mechanical ventilation, charges or length of stay.
Variation in use of non-surgical treatments among osteoarthritis patients in orthopaedic practice in the Netherlands
Authors: Hofstede Stefanie N , Vliet Vlieland Thea P M , van den Ende Cornelia H M , Nelissen Rob G H H , Marang-van de Mheen Perla J , van Bodegom-Vos Leti
Published: September 2015

Objectives

National and international evidence-based guidelines for hip and knee osteoarthritis (OA) recommend to start with non-surgical treatments, followed by surgical intervention if a patient does not respond sufficiently to non-surgical treatments, but there are indications that these are not optimally used. The aim of this study was to assess the extent to which all recommended non-surgical treatments were used by patients with hip or knee OA who receive(d) a total hip or knee replacement, as reported by patients and orthopaedic surgeons.

Setting

We performed two cross-sectional internet-based surveys among patients and orthopaedic surgeons throughout the Netherlands.

Participants

195 OA patients either have undergone total knee arthroplasty or total hip arthroplasty no longer than 12 months ago or being on the waiting list for surgery with a confirmed date within 3 months and 482 orthopaedic surgeons were invited to participate.

Primary and secondary outcome measures

The use of recommended non-surgical treatments including education about OA/treatment options, lifestyle advice, dietary therapy, physical therapy, acetaminophen, NSAIDs and glucocorticoid injections.

Results

174 OA patients (93%) and 172 orthopaedic surgeons (36%) completed the surveys. Most recommended non-surgical treatments were given to the majority of patients (eg, 80% education about OA, 73% physical therapy, 72% acetaminophen, 80% NSAIDs). However, only 6% of patients and 10% of orthopaedic surgeons reported using a combination of all recommended treatments. Dietary therapy was used least frequently. Only 11% of overweight and 30% of obese participants reported having received dietary therapy and 28% of orthopaedic surgeons reported to prescribe dietary therapy to overweight patients.

Conclusions

While most recommended non-surgical treatments were used frequently as single therapy, the combination is used in only a small percentage of OA patients. Especially, use of dietary therapy may be improved to help patients manage their symptoms, and potentially delay the need for joint arthroplasty.