bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of changes in facial skin temperature caused by ethyl chloride spraying, ice block rubbing and cold gel packing in healthy subjects
Authors: Im Y.‐G. , Park H.‐J. , Chae H.‐Y. , Kim B.‐G. , Lim H.‐S. , Park J.‐I. , Kim J.‐H. 
Published: September 2012

SummaryThe aim of this study was to compare the effects of three cryotherapeutic modalities (ethyl chloride spraying, ice block rubbing and cold gel packing) on facial skin temperature. Thirty healthy volunteers (15 men, 15 women; mean age, 29·4 ± 3·2 years) participated in this study. Each of the three modalities was randomly applied to the skin over the right masseter muscle. The skin surface temperature was recorded at baseline and every 5 min for 60 min after the application of one of the three cryotherapeutic modalities. Immediately after application, cold gel packing demonstrated the greatest reduction in surface temperature (10·6 °C), followed by ethyl chloride spraying (4·3 °C) and ice block rubbing (3·7 °C) (P < 0·001). During the 60‐min post‐application period, ethyl chloride spraying and ice block rubbing produced similar skin surface temperature changes. The skin surface remained coldest for the longest period of time after cold gel packing. The median time for recovery of the baseline temperature after application of the cold gel pack was about three to four times longer than that for the other modalities (P < 0·001). Ethyl chloride spraying and ice block rubbing resulted in less reduction and faster recovery of skin surface temperature than did cold gel packing. In conclusion, ethyl chloride spraying and ice block rubbing had a limited cooling effect on the facial skin tissue and could not reduce the skin surface temperature enough for local analgesia. Moreover, the cooling effect of cold gel packing was remarkable, but not sufficient for local analgesia.
Phosphoribosyl pyrophosphate synthetase, as a suppressor of the sepH mutation in Aspergillus nidulans, is required for the proper timing of septation
Authors: Zhong Guowei , Wei Wenfan , Guan Qi , Ma Zhaofei , Wei Hua , Xu Xushi , Zhang Shizhu , Lu Ling 
Published: September 2012

SummaryTimely cytokinesis/septation is essential for hyphal growth and conidiation in Aspergillus nidulans. Genetic analyses have identified that A. nidulans has components of the septum initiation network (SIN) pathway; one of these, SEPH, is a key player for early events during cytokinesis. However, little is known about how the SEPH kinase cascade is regulated by other components. Here, we demonstrate that the phosphoribosyl pyrophosphate synthetase family acts antagonistically against the SIN so that the downregulation of AnPRS family can bypass the requirements of the SIN for septum formation and conidiation. The transcription defect of the Anprs gene family accompanied with the reduction of AnPRS activity causes the formation of hyper‐septation as well as the restoration of septation and conidiation in the absence of SEPH. Clearly, the timing and positioning of septation is related to AnPRS activity. Moreover, with the extensive yeast two‐hybrid analysis and rescue combination experiments, it demonstrated that AnPRS members are able to form the heterodimers for functional interacting entities but they appear to contribute so unequally that Anprs1 mutant display relatively normal septation, but Anprs2 deletion is lethal. Thus, compared to in yeast, the AnPRS family may have a unique regulation mechanism during septation in filamentous fungi.
Profiling the Native Specific Human Humoral Immune Response to Sudan Ebola Virus Strain Gulu by Chemiluminescence Enzyme-Linked Immunosorbent Assay
Authors: Sobarzo Ariel , Perelman Eddie , Groseth Allison , Dolnik Olga , Becker Stephan , Lutwama Julius Julian , Dye John M. , Yavelsky Victoria , Lobel Leslie , Marks Robert S. 
Published: September 2012

ABSTRACTEbolavirus, a member of the familyFiloviridae, causes high lethality in humans and nonhuman primates. Research focused on protection and therapy for Ebola virus infection has investigated the potential role of antibodies. Recent evidence suggests that antibodies can be effective in protection from lethal challenge with Ebola virus in nonhuman primates. However, despite these encouraging results, studies have not yet determined the optimal antibodies and composition of an antibody cocktail, if required, which might serve as a highly effective and efficient prophylactic. To better understand optimal antibodies and their targets, which might be important for protection from Ebola virus infection, we sought to determine the profile of viral protein-specific antibodies generated during a natural cycle of infection in humans. To this end, we characterized the profile of antibodies against individual viral proteins of Sudan Ebola virus (Gulu) in human survivors and nonsurvivors of the outbreak in Gulu, Uganda, in 2000-2001. We developed a unique chemiluminescence enzyme-linked immunosorbent assay (ELISA) for this purpose based on the full-length recombinant viral proteins NP, VP30, and VP40 and two recombinant forms of the viral glycoprotein (GP1-294and GP1-649) of Sudan Ebola virus (Gulu). Screening results revealed that the greatest immunoreactivity was directed to the viral proteins NP and GP1-649, followed by VP40. Comparison of positive immunoreactivity between the viral proteins NP, GP1-649, and VP40 demonstrated a high correlation of immunoreactivity between these viral proteins, which is also linked with survival. Overall, our studies of the profile of immunorecognition of antibodies against four viral proteins of Sudan Ebola virus in human survivors may facilitate development of effective monoclonal antibody cocktails in the future.
Optimization of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Analysis for Bacterial Identification
Authors: Khot Prasanna D. , Couturier Marc R. , Wilson Andrew , Croft Ann , Fisher Mark A. 
Published: September 2012

ABSTRACTMatrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a relatively new addition to the clinical microbiology laboratory. The performance of the MALDI Biotyper system (Bruker Daltonics) was compared to those of phenotypic and genotypic identification methods for 690 routine and referred clinical isolates representing 102 genera and 225 unique species. We systematically compared direct-smear and extraction methods on a taxonomically diverse collection of isolates. The optimal score thresholds for bacterial identification were determined, and an approach to address multiple divergent results above these thresholds was evaluated. Analysis of identification scores revealed optimal species- and genus-level identification thresholds of 1.9 and 1.7, with 91.9% and 97.0% of isolates correctly identified to species and genus levels, respectively. Not surprisingly, routinely encountered isolates showed higher concordance than did uncommon isolates. The extraction method yielded higher scores than the direct-smear method for 78.3% of isolates. Incorrect species were reported in the top 10 results for 19.4% of isolates, and although there was no obvious cutoff to eliminate all of these ambiguities, a 10% score differential between the top match and additional species may be useful to limit the need for additional testing to reach single-species-level identifications.
Use of a Prequalification Panel for Rapid Scale-Up of High-Throughput HIV Viral Load Testing
Authors: Scott Lesley E. , Carmona Sergio , Gous Natasha , Horsfield Pamela , MacKay Melanie , Stevens Wendy 
Published: September 2012

ABSTRACT
Increased access to antiretroviral drugs expands needs for viral load (VL) testing. South Africa's National Health Laboratory Service responded to demands by implementing two testing platforms in 17 laboratories within 8 months. An industry partner's collaboration, training programs, and method verification with a VL prequalification panel ensured testing quality and rapid implementation.
Evaluation of a Simple Protein Extraction Method for Species Identification of Clinically Relevant Staphylococci by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Matsuda Naoto , Matsuda Mari , Notake Shigeyuki , Yokokawa Hirohide , Kawamura Yoshiaki , Hiramatsu Keiichi , Kikuchi Ken 
Published: September 2012

ABSTRACT

In clinical microbiology, bacterial identification is labor-intensive and time-consuming. A solution for this problem is the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). In this study, we evaluated a modified protein extraction method of identification performed on target plates (on-plate extraction method) with MALDI-TOF (Bruker Microflex LT with Biotyper version 3.0) and compared it to 2 previously described methods: the direct colony method and a standard protein extraction method (standard extraction method). We evaluated the species of 273 clinical strains and 14 reference strains of staphylococci. All isolates were characterized using the superoxide dismutase A sequence as a reference. For the species identification, the on-plate, standard extraction, and direct colony methods identified 257 isolates (89.5%), 232 isolates (80.8%), and 173 isolates (60.2%), respectively, with statistically significant differences among the three methods (
P
< 0.05). In conclusion, the on-plate extraction method is at least as good as standard extraction in identification rate and has the advantage of a shorter processing time.
Rapid Detection of Staphylococcus aureus in Lower Respiratory Tract Secretions from Patients with Suspected Ventilator-Associated Pneumonia: Evaluation of the Cepheid Xpert MRSA/SA SSTI Assay
Authors: Cercenado Emilia , Marín Mercedes , Burillo Almudena , Martín-Rabadán Pablo , Rivera Marisa , Bouza Emilio 
Published: September 2012

ABSTRACT

A preclinical evaluation was conducted to evaluate the performance of the Cepheid Xpert assay on 135 lower respiratory tract secretions for detection of methicillin-resistant
Staphylococcus aureus
and
S. aureus
. Compared with the quantitative culture, the sensitivity, specificity, and positive and negative predictive values were 99.0%, 72.2%, 90.7%, and 96.3%, respectively.
Ataxia Telangiectasia Mutated Kinase Controls Chronic Gammaherpesvirus Infection
Authors: Kulinski Joseph M. , Leonardo Steven M. , Mounce Bryan C. , Malherbe Laurent , Gauld Stephen B. , Tarakanova Vera L. 
Published: September 2012

ABSTRACT
Gammaherpesviruses, such as Epstein-Barr virus (EBV), are ubiquitous cancer-associated pathogens that interact with DNA damage response, a tumor suppressor network. Chronic gammaherpesvirus infection and pathogenesis in a DNA damage response-insufficient host are poorly understood. Ataxia-telangiectasia (A-T) is associated with insufficiency of ataxia-telangiectasia mutated (ATM), a critical DNA damage response kinase. A-T patients display a pattern of anti-EBV antibodies suggestive of poorly controlled EBV replication; however, parameters of chronic EBV infection and pathogenesis in the A-T population remain unclear. Here we demonstrate that chronic gammaherpesvirus infection is poorly controlled in an animal model of A-T. Intriguingly, in spite of a global increase in T cell activation and numbers in wild-type (wt) and ATM-deficient mice in response to mouse gammaherpesvirus 68 (MHV68) infection, the generation of an MHV68-specific immune response was altered in the absence of ATM. Our finding that ATM expression is necessary for an optimal adaptive immune response against gammaherpesvirus unveils an important connection between DNA damage response and immune control of chronic gammaherpesvirus infection, a connection that is likely to impact viral pathogenesis in an ATM-insufficient host.
Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients
Authors: Uchiyama Jumpei , Takeuchi Hiroaki , Kato Shin-ichiro , Takemura-Uchiyama Iyo , Ujihara Takako , Daibata Masanori , Matsuzaki Shigenobu 
Published: September 2012

ABSTRACT

Helicobacter pylori
causes peptic ulcers and gastric cancer, which lead to significantly higher morbidity in Japan than elsewhere in the world. As bacteriophage (phage) and host bacteria coevolve, the study of
H. pylori
phages is important to extend understanding of the evolution and pathogenesis of
H. pylori
. Here we report two complete genome sequences of
H. pylori
phages KHP30 and KHP40, which were released spontaneously from the most pathogenic East Asian-type isolates from Japanese patients.
A Network of Protein Interactions around the Herpes Simplex Virus Tegument Protein VP22
Authors: Maringer Kevin , Stylianou Julianna , Elliott Gillian 
Published: September 2012

ABSTRACT
Assembly of the herpesvirus tegument is poorly understood but is believed to involve interactions between outer tegument proteins and the cytoplasmic domains of envelope glycoproteins. Here, we present the detailed characterization of a multicomponent glycoprotein-tegument complex found in herpes simplex virus 1 (HSV-1)-infected cells. We demonstrate that the tegument protein VP22 bridges a complex between glycoprotein E (gE) and glycoprotein M (gM). Glycoprotein I (gI), the known binding partner of gE, is also recruited into this gE-VP22-gM complex but is not required for its formation. Exclusion of the glycoproteins gB and gD and VP22's major binding partner VP16 demonstrates that recruitment of virion components into this complex is highly selective. The immediate-early protein ICP0, which requires VP22 for packaging into the virion, is also assembled into this gE-VP22-gM-gI complex in a VP22-dependent fashion. Although subcomplexes containing VP22 and ICP0 can be formed when either gE or gM are absent, optimal complex formation requires both glycoproteins. Furthermore, and in line with complex formation, neither of these glycoproteins is individually required for VP22 or ICP0 packaging into the virion, but deletion of gE and gM greatly reduces assembly of both VP22 and ICP0. Double deletion of gE and gM also results in small plaque size, reduced virus yield, and defective secondary envelopment, similar to the phenotype previously shown for pseudorabies virus. Hence, we suggest that optimal gE-VP22-gM-gI-ICP0 complex formation correlates with efficient virus morphogenesis and spread. These data give novel insights into the poorly understood process of tegument acquisition.
Toward a Hepatitis C Virus Vaccine: the Structural Basis of Hepatitis C Virus Neutralization by AP33, a Broadly Neutralizing Antibody
Authors: Potter Jane A. , Owsianka Ania M. , Jeffery Nathan , Matthews David J. , Keck Zhen-Yong , Lau Patrick , Foung Steven K. H. , Taylor Garry L. , Patel Arvind H. 
Published: September 2012

ABSTRACT
The E2 envelope glycoprotein of hepatitis C virus (HCV) binds to the host entry factor CD81 and is the principal target for neutralizing antibodies (NAbs). Most NAbs recognize hypervariable region 1 on E2, which undergoes frequent mutation, thereby allowing the virus to evade neutralization. Consequently, there is great interest in NAbs that target conserved epitopes. One such NAb is AP33, a mouse monoclonal antibody that recognizes a conserved, linear epitope on E2 and potently neutralizes a broad range of HCV genotypes. In this study, the X-ray structure of AP33 Fab in complex with an epitope peptide spanning residues 412 to 423 of HCV E2 was determined to 1.8 Å. In the complex, the peptide adopts a β-hairpin conformation and docks into a deep binding pocket on the antibody. The major determinants of antibody recognition are E2 residues L413, N415, G418, and W420. The structure is compared to the recently described HCV1 Fab in complex with the same epitope. Interestingly, the antigen-binding sites of HCV1 and AP33 are completely different, whereas the peptide conformation is very similar in the two structures. Mutagenesis of the peptide-binding residues on AP33 confirmed that these residues are also critical for AP33 recognition of whole E2, confirming that the peptide-bound structure truly represents AP33 interaction with the intact glycoprotein. The slightly conformation-sensitive character of the AP33-E2 interaction was explored by cross-competition analysis and alanine-scanning mutagenesis. The structural details of this neutralizing epitope provide a starting point for the design of an immunogen capable of eliciting AP33-like antibodies.
Climate Change, High-Temperature Stress, Rice Productivity, and Water Use in Eastern China: A New Superensemble-Based Probabilistic Projection
Authors: Tao Fulu , Zhang Zhao 
Published: September 2012

AbstractThe impact of climate change on rice productivity in China remains highly uncertain because of uncertainties from climate change scenarios, parameterizations of biophysical processes, and extreme temperature stress in crop models. Here, the Model to Capture the Crop–Weather Relationship over a Large Area (MCWLA)-Rice crop model was developed by parameterizing the process-based general crop model MCWLA for rice crop. Bayesian probability inversion and a Markov chain Monte Carlo technique were then applied to MCWLA-Rice to analyze uncertainties in parameter estimations and to optimize parameters. Ensemble hindcasts showed that MCWLA-Rice could capture the interannual variability of the detrended historical yield series fairly well, especially over a large area. A superensemble-based probabilistic projection system (SuperEPPS) coupled to MCWLA-Rice was developed and applied to project the probabilistic changes of rice productivity and water use in eastern China under scenarios of future climate change. Results showed that across most cells in the study region, relative to 1961–90 levels, the rice yield would change on average by 7.5%–17.5% (from −10.4% to 3.0%), 0.0%–25.0% (from −26.7% to 2.1%), and from −10.0% to 25.0% (from −39.2% to −6.4%) during the 2020s, 2050s, and 2080s, respectively, in response to climate change, with (without) consideration of CO2 fertilization effects. The rice photosynthesis rate, biomass, and yield would increase as a result of increases in mean temperature, solar radiation, and CO2 concentration, although the rice development rate could accelerate particularly after the heading stage. Meanwhile, the risk of high-temperature stress on rice productivity would also increase notably with climate change. The effects of extreme temperature stress on rice productivity were explicitly parameterized and addressed in the study.
A Method for Adaptive Habit Prediction in Bulk Microphysical Models. Part II: Parcel Model Corroboration
Authors: Harrington Jerry Y. , Sulia Kara , Morrison Hugh 
Published: September 2012

AbstractIt is common for cloud microphysical models to use a single axis length to characterize ice crystals. These methods use either the diameter of an equivalent sphere or mass–size equations in conjunction with the capacitance model to close the equations for ice vapor diffusion. Single-axis methods unnaturally constrain growth because real crystals evolve along at least two axis directions. Thus, they are unable to reproduce the simultaneous variation in mass mixing ratio, maximum dimension, and mass-weighted fall speeds. While mass–size relations can at times capture the evolution of one of these with relatively low errors, the other properties are generally under- or overpredicted by 20%–40%. Part I of this study describes an adaptive habit method that evolves two axis dimensions, allowing feedbacks between aspect ratio changes and mass mixing-ratio evolution. The adaptive habit method evolves particle habit by prognosing number and mass mixing ratios along with two axis length mixing ratios. Compared with a detailed Lagrangian bin representation of ice habit distribution evolution in a parcel framework, the bulk method reproduces the ice mass mixing ratio, mean axis lengths, and mass-weighted fall speeds generally to within less than 5% relative error for layered and deeper mixed-phase clouds.
Concurrent Decadal Mesoscale Eddy Modulations in the Western North Pacific Subtropical Gyre
Authors: Qiu Bo , Chen Shuiming 
Published: September 2012

Abstract
Satellite altimeter data of the past two decades are used to investigate the low-frequency mesoscale eddy variability inside the western North Pacific subtropical gyre. Eddy activity modulations with a decadal time scale are detected concurrently within the 18°–28°N band, including the three branches of the Subtropical Countercurrent (STCC) and the Hawaiian Lee Countercurrent (HLCC). Lagging behind the Pacific decadal oscillation (PDO) index by six months, enhanced eddy activities were detected in 1995–98 and 2003–06, whereas the eddy activities were below the average in 1999–2002 and 2009–11. Analysis of the temperature and salinity data that became available after 2001 via the International Argo Program reveals that the modulating eddy activities are due to the decadal change in the upper-ocean eastward shear in the broad-scale STCC–HLCC band. By conducting an upper-ocean temperature budget analysis, the authors found that this observed eastward shear change can be effectively accounted for by the decadal-varying surface heat flux forcing. Using the Argo-based temperature and salinity data, it is further found that the decadal subsurface potential vorticity (PV) signals to the north and beneath the STCC–HLCC were vertically coherent and not confined to the mode water isopycnals. Adjusting to the PDO-related surface forcing, these subsurface PV anomalies lagged behind the upper-ocean eastward shear signals and likely made minor contributions to generate the decadal-varying eddy signals observed in the western North Pacific subtropical gyre.
Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing
Authors: ElSharawy Abdou , Warner Jason , Olson Jeff , Forster Michael , Schilhabel Markus B , Link Darren R , Rose-John Stefan , Schreiber Stefan , Rosenstiel Philip , Brayer James , Franke Andre 
Published: September 2012

Abstract

Background
Many hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA). We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing (NGS) to target 384 discrete exons from 373 genes involved in cancer. In our evaluation, we compared the performance of six non-amplified gDNA samples from two HapMap family trios. Three of these samples were also preamplified by WGA and evaluated. We tested sample pooling or multiplexing strategies at different stages of the tested targeted NGS (T-NGS) workflow.

Results
The results demonstrated comparable sequence performance between non-amplified and preamplified samples and between different indexing strategies [sequence specificity of 66.0% ± 3.4%, uniformity (coverage at 0.2× of the mean) of 85.6% ± 0.6%]. The average genotype concordance maintained across all the samples was 99.5% ± 0.4%, regardless of sample type or pooling strategy. We did not detect any errors in the Mendelian patterns of inheritance of genotypes between the parents and offspring within each trio. We also demonstrated the ability to detect minor allele frequencies within the pooled samples that conform to predicted models.

Conclusion
Our described PCR-based sample multiplex approach and the ability to use WGA material for NGS may enable researchers to perform deep resequencing studies and explore variants at very low frequencies and cost.