bluuebunny/crossref_metadata_2025 huggingface dataset:
A method for evaluating image quality of monochrome and color displays based on luminance by use of a commercially available color digital camera
Authors: Tokurei Shogo , Morishita Junji
Published: July 2015

Purpose:

The aim of this study is to propose a method for the quantitative evaluation of image quality of both monochrome and color liquid‐crystal displays (LCDs) using a commercially available color digital camera.

Methods:

The intensities of the unprocessed red (R), green (G), and blue (B) signals of a camera vary depending on the spectral sensitivity of the image sensor used in the camera. For consistent evaluation of image quality for both monochrome and color LCDs, the unprocessed RGB signals of the camera were converted into gray scale signals that corresponded to the luminance of the LCD. Gray scale signals for the monochrome LCD were evaluated by using only the green channel signals of the camera. For the color LCD, the RGB signals of the camera were converted into gray scale signals by employing weighting factors (WFs) for each RGB channel. A line image displayed on the color LCD was simulated on the monochrome LCD by using a software application for subpixel driving in order to verify the WF‐based conversion method. Furthermore, the results obtained by different types of commercially available color cameras and a photometric camera were compared to examine the consistency of the authors’ method. Finally, image quality for both the monochrome and color LCDs was assessed by measuring modulation transfer functions (MTFs) and Wiener spectra (WS).

Results:

The authors’ results demonstrated that the proposed method for calibrating the spectral sensitivity of the camera resulted in a consistent and reliable evaluation of the luminance of monochrome and color LCDs. The MTFs and WS showed different characteristics for the two LCD types owing to difference in the subpixel structure. The MTF in the vertical direction of the color LCD was superior to that of the monochrome LCD, although the WS in the vertical direction of the color LCD was inferior to that of the monochrome LCD as a result of luminance fluctuations in RGB subpixels.

Conclusions:

The authors’ method based on the use of a commercially available color camera is useful to evaluate and understand the display performances of both monochrome and color LCDs in radiology departments.
Undergraduate computational physics projects on quantum computing
Authors: Candela D.
Published: July 2015

Computational projects on quantum computing suitable for students in a junior-level quantum mechanics course are described. In these projects students write their own programs to simulate quantum computers. Knowledge is assumed of introductory quantum mechanics through the properties of spin 1/2. Initial, more easily programmed projects treat the basics of quantum computation, quantum gates, and Grover's quantum search algorithm. These are followed by more advanced projects to increase the number of qubits and implement Shor's quantum factoring algorithm. The projects can be run on a typical laptop or desktop computer, using most programming languages. Supplementing resources available elsewhere, the projects are presented here in a self-contained format especially suitable for a short computational module for physics students.
Application of the Fourier pseudospectral time-domain method in orthogonal curvilinear coordinates for near-rigid moderately curved surfaces
Authors: Hornikx Maarten , Dragna Didier
Published: July 2015

The Fourier pseudospectral time-domain method is an efficient wave-based method to model sound propagation in inhomogeneous media. One of the limitations of the method for atmospheric sound propagation purposes is its restriction to a Cartesian grid, confining it to staircase-like geometries. A transform from the physical coordinate system to the curvilinear coordinate system has been applied to solve more arbitrary geometries. For applicability of this method near the boundaries, the acoustic velocity variables are solved for their curvilinear components. The performance of the curvilinear Fourier pseudospectral method is investigated in free field and for outdoor sound propagation over an impedance strip for various types of shapes. Accuracy is shown to be related to the maximum grid stretching ratio and deformation of the boundary shape and computational efficiency is reduced relative to the smallest grid cell in the physical domain. The applicability of the curvilinear Fourier pseudospectral time-domain method is demonstrated by investigating the effect of sound propagation over a hill in a nocturnal boundary layer. With the proposed method, accurate and efficient results for sound propagation over smoothly varying ground surfaces with high impedances can be obtained.
Older Adults’ Uptake and Adherence to Exercise Classes: Instructors’ Perspectives
Authors: Hawley-Hague Helen , Horne Maria , Skelton Dawn A. , Todd Chris
Published: July 2015

Exercise classes provide a range of benefits for older adults, but adherence levels are poor. We know little of instructors’ experiences of delivering exercise classes to older adults. Semistructured interviews, informed by the Theory of Planned Behavior (TPB), were conducted with instructors (n = 19) delivering multicomponent exercise classes to establish their perspectives on older adults’ uptake and adherence to exercise classes. Analysis revealed ‘barriers’ to uptake related to identity, choice/control, cost, and venue, and ‘solutions’ included providing choice/control, relating exercise to identity, a personal touch, and social support. Barriers to adherence included unrealistic expectations and social influences, and solutions identified were encouraging commitment, creating social cohesion, and an emphasis on achieving outcomes. Older adults’ attitudes were an underlying theme, which related to all barriers and solutions. The instructor plays an important, but not isolated, role in older adults’ uptake and adherence to classes. Instructors’ perspectives help us to further understand how we can design successful exercise classes.
Revolution in human evolution
Authors: Gibbons Ann
Published: July 2015

As it smashes disciplinary boundaries, ancient DNA is rewriting much of human prehistory.
Generating the best superresolution microscopy data: Finding the right tool for the right job
Authors: Betzig Eric , Das Raman , Taraska Justin
Published: July 2015

Superresolution microscopy has recently been making headlines again, not least because it was the breakthrough that spurred Eric Betzig, Stefan Hell, and William Moerner to be awarded the Nobel Prize for Chemistry in 2014. The number of superresolution technologies keeps increasing, along with an alphabet soup of acronyms that includes SIM, SPIM, STED, PALM, and STORM. It is difficult enough for the microscopy experts to keep up, but even more challenging for the average biologist, particularly when they are looking for more from their data than a standard or confocal microscope can offer. When faced with the array of possible techniques, how does one decide which technique is going to get the results needed for that next major publication? In this webinar we will discuss the newest developments in superresolution microscopy and provide practical advice on obtaining the best imaging results. Our panelists, including 2014 Nobel Prize winner Eric Betzig, will help you find the right tool to answer your biological question. You will also hear case studies about how superresolution microscopy data has made the difference between acceptance and rejection of key papers by scientific journals.
Inhibition of the alternative complement pathway preserves photoreceptors after retinal injury
Authors: Sweigard J. Harry , Matsumoto Hidetaka , Smith Kaylee E. , Kim Leo A. , Paschalis Eleftherios I. , Okonuki Yoko , Castillejos Alexandra , Kataoka Keiko , Hasegawa Eiichi , Yanai Ryoji , Husain Deeba , Lambris John D. , Vavvas Demetrios , Miller Joan W. , Connor Kip M.
Published: July 2015

The alternative complement pathway is activated in response to retinal injury, and inhibiting this pathway prevents complement-mediated photoreceptor cell death.
Diverse diseases, diverse variants
Authors: Suzuki Masako
Published: July 2015

The disease-associated variants within different disease categories are preferentially targeted to specific regulatory elements.
Large Nosocomial Outbreak of Colistin-Resistant, Carbapenemase-Producing Klebsiella pneumoniae Traced to Clonal Expansion of an
mgrB
Deletion Mutant
Authors: Giani Tommaso , Arena Fabio , Vaggelli Guendalina , Conte Viola , Chiarelli Adriana , Henrici De Angelis Lucia , Fornaini Rossella , Grazzini Maddalena , Niccolini Fabrizio , Pecile Patrizia , Rossolini Gian Maria
Published: July 2015

We describe a large hospital outbreak (93 bloodstream infections) of colistin-resistant
Klebsiella pneumoniae
carbapenemase (KPC)-producing
K. pneumoniae
isolates which was mirrored by increased colistin consumption. The outbreak was mostly traced to the clonal expansion of an
mgrB
deletion mutant of an ST512 strain that produced KPC-3.
Molecular Epidemiology of Mycoplasma pneumoniae: Genotyping Using Single Nucleotide Polymorphisms and SNaPshot Technology
Authors: Touati A. , Blouin Y. , Sirand-Pugnet P. , Renaudin H. , Oishi T. , Vergnaud G. , Bébéar C. , Pereyre S.
Published: July 2015

Molecular typing of
Mycoplasma pneumoniae
is an important tool for identifying grouped cases and investigating outbreaks. In the present study, we developed a new genotyping method based on single nucleotide polymorphisms (SNPs) selected from the whole-genome sequencing of eight
M. pneumoniae
strains, using the SNaPshot minisequencing assay. Eight SNPs, localized in housekeeping genes, predicted lipoproteins, and adhesin P1 genes were selected for genotyping. These SNPs were evaluated on 140
M. pneumoniae
clinical isolates previously genotyped by multilocus variable-number tandem-repeat analysis (MLVA-5) and adhesin P1 typing. This method was also adapted for direct use with clinical samples and evaluated on 51 clinical specimens. The analysis of the clinical isolates using the SNP typing method showed nine distinct SNP types with a Hunter and Gaston diversity index (HGDI) of 0.836, which is higher than the HGDI of 0.583 retrieved for the MLVA-4 typing method, where the nonstable Mpn1 marker was removed. A strong correlation with the P1 adhesin gene typing results was observed. The congruence was poor between MLVA-5 and SNP typing, indicating distinct genotyping schemes. Combining the results increased the discriminatory power. This new typing method based on SNPs and the SNaPshot technology is a method for rapid
M. pneumoniae
typing directly from clinical specimens, which does not require any sequencing step. This method is based on stable markers and provides information distinct from but complementary to MLVA typing. The combined use of SNPs and MLVA typing provides powerful discrimination of strains.
First Report of Human Infection by Agromycesmediolanus, a Gram-Positive Organism Found in Soil
Authors: Sridhar Siddharth , Wang Angela Y. M. , Chan Jasper F. W. , Yip Cyril C. Y. , Lau Susanna K. P. , Woo Patrick C. Y. , Yuen Kwok-Yung
Published: July 2015

We report the first human infection by a member of the
Agromyces
genus, a group of Gram-positive bacteria found in soil. A patient with a long-term venous catheter developed bacteremia due to a non-vancomycin-susceptible isolate of
Agromyces
mediolanus
. Rapid identification was possible by matrix-assisted laser desorption ionization–time of flight mass spectrometry.
Reevaluation of an Acanthamoeba Molecular Diagnostic Algorithm following an Atypical Case of Amoebic Keratitis
Authors: Lau Rachel , Cunanan Marlou , Jackson Jonathan , Ali Ibne Karim M. , Chong-Kit Ann , Gasgas Jason , Tian Jinfang , Ralevski Filip , Boggild Andrea K.
Published: July 2015

Amoebic keratitis (AK) is a potentially blinding infection, the prompt diagnosis of which is essential for limiting ocular morbidity. We undertook a quality improvement initiative with respect to the molecular detection of acanthamoebae in our laboratory because of an unusual case of discordance. Nine ATCC strains of
Acanthamoeba
and 40 delinked, biobanked, surplus corneal scraping specimens were analyzed for the presence of acanthamoebae with four separate real-time PCR assays. The assay used by the Free-Living and Intestinal Amebas Laboratory of the CDC was considered the reference standard, and the performance characteristics of each individual assay and pairs of assays were calculated. Outcome measures were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Of 49 included specimens, 14 (28.6%) were positive by the gold standard assay, and 35 (71.4%) were negative. The sensitivities of the individual assays ranged from 64.3% to 92.9%, compared to the gold standard, while the specificities ranged from 88.6% to 91.4%. The PPVs and NPVs ranged from 69.2% to 78.6% and from 86.1% to 96.9%, respectively. Combinations of assay pairs led to improved performance, with sensitivities ranging from 92.9% to 100% and specificities ranging from 97.1% to 100%. ATCC and clinical strains of
Acanthamoeba
that failed to be detected by certain individual assays included
Acanthamoeba castellanii
,
Acanthamoeba culbertsoni
, and
Acanthamoeba lenticulata
. For three clinical specimens, false negativity of the gold standard assay could not be excluded. Molecular diagnostic approaches, especially combinations of highly sensitive and specific assays, offer a reasonably performing, operator-independent, rapid strategy for the detection of acanthamoebae in clinical specimens and are likely to be more practical than either culture or direct microscopic detection.
Intermolecular Complementation between Two Varicella-Zoster Virus pORF30 Terminase Domains Essential for DNA Encapsidation
Authors: Visalli Melissa A. , House Brittany L. , Lahrman Frances J. , Visalli Robert J.
Published: July 2015

The herpesviral terminase complex is part of the intricate machinery that delivers a single viral genome into empty preformed capsids (encapsidation). The varicella-zoster virus (VZV) terminase components (pORF25, pORF30, and pORF45/42) have not been studied as extensively as those of herpes simplex virus 1 and human cytomegalovirus (HCMV). In this study, VZV bacterial artificial chromosomes (BACs) were generated with small (Δ30S), medium (Δ30M), and large (Δ30L) ORF30 internal deletions. In addition, we isolated recombinant viruses with specific alanine substitutions in the putative zinc finger motif (30-ZF3A) or in a conserved region (region IX) with predicted structural similarity to the human topoisomerase I core subdomains I and II (30-IXAla, 30-620A, and 30-622A). Recombinant viruses replicated in an ORF30-complementing cell line (ARPE30) but failed to replicate in noncomplementing ARPE19 and MeWo cells. Transmission electron microscopy of 30-IXAla-, 30-620A-, and 30-622A-infected ARPE19 cells revealed only empty VZV capsids. Southern analysis showed that cells infected with parental VZV (VZVLUC) or a repaired virus (30R) contained DNA termini, whereas cells infected with Δ30L, 30-IXAla, 30-620A, or 30-622A contained little or no processed viral DNA. These results demonstrated that pORF30, specifically amino acids 619 to 624 (region IX), was required for DNA encapsidation. A luciferase-based assay was employed to assess potential intermolecular complementation between the zinc finger domain and conserved region IX. Complementation between 30-ZF3A and 30-IXAla provided evidence that distinct pORF30 domains can function independently. The results suggest that pORF30 may exist as a multimer or participate in higher-order assemblies during viral DNA encapsidation.

IMPORTANCEAntivirals with novel mechanisms of action are sought as additional therapeutic options to treat human herpesvirus infections. Proteins involved in the viral DNA encapsidation process have become promising antiviral targets. For example, letermovir is a small-molecule drug targeting HCMV terminase that is currently in phase III clinical trials. It is important to define the structural and functional characteristics of proteins that make up viral terminase complexes to identify or design additional terminase-specific compounds. The VZV ORF30 mutants described in this study represent the first VZV terminase mutants reported to date. Targeted mutations confirmed the importance of a conserved zinc finger domain found in all herpesvirus ORF30 terminase homologs but also identified a novel, highly conserved region (region IX) essential for terminase function. Homology modeling suggested that the structure of region IX is present in all human herpesviruses and thus represents a potential structurally conserved antiviral target.
Inhibition of Ebola and Marburg Virus Entry by G Protein-Coupled Receptor Antagonists
Authors: Cheng Han , Lear-Rooney Calli M. , Johansen Lisa , Varhegyi Elizabeth , Chen Zheng W. , Olinger Gene G. , Rong Lijun
Published: July 2015

Filoviruses, consisting of Ebola virus (EBOV) and Marburg virus (MARV), are among the most lethal infectious threats to mankind. Infections by these viruses can cause severe hemorrhagic fevers in humans and nonhuman primates with high mortality rates. Since there is currently no vaccine or antiviral therapy approved for humans, there is an urgent need to develop prophylactic and therapeutic options for use during filoviral outbreaks and bioterrorist attacks. One of the ideal targets against filoviral infection and diseases is at the entry step, which is mediated by the filoviral glycoprotein (GP). In this report, we screened a chemical library of small molecules and identified numerous inhibitors, which are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs, including histamine receptors, 5-HT (serotonin) receptors, muscarinic acetylcholine receptor, and adrenergic receptor. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. The time-of-addition experiment and microscopic studies suggest that GPCR antagonists block filoviral entry at a step following the initial attachment but prior to viral/cell membrane fusion. These results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.

IMPORTANCE
Infection of Ebola virus and Marburg virus can cause severe illness in humans with a high mortality rate, and currently there is no FDA-approved vaccine or therapeutic treatment available. The 2013-2015 epidemic in West Africa underscores a lack of our understanding in the infection and pathogenesis of these viruses and the urgency of drug discovery and development. In this study, we have identified numerous inhibitors that are known G protein-coupled receptor (GPCR) antagonists targeting different GPCRs. These inhibitors can effectively block replication of both infectious EBOV and MARV, indicating a broad antiviral activity of the GPCR antagonists. Our results strongly suggest that GPCRs play a critical role in filoviral entry and GPCR antagonists can be developed as an effective anti-EBOV/MARV therapy.
Polyphenols Inhibit Hepatitis C Virus Entry by a New Mechanism of Action
Authors: Calland Noémie , Sahuc Marie-Emmanuelle , Belouzard Sandrine , Pène Véronique , Bonnafous Pierre , Mesalam Ahmed Atef , Deloison Gaspard , Descamps Véronique , Sahpaz Sevser , Wychowski Czeslaw , Lambert Olivier , Brodin Priscille , Duverlie Gilles , Meuleman Philip , Rosenberg Arielle R. , Dubuisson Jean , Rouillé Yves , Séron Karin
Published: July 2015

Despite the validation of direct-acting antivirals for hepatitis C treatment, the discovery of new compounds with different modes of action may still be of importance for the treatment of special patient populations. We recently identified a natural molecule, epigallocatechin-3-gallate (EGCG), as an inhibitor of hepatitis C virus (HCV) targeting the viral particle. The aim of this work was to discover new natural compounds with higher anti-HCV activity than that of EGCG and determine their mode of action. Eight natural molecules with structure similarity to EGCG were selected. HCV JFH1 in cell culture and HCV pseudoparticle systems were used to determine the antiviral activity and mechanism of action of the compounds. We identified delphinidin, a polyphenol belonging to the anthocyanidin family, as a new inhibitor of HCV entry. Delphinidin inhibits HCV entry in a pangenotypic manner by acting directly on the viral particle and impairing its attachment to the cell surface. Importantly, it is also active against HCV in primary human hepatocytes, with no apparent cytotoxicity and in combination with interferon and boceprevir in cell culture. Different approaches showed that neither aggregation nor destruction of the particle occurred. Cryo-transmission electron microscopy observations of HCV pseudoparticles treated with delphinidin or EGCG showed a bulge on particles that was not observed under control conditions. In conclusion, EGCG and delphinidin inhibit HCV entry by a new mechanism, i.e., alteration of the viral particle structure that impairs its attachment to the cell surface.

IMPORTANCE
In this article, we identify a new inhibitor of hepatitis C virus (HCV) infection, delphinidin, that prevents HCV entry. This natural compound, a plant pigment responsible for the blue-purple color of flowers and berries, belongs to the flavonoid family, like the catechin EGCG, the major component present in green tea extract, which is also an inhibitor of HCV entry. We studied the mode of action of these two compounds against HCV and demonstrated that they both act directly on the virus, inducing a bulging of the viral envelope. This deformation might be responsible for the observed inhibition of virus attachment to the cell surface. The discovery of such HCV inhibitors with an unusual mode of action is important to better characterize the mechanism of HCV entry into hepatocytes and to help develop a new class of HCV entry inhibitors.
Going Viral with Fluorescent Proteins
Authors: Costantini Lindsey M. , Snapp Erik L.
Published: July 2015

Many longstanding questions about dynamics of virus-cell interactions can be answered by combining fluorescence imaging techniques with fluorescent protein (FP) tagging strategies. Successfully creating a FP fusion with a cellular or viral protein of interest first requires selecting the appropriate FP. However, while viral architecture and cellular localization often dictate the suitability of a FP, a FP's chemical and physical properties must also be considered. Here, we discuss the challenges of and offer suggestions for identifying the optimal FPs for studying the cell biology of viruses.
Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses
Authors: Caspeta Luis , Nielsen Jens
Published: July 2015

A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥40°C). Using adaptive laboratory evolution, we previously isolated sevenSaccharomyces cerevisiaestrains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3°C, whereas they showed a growth trade-off at temperatures below 34°C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49°C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes.

IMPORTANCEYeast thermotolerance can significantly reduce the production costs of biomass conversion to ethanol. However, little information is available about the underlying genetic changes and physiological functions required for yeast thermotolerance. We recently revealed the genetic changes of thermotolerance in thermotolerant yeast strains (TTSs) generated through adaptive laboratory evolution. Here, we examined these TTSs’ physiology and computed their proteome stability over the entire thermal niche, as well as their preadaptation to other stresses. Using this approach, we showed that TTSs exhibited evolutionary trade-offs in the ancestral thermal niche, as well as reduced numbers of growth functions and preadaptation to other stresses found in ethanol production processes. This information will be useful for rational engineering of yeast thermotolerance for the production of biofuels and chemicals.
Mapping the Evolution of Hypervirulent Klebsiella pneumoniae
Authors: Struve Carsten , Roe Chandler C. , Stegger Marc , Stahlhut Steen G. , Hansen Dennis S. , Engelthaler David M. , Andersen Paal S. , Driebe Elizabeth M. , Keim Paul , Krogfelt Karen A.
Published: July 2015

Highly invasive, community-acquired
Klebsiella pneumoniae
infections have recently emerged, resulting in pyogenic liver abscesses. These infections are caused by hypervirulent
K. pneumoniae
(hvKP) isolates primarily of capsule serotype K1 or K2. Hypervirulent K1 isolates belong to clonal complex 23 (CC23), indicating that this clonal lineage has a specific genetic background conferring hypervirulence. Here, we apply whole-genome sequencing to a collection of
K. pneumoniae
isolates to characterize the phylogenetic background of hvKP isolates with an emphasis on CC23. Most of the hvKP isolates belonged to CC23 and grouped into a distinct monophyletic clade, revealing that CC23 is a unique clonal lineage, clearly distinct from nonhypervirulent strains. Separate phylogenetic analyses of the CC23 isolates indicated that the CC23 lineage evolved recently by clonal expansion from a single common ancestor. Limited grouping according to geographical origin was observed, suggesting that CC23 has spread globally through multiple international transmissions. Conversely, hypervirulent K2 strains clustered in genetically unrelated groups. Strikingly, homologues of a large virulence plasmid were detected in all hvKP clonal lineages, indicating a key role in
K. pneumoniae
hypervirulence. The plasmid encodes two siderophores, aerobactin and salmochelin, and RmpA (regulator of the mucoid phenotype); all these factors were found to be restricted to hvKP isolates. Genomic comparisons revealed additional factors specifically associated with CC23. These included a distinct variant of a genomic island encoding yersiniabactin, colibactin, and microcin E492. Furthermore, additional novel genomic regions unique to CC23 were revealed which may also be involved in the increased virulence of this important clonal lineage.

IMPORTANCE
During the last 3 decades, hypervirulent
Klebsiella pneumoniae
(hvKP) isolates have emerged, causing severe community-acquired infections primarily in the form of pyogenic liver abscesses. This syndrome has so far primarily been found in Southeast Asia, but increasing numbers of cases are being reported worldwide, indicating that the syndrome is turning into a globally emerging disease. We applied whole-genome sequencing to a collection of
K. pneumoniae
clinical isolates to reveal the phylogenetic background of hvKP and to identify genetic factors associated with the increased virulence. The hvKP isolates primarily belonged to clonal complex 23 (CC23), and this clonal lineage was revealed to be clearly distinct from nonhypervirulent strains. A specific virulence plasmid was found to be associated with hypervirulence, and novel genetic determinants uniquely associated with CC23 were identified. Our findings extend the understanding of the genetic background of the emergence of hvKP clones.
An Intranasal Virus-Like Particle Vaccine Broadly Protects Mice from Multiple Subtypes of Influenza A Virus
Authors: Schwartzman Louis M. , Cathcart Andrea L. , Pujanauski Lindsey M. , Qi Li , Kash John C. , Taubenberger Jeffery K.
Published: July 2015

Influenza virus infections are a global public health problem, with a significant impact of morbidity and mortality from both annual epidemics and pandemics. The current strategy for preventing annual influenza is to develop a new vaccine each year against specific circulating virus strains. Because these vaccines are unlikely to protect against an antigenically divergent strain or a new pandemic virus with a novel hemagglutinin (HA) subtype, there is a critical need for vaccines that protect against all influenza A viruses, a so-called “universal” vaccine. Here we show that mice were broadly protected against challenge with a wide variety of lethal influenza A virus infections (94% aggregate survival following vaccination) with a virus-like particle (VLP) vaccine cocktail. The vaccine consisted of a mixture of VLPs individually displaying H1, H3, H5, or H7 HAs, and vaccinated mice showed significant protection following challenge with influenza viruses expressing 1918 H1, 1957 H2, and avian H5, H6, H7, H10, and H11 hemagglutinin subtypes. These experiments suggest a promising and practical strategy for developing a broadly protective “universal” influenza vaccine.

IMPORTANCEThe rapid and unpredictable nature of influenza A virus evolution requires new vaccines to be produced annually to match circulating strains. Human infections with influenza viruses derived from animals can cause outbreaks that may be associated with high mortality, and such strains may also adapt to humans to cause a future pandemic. Thus, there is a large public health need to create broadly protective, or “universal,” influenza vaccines that could prevent disease from a wide variety of human and animal influenza A viruses. In this study, a noninfectious virus-like particle (VLP) vaccine was shown to offer significant protection against a variety of influenza A viruses in mice, suggesting a practical strategy to develop a universal influenza vaccine.
Female anorectal malformation in a woman
Authors: Pandey Anand , Gupta Vipin , Singh Shailendra P , Verma Rajesh
Published: July 2015

Delayed presentation of patients with anorectal malformation is not uncommon, especially in developing countries. However, presentation beyond teenage years is not commonplace. We describe a case of a 28-year-old woman who presented for treatment due to marital issues.
Barriers and facilitators related to the implementation of surgical safety checklists: a systematic review of the qualitative evidence
Authors: Bergs Jochen , Lambrechts Frank , Simons Pascale , Vlayen Annemie , Marneffe Wim , Hellings Johan , Cleemput Irina , Vandijck Dominique
Published: July 2015

Objective

The objective of this review is to obtain a better understanding of the user-related barriers against, and facilitators for, the implementation of surgical safety checklists.

Methods

We searched MEDLINE for articles describing stakeholders’ perspectives regarding, and experiences with, the implementation of surgical safety checklists. The quality of the papers was assessed by means of the Qualitative Assessment and Review Instrument. Thematic synthesis was used to integrate the emergent descriptive themes into overall analytical themes.

Results

The synthesis of 18 qualitative studies indicated that implementation requires change in the workflow of healthcare professionals as well as in their perception of the checklist and the perception of patient safety in general. The factors impeding or advancing the required change concentrated around the checklist, the implementation process and the local context. We found that the required safety checks disrupt operating theatre staffs’ routines. Furthermore, conflicting priorities and different perspectives and motives of stakeholders complicate checklist implementation. When approaching the checklist as a simple technical intervention, the expectation of cooperation between surgeons, anaesthetists and nurses is often not addressed, reducing the checklist to a tick-off exercise.

Conclusions

The complex reality in which the checklist needs to be implemented requires an approach that includes more than eliminating barriers and supporting facilitating factors. Implementation leaders must facilitate team learning to foster the mutual understanding of perspectives and motivations, and the realignment of routines. This paper provides a pragmatic overview of the user-related barriers and facilitators upon which theories, hypothesising potential change strategies and interactions, can be developed and tested empirically.
Solvent-free preparation of amidoalkyl phenols catalyzed by trityl chloride under neutral media
Authors: Moosavi-Zare Ahmad Reza , Zolfigol Mohammad Ali , Derakhshan-Panah Fateme , Daraei Masoume
Published: July 2015

A one-pot, multicomponent condensation reaction of phenols, aromatic aldehydes, and amides in the presence of catalytic amount of trityl chloride as a homogeneous organocatalyst under solvent-free condition to prepare amidoalkyl phenols has been reported. It is interesting that trityl chloride by in situ generation of trityl carbocation with inherent instability catalyzes the reaction.
GIS analyses of ice-sheet erosional impacts on the exposed shield of Baffin Island, eastern Canadian Arctic
Authors: Ebert Karin
Published: July 2015

The erosional impacts of former ice sheets on the low-relief bedrock surfaces of Northern Hemisphere shields are not well understood. This paper assesses the variable impacts of glacial erosion on a portion of Baffin Island, eastern Canadian Arctic, between 68° and 72°N and 66° and 80°W. This tilted shield block was covered repeatedly by the Laurentide Ice Sheet during the late Cenozoic. The impact of ice-sheet erosion is examined with GIS analyses using two geomorphic parameters: lake density and terrain ruggedness. The resulting patterns generally conform to published data from other remote sensing studies, geological observations, cosmogenic exposure ages, and the distribution of the chemical index of alteration for tills. Lake density and terrain ruggedness are thereby demonstrated to be useful quantitative indicators of variable ice-sheet erosional impacts across Baffin Island. Ice-sheet erosion was most effective in the lower western parts of the lowlands, in a west–east-oriented band at around 350–400 m a.s.l., and in fjord-onset zones in the uplifted eastern region. Above the 350–400 m a.s.l. band and between the fjord-onset zones, ice-sheet erosion was not sufficient to create extensive ice-roughened or streamlined bedrock surfaces. The exception — where lake density and terrain ruggedness indicate that ice-sheet erosion had a scouring effect all across the study area — was in an area from Foxe Basin to Home Bay with elevations <400 m a.s.l. These morphological contrasts link to former ice-sheet basal thermal regimes during the Pleistocene. The zone of low glacial erosion surrounding the cold-based Barnes Ice Cap probably represents the ice cap’s greater extent during successive Pleistocene cold stages. Inter-fjord plateaus with few ice-sheet bedforms remained cold-based throughout multiple Pleistocene glaciations. In contrast, zones of high lake density and high terrain ruggedness are a result of the repeated development of fast-flowing, erosive ice in warm-based zones beneath the Laurentide Ice Sheet. These zones are linked to greater ice thickness over western lowland Baffin Island. However, adjacent lowland surfaces with similar elevations of non-eroded, weakly eroded, and ice-scoured shield bedrock indicate that—even in areas of high lake density and terrain ruggedness—the total depth of ice sheet erosion did not exceed 50 m.
Transport and magnetic properties of cobalt disulfide prepared by solid state hybrid microwave heating and hot pressing
Authors: Ouyang Ting , Xie Mianyu , Shi Yunfeng , Chen Bing , Lan Yu , Yue Song
Published: July 2015

In this study, single phase cobalt disulfide [Formula: see text] was synthesized by temperature-controlled solid state hybrid microwave heating. The structure, composition and morphology of the obtained samples were studied using X-ray diffraction (XRD), scanning electron spectroscopy (SEM), energy dispersive X-ray spectroscopy (EDX) and high resolution transmission electron microscopy (HRTEM), respectively. The loose [Formula: see text] polycrystalline precursor was then hot pressed to dense bulk sample. The subsequent transport and magnetic properties measurements reveal the ferromagnetic Curie temperature at the magnetic transition near 128 K. These results suggest that the magnetic transition in [Formula: see text] is susceptible to the preparation conditions and the microstructure of the samples.
A note on knot surgery
Authors: Sunukjian Nathan S.
Published: July 2015

In this paper we clarify an issue in the knot surgery construction of Fintushel and Stern. Using knot surgery, they construct an infinite number of smooth structures on 4-manifolds satisfying certain conditions, but they do not explicitly work out the circumstances under which two manifolds that arise from their construction will fail to be diffeomorphic on the grounds of Seiberg–Witten theory. This paper fills in that gap.
Markov trace on a tower of affine Temperley–Lieb algebras of type Ã
Authors: Al Harbat Sadek
Published: July 2015

We define a tower of affine Temperley–Lieb algebras of type Ã. We prove that there exists a unique Markov trace on this tower, this trace comes from the Markov–Ocneanu–Jones trace on the tower of Temperley–Lieb algebras of type A. We define an invariant of special kind of links as an application of this trace.
PORTFOLIO OPTIMIZATION IN AFFINE MODELS WITH MARKOV SWITCHING
Authors: ESCOBAR MARCOS , NEYKOVA DANIELA , ZAGST RUDI
Published: July 2015

We consider a stochastic-factor financial model wherein the asset price and the stochastic-factor processes depend on an observable Markov chain and exhibit an affine structure. We are faced with a finite investment horizon and derive optimal dynamic investment strategies that maximize the investor's expected utility from terminal wealth. To this end we apply Merton's approach, because we are dealing with an incomplete market. Based on the semimartingale characterization of Markov chains, we first derive the Hamilton–Jacobi–Bellman (HJB) equations that, in our case, correspond to a system of coupled nonlinear partial differential equations (PDE). Exploiting the affine structure of the model, we derive simple expressions for the solution in the case with no leverage, i.e. no correlation between the Brownian motions driving the asset price and the stochastic factor. In the presence of leverage, we propose a separable ansatz that leads to explicit solutions. General verification results are also proved. The results are illustrated for the special case of a Markov-modulated Heston model.
Crustal-scale structure of South Tien Shan: implications for subduction polarity and Cenozoic reactivation
Authors: Loury C. , Rolland Y. , Guillot S. , Mikolaichuk A. V. , Lanari P. , Bruguier O. , Bosch D.
Published: July 2015

Based on new structural and petrological investigations, we present two crustal-scale cross-sections of the Kyrgyz South Tien Shan, and correlations of main faults and units between Kyrgyzstan and China. The overall structure corresponds to a doubly-vergent mountain belt. The Kyrgyz and Chinese areas exhibit identical structural and metamorphic histories. To the west, the Atbashi Range comprises high-pressure oceanic and continental units stacked by north-verging thrusts above a low metamorphic accretionary prism. High-pressure (HP) gneisses are bound to their south by a south-dipping detachment exhibiting mantle relicts. The high-pressure oceanic and continental units underwent similar pressure–temperature (
P
–
T
) paths with peak conditions of around 500 °C–20 kbar, followed by rapid exhumation. The overall south-dipping structure and kinematics indicate a south-dipping subduction of the Central Tien Shan Ocean at 320–310 Ma, ending with the docking of the Tarim block to the Kazakh continent. To the east, the Pobeda Massif shows a narrow push-up structure. A major north-vergent thrust exhumes deep-crustal-level granulites, constituting the highest summits, which were thrust towards the north onto low-grade Devonian–Carboniferous schists. The southern part of South Tien Shan is made up of a south-verging thrust stack that formed later during ongoing convergence, reactivated throughout post-30 Ma phases.
Social Influence Based Clustering and Optimization over Heterogeneous Information Networks
Authors: Zhou Yang , Liu Ling
Published: July 2015

Social influence analysis has shown great potential for strategic marketing decision. It is well known that people influence one another based on both their social connections and the social activities that they have engaged in the past. In this article, we develop an innovative and high-performance social influence based graph clustering framework with four unique features. First, we explicitly distinguish social connection based influence (self-influence) and social activity based influence (co-influence). We compute the self-influence similarity between two members based on their social connections within a single collaboration network, and compute the co-influence similarity by taking into account not only the set of activities that people participate but also the semantic association between these activities. Second, we define the concept of influence-based similarity by introducing a unified influence-based similarity matrix that employs an iterative weight update method to integrate self-influence and co-influence similarities. Third, we design a dynamic learning algorithm, called SI-C
luster
, for social influence based graph clustering. It iteratively partitions a large social collaboration network into
K
clusters based on both the social network itself and the multiple associated activity information networks, each representing a category of activities that people have engaged. To make the SI-C
luster
algorithm converge fast, we transform sophisticated nonlinear fractional programming problem with respect to multiple weights into a straightforward nonlinear parametric programming problem of single variable. Finally, we develop an optimization technique of diagonalizable-matrix approximation to speed up the computation of self-influence similarity and co-influence similarities. Our SI-Cluster-Opt significantly improves the efficiency of SI-Cluster on large graphs while maintaining high quality of clustering results. Extensive experimental evaluation on three real-world graphs shows that, compared to existing representative graph clustering algorithms, our SI-C
luster
-O
pt
approach not only achieves a very good balance between self-influence and co-influence similarities but also scales extremely well for clustering large graphs in terms of time complexity while meeting the guarantee of high density, low entropy and low Davies--Bouldin Index.
Discovering Information Propagation Patterns in Microblogging Services
Authors: Yu Zhiwen , Wang Zhu , He Huilei , Tian Jilei , Lu Xinjiang , Guo Bin
Published: July 2015

During the last decade, microblog has become an important social networking service with billions of users all over the world, acting as a novel and efficient platform for the creation and dissemination of real-time information. Modeling and revealing the information propagation patterns in microblogging services cannot only lead to more accurate understanding of user behaviors and provide insights into the underlying sociology, but also enable useful applications such as trending prediction, recommendation and filtering, spam detection and viral marketing. In this article, we aim to reveal the information propagation patterns in Sina Weibo, the biggest microblogging service in China. First, the cascade of each message is represented as a tree based on its retweeting process. Afterwards, we divide the information propagation pattern into two levels, that is, the macro level and the micro level. On one hand, the macro propagation patterns refer to general propagation modes that are extracted by grouping propagation trees based on hierarchical clustering. On the other hand, the micro propagation patterns are frequent information flow patterns that are discovered using tree-based mining techniques. Experimental results show that several interesting patterns are extracted, such as popular message propagation, artificial propagation, and typical information flows between different types of users.
Smart Multitask Bregman Clustering and Multitask Kernel Clustering
Authors: Zhang Xianchao , Zhang Xiaotong , Liu Han
Published: July 2015

Traditional clustering algorithms deal with a single clustering task on a single dataset. However, there are many related tasks in the real world, which motivates multitask clustering. Recently some multitask clustering algorithms have been proposed, and among them multitask Bregman clustering (MBC) is a very applicable method. MBC alternatively updates clusters and learns relationships between clusters of different tasks, and the two phases boost each other. However, the boosting does not always have positive effects on improving the clustering performance, it may also cause negative effects. Another issue of MBC is that it cannot deal with nonlinear separable data. In this article, we show that in MBC, the process of using cluster relationship to boost the cluster updating phase may cause negative effects, that is, cluster centroids may be skewed under some conditions. We propose a smart multitask Bregman clustering (S-MBC) algorithm which can identify the negative effects of the boosting and avoid the negative effects if they occur. We then propose a multitask kernel clustering (MKC) framework for nonlinear separable data by using a similar framework like MBC in the kernel space. We also propose a specific optimization method, which is quite different from that of MBC, to implement the MKC framework. Since MKC can also cause negative effects like MBC, we further extend the framework of MKC to a smart multitask kernel clustering (S-MKC) framework in a similar way that S-MBC is extended from MBC. We conduct experiments on 10 real world multitask clustering datasets to evaluate the performance of S-MBC and S-MKC. The results on clustering accuracy show that: (1) compared with the original MBC algorithm MBC, S-MBC and S-MKC perform much better; (2) compared with the convex discriminative multitask relationship clustering (DMTRC) algorithms DMTRC-L and DMTRC-R which also avoid negative transfer, S-MBC and S-MKC perform worse in the (ideal) case in which different tasks have the same cluster number and the empirical label marginal distribution in each task distributes evenly, but better or comparable in other (more general) cases. Moreover, S-MBC and S-MKC can work on the datasets in which different tasks have different number of clusters, violating the assumptions of DMTRC-L and DMTRC-R. The results on efficiency show that S-MBC and S-MKC consume more computational time than MBC and less computational time than DMTRC-L and DMTRC-R. Overall S-MBC and S-MKC are competitive compared with the state-of-the-art multitask clustering algorithms in synthetical terms of accuracy, efficiency and applicability.