bluuebunny/crossref_metadata_2025 huggingface dataset:
Task‐based optimization of dedicated breast CT via Hotelling observer metrics
Authors: Sanchez Adrian A. , Sidky Emil Y. , Pan Xiaochuan
Published: October 2014

Purpose:

The purpose of this work is to develop and demonstrate a set of practical metrics for CT systems optimization. These metrics, based on the Hotelling observer (HO) figure of merit, are task‐based. The authors therefore take the specific example of optimizing a dedicated breast CT system, including the reconstruction algorithm, for two relevant tasks, signal detection and Rayleigh discrimination.

Methods:

A dedicated breast CT system is simulated using specifications in the literature from an existing prototype. The authors optimize configuration and image reconstruction algorithm parameters for two tasks: the detection of simulated microcalcifications and the discrimination of two adjacent, high‐contrast signals, known as the Rayleigh discrimination task. The effects on task performance of breast diameter, signal location, image grid size, projection view number, and reconstruction filter were all investigated. Two HO metrics were evaluated: the percentage of correct decisions in a two‐alternative forced choice experiment (equivalent to area under the ROC curve or AUC), and the HO efficiency, defined as the squared ratio of HO signal‐to‐noise ratio (SNR) in the reconstructed image to HO SNR in the projection data.

Results:

The ease and efficiency of the HO metric computation allows a rapid high‐resolution survey of many system parameters. Optimization of a range of system parameters using the HO results in images that subjectively appear optimal for the tasks investigated. Further, the results of assessment through the HO reproduce closely many existing results in the literature regarding the impact of parameter selection on image quality.

Conclusions:

This study demonstrates the utility of a task‐based approach to system design, evaluation, and optimization. The methodology presented is equally applicable to determining the impact of a wide range of factors, including patient parameters, system and acquisition design, and the reconstruction algorithm. The results demonstrate the versatility of the proposed HO formalism by not only generating a set of parameters that are optimal for a given task but also by qualitatively reproducing many existing results from the breast CT literature. Meanwhile, the implementation of the proposed methodology is straightforward and entirely simulation‐based. This is an attractive feature for many system optimization problems, where the goal is to analyze the individual system components such as the image reconstruction algorithm. Final assessment of the system as a whole should be based also on real data studies.
Ghost marker detection and elimination in marker‐based optical tracking systems for real‐time tracking in stereotactic body radiotherapy
Authors: Yan Guanghua , Li Jonathan , Huang Yin , Mittauer Kathryn , Lu Bo , Liu Chihray
Published: October 2014

Purpose:

To propose a simple model to explain the origin of ghost markers in marker‐based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers.

Methods:

In marker‐based OTS, ghost markers are virtual markers created due to the cross‐talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker‐free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five‐marker jig and a nine‐marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position uncertainties, and marker displacement.

Results:

The sensor positions and the limit for the CWL condition were measured with excellent reproducibility (standard deviation ≤ 0.39 mm). The ghost marker detection algorithm had perfect detection accuracy for both the jig (1544 samples) and the anthropomorphic phantom (2045 samples). Pattern matching was successful for all samples from both phantoms as well as the 40 patient marker patterns.

Conclusions:

The authors proposed a simple model to explain the origin of ghost markers and identified the CWL condition as the necessary condition for ghost marker occurrence. The retrospective ghost marker detection and elimination algorithms guarantee complete ghost marker elimination while providing the users with maximum flexibility in selecting the number of markers and their configuration to meet their clinic needs.
An integral program for tissue renewal and regeneration: Wnt signaling and stem cell control
Authors: Clevers Hans , Loh Kyle M. , Nusse Roel
Published: October 2014

Controlling stem cells and their niches

Adult organs such as the intestines and skin continually renew themselves every few days or weeks. In several mammalian tissues, this renewal relies on Wnt signaling. Clevers
et al.
review this crucial role in stem cell self renewal. Wnt plays a pivotal role in tissue regeneration even in the earliest animals. Wnt proteins function mainly as short-range signals between adjacent cells. The short-range, spatially-constrained nature of Wnt signals underpins mammalian stem cell niche architecture and tissue self-organization.

Science
, this issue
10.1126/science.1248012
Instantaneous energetics of puma kills reveal advantage of felid sneak attacks
Authors: Williams Terrie M. , Wolfe Lisa , Davis Tracy , Kendall Traci , Richter Beau , Wang Yiwei , Bryce Caleb , Elkaim Gabriel Hugh , Wilmers Christopher C.
Published: October 2014

The costs and benefits of stalking and chasing

Organisms live under a constant balance between getting and using energy. Large carnivores may feel this balance more acutely because of the large amounts of energy needed to capture and subdue their prey. Williams
et al.
and Scantlebury
et al.
used remote measures of physiology and behavior to identify the hunting strategies of the stalking North American puma and the speedy African cheetah (see the Perspective by Laundré). In both cases the cats' hunting strategies are well matched to produce a balance between the energy they spend on the hunt and the energy they acquire from their prey, despite their very different strategies and levels of competition.

Science
, this issue p.
81
, p.
79
; see also p.
33
Tracking cancer drugs in living cells by thermal profiling of the proteome
Authors: Savitski Mikhail M. , Reinhard Friedrich B. M. , Franken Holger , Werner Thilo , Savitski Maria Fälth , Eberhard Dirk , Molina Daniel Martinez , Jafari Rozbeh , Dovega Rebecca Bakszt , Klaeger Susan , Kuster Bernhard , Nordlund Pär , Bantscheff Marcus , Drewes Gerard
Published: October 2014

Mapping human drug targets in the cell

To understand both the beneficial and the side effects of a drug, one would need to know its full binding profile to all cellular proteins. Savitskiet al.take significant steps toward meeting this daunting challenge. They monitored the unfolding or “melting” of over 7000 human proteins and measured how small-molecule binding changes individual melting profiles. As a proof of principle, over 50 targets were identified for an inhibitor known to bind a broad spectrum of kinases. Two cancer drugs, vemurafib and Alectinib, are known to have a side effect of photosensitivity. The thermal profiling approach identified drug-protein interactions responsible for these side effects.

Science, this issue10.1126/science.1255784
Progress in measuring subjective well-being
Authors: Krueger Alan B. , Stone Arthur A.
Published: October 2014

Moving toward national indicators and policy evaluations
Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism
Authors: Scantlebury David M. , Mills Michael G. L. , Wilson Rory P. , Wilson John W. , Mills Margaret E. J. , Durant Sarah M. , Bennett Nigel C. , Bradford Peter , Marks Nikki J. , Speakman John R.
Published: October 2014

The costs and benefits of stalking and chasing

Organisms live under a constant balance between getting and using energy. Large carnivores may feel this balance more acutely because of the large amounts of energy needed to capture and subdue their prey. Williams
et al.
and Scantlebury
et al.
used remote measures of physiology and behavior to identify the hunting strategies of the stalking North American puma and the speedy African cheetah (see the Perspective by Laundré). In both cases the cats' hunting strategies are well matched to produce a balance between the energy they spend on the hunt and the energy they acquire from their prey, despite their very different strategies and levels of competition.

Science
, this issue p.
81
, p.
79
; see also p.
33
Engineering alcohol tolerance in yeast
Authors: Lam Felix H. , Ghaderi Adel , Fink Gerald R. , Stephanopoulos Gregory
Published: October 2014

Tricks for boosting yeast's ethanol yields

To become a widely used source of fuel, widespread industrial production of ethanol using yeast needs to be simple and efficient. However, two conditions ideal for boosting production—tolerance of higher temperatures and high concentrations of ethanol—have been limiting (see the Perspective by Cheng and Kao). Now, Caspeta
et al.
have used adaptive laboratory evolution to find yeast strains that can tolerate high temperatures and Lam
et al.
have identified a route to improve yeast's resistance to high concentrations of ethanol.

Science
, this issue p.
75
, p.
71
; see also p.
35
New global marine gravity model from CryoSat-2 and Jason-1 reveals buried tectonic structure
Authors: Sandwell David T. , Müller R. Dietmar , Smith Walter H. F. , Garcia Emmanuel , Francis Richard
Published: October 2014

High-resolution tectonic solutions

Detailed topographic maps are available for only a small fraction of the ocean floor, severely limited by the number of ship crossings. Global maps constructed using satellite-derived gravity data, in contrast, are limited in the size of features they can resolve. Sandwell
et al.
present a new marine gravity model that greatly improves this resolution (see the Perspective by Hwang and Chang). They identify several previously unknown tectonic features, including extinct spreading ridges in the Gulf of Mexico and numerous uncharted seamounts.

Science
, this issue p.
65
; see also p.
32
Seafloor secrets revealed
Authors: Hwang Cheinway , Chang Emmy T. Y.
Published: October 2014

Satellite data reveal formerly unknown tectonic structures

[Also see Report by

Sandwell
et al.

]
Good barriers make good neighbors
Authors: Ransohoff Richard M.
Published: October 2014

Cerebrospinal fluid may provide indicators of age-associated decline in brain function

[Also see Report by

Baruch
et al.

]
When Ebola protection fails
Authors: Cohen Jon
Published: October 2014

Repeated cases among health care workers are a puzzle, but more staff and better training may lower risks.
Early AIDS virus may have ridden Africa's rails
Authors: Cohen Jon
Published: October 2014

Genetic study reveals fresh details on HIV's emergence.
Breakthrough lost in coin toss?
Authors: Cho Adrian
Published: October 2014

A controversial quantum measurement that seems to bend the rules may not be very quantum after all.
Hope in a mouse
Authors: Couzin-Frankel Jennifer
Published: October 2014

Selling personalized mouse models to cancer patients, a firm draws thanks and reproach.
Emerging Technologies for the Clinical Microbiology Laboratory
Authors: Buchan Blake W. , Ledeboer Nathan A.
Published: October 2014

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
Pharmacokinetics and Pharmacodynamics of Aerosolized Antibacterial Agents in Chronically Infected Cystic Fibrosis Patients
Authors: Dalhoff Axel
Published: October 2014

Bacteria adapt to growth in lungs of patients with cystic fibrosis (CF) by selection of heterogeneously resistant variants that are not detected by conventional susceptibility testing but are selected for rapidly during antibacterial treatment. Therefore, total bacterial counts and antibiotic susceptibilities are misleading indicators of infection and are not helpful as guides for therapy decisions or efficacy endpoints. High drug concentrations delivered by aerosol may maximize efficacy, as decreased drug susceptibilities of the pathogens are compensated for by high target site concentrations. However, reductions of the bacterial load in sputum and improvements in lung function were within the same ranges following aerosolized and conventional therapies. Furthermore, the use of conventional pharmacokinetic/pharmacodynamic (PK/PD) surrogates correlating pharmacokinetics in serum with clinical cure and presumed or proven eradication of the pathogen as a basis for PK/PD investigations in CF patients is irrelevant, as minimization of systemic exposure is one of the main objectives of aerosolized therapy; in addition, bacterial pathogens cannot be eradicated, and chronic infection cannot be cured. Consequently, conventional PK/PD surrogates are not applicable to CF patients. It is nonetheless obvious that systemic exposure of patients, with all its sequelae, is minimized and that the burden of oral treatment for CF patients suffering from chronic infections is reduced.
Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans
Authors: Scales Brittan S. , Dickson Robert P. , LiPuma John J. , Huffnagle Gary B.
Published: October 2014

Pseudomonas fluorescensis not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the “species”P. fluorescensare now being reclassified as novelPseudomonasspecies within theP. fluorescens“species complex.” Although most widely studied for its role in the soil and the rhizosphere,P. fluorescenspossesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent thanP. aeruginosa,P. fluorescenscan cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association betweenP. fluorescensand human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies toP. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans andP. fluorescensduring health and disease.
Coagulase-Negative Staphylococci
Authors: Becker Karsten , Heilmann Christine , Peters Georg
Published: October 2014

The definition of the heterogeneous group of coagulase-negative staphylococci (CoNS) is still based on diagnostic procedures that fulfill the clinical need to differentiate betweenStaphylococcus aureusand those staphylococci classified historically as being less or nonpathogenic. Due to patient- and procedure-related changes, CoNS now represent one of the major nosocomial pathogens, withS. epidermidisandS. haemolyticusbeing the most significant species. They account substantially for foreign body-related infections and infections in preterm newborns. WhileS. saprophyticushas been associated with acute urethritis,S. lugdunensishas a unique status, in some aspects resemblingS. aureusin causing infectious endocarditis. In addition to CoNS found as food-associated saprophytes, many other CoNS species colonize the skin and mucous membranes of humans and animals and are less frequently involved in clinically manifested infections. This blurred gradation in terms of pathogenicity is reflected by species- and strain-specific virulence factors and the development of different host-defending strategies. Clearly, CoNS possess fewer virulence properties thanS. aureus, with a respectively different disease spectrum. In this regard, host susceptibility is much more important. Therapeutically, CoNS are challenging due to the large proportion of methicillin-resistant strains and increasing numbers of isolates with less susceptibility to glycopeptides.
Effectiveness of the E2-Classical Swine Fever Virus Recombinant Vaccine Produced and Formulated within Whey from Genetically Transformed Goats
Authors: Sánchez O. , Barrera M. , Farnós O. , Parra N. C. , Salgado E. R. , Saavedra P. A. , Meza C. D. , Rivas C. I. , Cortez-San Martín M. , Toledo J. R.
Published: October 2014

Subunit recombinant vaccines against classical swine fever virus (CSFV) are a promising alternative to overcome practical and biosafety issues with inactivated vaccines. One of the strategies in evaluation under field conditions is the use of a new marker E2-based vaccine produced in the milk of adenovirally transduced goats. Previously we had demonstrated the efficacy of this antigen, which conferred early protection and long-lasting immunity in swine against CSFV infection. Here, we have used a simpler downstream process to obtain and formulate the recombinant E2 glycoprotein expressed in the mammary gland. The expression levels reached approximately 1.7 mg/ml, and instead of chromatographic separation of the antigen, we utilized a clarification process that eliminates the fat content, retains a minor amount of caseins, and includes an adenoviral inactivation step that improves the biosafety of the final formulation. In a vaccination and challenge experiment in swine, different doses of the E2 antigen contained within the clarified whey generated an effective immune response of neutralizing antibodies that protected all of the animals against a lethal challenge with CSFV. During the immunization and after challenge, the swine were monitored for adverse reactions related to the vaccine or symptoms of CSF, respectively. No adverse reactions or clinical signs of disease were observed in vaccinated animals, in which no replication of CSFV could be detected after challenge. Overall, we consider that the simplicity of the procedures proposed here is a further step toward the introduction and implementation of a commercial subunit vaccine against CSF.
Multiple Low-Dose Challenges in a Rhesus Macaque AIDS Vaccine Trial Result in an Evolving Host Response That Affects Protective Outcome
Authors: Selinger Christian , Strbo Natasa , Gonzalez Louis , Aicher Lauri , Weiss Jeffrey M. , Law G. Lynn , Palermo Robert E. , Vaccari Monica , Franchini Genoveffa , Podack Eckhard R. , Katze Michael G.
Published: October 2014

Using whole-blood transcriptional profiling, we investigated differences in the host response to vaccination and challenge in a rhesus macaque AIDS vaccine trial. Samples were collected from animals prior to and after vaccination with live, irradiated vaccine cells secreting the modified endoplasmic reticulum chaperone gp96-Ig loaded with simian immunodeficiency virus (SIV) peptides, either alone or in combination with a SIV-gp120 protein boost. Additional samples were collected following multiple low-dose rectal challenges with SIVmac251. Animals in the boosted group had a 73% reduced risk of infection. Surprisingly, few changes in gene expression were observed during the vaccination phase. Focusing on postchallenge comparisons, in particular for protected animals, we identified a host response signature of protection comprised of strong interferon signaling after the first challenge, which then largely abated after further challenges. We also identified a host response signature, comprised of early macrophage-mediated inflammatory responses, in animals with undetectable viral loads 5 days after the first challenge but with unusually high viral titers after subsequent challenges. Statistical analysis showed that prime-boost vaccination significantly lowered the probability of infection in a time-consistent manner throughout several challenges. Given that humoral responses in the prime-boost group were highly significant prechallenge correlates of protection, the strong innate signaling after the first challenge suggests that interferon signaling may enhance vaccine-induced antibody responses and is an important contributor to protection from infection during repeated low-dose exposure to SIV.
Field Evaluation of the InBios Chagas Detect Plus Rapid Test in Serum and Whole-Blood Specimens in Bolivia
Authors: Shah Vishal , Ferrufino Lisbeth , Gilman Robert H. , Ramirez Margot , Saenza Eliana , Malaga Edith , Sanchez Gerardo , Okamoto Emi E. , Sherbuck Jacqueline E. , Clark Eva H. , Galdos-Cardenas Gerson , Bozo Ricardo , Flores-Franco Jorge Luis , Colanzi Rony , Verastegui Manuela , Bern Caryn
Published: October 2014

Trypanosoma cruzicauses Chagas disease, which affects an estimated 7 million to 8 million people. Chagas disease is endemic throughout Latin America, with the highest prevalence in Bolivia. Conventional diagnosis requires a well-equipped laboratory with experienced personnel. We evaluated the Chagas Detect Plus (CDP) (InBios, Seattle, WA), a rapid immunochromatographic assay for IgG antibodies toT. cruzi. CDP performance was compared to infection status based on results obtained by indirect hemagglutination assay, immunofluorescent-antibody test, and enzyme-linked immunosorbent assay. Confirmed infection required positive results by at least 2 conventional assays. We used specimens from adults of both sexes in a general hospital in the city of Santa Cruz and from pregnant women in a hospital and children in villages in the Bolivian Chaco, an area of hyperendemicity. CDP was performed in paired whole-blood and serum specimens from 385 individuals in the two hospital studies and in 200 serum specimens from the community study. CDP showed sensitivities/specificities of 96.2% (95% confidence interval, 92.7 to 98.4)/98.8% (95.9 to 99.9) in whole blood and 99.3% (97.5 to 99.9)/96.9% (94.2 to 98.6) in serum, with no differences by sex, age group, or study site. CDP showed excellent sensitivity and specificity in our study population, comparable to those of conventional serology. The test is reliable for field surveys, requires no laboratory equipment, and performed well in serum and whole blood. The CDP could also be used for accurate maternal screening to identify neonates at risk of congenital transmission. CDP performance data in diverse geographic areas are needed to strengthen the evidence base for its use.
Acidovorax oryzae Catheter-Associated Bloodstream Infection
Authors: Orsborne Christopher , Hardy Alison , Isalska Barbara , Williams Simon G. , Muldoon Eavan G.
Published: October 2014

Acidovorax oryzae
is a bacterium that has never before been reported as pathogenic in human subjects. Here we describe the first case of a successfully treated
A. oryzae
catheter-associated bloodstream infection in an immunocompetent patient prior to heart transplantation.
Pattern of Circulation of Norovirus GII Strains during Natural Infection
Authors: Ayukekbong James Ayukepi , Fobisong Cajetan , Tah Ferdinand , Lindh Magnus , Nkuo-Akenji Theresia , Bergström Tomas
Published: October 2014

Norovirus (NoV) is considered a major cause of nonbacterial gastroenteritis among people of all ages worldwide, but the natural course of infection is incompletely known. In this study, the pattern of circulation of NoVs was studied among 146 children and 137 adults in a small community in southwestern Cameroon. The participants provided monthly fecal samples during a year. NoV RNA was detected in at least one sample from 82 (29%) of the participants. The partial VP1 region could be sequenced in 36 NoV GII-positive samples. Three different genotypes were identified (GII.1, GII.4, and GII.17), with each genotype circulating within 2 to 3 months and reappearing after a relapse period of 2 to 3 months. Most infections occurred once, and 2 episodes at most within a year were detected. No difference in the frequency of NoV infection between children and adults was recorded. The same genotype was detected for a maximum of 2 consecutive months in 3 children only, suggesting that a less than 30-day duration of viral shedding in natural infection was common. Reinfection within a year with the same genotype was not observed, consistent with short-term homotypic immune protection. The study revealed that NoV strains are circulating with a limited duration of viral shedding both in the individuals and the population as part of their natural infection. The results also provide evidence of cross-protective immunity of limited duration between genotypes of the same genogroup.
Rapid Identification of Pathogens from Pediatric Blood Cultures by Use of the FilmArray Blood Culture Identification Panel
Authors: Zheng Xiaotian , Polanco Wanda , Carter Donna , Shulman Stanford
Published: October 2014

The performance of the FilmArray blood culture identification (BCID) panel has been studied in adult patients. We describe here an evaluation of this assay for the rapid identification of pathogens in Bactec Peds Plus/F and Bactec standard anaerobic/F bottles that contained blood samples from pediatric patients at a tertiary care children's hospital.
Development and Optimization of a Real-Time PCR Assay for Detection of Herpes Simplex and Varicella-Zoster Viruses in Skin and Mucosal Lesions by Use of the BD Max Open System
Authors: Cárdenas Ana María , Edelstein Paul H. , Alby Kevin
Published: October 2014

We transitioned laboratory-developed PCR assays for herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) to the BD Max system by using BD Max open system reagents. After optimization, the agreement with the reference PCR assay was 100% (123/123) for HSV-1, 96.7% (119/123) for HSV-2, and 100% (60/60) for VZV using retrospective clinical samples.
Multiplex PCR for Detection of Seven Virulence Factors and K1/K2 Capsular Serotypes of Klebsiella pneumoniae
Authors: Compain Fabrice , Babosan Ana , Brisse Sylvain , Genel Nathalie , Audo Jennifer , Ailloud Florent , Kassis-Chikhani Najiby , Arlet Guillaume , Decré Dominique
Published: October 2014

A single multiplex PCR assay targeting seven virulence factors and the
wzi
gene specific for the K1 and K2 capsular serotypes of
Klebsiella pneumoniae
was developed and tested on 65 clinical isolates, which included 45 isolates responsible for community-acquired severe human infections. The assay is useful for the surveillance of emerging highly virulent strains.
Direct Detection and Prediction of All Pneumococcal Serogroups by Target Enrichment-Based Next-Generation Sequencing
Authors: Ip Margaret , Liyanapathirana Veranja , Ang Irene , Fung Kitty S. C. , Ng T. K. , Zhou Haokui , Tsang Dominic N. C.
Published: October 2014

Despite the availability of standard methods for pneumococcal serotyping, there is room for improvement in the available methods, in terms of throughput, multiplexing capacity, and the number of serotypes identified. We describe a target enrichment-based next-generation sequencing method applied to nasopharyngeal samples for direct detection and serogroup prediction of all known serotypes of
Streptococcus pneumoniae
, 32 to the serotype level and the rest to the closely related serogroup level. The method was applied to detect and to predict the serogroups of pneumococci directly in clinical samples and from sweeps of primary culture DNA, with increased detection rates versus culture-based identification and agreement with the serotypes/serogroups determined by conventional serotyping methods. We propose this method, in conjunction with traditional serotyping methods, as an alternative to rapid detection and serotyping of pneumococci.
Evolution of Cocirculating Varicella-Zoster Virus Genotypes during a Chickenpox Outbreak in Guinea-Bissau
Authors: Depledge Daniel P. , Gray Eleanor R. , Kundu Samit , Cooray Samantha , Poulsen Anja , Aaby Peter , Breuer Judith
Published: October 2014

Varicella-zoster virus (VZV), a double-stranded DNA alphaherpesvirus, is associated with seasonal outbreaks of varicella in nonimmunized populations. Little is known about whether these outbreaks are associated with a single or multiple viral genotypes and whether new mutations rapidly accumulate during transmission. Here, we take advantage of a well-characterized population cohort in Guinea-Bissau and produce a unique set of 23 full-length genome sequences, collected over 7 months from eight households. Comparative sequence analysis reveals that four distinct genotypes cocirculated among the population, three of which were present during the first week of the outbreak, although no patients were coinfected, which indicates that exposure to infectious virus from multiple sources is common during VZV outbreaks. Transmission of VZV was associated with length polymorphisms in the R1 repeat region and the origin of DNA replication. In two cases, these were associated with the formation of distinct lineages and point to the possible coevolution of these loci, despite the lack of any known functional link in VZV or related herpesviruses. We show that these and all other sequenced clade 5 viruses possess a distinct R1 repeat motif that increases the acidity of an ORF11p protein domain and postulate that this has either arisen or been lost following divergence of the major clades. Thus, sequencing of whole VZV genomes collected during an outbreak has provided novel insights into VZV biology, transmission patterns, and (recent) natural history.

IMPORTANCE
VZV is a highly infectious virus and the causative agent of chickenpox and shingles, the latter being particularly associated with the risk of painful complications. Seasonal outbreaks of chickenpox are very common among young children, yet little is known about the dynamics of the virus during person-to-person to transmission or whether multiple distinct viruses seed and/or cocirculate during an outbreak. In this study, we have sequenced chickenpox viruses from an outbreak in Guinea-Bissau that are supported by detailed epidemiological data. Our data show that multiple different virus strains seeded and were maintained throughout the 6-month outbreak period and that viruses transmitted between individuals accumulated new mutations in specific genomic regions. Of particular interest is the potential coevolution of two distinct parts of the genomes and our calculations of the rate of viral mutation, both of which increase our understanding of how VZV evolves over short periods of time in human populations.
Differential Contribution of Adeno-Associated Virus Type 2 Rep Protein Expression and Nucleic Acid Elements to Inhibition of Adenoviral Replication in
cis
and in
trans
Authors: Weger Stefan , Hammer Eva , Heilbronn Regine
Published: October 2014

The helper-dependent adeno-associated virus type 2 (AAV-2) exhibits complex interactions with its helper adenovirus. Whereas AAV-2 is dependent on adenoviral functions for productive replication, it conversely inhibits adenoviral replication, both when its genome is present in
trans
after coinfection with both viruses and when it is present in
cis
, as in the production of recombinant adenovirus (rAd)/AAV-2 hybrid vectors. The notion that AAV-mediated inhibition of adenoviral replication is due predominantly to the expression of the AAV-2 Rep proteins was recently challenged by successful Rep78 expression in a rAd5 vector through recoding of the Rep open reading frame (ORF). We closely analyzed the relative contributions of AAV-2 nucleic acid elements and Rep protein expression to the inhibition of adenoviral replication in both of the above scenarios. When present in
cis
, a sequence element in the 3′ part of the
rep
gene, comprising only the AAV-2 p40 promoter and the AAV-2 intron sequence, which we termed the RIS-Ad, completely blocks adenoviral replication. p5/p19 promoter-driven Rep protein expression, on the other hand, only weakly inhibits rAd/AAV-2 vector propagation, and by inactivation of the RIS-Ad, it is feasible to generate first-generation rAd vectors expressing functional Rep proteins. The RIS-Ad plays no role in the inhibition of adenoviral replication in
trans
in a model closely mimicking AAV-2–Ad coinfection. In this case, expression of the Rep proteins is required, as well as the presence of an amplifiable inverted terminal repeat (ITR)-containing template. Thus, very different AAV-2 elements and mechanisms are involved in inhibition of adenoviral replication during rAd/AAV-2 vector propagation and after Ad-AAV coinfection.

IMPORTANCE
This is the first study to systematically compare the contributions of AAV-2 protein expression and AAV-2 nucleic acid elements to the inhibition of adenoviral replication in rAd/AAV-2 hybrid vector generation and in AAV-2–adenovirus coinfection. This study shows that the two inhibitory processes are very different with regard to AAV-2 functions and the mechanisms involved. Whereas inhibition of rAd/AAV-2 hybrid vector propagation mostly involves a 3′ nucleic acid element in the
rep
gene, inhibition of an adenoviral genome in
trans
requires the Rep proteins and the AAV ITRs. These findings have important implications both for a basic understanding of the AAV replication cycle and for generation of rAd/AAV-2 hybrid vectors expressing the nonstructural and structural proteins of AAV-2.
Linking Pig-Tailed Macaque Major Histocompatibility Complex Class I Haplotypes and Cytotoxic T Lymphocyte Escape Mutations in Simian Immunodeficiency Virus Infection
Authors: Gooneratne Shayarana L. , Alinejad-Rokny Hamid , Ebrahimi Diako , Bohn Patrick S. , Wiseman Roger W. , O'Connor David H. , Davenport Miles P. , Kent Stephen J.
Published: October 2014

The influence of major histocompatibility complex class I (MHC-I) alleles on human immunodeficiency virus (HIV) diversity in humans has been well characterized at the population level. MHC-I alleles likely affect viral diversity in the simian immunodeficiency virus (SIV)-infected pig-tailed macaque (Macaca nemestrina) model, but this is poorly characterized. We studied the evolution of SIV in pig-tailed macaques with a range of MHC-I haplotypes. SIVmac251genomes were amplified from the plasma of 44 pig-tailed macaques infected with SIVmac251at 4 to 10 months after infection and characterized by Illumina deep sequencing. MHC-I typing was performed on cellular RNA using Roche/454 pyrosequencing. MHC-I haplotypes and viral sequence polymorphisms at both individual mutations and groups of mutations spanning 10-amino-acid segments were linked using in-house bioinformatics pipelines, since cytotoxic T lymphocyte (CTL) escape can occur at different amino acids within the same epitope in different animals. The approach successfully identified 6 known CTL escape mutations within 3 Mane-A1*084-restricted epitopes. The approach also identified over 70 new SIV polymorphisms linked to a variety of MHC-I haplotypes. Using functional CD8 T cell assays, we confirmed that one of these associations, a Mane-B028 haplotype-linked mutation in Nef, corresponded to a CTL epitope. We also identified mutations associated with the Mane-B017 haplotype that were previously described to be CTL epitopes restricted by Mamu-B*017:01 in rhesus macaques. This detailed study of pig-tailed macaque MHC-I genetics and SIV polymorphisms will enable a refined level of analysis for future vaccine design and strategies for treatment of HIV infection.

IMPORTANCECytotoxic T lymphocytes select for virus escape mutants of HIV and SIV, and this limits the effectiveness of vaccines and immunotherapies against these viruses. Patterns of immune escape variants are similar in HIV type 1-infected human subjects that share the same MHC-I genes, but this has not been studied for SIV infection of macaques. By studying SIV sequence diversity in 44 MHC-typed SIV-infected pigtail macaques, we defined over 70 sites within SIV where mutations were common in macaques sharing particular MHC-I genes. Further, pigtail macaques sharing nearly identical MHC-I genes with rhesus macaques responded to the same CTL epitope and forced immune escape. This allows many reagents developed to study rhesus macaques to also be used to study pigtail macaques. Overall, our study defines sites of immune escape in SIV in pigtailed macaques, and this enables a more refined level of analysis of future vaccine design and strategies for treatment of HIV infection.
Role of the Short Telomeric Repeat Region in Marek's Disease Virus Replication, Genomic Integration, and Lymphomagenesis
Authors: Greco Annachiara , Fester Nadine , Engel Annemarie T. , Kaufer Benedikt B.
Published: October 2014

Marek's disease virus (MDV) is a cell-associated alphaherpesvirus that causes generalized polyneuritis and T-cell lymphomas in chickens. MDV is able to integrate its genome into host telomeres, but the mechanism of integration is poorly understood. The MDV genome harbors two arrays of telomeric repeats (TMR) at the ends of its linear genome: multiple telomeric repeats (mTMR), with a variable number of up to 100 repeats, and short telomeric repeats (sTMR), with a fixed number of 6 repeats. The mTMR have recently been shown to play an important role in MDV integration and tumor formation; however, the functions of the sTMR have remained unknown. In this study, we demonstrate that deletion of the sTMR in the MDV genome abrogates virus replication, while extensive mutation of the sTMR does not, indicating that the presence of the sTMR but not the sTMR sequence itself is important. Furthermore, we generated a panel of truncation mutants to determine the minimal length of the sTMR and observed a direct correlation between sTMR length and MDV replication. To address the role of sTMR in MDV replication, integration, and tumorigenesis, sTMR sequences were replaced by a scrambled repeated sequence (vsTMR_mut). vsTMR_mut replicated comparably to parental and revertant viruses
in vitro. In vivo
, however, a significant reduction in disease and tumor incidence was observed in chickens infected with vsTMR_mut that also correlated with a reduced number of viral integration sites in tumor cells. Taken together, our data demonstrate that the sTMR play a central role in MDV genome replication, pathogenesis, and MDV-induced tumor formation.

IMPORTANCE
Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that infects chickens and causes high economic losses in the poultry industry. MDV integrates its genetic material into host telomeres, a process that is crucial for efficient tumor formation. The MDV genome harbors two arrays of telomeric repeats (TMR) at the ends of its linear genome that are identical to host telomeres and that are termed mTMR and sTMR. mTMR have been recently shown to be involved in MDV integration, while the functions of sTMR remain unknown. Here, we demonstrate that the presence and length of sTMR sequence, but not the exact nucleotide sequence, are crucial for MDV replication. Furthermore, the sTMR contribute to the high integration frequency of MDV and are important for MDV pathogenesis and tumor formation. As a number of herpesviruses harbor arrays of telomeric repeats (TMR), MDV serves as a model to determine the role of the herpesvirus TMR in replication, integration, and pathogenesis.
Prevalence, nature and predictors of prescribing errors in mental health hospitals: a prospective multicentre study
Authors: Keers Richard N , Williams Steven D , Vattakatuchery Joe J , Brown Petra , Miller Joan , Prescott Lorraine , Ashcroft Darren M
Published: October 2014

Objective

To determine the prevalence, nature and predictors of prescribing errors (PEs) in three mental health hospitals.

Setting

Inpatient units in three National Health Service (NHS) mental health hospitals in the North West of England.

Participants

Trained clinical pharmacists prospectively recorded the number of PEs in newly written or omitted prescription items screened during their routine work on 10 data collection days. A multidisciplinary panel reviewed PE data using established methods to confirm (1) the presence of a PE, (2) the type of PE and (3) whether errors were clinically relevant and likely to cause harm.

Primary outcome measures

Frequency, nature and predictors of PEs.

Results

Of 4427 screened prescription items, 281 were found to have one or more PEs (error rate 6.3% (95% CI 5.6 to 7.1%)). Multivariate analysis revealed that specialty trainees (OR 1.23 (1.01 to 1.51)) and staff grade psychiatrists (OR 1.50 (1.05 to 2.13)) were more likely to make PEs when compared to foundation year (FY) one doctors, and that specialty trainees and consultant psychiatrists were twice as likely to make clinically relevant PEs (OR 2.61 (2.11 to 3.22) and 2.03 (1.66 to 2.50), respectively) compared to FY one staff. Prescription items screened during the prescription chart rewrite (OR 0.52 (0.33 to 0.82)) or at discharge (OR 0.87 (0.79 to 0.97)) were less likely to be associated with PEs than items assessed during inpatient stay, although they were more likely to be associated with clinically relevant PEs (OR 2.27 (1.72 to 2.99) and 4.23 (3.68 to 4.87), respectively). Prescription items screened at hospital admission were five times more likely (OR 5.39 (2.72 to 10.69)) to be associated with clinically relevant errors than those screened during patient stay.

Conclusions

PEs may be more common in mental health hospitals than previously reported and important targets to minimise these errors have been identified.
Starting early: integration of self-management support into an acute stroke service
Authors: Mäkelä Petra , Gawned Sara , Jones Fiona
Published: October 2014

Self-management support following stroke is rare, despite emerging evidence for impact on patient outcomes. The promotion of a common approach to self-management support across a stroke pathway requires collaboration between professionals. To date, the feasibility of self-management support in acute stroke settings has not been evaluated.

The Bridges stroke self-management package (SMP) is based on self-efficacy principles. It is delivered by professionals and supported by a patient-held workbook. The aim of this project was to introduce the Bridges stroke SMP to the multidisciplinary staff of a London hyperacute and acute stroke unit.

The ‘Plan Do Study Act’ (PDSA) cycle guided iterative stages of project development, with normalisation process theory helping to embed the intervention into existing ways of working. Questionnaires explored attitudes, beliefs and experiences of the staff who were integrating self-management support into ways of working in the acute stroke setting.

Self-management support training was delivered to a total of 46 multidisciplinary stroke staff. Of the staff who attended the follow-up training, 66% had implemented Bridges self-management support with patients since initial training, and 100% felt their practice had changed. Questionnaire findings demonstrated that staff attitudes and beliefs had changed following training, particularly regarding ownership and type of rehabilitation goals set, and prioritisation of self-management support within acute stroke care.

Staff initiated an audit of washing and dressing practices pre- and post-training. This was designed to evaluate the number of occasions when techniques were used by staff to facilitate patients’ independence and self-management. They found that the number of occasions featuring optimum practice went from 54% at baseline to 63% at three months post-training.

This project demonstrated the feasibility of integrating self-management support into an acute stroke setting. Further work is required to evaluate sustainability of the Bridges stroke SMP, to understand the barriers and opportunities involved in engaging all professional groups in integrated self-management support in acute stroke settings, and to assess patient reported outcomes.
A nontraditional undergraduate astronomy course: Changing pedagogy to better meet students’ needs
Authors: MacLeod Katarin , Razul Mohamed Shajahan Gulam , Powell Jamie
Published: October 2014

The authors examined a change of pedagogy in the delivery of a three-credit, first-year astronomy course offered to nonphysics majors by the Department of Physics at a small undergraduate university in Canada. The pedagogy was changed to better meet the needs of the students enrolled in the course. The research includes a description of some of the activities and teaching strategies utilized by the professor; an analysis of the students’ perspectives, attitudes, and reactions towards this nontraditional astronomy course; and what this meant for the students, their level of understanding of science, scientific literacy, and connection between science and society. The article provides insight into the professor’s perceptions, views, classroom observations, and overall analysis of the effectiveness of changing the pedagogy and concludes with thoughts on whether the effort was worth the end result.
Asymmetric effects of low doses of progesterone on GABA(A) receptor α4 subunit protein expression in the olfactory bulb of female rats
Authors: Arbo Bruno D. , Andrade Susie , Osterkamp Gabriela , Gomez Rosane , Ribeiro Maria Flávia
Published: October 2014

The aim of this study was to evaluate the effect of progesterone on the protein expression of α4 subunit of GABA(A) receptor, serotonin transporter (SERT), Akt, Erk, and caspase-3 in the olfactory bulb (OB) of female rats exposed to the forced swimming test (FST). Female rats were injected daily with progesterone (0.4 mg/kg body mass) or vehicle during 2 complete oestrous cycles and exposed to the FST, and the protein expression of GABA(A) receptor α4 subunit, SERT, Akt, Erk, and caspase-3 in the OB were evaluated. Progesterone increased the expression of the α4 subunit in the right OB and decreased its expression in the left OB, although it did not change the expression of other proteins. In summary, our findings indicate that progesterone has an asymmetric modulatory effect on the expression of GABA(A) receptor α4 subunit in the OB. This effect could be related to the antidepressant-like effect of progesterone in female rats.