bluuebunny/crossref_metadata_2025 huggingface dataset:
Matching and Minimizing Movement Time in Speed-Accuracy Tasks
Authors: Hsieh Tsung-Yu , Pacheco Matheus M. , Newell Karl M.
Published: October 2015

The goal of present experiment was to test whether different speed-accuracy paradigms outcomes (time minimization and time matching) were due to different temporal and spatial task constraints. Fifteen participants twice performed 100 trials of time minimization and time matching tasks with the yoked temporal and spatial requirements (criterion time and target width). The results showed that performing an aiming movement under the same spatial and temporal constraints resulted in similar outcomes with distributional properties (skewness and kurtosis) being slightly affected by practice effects. There was a trade-off in the information entropy for space and time (temporal information entropy decreased as spatial information entropy increased) with practice. Nevertheless, the joint space-time entropy of outcome did not change across tasks and conditions—revealing a common level of space-time entropy between these two categories of aiming tasks. These findings support the hypothesis that under the same spatial and temporal constraints the movement speed-accuracy function shares the same properties independent of task category.
Proinflammatory GM-CSF–producing B cells in multiple sclerosis and B cell depletion therapy
Authors: Li Rui , Rezk Ayman , Miyazaki Yusei , Hilgenberg Ellen , Touil Hanane , Shen Ping , Moore Craig S. , Michel Laure , Althekair Faisal , Rajasekharan Sathy , Gommerman Jennifer L. , Prat Alexandre , Fillatreau Simon , Bar-Or Amit ,   on behalf of the Canadian B cells in MS Team
Published: October 2015

GM-CSF–producing B cells contribute to multiple sclerosis pathogenesis and the therapeutic action of B cell depletion.
Impact of guidance documents on translational large animal studies of cartilage repair
Authors: Pfeifer Christian G. , Fisher Matthew B. , Carey James L. , Mauck Robert L.
Published: October 2015

A systematic review of large animal cartilage repair studies demonstrates that few investigators attend to guidance documents published by regulatory agencies.
Beep, beeep, beeeep, beeeeeep
Authors: Heldt Thomas
Published: October 2015

Leveraging redundant information among physiological signals helps reduce false alarms in critical care.
What the elephant knew
Authors: Lalazar Gadi
Published: October 2015

Multiple copies of P53 may lie at the basis of the elephant’s resistance to cancer.
Oxygen as Acceptor
Authors: Borisov Vitaliy B. , Verkhovsky Michael I.
Published: October 2015

Like most bacteria,
Escherichia coli
has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O
2
is served by two major oxidoreductases (oxidases), cytochrome
bo
3
encoded by
cyoABCDE
and cytochrome
bd
encoded by
cydABX
. Terminal oxidases of aerobic respiratory chains of bacteria, which use O
2
as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome
c
or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome
bo
3
and cytochrome
bd
in
E. coli
. It also presents a discussion on the genetics and the prosthetic groups of cytochrome
bo
3
and cytochrome
bd
. The
E. coli
membrane contains three types of quinones that all have an octaprenyl side chain (C
40
). It has been proposed that the
bo
3
oxidase can have two ubiquinone-binding sites with different affinities.

“What’s new” in the revised article
: The revised article comprises additional information about subunit composition of cytochrome
bd
and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of
appBCX
-encoded cytochrome
bd
-II, a second
bd
-type oxidase that had been thought not to contribute to generation of a proton motive force in
E. coli
, although its spectral properties closely resemble those of
cydABX
-encoded cytochrome
bd
.
Interlaboratory Collaboration for Optimized Screening for Urinary Tract Infection
Authors: Russcher Anne , Kusters Elske , Wolterbeek Ron , Kuijper Ed J. , Cobbaert Christa M. , van der Beek Martha T.
Published: October 2015

As the majority of urine samples submitted for culture yields a negative result, rapid screening that accurately predicts culture outcome benefits clinicians by reducing the time to result and improves the efficiency of the microbiological laboratory. Automated urinalysis using the IRIS Diagnostics iQ200 Elite (iQ200) analyzer permits just such a fast and large-scale screening. We aimed to predict and thus to reduce negative cultures with a screening algorithm based on iQ200 urinalysis in a tertiary university hospital. In parallel, we evaluated the performance of the iQ200 screen compared to that of Gram stain for sample quality. We screened 1,442 samples submitted for bacterial culture using the iQ200 analyzer; of these samples, 357 (24.8%) had a positive culture result. We identified the absence of microorganisms in the iQ200 screen as the strongest solitary predictor for a negative culture, with a sensitivity of 90.5% (323/357). The algorithm was further improved by performing logistic regression on leukocyte counts, which gave a cutoff of 65 leukocytes/μl to obtain the desired sensitivity of >95% (95.2%; 95% confidence interval [CI], 92.5 to 97.0), a negative predictive value of 97.3% (95% CI, 95.7 to 98.3), and an anticipated culture workload reduction of 44% (95% CI, 41 to 46). Concordance between sample quality based on Gram stain and iQ200 screening was only 72%, which was probably a result of interobserver effect in evaluation of the Gram stain. In conclusion, in our setting, screening by iQ200 proved to be a safe and cost-effective means to provide faster culture results, and it has the added benefit of a more objective evaluation of sample quality.
Cost-Effectiveness of 30- Compared to 20-Milliliter Blood Cultures: a Retrospective Study
Authors: Cheruvanky Anita , Kirn Thomas J. , Weinstein Melvin P.
Published: October 2015

The importance of blood culture (BC) volume for detection of bloodstream infections (BSIs) is documented. Recently, improved diagnostic sensitivity was demonstrated for 30- versus 20-ml BCs in adults (Cockerill FR, Wilson JW, Vetter EA, Goodman KM, Torgerson CA, Harmsen WS, Schleck CD, IIstrup DM, Washington JA, Wilson WR. Clin Infect Dis 38:1724–1730, 2004,
http://dx.doi.org/10.1128/JCM.01314-11
). Hospitals receive higher reimbursement for patients with documented septicemia. We determined the cost-effectiveness of 30-ml versus 20-ml BCs using results from our institution and previously published data. Positive BC results from 292 bacteremic episodes were reviewed. The costs of the reagents, equipment, phlebotomist, and technologist time were determined. The medical records department provided Medicare reimbursement (MR) data for patients with selected ICD-9 codes. These data provided an estimate of the annualized increase in MR versus costs associated with conversion to 30-ml BCs. MR for 464 annual primary BSIs was $24,808/episode. An expected 7.2% increase in BSIs detected using 30-ml BCs would add 34 additional cases annually and increase MR by $843,472. Comparative MR data for cases where septicemia complicated another diagnosis were available for 4 International Classification of Diseases, Ninth Revision (ICD-9) codes: laparoscopic cholecystectomy, biliary tract disorders, pneumonia, and cellulitis. The mean incremental MR was $9,667 per episode, which projected to a $483,350 revenue increase annually. The annual cost associated with conversion to 30-ml BCs was estimated to be $157,798. Thus, the potential net increase in hospital revenue would be $1,169,031 for 30-ml versus 20-ml BCs. Our results suggest that conversion to 30-ml BCs may not only improve patient care by detecting more BSIs but also increase hospital revenue substantially.
Detection of
mecA
- and
mecC
-Positive Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates by the New Xpert MRSA Gen 3 PCR Assay
Authors: Becker Karsten , Denis Olivier , Roisin Sandrine , Mellmann Alexander , Idelevich Evgeny A. , Knaack Dennis , van Alen Sarah , Kriegeskorte André , Köck Robin , Schaumburg Frieder , Peters Georg , Ballhausen Britta
Published: October 2015

An advanced methicillin-resistant
Staphylococcus aureus
(MRSA) detection PCR approach targeting SCC
mec-orfX
along with
mecA
and
mecC
was evaluated for
S. aureus
and coagulase-negative staphylococci. The possession of
mecA
and/or
mecC
was correctly confirmed in all cases. All methicillin-susceptible
S. aureus
strains (
n
= 98; including staphylococcal cassette chromosome
mec
element [SCC
mec
] remnants) and 98.1% of the MRSA strains (
n
= 160, including 10
mecC
-positive MRSA) were accurately categorized.
High Incidence of Invasive Group A Streptococcus Disease Caused by Strains of Uncommon
emm
Types in Thunder Bay, Ontario, Canada
Authors: Athey Taryn B. T. , Teatero Sarah , Sieswerda Lee E. , Gubbay Jonathan B. , Marchand-Austin Alex , Li Aimin , Wasserscheid Jessica , Dewar Ken , McGeer Allison , Williams David , Fittipaldi Nahuel
Published: October 2015

An outbreak of type
emm59
invasive group A
Streptococcus
(iGAS) disease was declared in 2008 in Thunder Bay District, Northwestern Ontario, 2 years after a countrywide
emm59
epidemic was recognized in Canada. Despite a declining number of
emm59
infections since 2010, numerous cases of iGAS disease continue to be reported in the area. We collected clinical information on all iGAS cases recorded in Thunder Bay District from 2008 to 2013. We also
emm
typed and sequenced the genomes of all available strains isolated from 2011 to 2013 from iGAS infections and from severe cases of soft tissue infections. We used whole-genome sequencing data to investigate the population structure of GAS strains of the most frequently isolated
emm
types. We report an increased incidence of iGAS in Thunder Bay compared to the metropolitan area of Toronto/Peel and the province of Ontario. Illicit drug use, alcohol abuse, homelessness, and hepatitis C infection were underlying diseases or conditions that might have predisposed patients to iGAS disease. Most cases were caused by clonal strains of skin or generalist
emm
types (i.e.,
emm82
,
emm87
,
emm101
,
emm4
,
emm83
, and
emm114
) uncommonly seen in other areas of the province. We observed rapid waxing and waning of
emm
types causing disease and their replacement by other
emm
types associated with the same tissue tropisms. Thus, iGAS disease in Thunder Bay District predominantly affects a select population of disadvantaged persons and is caused by clonally related strains of a few skin and generalist
emm
types less commonly associated with iGAS in other areas of Ontario.
Evaluation of the Lyra Direct Strep Assay To Detect Group A Streptococcus and Group C and G Beta-Hemolytic Streptococcus from Pharyngeal Specimens
Authors: Boyanton Bobby L. , Darnell Elizabeth M. , Prada Anne E. , Hansz Dana M. , Robinson-Dunn Barbara
Published: October 2015

The Lyra Direct strep assay was compared to culture for its ability to detect
Streptococcus
group A and β-hemolytic groups C/G using rapid antigen-negative pharyngeal specimens (
n
= 161). The Lyra assay correctly detected all β-hemolytic streptococci (group A,
n
= 19; group C/G,
n
= 5). In batch mode, the Lyra assay reduced intralaboratory turnaround time by 60% (18.1 h versus 45.0 h) but increased hands-on time by 96% (3 min 16 s versus 1 min 40 s per specimen).
Hepatocyte Heparan Sulfate Is Required for Adeno-Associated Virus 2 but Dispensable for Adenovirus 5 Liver Transduction
In Vivo
Authors: Zaiss Anne K. , Foley Erin M. , Lawrence Roger , Schneider Lina S. , Hoveida Hamidreza , Secrest Patrick , Catapang Arthur B. , Yamaguchi Yu , Alemany Ramon , Shayakhmetov Dmitry M. , Esko Jeffrey D. , Herschman Harvey R.
Published: October 2015

Adeno-associated virus 2 (AAV2) and adenovirus 5 (Ad5) are promising gene therapy vectors. Both display liver tropism and are currently thought to enter hepatocytes
in vivo
through cell surface heparan sulfate proteoglycans (HSPGs). To test directly this hypothesis, we created mice that lack
Ext1
, an enzyme required for heparan sulfate biosynthesis, in hepatocytes.
Ext1

HEP

mutant mice exhibit an 8-fold reduction of heparan sulfate in primary hepatocytes and a 5-fold reduction of heparan sulfate in whole liver tissue. Conditional hepatocyte
Ext1
gene deletion greatly reduced AAV2 liver transduction following intravenous injection. Ad5 transduction requires blood coagulation factor X (FX); FX binds to the Ad5 capsid hexon protein and bridges the virus to HSPGs on the cell surface. Ad5.FX transduction was abrogated in primary hepatocytes from
Ext1

HEP

mice. However, in contrast to the case with AAV2, Ad5 transduction was not significantly reduced in the livers of
Ext1

HEP

mice. FX remained essential for Ad5 transduction
in vivo
in
Ext1

HEP

mice. We conclude that while AAV2 requires HSPGs for entry into mouse hepatocytes, HSPGs are dispensable for Ad5 hepatocyte transduction
in vivo
. This study reopens the question of how adenovirus enters cells
in vivo
.

IMPORTANCE
Our understanding of how viruses enter cells, and how they can be used as therapeutic vectors to manage disease, begins with identification of the cell surface receptors to which viruses bind and which mediate viral entry. Both adeno-associated virus 2 and adenovirus 5 are currently thought to enter hepatocytes
in vivo
through heparan sulfate proteoglycans (HSPGs). However, direct evidence for these conclusions is lacking. Experiments presented herein, in which hepatic heparan sulfate synthesis was genetically abolished, demonstrated that HSPGs are not likely to function as hepatocyte Ad5 receptors
in vivo
. The data also demonstrate that HSPGs are required for hepatocyte transduction by AAV2. These results reopen the question of the identity of the Ad5 receptor
in vivo
and emphasize the necessity of demonstrating the nature of the receptor by genetic means, both for understanding Ad5 entry into cells
in vivo
and for optimization of Ad5 vectors as therapeutic agents.
Functional Characterization of Glycoprotein H Chimeras Composed of Conserved Domains of the Pseudorabies Virus and Herpes Simplex Virus 1 Homologs
Authors: Böhm Sebastian W. , Backovic Marija , Klupp Barbara G. , Rey Felix A. , Mettenleiter Thomas C. , Fuchs Walter
Published: October 2015

Membrane fusion is indispensable for entry of enveloped viruses into host cells. The conserved core fusion machinery of the
Herpesviridae
consists of glycoprotein B (gB) and the gH/gL complex. Recently, crystal structures of gH/gL of herpes simplex virus 2 (HSV-2) and Epstein-Barr virus and of a core fragment of pseudorabies virus (PrV) gH identified four structurally conserved gH domains. To investigate functional conservation, chimeric genes encoding combinations of individual domains of PrV and herpes simplex virus 1 (HSV-1) gH were expressed in rabbit kidney cells, and their processing and transport to the cell surface, as well as activity in fusion assays including gB, gD, and gL of PrV or HSV-1, were analyzed. Chimeric gH containing domain I of HSV-1 and domains II to IV of PrV exhibited limited fusion activity in the presence of PrV gB and gD and HSV-1 gL, but not of PrV gL. More strikingly, chimeric gH consisting of PrV domains I to III and HSV-1 domain IV exhibited considerable fusion activity together with PrV gB, gD, and gL. Replacing PrV gB with the HSV-1 protein significantly enhanced this activity. A cell line stably expressing this chimeric gH supported replication of gH-deleted PrV. Our results confirm the specificity of domain I for gL binding, demonstrate functional conservation of domain IV in two alphaherpesviruses from different genera, and indicate species-specific interactions of this domain with gB. They also suggest that gH domains II and III might form a structural and functional unit which does not tolerate major substitutions.

IMPORTANCE
Envelope glycoprotein H (gH) is essential for herpesvirus-induced membrane fusion, which is required for host cell entry and viral spread. Although gH is structurally conserved within the
Herpesviridae
, its precise role and its interactions with other components of the viral fusion machinery are not fully understood. Chimeric proteins containing domains of gH proteins from different herpesviruses can serve as tools to elucidate the molecular basis of gH function. The present study shows that the C-terminal part of human herpesvirus 1 (herpes simplex virus 1) gH can functionally substitute for the corresponding part of suid herpesvirus 1 (pseudorabies virus) gH, whereas other tested combinations proved to be nonfunctional. Interestingly, the exchangeable fragment included the membrane-proximal end of the gH ectodomain (domain IV), which is most conserved in sequence and structure and might be capable of transient membrane interaction during fusion.
γδ T Cells Play a Protective Role in Chikungunya Virus-Induced Disease
Authors: Long Kristin M. , Ferris Martin T. , Whitmore Alan C. , Montgomery Stephanie A. , Thurlow Lance R. , McGee Charles E. , Rodriguez Carlos A. , Lim Jean K. , Heise Mark T.
Published: October 2015

Chikungunya virus (CHIKV) is an alphavirus responsible for causing epidemic outbreaks of polyarthralgia in humans. Because CHIKV is initially introduced via the skin, where γδ T cells are prevalent, we evaluated the response of these cells to CHIKV infection. CHIKV infection led to a significant increase in γδ T cells in the infected foot and draining lymph node that was associated with the production of proinflammatory cytokines and chemokines in C57BL/6J mice. γδ T cell−/−mice demonstrated exacerbated CHIKV disease characterized by less weight gain and greater foot swelling than occurred in wild-type mice, as well as a transient increase in monocytes and altered cytokine/chemokine expression in the foot. Histologically, γδ T cell−/−mice had increased inflammation-mediated oxidative damage in the ipsilateral foot and ankle joint compared to wild-type mice which was independent of differences in CHIKV replication. These results suggest that γδ T cells play a protective role in limiting the CHIKV-induced inflammatory response and subsequent tissue and joint damage.

IMPORTANCERecent epidemics, including the 2004 to 2007 outbreak and the spread of CHIKV to naive populations in the Caribbean and Central and South America with resultant cases imported into the United States, have highlighted the capacity of CHIKV to cause explosive epidemics where the virus can spread to millions of people and rapidly move into new areas. These studies identified γδ T cells as important to both recruitment of key inflammatory cell populations and dampening the tissue injury due to oxidative stress. Given the importance of these cells in the early response to CHIKV, this information may inform the development of CHIKV vaccines and therapeutics.
RNA Silencing May Play a Role in but Is Not the Only Determinant of the Multiplicity of Infection
Authors: Donaire Livia , Burgyán József , García-Arenal Fernando
Published: October 2015

The multiplicity of infection (MOI), i.e., the number of viral genomes that infect a cell, is an important parameter in virus evolution, which for each virus and environment may have an optimum value that maximizes virus fitness. Thus, the MOI might be controlled by virus functions, an underexplored hypothesis in eukaryote-infecting viruses. To analyze if the MOI is controlled by virus functions, we estimated the MOI in plants coinfected by two genetic variants of
Tomato bushy stunt virus
(TBSV); by TBSV and a TBSV-derived defective interfering RNA (DI-RNA); or by TBSV and a second tombusvirus,
Cymbidium ringspot virus
(CymRSV). The MOI was significantly larger in TBSV-CymRSV coinfections (∼4.0) than in TBSV-TBSV or TBSV–DI-RNA coinfections (∼1.7 to 2.2). Coinfections by CymRSV or TBSV with chimeras in which an open reading frame (ORF) of one virus species was replaced by that of the other identified a role of viral proteins in determining the MOI, which ranged from 1.6 to 3.9 depending on the coinfecting genotypes. However, no virus-encoded protein or genomic region was the sole MOI determinant. Coinfections by CymRSV and TBSV mutants in which the expression of the gene-silencing suppressor protein p19 was abolished also showed a possible role of gene silencing in MOI determination. Taken together, these results demonstrate that the MOI is a quantitative trait showing continuous variation and that as such it has a complex determination involving different virus-encoded functions.

IMPORTANCE
The number of viral genomes infecting a cell, or the multiplicity of infection (MOI), is an important parameter in virus evolution affecting recombination rates, selection intensity on viral genes, evolution of multipartite genomes, or hyperparasitism by satellites or defective interfering particles. For each virus and environment, the MOI may have an optimum value that maximizes virus fitness, but little is known about MOI control in eukaryote-infecting viruses. We show here that in plants coinfected by two genotypes of
Tomato bushy stunt virus
(TBSV), the MOI was lower than in plants coinfected by TBSV and
Cymbidium ringspot virus
(CymRSV). Coinfections by CymRSV or TBSV with TBSV-CymRSV chimeras showed a role of viral proteins in MOI determination. Coinfections by CymRSV and TBSV mutants not expressing the gene-silencing suppressor protein also showed a role of gene silencing in MOI determination. The results demonstrate that the MOI is a quantitative trait with a complex determination involving different viral functions.
Defensive Perimeter in the Central Nervous System: Predominance of Astrocytes and Astrogliosis during Recovery from Varicella-Zoster Virus Encephalitis
Authors: Carpenter John E. , Clayton Amy C. , Halling Kevin C. , Bonthius Daniel J. , Buckingham Erin M. , Jackson Wallen , Dotzler Steven M. , Card J. Patrick , Enquist Lynn W. , Grose Charles
Published: October 2015

Varicella-zoster virus (VZV) is a highly neurotropic virus that can cause infections in both the peripheral nervous system and the central nervous system. Several studies of VZV reactivation in the peripheral nervous system (herpes zoster) have been published, while exceedingly few investigations have been carried out in a human brain. Notably, there is no animal model for VZV infection of the central nervous system. In this report, we characterized the cellular environment in the temporal lobe of a human subject who recovered from focal VZV encephalitis. The approach included not only VZV DNA/RNA analyses but also a delineation of infected cell types (neurons, microglia, oligodendrocytes, and astrocytes). The average VZV genome copy number per cell was 5. Several VZV regulatory and structural gene transcripts and products were detected. When colocalization studies were performed to determine which cell types harbored the viral proteins, the majority of infected cells were astrocytes, including aggregates of astrocytes. Evidence of syncytium formation within the aggregates included the continuity of cytoplasm positive for the VZV glycoprotein H (gH) fusion-complex protein within a cellular profile with as many as 80 distinct nuclei. As with other causes of brain injury, these results suggested that astrocytes likely formed a defensive perimeter around foci of VZV infection (astrogliosis). Because of the rarity of brain samples from living humans with VZV encephalitis, we compared our VZV results with those found in a rat encephalitis model following infection with the closely related pseudorabies virus and observed similar perimeters of gliosis.

IMPORTANCE
Investigations of VZV-infected human brain from living immunocompetent human subjects are exceedingly rare. Therefore, much of our knowledge of VZV neuropathogenesis is gained from studies of VZV-infected brains obtained at autopsy from immunocompromised patients. These are not optimal samples with which to investigate a response by a human host to VZV infection. In this report, we examined both flash-frozen and paraffin-embedded formalin-fixed brain tissue of an otherwise healthy young male with focal VZV encephalitis, most likely acquired from VZV reactivation in the trigeminal ganglion. Of note, the cellular response to VZV infection mimicked the response to other causes of trauma to the brain, namely, an ingress of astrocytes and astrogliosis around an infectious focus. Many of the astrocytes themselves were infected; astrocytes aggregated in clusters. We postulate that astrogliosis represents a successful defense mechanism by an immunocompetent human host to eliminate VZV reactivation within neurons.
Conditional Immune Escape during Chronic Simian Immunodeficiency Virus Infection
Authors: Gellerup Dane D. , Balgeman Alexis J. , Nelson Chase W. , Ericsen Adam J. , Scarlotta Matthew , Hughes Austin L. , O'Connor Shelby L.
Published: October 2015

Anti-HIV CD8 T cells included in therapeutic treatments will need to target epitopes that do not accumulate escape mutations. Identifying the epitopes that do not accumulate variants but retain immunogenicity depends on both host major histocompatibility complex (MHC) genetics and the likelihood for an epitope to tolerate variation. We previously found that immune escape during acute SIV infection is conditional; the accumulation of mutations in T cell epitopes is limited, and the rate of accumulation depends on the number of epitopes being targeted. We have now tested the hypothesis that conditional immune escape extends into chronic SIV infection and that epitopes with a preserved wild-type sequence have the potential to elicit epitope-specific CD8 T cells. We deep sequenced simian immunodeficiency virus (SIV) from Mauritian cynomolgus macaques (MCMs) that were homozygous and heterozygous for the M3 MHC haplotype and had been infected with SIV for about 1 year. When interrogating variation within individual epitopes restricted by M3 MHC alleles, we found three categories of epitopes, which we called categories A, B, and C. Category B epitopes readily accumulated variants in M3-homozygous MCMs, but this was less common in M3-heterozygous MCMs. We then determined that chronic CD8 T cells specific for these epitopes were more likely preserved in the M3-heterozygous MCMs than M3-homozygous MCMs. We provide evidence that epitopes known to escape from chronic CD8 T cell responses in animals that are homozygous for a set of MHC alleles are preserved and retain immunogenicity in a host that is heterozygous for the same MHC alleles.

IMPORTANCE
Anti-HIV CD8 T cells that are part of therapeutic treatments will need to target epitopes that do not accumulate escape mutations. Defining these epitope sequences is a necessary precursor to designing approaches that enhance the functionality of CD8 T cells with the potential to control virus replication during chronic infection or after reactivation of latent virus. Using MHC-homozygous and -heterozygous Mauritian cynomolgus macaques, we have now obtained evidence that epitopes known to escape from chronic CD8 T cell responses in animals that are MHC homozygous are preserved and retain immunogenicity in a host that is heterozygous for the same MHC alleles. Importantly, our findings support the conditional immune escape hypothesis, such that the potential to present a greater number of CD8 T cell epitopes within a single animal can delay immune escape in targeted epitopes. As a result, certain epitope sequences can retain immunogenicity into chronic infection.
A Naturally Occurring Domestic Cat APOBEC3 Variant Confers Resistance to Feline Immunodeficiency Virus Infection
Authors: Yoshikawa Rokusuke , Izumi Taisuke , Yamada Eri , Nakano Yusuke , Misawa Naoko , Ren Fengrong , Carpenter Michael A. , Ikeda Terumasa , Münk Carsten , Harris Reuben S. , Miyazawa Takayuki , Koyanagi Yoshio , Sato Kei
Published: October 2015

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) DNA cytosine deaminases can be incorporated into progeny virions and inhibit lentiviral replication. On the other hand, viral infectivity factor (Vif) of lentiviruses antagonizes A3-mediated antiviral activities by degrading A3 proteins. It is known that domestic cat (
Felis catus
) APOBEC3Z3 (A3Z3), the ortholog of human APOBEC3H, potently suppresses the infectivity of
vif
-defective feline immunodeficiency virus (FIV). Although a recent report has shown that domestic cat encodes 7 haplotypes (hap I to hap VII) of A3Z3, the relevance of A3Z3 polymorphism in domestic cats with FIV Vif has not yet been addressed. In this study, we demonstrated that these feline A3Z3 variants suppress
vif
-defective FIV infectivity. We also revealed that codon 65 of feline A3Z3 is a positively selected site and that A3Z3 hap V is subject to positive selection during evolution. It is particularly noteworthy that feline A3Z3 hap V is resistant to FIV Vif-mediated degradation and still inhibits
vif
-proficient viral infection. Moreover, the side chain size, but not the hydrophobicity, of the amino acid at position 65 determines the resistance to FIV Vif-mediated degradation. Furthermore, phylogenetic analyses have led to the inference that feline A3Z3 hap V emerged approximately 60,000 years ago. Taken together, these findings suggest that feline A3Z3 hap V may have been selected for escape from an ancestral FIV. This is the first evidence for an evolutionary “arms race” between the domestic cat and its cognate lentivirus.

IMPORTANCE
Gene diversity and selective pressure are intriguing topics in the field of evolutionary biology. A direct interaction between a cellular protein and a viral protein can precipitate an evolutionary arms race between host and virus. One example is primate APOBEC3G, which potently restricts the replication of primate lentiviruses (e.g., human immunodeficiency virus type 1 [HIV-1] and simian immunodeficiency virus [SIV]) if its activity is not counteracted by the viral Vif protein. Here we investigate the ability of 7 naturally occurring variants of feline APOBEC3, APOBEC3Z3 (A3Z3), to inhibit FIV replication. Interestingly, one feline A3Z3 variant is dominant, restrictive, and naturally resistant to FIV Vif-mediated degradation. Phylogenetic analyses revealed that the ancestral change that generated this variant could have been caused by positive Darwinian selection, presumably due to an ancestral FIV infection. The experimental-phylogenetic investigation sheds light on the evolutionary history of the domestic cat, which was likely influenced by lentiviral infection.
Evolutionary Landscape of the Mycobacterium tuberculosis Complex from the Viewpoint of PhoPR: Implications for Virulence Regulation and Application to Vaccine Development
Authors: Broset Esther , Martín Carlos , Gonzalo-Asensio Jesús
Published: October 2015

Different members of theMycobacteriumgenus have evolved to cause tuberculosis in diverse human populations and in a variety of animal species. Our cumulative knowledge of mycobacterial genomes indicates that mutations in the PhoPR two-component virulence system were acquired not only during the natural evolution of mycobacterial species but also duringin vitrosubculture, which has given rise to the attenuated reference strain H37Ra or to different daughter strains ofMycobacterium bovisBCG. PhoPR is a well-known regulator of pathogenic phenotypes, including secretion of the virulence factor ESAT-6, biosynthesis of acyltrehalose-based lipids, and modulation of antigen export, in members of theMycobacterium tuberculosiscomplex (MTBC). Evolutionarily conserved polymorphisms in PhoPR fromMycobacterium africanum,M. bovis, orM. tuberculosisH37Ra result in loss of functional phenotypes. Interestingly, some members of the MTBC have acquired compensatory mutations to counteract these polymorphisms and, probably, to maintain their pathogenic potential. Some of these compensatory mutations include the insertion of the IS6110element upstream fromphoPRin a particularM. bovisstrain that is able to transmit between humans or polymorphisms inM. africanumandM. bovisthat affect the regulatory region of theespACDoperon, allowing PhoPR-independent ESAT-6 secretion. This review highlights the increasing knowledge of the significance of PhoPR in the evolution of the MTBC and its potential application in the construction of new attenuated vaccines based onphoPRinactivation. In this context, the live attenuated vaccine MTBVAC, based on aphoP fadD26deletion mutant ofM. tuberculosis, is the first vaccine of this kind to successfully enter into clinical development, representing a historic milestone in the field of human vaccinology.
Large-scale data reporting of paediatric morbidity and mortality in developing countries: it can be done
Authors: Duke Trevor , Yano Edilson , Hutchinson Adrian , Hwaihwanje Ilomo , Aipit Jimmy , Tovilu Mathias , Uluk Tarcisius , Rongap Theresia , Vetuna Beryl , Lagani William , Amini James
Published: October 2015

Although the WHO recommends all countries use International Classification of Diseases (ICD)-10 coding for reporting health data, accurate health facility data are rarely available in developing or low and middle income countries. Compliance with ICD-10 is extremely resource intensive, and the lack of real data seriously undermines evidence-based approaches to improving quality of care and to clinical and public health programme management. We developed a simple tool for the collection of accurate admission and outcome data and implemented it in 16 provincial hospitals in Papua New Guinea over 6 years. The programme was low cost and easy to use by ward clerks and nurses. Over 6 years, it gathered data on the causes of 96 998 admissions of children and 7128 deaths. National reports on child morbidity and mortality were produced each year summarising the incidence and mortality rates for 21 common conditions of children and newborns, and the lessons learned for policy and practice. These data informed the National Policy and Plan for Child Health, triggered the implementation of a process of clinical quality improvement and other interventions to reduce mortality in the neediest areas, focusing on diseases with the highest burdens. It is possible to collect large-scale data on paediatric morbidity and mortality, to be used locally by health workers who gather it, and nationally for improving policy and practice, even in very resource-limited settings where ICD-10 coding systems such as those that exist in some high-income countries are not feasible or affordable.
Just hypercalcaemia or acute ST elevation myocardial infarction? A review of hypercalcaemia-related electrocardiographic changes
Authors: Patnaik Soumya , Lai Yu Kuang
Published: October 2015

In elderly patients presenting with confusion and recurrent falls, conditions including infection, acute stroke, acute coronary events and electrolyte abnormalities have to be strongly considered as diagnostic possibilities. ECG is a non-invasive test that often serves as a useful tool in suggesting the underlying electrolyte disturbance. However, ECG must be interpreted with caution as it can, at times, be misleading, as in this case of hypercalcaemia seen by us. We discuss the different ECG findings in hypercalcaemic situations.
Bilateral BRVO in a patient with recurrent prostate cancer
Authors: Castro-Navarro Veronica , Odaibo Stephen G , Ghodasra Devon H , Besirli Cagri G
Published: October 2015

Bilateral cases of branch retinal vein occlusions (BRVO) are infrequent and often related to systemic disease. A 72-year-old man with biochemical recurrence of prostate cancer was referred for decreased vision in his left eye. Fundus examination and fluorescein angiography disclosed bilateral BRVO with patches of peripheral non-perfusion and macular oedema in the left eye. A systemic work up revealed elevated fibrinogen and reduced free protein S antigen, consistent with an underlying hypercoagulable state. Cancer is a well-known cause of hypercoagulability. We report the first case of bilateral BRVO related to biochemical recurrence of prostate cancer and a proven coagulation derangement.
Quantifying the prevalence of frailty in English hospitals
Authors: Soong J , Poots AJ , Scott S , Donald K , Woodcock T , Lovett D , Bell D
Published: October 2015

Objectives

Population ageing has been associated with an increase in comorbid chronic disease, functional dependence, disability and associated higher health care costs. Frailty Syndromes have been proposed as a way to define this group within older persons. We explore whether frailty syndromes are a reliable methodology to quantify clinically significant frailty within hospital settings, and measure trends and geospatial variation using English secondary care data set Hospital Episode Statistics (HES).

Setting

National English Secondary Care Administrative Data HES.

Participants

All 50 540 141 patient spells for patients over 65 years admitted to acute provider hospitals in England (January 2005—March 2013) within HES.

Primary and secondary outcome measures

We explore the prevalence of Frailty Syndromes as coded by International Statistical Classification of Diseases, Injuries and Causes of Death (ICD-10) over time, and their geographic distribution across England. We examine national trends for admission spells, inpatient mortality and 30-day readmission.

Results

A rising trend of admission spells was noted from January 2005 to March 2013(daily average admissions for month rising from over 2000 to over 4000). The overall prevalence of coded frailty is increasing (64 559 spells in January 2005 to 150 085 spells by Jan 2013). The majority of patients had a single frailty syndrome coded (10.2% vs total burden of 13.9%). Cognitive impairment and falls (including significant fracture) are the most common frailty syndromes coded within HES. Geographic variation in frailty burden was in keeping with known distribution of prevalence of the English elderly population and location of National Health Service (NHS) acute provider sites. Overtime, in-hospital mortality has decreased (>65 years) whereas readmission rates have increased (esp.>85 years).

Conclusions

This study provides a novel methodology to reliably quantify clinically significant frailty. Applications include evaluation of health service improvement over time, risk stratification and optimisation of services.
BET 2: does a normal CT scan within 6 h rule out subarachnoid haemorrhage?
Authors: Gray Chris , Foëx Bernard A
Published: October 2015

A short cut review was carried out to establish whether a normal CT scan within 6 h of onset of a severe, sudden onset headache can be used to rule out a subarachnoid haemorrhage. Four studies were directly relevant to the question. The author, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses of these papers are tabulated. The clinical bottom line is that a CT scan performed on a third generation scanner with thin slices, reported by a radiologist experienced in reporting CT brain scans, within 6 h of onset of the headache can be used to rule out a subarachnoid haemorrhage.
Abstracts from international Emergency Medicine journals
Authors: Weber Ellen J
Published: October 2015

Editor's note:EMJhas partnered with the journals of multiple international emergency medicine societies to share from each a highlighted research study, as selected by their editors.
Meckel’s diverticulum: new solutions for an old problem?
Authors: Chauhan Abhishek , Suggett Nigel , Guest Peter , Goh Jason
Published: October 2015

Meckel's diverticulum (MD) is the most commonly encountered true diverticulum in the small bowel. Although overall a rare cause of gastrointestinal bleeding, it remains an important differential in a child/young adult presenting with lower gastrointestinal bleeding. We present two MD cases, one associated with brisk bleeding resulting in haemodynamic instability and the other in insidious blood loss causing symptoms of chronic iron deficiency. These cases illustrate the heterogeneous nature of the clinical picture associated with Meckel's diverticulae, a condition most gastroenterological and surgical units will encounter. We subsequently discuss the diagnostic and management dilemma Meckel's diverticulae pose and appraise the latest evidence and management strategies in this regard.
Pyrexia of unknown origin 90 years on: a paradigm of modern clinical medicine
Authors: Brown Michael
Published: October 2015

In 1925, Sir Thomas Horder, a leading physician of his day, gave a lecture, published in this journal, entitled ‘Some cases of pyrexia without physical signs’. The paper highlighted what was already a familiar clinical presentation “which taxes our resources to the utmost”. Fast-forward through 90 years of careful clinical description, technological innovation in diagnosis and treatment, emergent infections, novel diagnoses, demographic shifts, and radical changes in the health economy. Sir Thomas would find certain aspects familiar, and others revolutionary, in the differential diagnosis and management of the 21st century patient with pyrexia of unknown origin (PUO). Within high-income settings, the proportion of cases due to infection has declined, albeit unevenly. The era of untreated HIV, and the consequences of iatrogenic intervention and immunosuppression, led to Durack and Street’s subclassification of the condition in the early 1990s into classic, nosocomial, neutropenic and HIV-associated PUO. Shifts towards ambulatory care have driven a change in the definition of many diseases. An era of observant clinicians, who lent their names to eponymous syndromes, followed by meticulous serological, genetic and clinicopathological correlation, generated a battery of diagnoses that, along with malignancy, form a large proportion of diagnoses in more recent clinical care. In the current era, universal access to cross-sectional imaging and an infinite array of laboratory tests has undermined the attention paid to history and examination. In some areas of the clinical assessment, such as assessing the fever pattern, this shift is supported by research evidence. The issues that need to be addressed in the next 90 years of technological innovation, information sharing and health service transformation are likely to include: transcriptomic approaches to diagnosis; the place of positron emission tomography (PET) in the diagnostic pathway; the optimal management of high ferritin states; and the most cost-effective diagnostic environment, in the face of this era of specialisation and fragmentation of care. In the meantime, this review covers some important early 21st century lessons to be shared in avoiding diagnostic pitfalls and choosing empirical therapy.
Iatrogenic tracheal rent in a Clydesdale colt
Authors: Little Erika
Published: October 2015

A one‐month‐old Clydesdale colt presented for bilateral scrotal hernia and a patent urachus. Manual reduction of the hernia followed by castration and primary closure of the superficial inguinal rings bilaterally was performed. The umbilical stump was resected along with the apex of the bladder, and the abdomen was closed routinely. During the procedure, the anaesthetist noted difficulty maintaining an appropriate anaesthetic plane. Diagnostics while under general anaesthesia including arterial blood gas evaluation revealed a blood pH of 7.190 and 7.220. In addition, a large mass was noted in the ventral cervical region that was not present prior to surgery. The mass dramatically reduced in size as the endotracheal cuff was deflated. Postoperatively a tracheal rent was identified, and a temporary tracheostomy was performed under endoscopic guidance. The colt was maintained on systemic antimicrobials, NSAIDs and gastric ulcer prophylaxis and was discharged without complication four weeks later.
Presumptive cystic haemorrhages in a cat with polycystic kidney and hepatic disease
Authors: Longo Maurizio , Zini Eric , Specchi Swan , Piseddu Eleonora , Auriemma Edoardo
Published: October 2015

An adult Persian cat was referred after an abdominal ultrasound revealed a polycystic renal and hepatic disease along with a suspected renal mass on the left kidney. Two non‐enhancing, hyperattenuating cysts were detected on CT on the left and on the right kidney, respectively. A presumptive diagnosis of intracystic bleeding was made, and the subsequently performed aspiration biopsies confirmed a chronic haemorrhage. At 12 months, the CT showed that the same renal lesions appeared similar. The present findings suggest that bleeding from cystic lesions should be considered in case of non‐enhancing, heterogeneous and hyperattenuating renal lesions in cats.
Liver copper concentrations in cull cattle in the UK: are cattle being copper loaded?
Authors: Kendall N. R. , Holmes‐Pavord H. R. , Bone P. A. , Ander E. L. , Young S. D.
Published: October 2015

With the release of the Department for the Environment, Food and Rural Affairs/Advisory Committee on Animal Feed Guidance Note for Supplementing Copper to Bovines it was noted that the current copper status of the national herd was not known. Liver samples were recovered from 510 cull cattle at a single abattoir across a period of three days. The samples were wet‐ashed and liver copper concentrations determined by inductively coupled plasma mass spectrometry analysis. Breed, age and previous location information were obtained from the British Cattle Movement Service. Dairy breeds had higher liver copper concentrations than beef breeds. Holstein‐Friesian and ‘other’ dairy breeds had 38.3 per cent and 40 per cent of cattle above the Animal Health and Veterinary Laboratories Agency (AHVLA) reference range (8000 µmol/kg dry matter), respectively, whereas only 16.9 per cent of animals in the combined beef breeds exceeded this value. It was found that underlying topsoil copper concentration was not related to liver copper content and that age of the animal also had little effect on liver concentration. In conclusion, over 50 per cent of the liver samples tested had greater‐than‐normal concentrations of copper with almost 40 per cent of the female dairy cattle having liver copper concentrations above the AHVLA reference range, indicating that a significant proportion of the UK herd is at risk of chronic copper toxicity.