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1.  Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts To Educate High School Students about Alcohol 
Journal of Chemical Education  2014;91(2):165-172.
We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional development either at a conference-based workshop (NSTA or NCSTA) or via distance learning to learn how to incorporate the APEP modules into their teaching. They field-tested the modules in their classes during the following year. Teacher knowledge of chemistry and biology concepts increased significantly following professional development, and was maintained for at least a year. Their students (n = 14 014) demonstrated significantly higher scores when assessed for knowledge of both basic and advanced chemistry and biology concepts compared to students not using APEP modules in their classes the previous year. Higher scores were achieved as the number of modules used increased. These findings are consistent with our previous studies, demonstrating higher scores in chemistry and biology after students use modules that integrate topics interesting to them, such as drugs (the Pharmacology Education Partnership).
PMCID: PMC3983151  PMID: 24803686
High School/Introductory Chemistry; Chemical Education Research; Interdisciplinary/Multidisciplinary; Distance Learning/Self Instruction; Inquiry-Based/Discovery Learning; Testing/Assessment; Alcohols; Drugs/Pharmaceuticals; Enzymes; Oxidation/Reduction
2.  Annual rates of change in pre- vs. post- bronchodilator FEV1 and FVC over 4 years in moderate to very severe COPD 
Respiratory medicine  2013;107(12):1904-1911.
While the slope of decline in FEV1 has traditionally been calculated from the post- rather than the pre-bronchodilator measurement in COPD interventional trials, it is not clear whether and to what extent these two slopes differ in symptomatic patients with COPD. Therefore, we used data from the 4-year UPLIFT trial of tiotropium 18 mcg QD vs. placebo to compare annual rates of change in pre- vs. post-bronchodilator FEV1 in 5041 patients with moderate to very severe COPD (mean FEV1 48% pred) in whom the post-bronchodilator FEV1 was measured after 4 inhalations of two different classes of short-acting inhaled bronchodilators at baseline and 1 month and every 6 months post-randomization over 4 years. Linear mixed effects models were used to estimate annual rates of decline in FEV1 and FVC pre- and post- bronchodilator in each treatment group separately, after adjusting for height, gender, smoking status, baseline % predicted FEV1 or FVC, and baseline acute % improvement in lung function. The slopes of the post-bronchodilator FEV1 and FVC were significantly steeper than the pre-bronchodilator slopes regardless of treatment arm (p < 0.001), while the estimated variances of the slopes were similar. Post-bronchodilator increases in FEV1 and FVC diminished progressively and significantly (p < 0.0001) over the 4-year trial, suggesting a possible explanation for the significant differences between the pre- and post-bronchodilator slopes. While the reasons for these differences are not completely clear, they are important to consider when assessing treatment effects on rates of decline in FEV1 and FVC.
PMCID: PMC4284059  PMID: 23972968
slope of FEV1 decline; post-bronchodilator; COPD; UPLIFT
3.  Analysis of Recombinant H7N9 Wild-Type and Mutant Viruses in Pigs Shows that the Q226L Mutation in HA Is Important for Transmission 
Journal of Virology  2014;88(14):8153-8165.
The fact that there have been more than 300 human infections with a novel avian H7N9 virus in China indicates that this emerging strain has pandemic potential. Furthermore, many of the H7N9 viruses circulating in animal reservoirs contain putative mammalian signatures in the HA and PB2 genes that are believed to be important in the adaptation of other avian strains to humans. To date, the definitive roles of these mammalian-signature substitutions in transmission and pathogenesis of H7N9 viruses remain unclear. To address this we analyzed the biological characteristics, pathogenicity, and transmissibility of A/Anhui/1/2013 (H7N9) virus and variants in vitro and in vivo using a synthetically created wild-type virus (rAnhui-WT) and two mutants (rAnhui-HA-226Q and rAnhui-PB2-627E). All three viruses replicated in lungs of intratracheally inoculated pigs, yet nasal shedding was limited. The rAnhui-WT and rAnhui-PB2-627E viruses were transmitted to contact animals. In contrast, the rAnhui-HA-226Q virus was not transmitted to sentinel pigs. Deep sequencing of viruses from the lungs of infected pigs identified substitutions arising in the viral population (e.g., PB2-T271A, PB2-D701N, HA-V195I, and PB2-E627K reversion) that may enhance viral replication in pigs. Collectively, the results demonstrate that critical mutations (i.e., HA-Q226L) enable the H7N9 viruses to be transmitted in a mammalian host and suggest that the myriad H7N9 genotypes circulating in avian species in China and closely related strains (e.g., H7N7) have the potential for further adaptation to human or other mammalian hosts (e.g., pigs), leading to strains capable of sustained human-to-human transmission.
IMPORTANCE The genomes of the zoonotic avian H7N9 viruses emerging in China have mutations in critical genes (PB2-E627K and HA-Q226L) that may be important in their pandemic potential. This study shows that (i) HA-226L of zoonotic H7N9 strains is critical for binding the α-2,6-linked receptor and enables transmission in pigs; (ii) wild-type A/Anhui/1/2013 (H7N9) shows modest replication, virulence, and transmissibility in pigs, suggesting that it is not well adapted to the mammalian host; and (iii) both wild-type and variant H7N9 viruses rapidly develop additional mammalian-signature mutations in pigs, indicating that they represent an important potential intermediate host. This is the first study analyzing the phenotypic effects of specific mutations within the HA and PB2 genes of the novel H7N9 viruses created by reverse genetics in an important mammalian host model. Finally, this study illustrates that loss-of-function mutations can be used to effectively identify residues critical to zoonosis/transmission.
PMCID: PMC4097782  PMID: 24807722
4.  Engaging Teenagers with Science Through Comics 
Research in science education  2013;43(6):10.1007/s11165-013-9358-x.
PMCID: PMC3859376  PMID: 24347748
5.  Equine Influenza A(H3N8) Virus Isolated from Bactrian Camel, Mongolia 
Emerging Infectious Diseases  2014;20(12):2144-2147.
Because little is known about the ecology of influenza viruses in camels, 460 nasal swab specimens were collected from healthy (no overt illness) Bactrian camels in Mongolia during 2012. One specimen was positive for influenza A virus (A/camel/Mongolia/335/2012[H3N8]), which is phylogenetically related to equine influenza A(H3N8) viruses and probably represents natural horse-to-camel transmission.
PMCID: PMC4257804  PMID: 25418532
influenza A virus; Mongolia; interspecies transmission; Camelus bactrianus; Bactrian camel; viruses; influenza
6.  Hearing and facial function outcomes for neurofibromatosis 2 clinical trials 
Neurology  2013;81(21 Suppl 1):S25-S32.
Vestibular schwannomas are the hallmark of neurofibromatosis 2 (NF2), occurring in >95% of patients. These tumors develop on the vestibulocochlear nerve and are associated with significant morbidity due to hearing loss, tinnitus, imbalance, facial weakness, and risk of early mortality from brainstem compression. Although hearing loss and facial weakness have been identified as important functional outcomes for patients with NF2, there is a lack of consensus regarding appropriate endpoints in clinical trials.
The functional outcomes group reviewed existing endpoints for hearing and facial function and developed consensus recommendations for response evaluation in NF2 clinical trials.
For hearing endpoints, the functional group endorsed the use of maximum word recognition score as a primary endpoint, with the 95% critical difference as primary hearing outcomes. The group recommended use of the scaled measurement of improvement in lip excursion (SMILE) system for studies of facial function.
These recommendations are intended to provide researchers with a common set of endpoints for use in clinical trials of patients with NF2. The use of common endpoints should improve the quality of clinical trials and foster comparison among studies for hearing loss and facial weakness.
PMCID: PMC3908336  PMID: 24249803
7.  Ten-year audit of clients presenting to a specialised service for young people experiencing or at increased risk for psychosis 
BMC Psychiatry  2014;14(1):318.
Despite strong research interest in psychosis risk identification and the potential for early intervention, few papers have sought to document the implementation and evaluation of specialised psychosis related services. Assessment of Ultra High Risk (UHR) has been given priority, but it is equally as important to identify appropriate comparison groups and other baseline differences. This largely descriptive service evaluation paper focuses on the ‘baseline characteristics’ of referred clients (i.e., previously assessed characteristics or those identified within the first two months following service presentation).
Data are reported from a 10-year layered service audit of all presentations to a ‘Psychological Assistance Service’ for young people (PAS, Newcastle, Australia). Baseline socio-demographic and clinical characteristics (N =1,997) are described (including clients’ psychosis and UHR status, previous service contacts, hospitalisation rates, and diagnostic and comorbidity profiles). Key groups are identified and comparisons made between clients who received ongoing treatment and those who were primarily assessed and referred elsewhere.
Clients averaged 19.2 (SD =4.5) years of age and 59% were male. One-tenth of clients (9.6%) were categorised as UHR, among whom there were relatively high rates of attenuated psychotic symptoms (69.1%), comorbid depression (62.3%), anxiety (42.9%), and attentional and related problems (67.5%). Overall, one-fifth (19.8%) experienced a recent psychotic episode, while a further 14.5% were categorised as having an existing psychosis (46.7% with a schizophrenia diagnosis), amongst whom there were relatively high rates of comorbid substance misuse (52.9%), psychosocial (70.2%) and physical health (37.7%) problems. The largest group presenting to PAS were those with non-psychotic disorders (43.7%), who provide a valuable comparison group against which to contrast the health trajectories of those with UHR and recent psychosis. Ongoing treatment by PAS was preferentially given to those experiencing or at risk for psychosis and those reporting greater current distress or dysfunction.
Whether or not UHR clients transition to psychosis, they displayed high rates of comorbid depression and anxiety at service presentation, with half receiving ongoing treatment from PAS. Although international comparisons with similar services are difficult, the socio-demographic and comorbidity patterns observed here were viewed as largely consistent with those reported elsewhere.
PMCID: PMC4239381  PMID: 25403891
Psychosis; Risk status; Service evaluation; Comorbidity; Youth; Early intervention
8.  A phase II randomized trial of induction chemotherapy versus no induction chemotherapy followed by preoperative chemoradiation in patients with esophageal cancer 
Annals of Oncology  2013;24(11):2844-2849.
The contribution of induction chemotherapy (IC) before preoperative chemoradiation for esophageal cancer (EC) is not known. We hypothesized that IC would increase the rate of pathologic complete response (pathCR).
Trimodality-eligibile patients were randomized to receive no IC (Arm A) or IC (oxaliplatin/FU; Arm B) before oxaliplatin/FU/radiation. Surgery was attempted ∼5–6 weeks after chemoradiation. The pathCR rate, post-surgery 30-day mortality, overall survival (OS), and toxic effects were assessed. Bayesian methods and Fisher's exact test were used.
One hundred twenty-six patients were randomized dynamically to balance the two arms for histology, baseline stage, gender, race, and age. Fifty-five patients in Arm A and 54 in Arm B underwent surgery. The median actuarial OS for all patients (54 deaths) was 45.62 months [95% confidence interval (CI), 27.63–NA], with median OS 45.62 months (95% CI 25.56–NA) in Arm A and 43.68 months (95% CI 27.63–NA) in Arm B (P = 0.69). The pathCR rate in Arm A was 13% (7 of 55) and 26% (14 of 54) in Arm B (two-sided Fisher's exact test, P = 0.094). Safety was similar in both arms.
These data suggest that IC produces non-significant increase in the pathCR rate and does not prolong OS. Further development of IC before chemoradiation may not be beneficial.
Clinical trial no.: NCT 00525915 (
PMCID: PMC3937600  PMID: 23975663
esophageal carcinoma; induction chemotherapy; chemoradiation; randomized trial; pathologic complete response; esophageal preservation
9.  A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys 
BMC Genomics  2014;15(1):907.
(1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on human health.
We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes.
We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containing CslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-907) contains supplementary material, which is available to authorized users.
PMCID: PMC4213503  PMID: 25326272
Barley; (1,3;1,4)-β-glucan; Cell walls; GWAS; Soluble fibre
10.  Do you know your patient? 
PMCID: PMC3930328  PMID: 23980659
11.  Genomewide Analysis of Reassortment and Evolution of Human Influenza A(H3N2) Viruses Circulating between 1968 and 2011 
Journal of Virology  2014;88(5):2844-2857.
Influenza A(H3N2) viruses became widespread in humans during the 1968 H3N2 virus pandemic and have been a major cause of influenza epidemics ever since. These viruses evolve continuously by reassortment and genomic evolution. Antigenic drift is the cause for the need to update influenza vaccines frequently. Using two data sets that span the entire period of circulation of human influenza A(H3N2) viruses, it was shown that influenza A(H3N2) virus evolution can be mapped to 13 antigenic clusters. Here we analyzed the full genomes of 286 influenza A(H3N2) viruses from these two data sets to investigate the genomic evolution and reassortment patterns. Numerous reassortment events were found, scattered over the entire period of virus circulation, but most prominently in viruses circulating between 1991 and 1998. Some of these reassortment events persisted over time, and one of these coincided with an antigenic cluster transition. Furthermore, selection pressures and nucleotide and amino acid substitution rates of all proteins were studied, including those of the recently discovered PB1-N40, PA-X, PA-N155, and PA-N182 proteins. Rates of nucleotide and amino acid substitutions were most pronounced for the hemagglutinin, neuraminidase, and PB1-F2 proteins. Selection pressures were highest in hemagglutinin, neuraminidase, matrix 1, and nonstructural protein 1. This study of genotype in relation to antigenic phenotype throughout the period of circulation of human influenza A(H3N2) viruses leads to a better understanding of the evolution of these viruses.
IMPORTANCE Each winter, influenza virus infects approximately 5 to 15% of the world's population, resulting in significant morbidity and mortality. Influenza A(H3N2) viruses evolve continuously by reassortment and genomic evolution. This leads to changes in antigenic recognition (antigenic drift) which make it necessary to update vaccines against influenza A(H3N2) viruses frequently. In this study, the relationship of genetic evolution to antigenic change spanning the entire period of A(H3N2) virus circulation was studied for the first time. The results presented in this study contribute to a better understanding of genetic evolution in correlation with antigenic evolution of influenza A(H3N2) viruses.
PMCID: PMC3958060  PMID: 24371052
12.  Acute bronchodilator responses decline progressively over 4 years in patients with moderate to very severe COPD 
Respiratory Research  2014;15(1):102.
We previously reported a progressive decline in absolute responses of FEV1 and FVC to a near-maximal dose of 2 different short-acting bronchodilators over 4 years. Since varying host factors and the method of expressing the response may impact the time trend of acute bronchodilator responses, we now examined the potential influence of salient host characteristics on changes in bronchodilator responses over time expressed in different ways.
As part of the 4-year, placebo-controlled Understanding Potential Long-term Impacts on Function with Tiotropium (UPLIFT) trial, pre- and post-bronchodilator spirometry was performed at baseline and 1 month and every 6 months thereafter. Post-bronchodilator values for FEV1 and FVC were analyzed for subjects completing at least the 1 year visit (Placebo – N = 2463; Tiotropium – N = 2579), stratified by GOLD stage, age, gender and smoking status and expressed as absolute, relative (%) and % predicted changes from pre-bronchodilator values. Annual changes in bronchodilator response were estimated using linear mixed effects models.
For all subjects analyzed, FEV1 and FVC bronchodilator responses showed progressive and highly significant (p < 0.0001) declines over 4 years. Declines were generally larger in patients with severe/very severe than mild/moderate airflow obstruction, in older patients (≥65 yrs) and in former than continuing smokers.
Acute FEV1 and FVC responses to bronchodilators decline significantly over time in COPD patients, whether expressed as absolute, relative or % predicted changes, potentially impacting on the clinical responses to bronchodilator therapy as well as on the annual rate of decline in post-bronchodilator lung function. number
Electronic supplementary material
The online version of this article (doi:10.1186/s12931-014-0102-5) contains supplementary material, which is available to authorized users.
PMCID: PMC4244051  PMID: 25175805
COPD; Bronchodilator response; UPLIFT trial
13.  MRI markers of small vessel disease in lobar and deep hemispheric intracerebral hemorrhage 
MRI evidence of small vessel disease is common in intracerebral hemorrhage (ICH). We hypothesized that ICH caused by cerebral amyloid angiopathy (CAA) or hypertensive vasculopathy would have different distributions of MRI T2 white matter hyperintensity (WMH) and microbleeds (MB).
Data were analyzed from 133 consecutive patients with primary supratentorial ICH and adequate MRI sequences. CAA was diagnosed using the Boston criteria. WMH segmentation was performed using a validated semi-automated method. WMH and MB were compared according to site of symptomatic hematoma origin (lobar vs. deep) or by pattern of hemorrhages, including both hematomas and MB, on MRI GRE sequence (grouped as lobar only--probable CAA, lobar only--possible CAA, deep hemispheric only, or mixed lobar and deep hemorrhages).
Lobar and deep hemispheric hematoma patients had similar median nWMH volumes (19.5 cm vs. 19.9 cm3, p=0.74) and prevalence of ≥1 MB (54% vs. 52%, p=0.99). The supratentorial WMH distribution was similar according to hemorrhage location category, however the prevalence of brainstem T2 hyperintensity was lower in lobar hematoma vs. deep hematoma (54% vs. 70%, p=0.004). Mixed ICH was common (23%). Mixed ICH patients had large nWMH volumes and a posterior distribution of cortical hemorrhages similar to that seen in CAA.
WMH distribution is largely similar between CAA-related and non-CAA-related ICH. Mixed lobar and deep hemorrhages are seen on MRI GRE in up to one quarter of patients; in these patients both hypertension and CAA may be contributing to the burden of WMH.
PMCID: PMC4084787  PMID: 20689084
intracerebral hemorrhage; MRI; white matter disease; leukoaraiosis; cerebral amyloid angiopathy
14.  Suggested response criteria for phase II antitumor drug studies for neurofibromatosis type 2 related vestibular schwannoma 
Journal of neuro-oncology  2009;93(1):61-77.
Neurofibromatosis type 2 (NF2) is a tumor suppressor gene syndrome characterized by multiple schwannomas, especially vestibular schwannomas (VS), and meningiomas. Anticancer drug trials are now being explored, but there are no standardized endpoints in NF2. We review the challenges of NF2 clinical trials and suggest possible response criteria for use in initial phase II studies. We suggest two main response criteria in such trials. Objective radiographic response is defined as a durable 20% or greater reduction in VS volume based on postcontrast T1-weighted MRI images collected with 3 mm or finer cuts through the internal auditory canal. Hearing response is defined as a statistically significant improvement in word recognition scores using 50-word recorded lists in audiology. A possible composite endpoint incorporating both radiographic response and hearing response is outlined. We emphasize pitfalls in response assessment and suggest guidelines to minimize misinterpretations of response. We also identify research goals in NF2 to facilitate future trial conduct, such as identifying the expectations for time to tumor progression and time to measurable hearing loss in untreated NF2-related VS, and the relation of both endpoints to patient prognostic factors (such as age, baseline tumor volume, and measures of disease severity). These data would facilitate future use of endpoints based on stability of tumor size and hearing, which might be more appropriate for testing certain drugs. We encourage adoption of standardized endpoints early in the development of phase II trials for this population to facilitate comparison of results across trials of different agents.
PMCID: PMC4036446  PMID: 19430883
Vestibular schwannoma; Acoustic neuroma; Neurofibromatosis type 2; Trial design; Phase II trial
15.  Teaching High School Chemistry in the Context of Pharmacology Helps Both Teachers and Students Learn 
Journal of chemical education  2011;88(6):744-750.
Few studies demonstrate the impact of teaching chemistry embedded in a context that has relevance to high school students. We build upon our prior work showing that pharmacology topics (i.e., drugs), which are inherently interesting to high school students, provide a useful context for teaching chemistry and biology. In those studies, teachers were provided professional development for the Pharmacology Education Partnership (PEP) in an onsite venue (either five-day or one-day workshop). Given financial difficulties to travel, teachers have asked for alternatives for professional development. Thus, we developed the same PEP training workshop using a distance learning (DL) (two-way live video) approach. In this way, 121 chemistry and biology teachers participated in the DL workshops to learn how to incorporate the PEP modules into their teaching. They field-tested the modules over the year in high school chemistry and biology classes. Teacher knowledge of chemistry and biology increased significantly after the workshop and was maintained for at least a year. Their students (N = 2309) demonstrated a significant increase in knowledge of chemistry and biology concepts, with higher scores as the number of modules used increased. The increase in both teacher and student knowledge in these subjects was similar to that found previously when teachers were provided with onsite professional development.
PMCID: PMC4037129  PMID: 24882881
High School/Introductory Chemistry; Chemical Education Research; Interdisciplinary/Multidisciplinary; Distance Learning/Self Instruction; Inquiry-Based/Discovery Learning; Testing/Assessment; Acids/Bases; Drugs/Pharmaceuticals; Enzymes; Oxidation/Reduction
16.  Erlotinib for Progressive Vestibular Schwannoma in Neurofibromatosis 2 Patients 
In vitro treatment of Nf2-deficient cells with epidermal growth factor receptor (EGFR) inhibitors can inhibit cellular proliferation. We retrospectively assessed the effect of erlotinib (150 mg daily) on eleven consecutive NF2 patients with progressive VS who were poor candidates for standard therapy. A radiographic response was defined as ≥ 20% decrease in tumor volume compared to baseline. A hearing response was defined as a statistically significant increase in word recognition score (WRS) compared to baseline; a minor hearing response was defined as a 10 dB improvement in pure-tone average with stable WRS. Before treatment, the median and mean annual volumetric growth rate for eleven index VS were 26% and 46%, respectively. Among 10 evaluable patients, the median time-to-tumor progression was 9.2 months. Three patients with stable disease experienced maximum tumor shrinkage of 4%, 13%, and 14%. Nine patients underwent audiologic evaluations. One experienced a transient hearing response, two experienced minor hearing responses, three remained stable, and two developed progressive hearing loss. The median time-to-progressive hearing loss was 9.2 months and to either tumor growth or progressive hearing loss was 7.1 months. Adverse treatment effects included mild-to-moderate rash, diarrhea, and hair thinning, with 2 episodes of grade 3 toxicity. Erlotinib treatment was not associated with radiographic or hearing responses in NF2 patients with progressive VS. Because a subset of patients experienced prolonged stable disease, time-to-progression may be more appropriate than radiographic or hearing response for anti-EGFR agents in NF2-associated VS.
PMCID: PMC4030413  PMID: 20736812
neurofibromatosis; vestibular schwannoma; acoustic neuroma; erlotinib; hearing
17.  Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics 
Journal of Clinical Microbiology  2014;52(5):1330-1337.
Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock.
PMCID: PMC3993638  PMID: 24501036
18.  Comparison of umbo velocity in air and bone conduction 
Hearing research  2012;290(0):83-90.
This study investigates the ossicular motion produced by bone-conducted (BC) sound in live human ears. Laser Doppler Vibrometry was used to measure air conduction (AC) and BC induced umbo velocity (Vu) in both ears of 10 subjects, 20 ears total. Sound pressure in the ear canal (PEC) was measured simultaneously. For air conduction, Vu at threshold was calculated. For BC, ΔV was defined as the difference between Vu and the tympanic ring velocity (an estimate of the skull velocity measured in the ear canal). ΔV and PEC at BC threshold were calculated and compared to the corresponding air conduction measurements.
ΔV at BC threshold was significantly smaller than Vu at AC threshold between 500 Hz and 2000 Hz. Ear canal pressure at BC threshold tended to be smaller than for AC below 3000 Hz (with significant differences at 1000 Hz and 2000 Hz). Our results are most consistent with inertia of the ossicles and cochlear fluid driving BC hearing below 500 Hz, but with other mechanisms playing a significant role at higher frequencies. Sound radiated into the external ear canal might contribute to BC hearing at 3000 Hz and above.
PMCID: PMC3998651  PMID: 22609771
umbo velocity; bone conduction; middle ear inertia; cochlear inertia; sound radiated in the external ear canal
19.  Topography of dilated perivascular spaces in subjects from a memory clinic cohort 
Neurology  2013;80(17):1551-1556.
To investigate whether the topography of dilated perivascular spaces (DPVS) corresponds with markers of particular small-vessel diseases such as cerebral amyloid angiopathy and hypertensive vasculopathy.
Patients were recruited from an ongoing single-center prospective longitudinal cohort study of patients evaluated in a memory clinic. All patients underwent structural, high-resolution MRI, and had a clinical assessment performed within 1 year of scan. DPVS were rated in basal ganglia (BG-DPVS) and white matter (WM-DPVS) on T1 sequences, using an established 4-point semiquantitative score. DPVS degree was classified as high (score > 2) or low (score ≤ 2). Independent risk factors for high degree of BG-DPVS and WM-DPVS were investigated.
Eighty-nine patients were included (mean age 72.7 ± 9.9 years, 57% female). High degree of WM-DPVS was more frequent than low degree in patients with presence of strictly lobar microbleeds (45.5% vs 28.4% of subjects). High BG-DPVS degree was associated with older age, hypertension, and higher white matter hyperintensity volumes. In multivariate analysis, increased lobar microbleed count was an independent predictor of high degree of WM-DPVS (odds ratio [OR] 1.53 [95% confidence interval (CI) 1.06–2.21], p = 0.02). By contrast, hypertension was an independent predictor of high degree of BG-DPVS (OR 9.4 [95% CI 1–85.2], p = 0.04).
The associations of WM-DPVS with lobar microbleeds and BG-DPVS with hypertension raise the possibility that the distribution of DPVS may indicate the presence of underlying small-vessel diseases such as cerebral amyloid angiopathy and hypertensive vasculopathy in patients with cognitive impairment.
PMCID: PMC3662325  PMID: 23553482
20.  Increased predation of nutrient-enriched aposematic prey 
Avian predators readily learn to associate the warning coloration of aposematic prey with the toxic effects of ingesting them, but they do not necessarily exclude aposematic prey from their diets. By eating aposematic prey ‘educated’ predators are thought to be trading-off the benefits of gaining nutrients with the costs of eating toxins. However, while we know that the toxin content of aposematic prey affects the foraging decisions made by avian predators, the extent to which the nutritional content of toxic prey affects predators' decisions to eat them remains to be tested. Here, we show that European starlings (Sturnus vulgaris) increase their intake of a toxic prey type when the nutritional content is artificially increased, and decrease their intake when nutritional enrichment is ceased. This clearly demonstrates that birds can detect the nutritional content of toxic prey by post-ingestive feedback, and use this information in their foraging decisions, raising new perspectives on the evolution of prey defences. Nutritional differences between individuals could result in equally toxic prey being unequally predated, and might explain why some species undergo ontogenetic shifts in defence strategies. Furthermore, the nutritional value of prey will likely have a significant impact on the evolutionary dynamics of mimicry systems.
PMCID: PMC3953848  PMID: 24598424
educated predator; prey defences; nutrients; toxic prey; mimicry
21.  North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses 
PLoS ONE  2014;9(3):e92075.
Avian influenza virus (AIV) in wild birds has been of increasing interest over the last decade due to the emergence of AIVs that cause significant disease and mortality in both poultry and humans. While research clearly demonstrates that AIVs can move across the Pacific or Atlantic Ocean, there has been no data to support the mechanism of how this occurs. In spring and autumn of 2010 and autumn of 2011 we obtained cloacal swab samples from 1078 waterfowl, gulls, and shorebirds of various species in southwest and west Iceland and tested them for AIV. From these, we isolated and fully sequenced the genomes of 29 AIVs from wild caught gulls (Charadriiformes) and waterfowl (Anseriformes) in Iceland. We detected viruses that were entirely (8 of 8 genomic segments) of American lineage, viruses that were entirely of Eurasian lineage, and viruses with mixed American-Eurasian lineage. Prior to this work only 2 AIVs had been reported from wild birds in Iceland and only the sequence from one segment was available in GenBank. This is the first report of finding AIVs of entirely American lineage and Eurasian lineage, as well as reassortant viruses, together in the same geographic location. Our study demonstrates the importance of the North Atlantic as a corridor for the movement of AIVs between Europe and North America.
PMCID: PMC3960164  PMID: 24647410
22.  Shifts in Geographic Distribution and Antimicrobial Resistance during a Prolonged Typhoid Fever Outbreak — Bundibugyo and Kasese Districts, Uganda, 2009–2011 
Salmonella enterica serovar Typhi is transmitted by fecally contaminated food and water and causes approximately 22 million typhoid fever infections worldwide each year. Most cases occur in developing countries, where approximately 4% of patients develop intestinal perforation (IP). In Kasese District, Uganda, a typhoid fever outbreak notable for a high IP rate began in 2008. We report that this outbreak continued through 2011, when it spread to the neighboring district of Bundibugyo.
Methodology/Principal Findings
A suspected typhoid fever case was defined as IP or symptoms of fever, abdominal pain, and ≥1 of the following: gastrointestinal disruptions, body weakness, joint pain, headache, clinically suspected IP, or non-responsiveness to antimalarial medications. Cases were identified retrospectively via medical record reviews and prospectively through laboratory-enhanced case finding. Among Kasese residents, 709 cases were identified from August 1, 2009–December 31, 2011; of these, 149 were identified during the prospective period beginning November 1, 2011. Among Bundibugyo residents, 333 cases were identified from January 1–December 31, 2011, including 128 cases identified during the prospective period beginning October 28, 2011. IP was reported for 507 (82%) and 59 (20%) of Kasese and Bundibugyo cases, respectively. Blood and stool cultures performed for 154 patients during the prospective period yielded isolates from 24 (16%) patients. Three pulsed-field gel electrophoresis pattern combinations, including one observed in a Kasese isolate in 2009, were shared among Kasese and Bundibugyo isolates. Antimicrobial susceptibility was assessed for 18 isolates; among these 15 (83%) were multidrug-resistant (MDR), compared to 5% of 2009 isolates.
Molecular and epidemiological evidence suggest that during a prolonged outbreak, typhoid spread from Kasese to Bundibugyo. MDR strains became prevalent. Lasting interventions, such as typhoid vaccination and improvements in drinking water infrastructure, should be considered to minimize the risk of prolonged outbreaks in the future.
Author Summary
Typhoid fever is an acute febrile illness caused by the bacteria Salmonella Typhi and transmitted through food and water contaminated with the feces of typhoid fever patients or carriers. We investigated typhoid fever outbreaks in two neighboring Ugandan districts, Kasese and Bundibugyo, where typhoid fever outbreaks began in 2008 and 2011, respectively. In Kasese from August 2009–December 2011, we documented 709 cases of typhoid fever. In Bundibugyo from January–December 2011, we documented 333 cases. Salmonella Typhi from Bundibugyo and Kasese had indistinguishable molecular fingerprints; laboratory and epidemiological evidence indicate that the outbreak spread from Kasese to Bundibugyo. Salmonella Typhi isolated during our investigation were resistant to more antibiotics than isolates obtained from Kasese in 2009. Drinking water in both districts was fecally contaminated and the likely vehicle for the outbreaks. Our investigation highlights that in unchecked typhoid fever outbreaks, illness can become geographically dispersed and outbreak strains can become increasingly resistant to antibiotics. Lasting interventions, including investments in drinking water infrastructure and typhoid vaccination, are needed to control these outbreaks and prevent future outbreaks.
PMCID: PMC3945727  PMID: 24603860
23.  The Barley Genome Sequence Assembly Reveals Three Additional Members of the CslF (1,3;1,4)-β-Glucan Synthase Gene Family 
PLoS ONE  2014;9(3):e90888.
An important component of barley cell walls, particularly in the endosperm, is (1,3;1,4)-β- glucan, a polymer that has proven health benefits in humans and that influences processability in the brewing industry. Genes of the cellulose synthase-like (Csl) F gene family have been shown to be involved in (1,3;1,4)-β-glucan synthesis but many aspects of the biosynthesis are still unclear. Examination of the sequence assembly of the barley genome has revealed the presence of an additional three HvCslF genes (HvCslF11, HvCslF12 and HvCslF13) which may be involved in (1,3;1,4)-β-glucan synthesis. Transcripts of HvCslF11 and HvCslF12 mRNA were found in roots and young leaves, respectively. Transient expression of these genes in Nicotiana benthamiana resulted in phenotypic changes in the infiltrated leaves, although no authentic (1,3;1,4)-β-glucan was detected. Comparisons of the CslF gene families in cereals revealed evidence of intergenic recombination, gene duplications and translocation events. This significant divergence within the gene family might be related to multiple functions of (1,3;1,4)-β-glucans in the Poaceae. Emerging genomic and global expression data for barley and other cereals is a powerful resource for characterising the evolution and dynamics of complete gene families. In the case of the CslF gene family, the results will contribute to a more thorough understanding of carbohydrate metabolism in grass cell walls.
PMCID: PMC3940952  PMID: 24595438
24.  Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 1: Fabrication and Characterization 
The Analyst  2012;138(1):129-136.
In Part I of a two-part series, we describe a simple, and inexpensive approach to fabricate polystyrene devices that is based upon melting polystyrene (from either a Petri dish or powder form) against PDMS molds or around electrode materials. The ability to incorporate microchannels in polystyrene and integrate the resulting device with standard laboratory equipment such as an optical plate reader for analyte readout and micropipettors for fluid propulsion is first described. A simple approach for sample and reagent delivery to the device channels using a standard, multi-channel micropipette and a PDMS-based injection block is detailed. Integration of the microfluidic device with these off-chip functions (sample delivery and readout) enables high throughput screens and analyses. An approach to fabricate polystyrene-based devices with embedded electrodes is also demonstrated, thereby enabling the integration of microchip electrophoresis with electrochemical detection through the use of a palladium electrode (for a decoupler) and carbon-fiber bundle (for detection). The device was sealed against a PDMS-based microchannel and used for the electrophoretic separation and amperometric detection of dopamine, epinephrine, catechol, and 3,4-dihydroxyphenylacetic acid. Finally, these devices were compared against PDMS-based microchips in terms of their optical transparency and absorption of an anti-platelet drug, clopidogrel. Part I of this series lays the foundation for Part II, where these devices were utilized for various on-chip cellular analysis.
PMCID: PMC3523208  PMID: 23120747
25.  Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 2: Cellular Analysis 
The Analyst  2012;138(1):137-143.
In Part II of this series describing the use of polystyrene (PS) devices for microfluidic-based cellular assays, various cellular types and detection strategies are employed to determine three fundamental assays often associated with cells. Specifically, using either integrated electrochemical sensing or optical measurements with a standard multi-well plate reader, cellular uptake, production, or release of important cellular analytes are determined on a PS-based device. One experiment involved the fluorescence measurement of nitric oxide (NO) produced within an endothelial cell line following stimulation with ATP. The result was a four-fold increase in NO production (as compared to a control), with this receptor-based mechanism of NO production verifying the maintenance of cell receptors following immobilization onto the PS substrate. The ability to monitor cellular uptake was also demonstrated by optical determination of Ca2+ into endothelial cells following stimulation with the Ca2+ ionophore A20317. The result was a significant increase (42%) in the calcium uptake in the presence of the ionophore, as compared to a control (17%) (p < 0.05). Finally, the release of catecholamines from a dopaminergic cell line (PC 12 cells) was electrochemically monitored, with the electrodes being embedded into the PS-based device. The PC 12 cells had better adherence on the PS devices, as compared to use of PDMS. Potassium-stimulation resulted in the release of 114 ± 11 µM catecholamines, a significant increase (p < 0.05) over the release from cells that had been exposed to an inhibitor (reserpine, 20 ± 2 µM of catecholamines). The ability to successfully measure multiple analytes, generated in different means from various cells under investigation, suggests that PS may be a useful material for microfluidic device fabrication, especially considering the enhanced cell adhesion to PS, its enhanced rigidity/amenability to automation, and its ability to enable a wider range of analytes to be investigated, even analytes with a high degree of hydrophobicity.
PMCID: PMC3523209  PMID: 23120748

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