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1.  Immunoglobulin G, Plasma Cells, and Lymphocytes in the Murine Vagina after Vaginal or Parenteral Immunization with Attenuated Herpes Simplex Virus Type 2 
Journal of Virology  1998;72(6):5137-5145.
This investigation evaluated immunity to vaginal herpes simplex virus type 2 (HSV-2) infection after local or parenteral immunization with attenuated HSV-2. Vaginal immunization induced sterilizing immunity against challenge with a high dose of wild-type virus, whereas parenteral immunizations protected against neurologic disease but did not entirely prevent infection of the vagina. Vaginal immunization caused 86- and 31-fold increases in the numbers of immunoglobulin G (IgG) plasma cells in the vagina at 6 weeks and 10 months after immunization, whereas parenteral immunizations did not increase plasma cell numbers in the vagina. Vaginal secretion/serum titer ratios and specific antibody activities in vaginal secretions and serum indicated that IgG viral antibody was produced in the vagina and released into vaginal secretions at 6 weeks and 10 months after vaginal immunization but not after parenteral immunizations. In contrast to the case for plasma cells, the numbers of T and B lymphocytes in the vagina were similar in vaginally and parenterally immunized mice. Also, lymphocyte numbers in the vagina were markedly but similarly increased by vaginal challenge with HSV-2 in both vaginally and parenterally immunized mice. Lymphocyte recruitment to the vagina after virus challenge appeared to involve memory lymphocytes, because it was not observed in nonimmunized mice. Thus, local vaginal immunization with attenuated HSV-2 increased the number of IgG plasma cells in the vagina and increased vaginal secretion/serum titer ratios to 3.0- to 4.7-fold higher than in parenterally immunized groups but caused little if any selective homing of T and B lymphocytes to the vagina.
PMCID: PMC110083  PMID: 9573285
2.  Mucosal Immunity to Herpes Simplex Virus Type 2 Infection in the Mouse Vagina Is Impaired by In Vivo Depletion of T Lymphocytes 
Journal of Virology  1998;72(4):2677-2685.
Intravaginal (IVAG) inoculation of wild-type herpes simplex virus type 2 (HSV-2) in mice causes epithelial infection followed by lethal neurological illness, while IVAG inoculation of attenuated HSV-2 causes epithelial infection followed by development of protective immunity against subsequent IVAG challenge with wild-type virus. The role of T cells in this immunity was studied by in vivo depletion of these cells with monoclonal antibodies. Three groups of mice were used for each experiment: nonimmune/challenged mice, immune/challenged mice, and immune depleted mice [immune mice depleted of a T-cell subset(s) shortly before challenge with HSV-2]. Mice were assessed for epithelial infection 24 h after challenge, virus protein in the vaginal lumen 3 days after challenge, and neurological illness 8 to 14 days after challenge. Monoclonal antibodies to CD4, CD8, or Thy-1 markedly reduced T cells in blood, spleen, and vagina, but major histocompatibility complex class II antigens were still partially upregulated in the vaginal epithelium after virus challenge, indicating that virus-specific memory T-cell function was not entirely eliminated from the vagina. Nevertheless, immune mice depleted of CD4+ and CD8+ T cells, Thy-1+ T cells, or CD8+ T cells alone had greater viral infection in the vaginal epithelium than nondepleted immune mice, indicating that T cells contribute to immunity against vaginal HSV-2 infection. All immune depleted mice retained substantial immunity to epithelial infection and were immune to neurological illness, suggesting that other immune mechanisms such as virus-specific antibody may also contribute to immunity.
PMCID: PMC109710  PMID: 9525585
3.  Immunoglobulin G is the main protective antibody in mouse vaginal secretions after vaginal immunization with attenuated herpes simplex virus type 2. 
Journal of Virology  1997;71(11):8109-8115.
We investigated the protective role of antibodies in vaginal secretions of mice that were immune to vaginal challenge with herpes simplex virus type 2 (HSV-2). Unfractionated vaginal immunoglobulins from immune and nonimmune mice and affinity-purified immunoglobulin G (IgG) and secretory IgA (S-IgA) from immune secretions were adjusted to their concentrations in vivo. Wild-type HSV-2 was incubated in the immunoglobulin preparations for 15 min in vitro, followed by inoculation into vaginae of nonimmune mice. HSV-2 was neutralized by unfractionated antibody and purified IgG from immune secretions but not by unfractionated nonimmune antibody or by purified immune S-IgA. The protective effect of IgG in vivo was investigated by passively transferring purified serum IgG from immune and nonimmune donors to nonimmune recipients before vaginal challenge infection. Immune IgG significantly reduced the percentage of vaginal epithelium infected, concentrations of shed virus protein in the vaginal lumen, and illness scores, even though the viral antibody titers in serum and vaginal secretions of recipient mice at the time of challenge were only 29 and 8%, respectively, of those in actively immunized mice. Additionally, removal of vaginal secretions from immune mice 10 min before vaginal challenge with HSV-2 significantly increased the concentration of shed virus protein in the vaginal lumen after challenge. Collectively, the data indicate that IgG antibody in vaginal secretions of immune mice provides early protection against vaginal challenge infection, probably by neutralizing virus in the vaginal lumen. In contrast, S-IgA antibody contributed relatively little to immune protection of the vagina.
PMCID: PMC192266  PMID: 9343160
4.  Virtual Reconstruction and Prey Size Preference in the Mid Cenozoic Thylacinid, Nimbacinus dicksoni (Thylacinidae, Marsupialia) 
PLoS ONE  2014;9(4):e93088.
Thylacinidae is an extinct family of Australian and New Guinean marsupial carnivores, comprizing 12 known species, the oldest of which are late Oligocene (∼24 Ma) in age. Except for the recently extinct thylacine (Thylacinus cynocephalus), most are known from fragmentary craniodental material only, limiting the scope of biomechanical and ecological studies. However, a particularly well-preserved skull of the fossil species Nimbacinus dicksoni, has been recovered from middle Miocene (∼16-11.6 Ma) deposits in the Riversleigh World Heritage Area, northwestern Queensland. Here, we ask whether N. dicksoni was more similar to its recently extinct relative or to several large living marsupials in a key aspect of feeding ecology, i.e., was N. dicksoni a relatively small or large prey specialist. To address this question we have digitally reconstructed its skull and applied three-dimensional Finite Element Analysis to compare its mechanical performance with that of three extant marsupial carnivores and T. cynocephalus. Under loadings adjusted for differences in size that simulated forces generated by both jaw closing musculature and struggling prey, we found that stress distributions and magnitudes in the skull of N. dicksoni were more similar to those of the living spotted-tailed quoll (Dasyurus maculatus) than to its recently extinct relative. Considering the Finite Element Analysis results and dental morphology, we predict that N. dicksoni likely occupied a broadly similar ecological niche to that of D. maculatus, and was likely capable of hunting vertebrate prey that may have exceeded its own body mass.
PMCID: PMC3981708  PMID: 24718109
5.  Knowledge Extraction and Semantic Annotation of Text from the Encyclopedia of Life 
PLoS ONE  2014;9(3):e89550.
Numerous digitization and ontological initiatives have focused on translating biological knowledge from narrative text to machine-readable formats. In this paper, we describe two workflows for knowledge extraction and semantic annotation of text data objects featured in an online biodiversity aggregator, the Encyclopedia of Life. One workflow tags text with DBpedia URIs based on keywords. Another workflow finds taxon names in text using GNRD for the purpose of building a species association network. Both workflows work well: the annotation workflow has an F1 Score of 0.941 and the association algorithm has an F1 Score of 0.885. Existing text annotators such as Terminizer and DBpedia Spotlight performed well, but require some optimization to be useful in the ecology and evolution domain. Important future work includes scaling up and improving accuracy through the use of distributional semantics.
PMCID: PMC3940440  PMID: 24594988
6.  The Community Leaders Institute: An Innovative Program to Train Community Leaders in Health Research 
An emerging best practice of addressing health and improving health disparities in communities is ensuring that academic health centers (AHCs) are engaged with area schools, primary care practices, and community advocates as equal partners in research, services, and programs. The literature documents the importance of ensuring that academic-community collaboration is based on equity, trust, and respect, and that there is capacity (time and resources) and a shared culture (language, skills, and applied knowledge) for accomplishing mutual goals in academic-community research partnerships. It is also essential that an academic-community collaboration results in tangible and measurable goals and outcomes for both the target community and the AHC. Currently, the models for implementing best practices in community health partnerships, especially training programs, are limited.
This paper article summarizes the goals and outcomes for the Community Leaders Institute (CLI), a six-week innovative leadership development training program designed to enhance academic-community research, integrate the interests of community leaders and AHC researchers, and build research capacity and competencies within the community. Based on two years of outcome data, the CLI is achieving its intended goals of engaging faculty as trainer-scholars while promoting academic-community partnerships that align with community and AHC priorities. The training and collaborative research paradigm utilized by the CLI has served to accelerate AHC-community engagement and integration efforts, as CLI graduates are now serving on AHC steering, bioethics, and other committees.
PMCID: PMC3584236  PMID: 23348087
7.  Quantitative computed tomography–derived clusters: Redefining airway remodeling in asthmatic patients☆ 
Asthma heterogeneity is multidimensional and requires additional tools to unravel its complexity. Computed tomography (CT)–assessed proximal airway remodeling and air trapping in asthmatic patients might provide new insights into underlying disease mechanisms.
The aim of this study was to explore novel, quantitative, CT-determined asthma phenotypes.
Sixty-five asthmatic patients and 30 healthy subjects underwent detailed clinical, physiologic characterization and quantitative CT analysis. Factor and cluster analysis techniques were used to determine 3 novel, quantitative, CT-based asthma phenotypes.
Patients with severe and mild-to-moderate asthma demonstrated smaller mean right upper lobe apical segmental bronchus (RB1) lumen volume (LV) in comparison with healthy control subjects (272.3 mm3 [SD, 112.6 mm3], 259.0 mm3 [SD, 53.3 mm3], 366.4 mm3 [SD, 195.3 mm3], respectively; P = .007) but no difference in RB1 wall volume (WV). Air trapping measured based on mean lung density expiratory/inspiratory ratio was greater in patients with severe and mild-to-moderate asthma compared with that seen in healthy control subjects (0.861 [SD, 0.05)], 0.866 [SD, 0.07], and 0.830 [SD, 0.06], respectively; P = .04). The fractal dimension of the segmented airway tree was less in asthmatic patients compared with that seen in control subjects (P = .007). Three novel, quantitative, CT-based asthma clusters were identified, all of which demonstrated air trapping. Cluster 1 demonstrates increased RB1 WV and RB1 LV but decreased RB1 percentage WV. On the contrary, cluster 3 subjects have the smallest RB1 WV and LV values but the highest RB1 percentage WV values. There is a lack of proximal airway remodeling in cluster 2 subjects.
Quantitative CT analysis provides a new perspective in asthma phenotyping, which might prove useful in patient selection for novel therapies.
PMCID: PMC3969578  PMID: 24238646
Asthma; airway remodeling; distal airway; CT; quantitative imaging; phenotypes; cluster analysis; fractal analysis; ATS, American Thoracic Society; BSA, Body surface area; CT, Computed tomography; Dav, Averaged fractal dimension; De, Most efficient cover fractal dimension; Dsc, Slope-corrected fractal dimension; Dsce, Slope-corrected most-efficient covering fractal dimension; FRC, Functional residual capacity; HU, Hounsfield units; ICC, Intraclass correlation coefficient; LA, Lumen area; LV, Lumen volume; MLD E/I, Mean lung density expiratory/inspiratory ratio; Pi10, Hypothetical airway with internal perimeter of 10 mm; Po20, Hypothetical airways with outer airway perimeter of 20 mm; RB1, Right upper lobe apical segmental bronchus; ROI, Region of interest; RV, Residual volume; TLC, Total lung capacity; VI, Voxel index; VI−850 E-I, VI−850 change on paired inspiratory and expiratory CT scan; VI−850/−950 E-I, Voxel index change of percent voxels between −950 and −850 HU on paired inspiratory and expiratory CT scan; WA, Wall area; WV, Wall volume
8.  Differences in Neural Activation for Object-Directed Grasping in Chimpanzees and Humans 
The Journal of Neuroscience  2013;33(35):14117-14134.
The human faculty for object-mediated action, including tool use and imitation, exceeds that of even our closest primate relatives and is a key foundation of human cognitive and cultural uniqueness. In humans and macaques, observing object-directed grasping actions activates a network of frontal, parietal, and occipitotemporal brain regions, but differences in human and macaque activation suggest that this system has been a focus of selection in the primate lineage. To study the evolution of this system, we performed functional neuroimaging in humans' closest living relatives, chimpanzees. We compare activations during performance of an object-directed manual grasping action, observation of the same action, and observation of a mimed version of the action that consisted of only movements without results. Performance and observation of the same action activated a distributed frontoparietal network similar to that reported in macaques and humans. Like humans and unlike macaques, these regions were also activated by observing movements without results. However, in a direct chimpanzee/human comparison, we also identified unique aspects of human neural responses to observed grasping. Chimpanzee activation showed a prefrontal bias, including significantly more activity in ventrolateral prefrontal cortex, whereas human activation was more evenly distributed across more posterior regions, including significantly more activation in ventral premotor cortex, inferior parietal cortex, and inferotemporal cortex. This indicates a more “bottom-up” representation of observed action in the human brain and suggests that the evolution of tool use, social learning, and cumulative culture may have involved modifications of frontoparietal interactions.
PMCID: PMC3756757  PMID: 23986247
9.  Clinical audit to enhance safe practice of skilled birth attendants for the fetus with nuchal cord: evidence from a refugee and migrant cohort 
Current evidence for optimal management of fetal nuchal cord detected after the head has birthed supports techniques that avoid ligation of the umbilical cord circulation. Routine audit found frequent unsafe management of nuchal cord by skilled birth attendants (SBAs) in migrant and refugee birth centres on the Thai-Burmese border.
The audit cycle was used to enhance safe practice by SBA for the fetus with nuchal cord. In the three birth centres the action phase of the audit cycle was initially carried out by the doctor responsible for the site. Six months later a registered midwife, present six days per week for three months in one birth facility, encouraged SBAs to facilitate birth with an intact umbilical circulation for nuchal cord. Rates of cord ligation before birth were recorded over a 24 month period (1-July-2011 to 30-June-2013) and in-depth interviews and a knowledge survey of the SBAs took place three months after the registered midwife departure.
The proportion of births with nuchal cord ligation declined significantly over the four six monthly quarters from 15.9% (178/1123) before the action phase of the audit cycle; to 11.1% (107/966) during the action phase of the audit cycle with the doctors; to 2.4% (28/1182) with the registered midwife; to 0.9% (9/999) from three to nine months after the departure of the registered midwife, (p < 0.001, linear trend). Significant improvements in safe practice were observed at all three SMRU birth facilities. Knowledge of fetal nuchal cord amongst SBAs was sub-optimal and associated with fear and worry despite improved practice. The support of a registered midwife increased confidence of SBAs.
The audit cycle and registered midwife interprofessional learning for SBAs led to a significant improvement in safe practice for the fetus with nuchal cord. The authors would encourage this type of learning in organizations with birth facilities on the Thai-Burmese border and in other similar resource limited settings with SBAs.
PMCID: PMC3943506  PMID: 24552462
Audit cycle; Interprofessional learning; Nuchal cord; Quality improvement; Registered midwife; Skilled birth attendant
10.  The drooling reduction intervention trial (DRI): a single blind trial comparing the efficacy of glycopyrronium and hyoscine on drooling in children with neurodisability 
Trials  2014;15:60.
Drooling saliva is a common problem in children with neurodevelopmental disorders. The negative consequences of drooling include skin breakdown, dehydration, and damage to clothing and equipment. Children and families often suffer social embarrassment due to drooling. There is no evidence about the relative effectiveness, side effect profiles or patient acceptability of the two medications most commonly used to reduce drooling - glycopyrronium and hyoscine. Consequently, there is no consensus or guideline to aid clinical decisions about which drug to use, and at what dose.
A multi-centre, randomised trial of treatment with glycopyrronium or hyoscine in children with problematic drooling and non-progressive neurodisability. Ninety children aged between 3 and 15 years who have never received medication for drooling will be stratified by severity of drooling and care centre. Randomisation to receive treatment with glycopyrronium or hyoscine will be computer generated from the trial randomisation website. Dose adjustment and side effect monitoring will occur via telephone consultation. Medication arm will be known to participants and clinicians but not the Trial Outcome Assessor.
The primary outcome measure is the Drooling Impact Scale score at four weeks, at which time all children will be on the maximum tolerated dose of their medication. Secondary outcome measures include change in Drooling Impact Scale score between baseline, 4, 12 and 52 weeks, change in Drooling Severity and Frequency Scale score and difference between groups in the Treatment Satisfaction Questionnaire for Medication score. A structured interview with children and young people of sufficient age, cognitive and communication ability will explore their perceptions of drooling and the effectiveness and acceptability of the medications.
The primary objective of the study is to identify whether glycopyrronium or hyoscine is more effective in treating drooling in children with non-progressive neurodisability. The study will also determine which medications at what doses are most acceptable and have fewest side effects. This information will be used to develop evidence based guidance to inform the medical treatment of drooling.
DRI trial registration
Current Controlled Trials: ISRCTN75287237.
EUDRACT: 2013-000863-94.
Medicines and Healthcare products Regulatory Agency (MHRA): 17136/0264/001-0003.
PMCID: PMC3937527  PMID: 24533890
Randomised trial; Drooling; Neurodisability; Glycopyrronium; Hyoscine; Children; Treatment satisfaction; Drooling impact scale
11.  Alcohol Ingestion Impairs Maximal Post-Exercise Rates of Myofibrillar Protein Synthesis following a Single Bout of Concurrent Training 
PLoS ONE  2014;9(2):e88384.
The culture in many team sports involves consumption of large amounts of alcohol after training/competition. The effect of such a practice on recovery processes underlying protein turnover in human skeletal muscle are unknown. We determined the effect of alcohol intake on rates of myofibrillar protein synthesis (MPS) following strenuous exercise with carbohydrate (CHO) or protein ingestion.
In a randomized cross-over design, 8 physically active males completed three experimental trials comprising resistance exercise (8×5 reps leg extension, 80% 1 repetition maximum) followed by continuous (30 min, 63% peak power output (PPO)) and high intensity interval (10×30 s, 110% PPO) cycling. Immediately, and 4 h post-exercise, subjects consumed either 500 mL of whey protein (25 g; PRO), alcohol (1.5 g·kg body mass−1, 12±2 standard drinks) co-ingested with protein (ALC-PRO), or an energy-matched quantity of carbohydrate also with alcohol (25 g maltodextrin; ALC-CHO). Subjects also consumed a CHO meal (1.5 g CHO·kg body mass−1) 2 h post-exercise. Muscle biopsies were taken at rest, 2 and 8 h post-exercise.
Blood alcohol concentration was elevated above baseline with ALC-CHO and ALC-PRO throughout recovery (P<0.05). Phosphorylation of mTORSer2448 2 h after exercise was higher with PRO compared to ALC-PRO and ALC-CHO (P<0.05), while p70S6K phosphorylation was higher 2 h post-exercise with ALC-PRO and PRO compared to ALC-CHO (P<0.05). Rates of MPS increased above rest for all conditions (∼29–109%, P<0.05). However, compared to PRO, there was a hierarchical reduction in MPS with ALC-PRO (24%, P<0.05) and with ALC-CHO (37%, P<0.05).
We provide novel data demonstrating that alcohol consumption reduces rates of MPS following a bout of concurrent exercise, even when co-ingested with protein. We conclude that alcohol ingestion suppresses the anabolic response in skeletal muscle and may therefore impair recovery and adaptation to training and/or subsequent performance.
PMCID: PMC3922864  PMID: 24533082
12.  Validation of a field technique and characterization of fecal glucocorticoid metabolite analysis in wild chimpanzees (Pan troglodytes) 
Monitoring adrenocortical activity in wild primate populations is critical, given the well-documented relationship between stress, health and reproduction. Although many primate studies have quantified fecal glucocorticoid metabolite (FGM) concentrations, it is imperative that researchers validate their method for each species. Here, we describe and validate a technique for field extraction and storage of FGMs in wild chimpanzees (Pan troglodytes). Our method circumvents many of the logistical challenges associated with field studies while yielding similar results to a commonly-used laboratory method. We further validate that our method accurately reflects stress physiology using an ACTH challenge in a captive chimpanzee and a FGM peak at parturition in a wild subject. Finally, we quantify circadian patterns for FGMs for the first time in this species. Understanding these patterns may allow researchers to directly link specific events with the stress response.
PMCID: PMC3619224  PMID: 22968979
chimpanzee; fecal glucocorticoid metabolites; field methods; ACTH; parturition; circadian rhythm
13.  Disseminated extragenital bullous lichen sclerosus 
Lichen sclerosus commonly affects the genitalia of post-menopausal women. We describe a woman with painful, disseminated, bullous, extragenital lichen sclerosus that responded to oral acitretin and topical calcitriol and triamcinolone.
PMCID: PMC3937493  PMID: 24616861
Acitretin; bullous; calcitriol; disseminated; lichen sclerosis et atrophicus; non-genital; painful
14.  Micro-Biomechanics of the Kebara 2 Hyoid and Its Implications for Speech in Neanderthals 
PLoS ONE  2013;8(12):e82261.
The description of a Neanderthal hyoid from Kebara Cave (Israel) in 1989 fuelled scientific debate on the evolution of speech and complex language. Gross anatomy of the Kebara 2 hyoid differs little from that of modern humans. However, whether Homo neanderthalensis could use speech or complex language remains controversial. Similarity in overall shape does not necessarily demonstrate that the Kebara 2 hyoid was used in the same way as that of Homo sapiens. The mechanical performance of whole bones is partly controlled by internal trabecular geometries, regulated by bone-remodelling in response to the forces applied. Here we show that the Neanderthal and modern human hyoids also present very similar internal architectures and micro-biomechanical behaviours. Our study incorporates detailed analysis of histology, meticulous reconstruction of musculature, and computational biomechanical analysis with models incorporating internal micro-geometry. Because internal architecture reflects the loadings to which a bone is routinely subjected, our findings are consistent with a capacity for speech in the Neanderthals.
PMCID: PMC3867335  PMID: 24367509
15.  Mutational analysis of the rotavirus NSP4 enterotoxic domain that binds to caveolin-1 
Virology Journal  2013;10:336.
Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction.
A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed to alanine (NSP446-175-ala6); and three residues in the hydrophobic face were altered to charged amino acids (NSP446-175-HydroMut). In total, twelve mutants of NSP4 were generated to define the cav-1 binding site. Synthetic peptides corresponding to the hydrophobic and charged faces of NSP4 were examined for structural changes by circular dichroism (CD) and diarrhea induction by a neonatal mouse study.
Mutations of the hydrophilic face (NSP446-175-Ala6) bound cav-1 akin to wild type NSP4. In contrast, disruption of the hydrophobic face (NSP446-175-HydroMut) failed to bind cav-1. These data suggest NSP4 and cav-1 associate via a hydrophobic interaction. Analyses of mutant synthetic peptides in which the hydrophobic residues in the enterotoxic domain of NSP4 were altered suggested a critical hydrophobic residue. Both NSP4HydroMut112-140, that contains three charged amino acids (aa113, 124, 131) changed from the original hydrophobic residues and NSP4AlaAcidic112-140 that contained three alanine residues substituted for negatively charged (aa114, 125, 132) amino acids failed to induce diarrhea. Whereas peptides NSP4wild type 112−140 and NSP4AlaBasic112-140 that contained three alanine substituted for positively charged (aa115, 119, 133) amino acids, induced diarrhea.
These data show that the cav-1 binding domain is within the hydrophobic face of the NSP4 amphipathic helix. The integrity of the helical structure is important for both cav-1 binding and diarrhea induction implying a connection between NSP4 functional and binding activities.
PMCID: PMC3924327  PMID: 24220211
16.  Evaluation of Real-Time PCR, Galactomannan Enzyme-Linked Immunosorbent Assay (ELISA), and a Novel Lateral-Flow Device for Diagnosis of Invasive Aspergillosis 
Journal of Clinical Microbiology  2013;51(5):1510-1516.
Diagnosis of invasive aspergillosis (IA) remains challenging. With a relatively low incidence of disease, the use of expensive empirical antifungal therapy exposes many patients to unnecessary toxicity. Diagnosis places emphasis on specific but temporal radiological evidence. Circulating biomarker diagnosis has shown potential, but assays show variable performance, take several hours to perform, and require a degree of technical ability. A novel and simple lateral-flow device (LFD) using monoclonal antibody JF5, which targets an extracellular glycoprotein, has been developed and potentially removes any technical requirements, reducing processing time considerably. In this study, we evaluate the performance of this LFD compared to real-time PCR (targeting the 28S rRNA gene) and galactomannan (GM) detection when testing serum from a European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group, National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG)-defined hematological population. In a proven/probable-IA population versus a no-IA population, the LFD performance was comparable to that of both PCR and galactomannan enzyme immunoassay. Specificity (98.0%) was similar to that of PCR (96.6%) and slightly superior to that of GM (91.5%). Sensitivity (81.8%) was inferior to that of PCR (95.5%) but better than that of GM (77.3%). In combination with PCR, it provided both 100% sensitivity and 100% specificity. The LFD permits rapid testing of easily obtainable specimens, to be used as an adjunct test, before confirmation by other investigations. Its simplicity provides centers without specialist diagnostics with a test with clinical performance superior to that of classical microbiological approaches and results that can be used to direct antifungal management. In summary, microbiological diagnosis of IA is difficult and options are limited, with variable performance. An LFD assay targeting a novel specific biomarker has been developed, one which is methodologically simple and provides good clinical performance, particularly if combined with PCR.
PMCID: PMC3647888  PMID: 23486712
17.  Collecting Duct Carcinomas Represent a Unique Tumor Entity Based on Genetic Alterations 
PLoS ONE  2013;8(10):e78137.
Collecting duct carcinoma (CDC) is a rare renal neoplasm that is associated with poor prognosis due to its highly aggressive course and limited response to immuno- or chemotherapy. Histologically, CDC is defined as a subtype of renal cell carcinomas, but in some cases, it is difficult to differentiate from urothelial carcinomas (UC). Therefore the aim of this study was to determine genetic alterations of CDC in comparison to that of urothelial carcinomas of the upper urinary tract (UUT-UC) to clarify the histological origin of this rare tumor entity. Twenty-nine CDC samples were obtained from seven different German centers and compared with twenty-six urothelial carcinomas of the upper urinary tract. Comparative genomic hybridization (CGH) was used to investigate the genetic composition of patients’ tumors and allowed the detection of losses and gains of DNA copy numbers throughout the entire genome. The clinical data were correlated with CGH results. CGH analysis of CDC revealed DNA aberrations in many chromosomes. DNA losses were more frequently observed than gains, while high-level amplifications were not detected. The mean frequency of CDC chromosomal aberrations (4.9/case) was slightly lower than that in UUT-UC (5.4/case). Recurrent CDC DNA losses occurred at 8p (n=9/29), 16p (9/29), 1p (n=7/29) and 9p (n=7/29), and gains occurred in 13q (n=9/29). In contrast to CDC, the most frequently detected UUT-UC DNA aberration was a loss at 9q (n=13/26). DNA losses at 9q, 13q and 8q as well as gains at 8p showed significant variations in UUT-UC compared to CDC. There was no correlation between the patients’ clinical course and the presence or absence of these recurrent genetic alterations. CDCs are characterized by a different genetic pattern compared to UUT-UC. Regarding the published data on renal cell carcinoma, we conclude that CDC appears to be a unique entity among kidney carcinomas.
PMCID: PMC3805592  PMID: 24167600
18.  Potential of Global Cropland Phytolith Carbon Sink from Optimization of Cropping System and Fertilization 
PLoS ONE  2013;8(9):e73747.
The occlusion of carbon (C) by phytoliths, the recalcitrant silicified structures deposited within plant tissues, is an important persistent C sink mechanism for croplands and other grass-dominated ecosystems. By constructing a silica content-phytolith content transfer function and calculating the magnitude of phytolith C sink in global croplands with relevant crop production data, this study investigated the present and potential of phytolith C sinks in global croplands and its contribution to the cropland C balance to understand the cropland C cycle and enhance long-term C sequestration in croplands. Our results indicate that the phytolith sink annually sequesters 26.35±10.22 Tg of carbon dioxide (CO2) and may contribute 40±18% of the global net cropland soil C sink for 1961–2100. Rice (25%), wheat (19%) and maize (23%) are the dominant contributing crop species to this phytolith C sink. Continentally, the main contributors are Asia (49%), North America (17%) and Europe (16%). The sink has tripled since 1961, mainly due to fertilizer application and irrigation. Cropland phytolith C sinks may be further enhanced by adopting cropland management practices such as optimization of cropping system and fertilization.
PMCID: PMC3774741  PMID: 24066067
19.  BET Inhibition Silences Expression of MYCN and BCL2 and Induces Cytotoxicity in Neuroblastoma Tumor Models 
PLoS ONE  2013;8(8):e72967.
BET family proteins are epigenetic regulators known to control expression of genes involved in cell growth and oncogenesis. Selective inhibitors of BET proteins exhibit potent anti-proliferative activity in a number of hematologic cancer models, in part through suppression of the MYC oncogene and downstream Myc-driven pathways. However, little is currently known about the activity of BET inhibitors in solid tumor models, and whether down-regulation of MYC family genes contributes to sensitivity. Here we provide evidence for potent BET inhibitor activity in neuroblastoma, a pediatric solid tumor associated with a high frequency of MYCN amplifications. We treated a panel of neuroblastoma cell lines with a novel small molecule inhibitor of BET proteins, GSK1324726A (I-BET726), and observed potent growth inhibition and cytotoxicity in most cell lines irrespective of MYCN copy number or expression level. Gene expression analyses in neuroblastoma cell lines suggest a role of BET inhibition in apoptosis, signaling, and N-Myc-driven pathways, including the direct suppression of BCL2 and MYCN. Reversal of MYCN or BCL2 suppression reduces the potency of I-BET726-induced cytotoxicity in a cell line-specific manner; however, neither factor fully accounts for I-BET726 sensitivity. Oral administration of I-BET726 to mouse xenograft models of human neuroblastoma results in tumor growth inhibition and down-regulation MYCN and BCL2 expression, suggesting a potential role for these genes in tumor growth. Taken together, our data highlight the potential of BET inhibitors as novel therapeutics for neuroblastoma, and suggest that sensitivity is driven by pleiotropic effects on cell growth and apoptotic pathways in a context-specific manner.
PMCID: PMC3751846  PMID: 24009722
20.  Study protocol: longitudinal study of the transition of young people with complex health needs from child to adult health services 
BMC Public Health  2013;13:675.
Young people with complex health needs have impairments that can limit their ability to carry out day-to-day activities. As well as coping with other developmental transitions, these young people must negotiate the transfer of their clinical care from child to adult services. The process of transition may not be smooth and both health and social outcomes may suffer.
Increasingly, policy-makers have recognised the need to ensure a smoother transition between children’s and adult services, with processes that are holistic, individualised, and person-centred; however, there is little outcome data to support proposed models of care. This study aims to identify the features of transitional care that are potentially effective and efficient for young people with complex health needs making their transition.
Longitudinal cohort study. 450 young people aged 14 years to 18 years 11 months (with autism spectrum disorder and an additional mental health problem, cerebral palsy or diabetes) will be followed through their transition from child to adult services and will contribute data at baseline, 12, 24 and 36 months. We will collect data on: health and wellbeing outcomes (participation, quality of life, satisfaction with services, generic health status (EQ-5D-Y) and condition specific measure of disease control or management); exposure to proposed beneficial features of services (such as having a key worker, appropriate involvement of parents); socio-economic characteristics of the sample; use of condition-related health and personal social services; preferences for the characteristics of transitional care.
We will us regression techniques to explore how outcomes vary by exposure to service features and by characteristics of the young people. These data will populate a decision-analytic model comparing the costs and benefits of potential alternative ways of organising transition services.
In order to better understand mechanisms and aid interpretation, we will undertake qualitative work with 15 young people, including interviews, non-participant observation and diary collection.
This study will evaluate the effect of service components of transitional care, rather than evaluation of specific models that may be unsustainable or not generalisable. It has been developed in response to numerous national and international calls for such evaluation.
PMCID: PMC3724698  PMID: 23875722
Transition; Adolescence; Chronic illness; Disability; Evaluation; Protocol
21.  Highly Stereoselective C—C Bond Formation by Rhodium-Catalyzed Tandem Ylide Formation/[2,3]-Sigmatropic Rearrangement Between Donor/Acceptor Carbenoids and Chiral Allylic Alcohols 
Journal of the American Chemical Society  2012;134(26):10942-10946.
The tandem ylide-formation/[2,3]-sigmatropic rearrangement between donor/acceptor rhodium-carbenoids and chiral allyl alcohols is a convergent C—C bond forming process, which generates two vicinal stereogenic centers. Any of the four possible stereoisomers can be selectively synthesized by appropriate combination of the chiral catalyst Rh2(DOSP)4 and the chiral alcohol.
PMCID: PMC3413634  PMID: 22694052
22.  Comparative Biomechanical Modeling of Metatherian and Placental Saber-Tooths: A Different Kind of Bite for an Extreme Pouched Predator 
PLoS ONE  2013;8(6):e66888.
Questions surrounding the dramatic morphology of saber-tooths, and the presumably deadly purpose to which it was put, have long excited scholarly and popular attention. Among saber-toothed species, the iconic North American placental, Smilodon fatalis, and the bizarre South American sparassodont, Thylacosmilus atrox, represent extreme forms commonly forwarded as examples of convergent evolution. For S. fatalis, some consensus has been reached on the question of killing behaviour, with most researchers accepting the canine-shear bite hypothesis, wherein both head-depressing and jaw closing musculatures played a role in delivery of the fatal bite. However, whether, or to what degree, T. atrox may have applied a similar approach remains an open question. Here we apply a three-dimensional computational approach to examine convergence in mechanical performance between the two species. We find that, in many respects, the placental S. fatalis (a true felid) was more similar to the metatherian T. atrox than to a conical-toothed cat. In modeling of both saber-tooths we found that jaw-adductor-driven bite forces were low, but that simulations invoking neck musculature revealed less cranio-mandibular stress than in a conical-toothed cat. However, our study also revealed differences between the two saber-tooths likely reflected in the modus operandi of the kill. Jaw-adductor-driven bite forces were extremely weak in T. atrox, and its skull was even better-adapted to resist stress induced by head-depressors. Considered together with the fact that the center of the arc described by the canines was closer to the jaw-joint in Smilodon, our results are consistent with both jaw-closing and neck musculature playing a role in prey dispatch for the placental, as has been previously suggested. However, for T. atrox, we conclude that the jaw-adductors probably played no major part in the killing bite. We propose that the metatherian presents a more complete commitment to the already extreme saber-tooth ‘lifestyle’.
PMCID: PMC3694156  PMID: 23840547
23.  Re-introduction of a Novel Approach to the Use of Stable Isotopes in Pharmacokinetic Studies 
The AAPS Journal  2012;14(3):639-645.
The purpose of this investigation is to evaluate the scientific benefits of a novel approach in using stable isotopes to reduce the number of subjects needed to perform relative bioavailability and bioequivalence pharmacokinetic studies for formulations that are qualitatively and quantitatively the same and quality by design (QbD) pharmacokinetic studies. The stable isotope approach was investigated using simulations to determine the impact this approach would have on the estimation of variability and, subsequently, the sample size for a bioequivalence study. A biostudy was conducted in dogs in a two period crossover to explore the viability of the stable isotope approach. For a drug product with within-subject variability (CVw) of 50% and assuming a correlation of 0.95 between the enriched and non-enriched pharmacokinetics (PK), simulations showed that the variability can be reduced by 70% and the required sample size can be reduced by 90% while maintaining 90% power to demonstrate bioequivalence. The dog study showed a strong correlation (R2, > 0.99) between the enriched and non-enriched area under the curve and maximum observed concentration, and a significant reduction in the variability (reduction in % coefficient of variation from 79.9% to 6.3%). Utilization of a stable isotope approach can markedly improve the efficiency and accuracy of bioavailability and bioequivalence studies particularly for highly variable drugs in formulations that are qualitatively and quantitatively the same and for studies designed for QbD investigations.
PMCID: PMC3385839  PMID: 22684401
bioequivalence; biopharmaceutics; quality by design; relative bioavailability; stable isotope
24.  Selective Inactivation of PTEN in Smooth Muscle Cells Synergizes With Hypoxia to Induce Severe Pulmonary Hypertension 
Pulmonary vascular remodeling in pulmonary hypertension (PH) is characterized by increased vascular smooth muscle cell (SMC) and adventitial fibroblast proliferation, small vessel occlusion, and inflammatory cell accumulation. The underlying molecular mechanisms driving progression remain poorly defined. We have focused on loss of the phosphatase PTEN in SMCs as a major driver of pathological vascular remodeling. Our goal was to define the role of PTEN in human PH and in hypoxia‐induced PH using a mouse model with inducible deletion of PTEN in SMCs.
Methods and Results
Staining of human biopsies demonstrated enhanced inactive PTEN selectively in the media from hypertensive patients compared to controls. Mice with induced deletion of PTEN in SMCs were exposed to normoxia or hypoxia for up to 4 weeks. Under normoxia, SMC PTEN depletion was sufficient to induce features of PH similar to those observed in wild‐type mice exposed to chronic hypoxia. Under hypoxia, PTEN depletion promoted an irreversible progression of PH characterized by increased pressure, extensive pulmonary vascular remodeling, formation of complex vascular lesions, and increased macrophage accumulation associated with synergistic increases in proinflammatory cytokines and proliferation of both SMCs and nonSMCs.
Chronic inactivation of PTEN selectively in SMC represents a critical mediator of PH progression, leading to cell autonomous events and increased production of factors correlated to proliferation and recruitment of adventitial and inflammatory cells, resulting in irreversible progression of the disease.
PMCID: PMC3698782  PMID: 23727701
hypoxia; inflammation; pulmonary hypertension; remodeling; smooth muscle

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