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1.  The “Puck” energetic charged particle detector: Design, heritage, and advancements 
Abstract
Energetic charged particle detectors characterize a portion of the plasma distribution function that plays critical roles in some physical processes, from carrying the currents in planetary ring currents to weathering the surfaces of planetary objects. For several low‐resource missions in the past, the need was recognized for a low‐resource but highly capable, mass‐species‐discriminating energetic particle sensor that could also obtain angular distributions without motors or mechanical articulation. This need led to the development of a compact Energetic Particle Detector (EPD), known as the “Puck” EPD (short for hockey puck), that is capable of determining the flux, angular distribution, and composition of incident ions between an energy range of ~10 keV to several MeV. This sensor makes simultaneous angular measurements of electron fluxes from the tens of keV to about 1 MeV. The same measurements can be extended down to approximately 1 keV/nucleon, with some composition ambiguity. These sensors have a proven flight heritage record that includes missions such as MErcury Surface, Space ENvironment, GEochemistry, and Ranging and New Horizons, with multiple sensors on each of Juno, Van Allen Probes, and Magnetospheric Multiscale. In this review paper we discuss the Puck EPD design, its heritage, unexpected results from these past missions and future advancements. We also discuss high‐voltage anomalies that are thought to be associated with the use of curved foils, which is a new foil manufacturing processes utilized on recent Puck EPD designs. Finally, we discuss the important role Puck EPDs can potentially play in upcoming missions.
Key Points
Review of the compact Energetic Particle Detector known as the PuckPuck EPD heritage includes five successful scientific missionsUnexpected results and potential advancements of the Puck are discussed
doi:10.1002/2016JA022579
PMCID: PMC5101846  PMID: 27867799
Energetic Particle Detectors; space plasma; energetic charged particles; energetic ions; energetic electrons
2.  The Low‐Energy Neutral Imager (LENI) 
Abstract
To achieve breakthroughs in the areas of heliospheric and magnetospheric energetic neutral atom (ENA) imaging, a new class of instruments is required. We present a high angular resolution ENA imager concept aimed at the suprathermal plasma populations with energies between 0.5 and 20 keV. This instrument is intended for understanding the spatial and temporal structure of the heliospheric boundary recently revealed by Interstellar Boundary Explorer instrumentation and the Cassini Ion and Neutral Camera. The instrument is also well suited to characterize magnetospheric ENA emissions from low‐altitude ENA emissions produced by precipitation of magnetospheric ions into the terrestrial upper atmosphere, or from the magnetosheath where solar wind protons are neutralized by charge exchange, or from portions of the ring current region. We present a new technique utilizing ultrathin carbon foils, 2‐D collimation, and a novel electron optical design to produce high angular resolution (≤2°) and high‐sensitivity (≥10−3 cm2 sr/pixel) ENA imaging in the 0.5–20 keV energy range.
Key Points
The LENI instrument is capable of high angular resolution ENA imagingThe LENI instrument utilizes novel MCP collimation for ENA imagingThe LENI instrument is designed for heliospheric and magnetospheric imaging
doi:10.1002/2016JA022547
PMCID: PMC5101854  PMID: 27867800
ENA; heliospheric imaging; magnetospheric imaging; energetic particles; measurement techniques; instrument
3.  Mitogen-activated protein kinases (MAPKs) are modulated during Francisella tularensis infection, but inhibition of extracellular-signal-regulated kinases (ERKs) is of limited therapeutic benefit 
Francisella tularensis is a Gram-negative intracellular bacterium that causes the disease tularemia. The disease can be fatal if left untreated and there is currently no licenced vaccine available; the identification of new therapeutic targets is therefore required. Toll-like receptors represent an interesting target for therapeutic modulation due to their essential role in generating immune responses. In this study, we analysed the in vitro expression of the key mitogen-activated protein kinases (MAPKs) p38, JNK and ERK in murine alveolar macrophages during infection with F. tularensis. The phosphorylation profile of ERK highlighted its potential as a target for therapeutic modulation and subsequently the effect of ERK manipulation was measured in a lethal intranasal F. tularensis in vivo model of infection. The selective ERK1/2 inhibitor PD0325901 was administered orally to mice either pre- or post-challenge with F. tularensis strain LVS. Both treatment regimens selectively reduced ERK expression, but only the pre-exposure treatment produced decreased bacterial burden in the spleen and liver, which correlated with a significant reduction in the pro-inflammatory cytokines IFN-γ, MCP-1, IL-6, and TNF-α. However, no overall improvements in survival were observed for treated animals in this study. ERK may represent a useful therapeutic target where selective dampening of the immune response (to control the damaging pathology seen during infection) is combined with antibiotic treatment required to eradicate bacterial infection. This combination treatment strategy has been shown to be effective in other models of tularemia.
doi:10.1007/s10096-016-2754-1
PMCID: PMC5138274  PMID: 27714591
4.  miR-9 Acts as an OncomiR in Prostate Cancer through Multiple Pathways That Drive Tumour Progression and Metastasis 
PLoS ONE  2016;11(7):e0159601.
Identification of dysregulated microRNAs (miRNAs) in prostate cancer is critical not only for diagnosis, but also differentiation between the aggressive and indolent forms of the disease. miR-9 was identified as an oncomiR through both miRNA panel RT-qPCR as well as high-throughput sequencing analysis of the human P69 prostate cell line as compared to its highly tumorigenic and metastatic subline M12, and found to be consistently upregulated in other prostate cell lines including DU-145 and PC3. While miR-9 has been characterized as dysregulated either as an oncomiR or tumour suppressor in a variety of other cancers including breast, ovarian, and nasopharyngeal carcinomas, it has not been previously evaluated and proven as an oncomiR in prostate cancer. miR-9 was confirmed an oncomiR when found to be overexpressed in tumour tissue as compared to adjacent benign glandular epithelium through laser-capture microdissection of radical prostatectomy biopsies. Inhibition of miR-9 resulted in reduced migratory and invasive potential of the M12 cell line, and reduced tumour growth and metastases in male athymic nude mice. Analysis showed that miR-9 targets e-cadherin and suppressor of cytokine signalling 5 (SOCS5), but not NF-ĸB mRNA. Expression of these proteins was shown to be affected by modulation in expression of miR-9.
doi:10.1371/journal.pone.0159601
PMCID: PMC4957825  PMID: 27447934
5.  Non-conflict theories for the evolution of genomic imprinting 
Heredity  2014;113(2):112-118.
Theories focused on kinship and the genetic conflict it induces are widely considered to be the primary explanations for the evolution of genomic imprinting. However, there have appeared many competing ideas that do not involve kinship/conflict. These ideas are often overlooked because kinship/conflict is entrenched in the literature, especially outside evolutionary biology. Here we provide a critical overview of these non-conflict theories, providing an accessible perspective into this literature. We suggest that some of these alternative hypotheses may, in fact, provide tenable explanations of the evolution of imprinting for at least some loci.
doi:10.1038/hdy.2013.129
PMCID: PMC4105448  PMID: 24398886
evolutionary hypotheses; genetic imprinting; kinship; genetic conflict
6.  Using next-generation RNA sequencing to identify imprinted genes 
Heredity  2014;113(2):156-166.
Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.
doi:10.1038/hdy.2014.18
PMCID: PMC4105452  PMID: 24619182
7.  Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England 
Journal of Clinical Microbiology  2015;53(10):3141-3147.
Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.
doi:10.1128/JCM.00648-15
PMCID: PMC4572532  PMID: 26179308
8.  Evaluation of the packaging and encapsulation reliability in fully integrated, fully wireless 100 channel Utah Slant Electrode Array (USEA): Implications for long term functionality 
The encapsulation and packaging reliability in fully integrated, fully wireless 100 channel Utah Slant Electrode Array (USEA)/integrated neural interface-recording version 5 (INI-R5) has been evaluated by monitoring the extended long term in-vitro functional stability and recording longevity. The INI encapsulated with 6-μm Parylene-C was immersed in phosphate buffer saline (PBS) at room temperature for a period of over 12 months. The USEA/INI-R5, while being soaked was powered and configured wirelessly through 2.765 MHz inductive link and the transmitted frequency shift keying (FSK) modulated radio-frequency (RF) (900 MHz Industrial, scientific, medical-ISM band) signal was also recorded wirelessly as a function of soak time. In order to test the long term recording ability, in-vitro wireless recording was performed in agarose for few channels. The full functionality and the ability of the electrodes to record artificial neural signals even after 12 months of PBS soak provides a measure of encapsulation reliability, the functional and recording stability in fully integrated wireless neural interface and potential usefulness for future chronic implants.
doi:10.1016/j.sna.2011.11.015
PMCID: PMC3533439  PMID: 23288983
9.  COORDINATED, MULTI-JOINT, FATIGUE-RESISTANT FELINE STANCE PRODUCED WITH INTRAFASCICULAR HIND LIMB NERVE STIMULATION 
Journal of Neural Engineering  2012;9(2):026019.
The production of graceful skeletal movements requires coordinated activation of multiple muscles that produce torques around multiple joints. The work described herein is focused on one such movement, stance, that requires coordinated activation of extensor muscles acting around the hip, knee and ankle joints. The forces evoked in these muscles by external stimulation all have a complex dependence on muscle length and shortening velocities, and some of these muscles are bi-articular. In order to recreate sit-to-stand maneuvers in the anesthetized feline, we excited the hind limb musculature using intrafascicular multielectrode stimulation (IFMS) of the muscular branch of the sciatic nerve, the femoral nerve, and the main branch of the sciatic nerve. Stimulation was achieved with either acutely or chronically implanted Utah Slanted Electrode Arrays (USEAs) via subsets of electrodes 1) that activated motor units in the extensor muscles of the hip, knee, and ankle joints, 2) that were able to evoke large extension forces, and 3) that manifested minimal coactivation of the targeted motor units. Three hind limb force-generation strategies were investigated, including sequential activation of independent motor units to increase force, and interleaved or simultaneous IFMS of three sets of six or more USEA electrodes that excited the hip, knee, and ankle extensors. All force-generation strategies evoked stance, but the interleaved IFMS strategy also reduced muscle fatigue produced by repeated sit-to-stand maneuvers compared with fatigue produced by simultaneous activation of different motor neuron pools. These results demonstrate the use of interleaved IFMS as a means to recreate coordinated, fatigue-resistant multi-joint muscle forces in the unilateral hind limb. This muscle activation paradigm could provide a promising neuroprosthetic approach for the restoration of sit-to-stand transitions in individuals who are paralyzed by spinal cord injury, stroke, or disease.
doi:10.1088/1741-2560/9/2/026019
PMCID: PMC3377012  PMID: 22414699
Neural prosthetics; intrafascicular stimulation; motor system; stance
10.  Characterization of a 3D optrode array for infrared neural stimulation 
Biomedical Optics Express  2012;3(9):2200-2219.
This paper characterizes the Utah Slant Optrode Array (USOA) as a means to deliver infrared light deep into tissue. An undoped crystalline silicon (100) substrate was used to fabricate 10 × 10 arrays of optrodes with rows of varying lengths from 0.5 mm to 1.5 mm on a 400-μm pitch. Light delivery from optical fibers and loss mechanisms through these Si optrodes were characterized, with the primary loss mechanisms being Fresnel reflection, coupling, radiation losses from the tapered shank and total internal reflection in the tips. Transmission at the optrode tips with different optical fiber core diameters and light in-coupling interfaces was investigated. At λ = 1.55μm, the highest optrode transmittance of 34.7%, relative to the optical fiber output power, was obtained with a 50-μm multi-mode fiber butt-coupled to the optrode through an intervening medium of index n = 1.66. Maximum power is directed into the optrodes when using fibers with core diameters of 200 μm or less. In addition, the output power varied with the optrode length/taper such that longer and less tapered optrodes exhibited higher light transmission efficiency. Output beam profiles and potential impacts on physiological tests were also examined. Future work is expected to improve USOA efficiency to greater than 64%.
doi:10.1364/BOE.3.002200
PMCID: PMC3447562  PMID: 23024914
(170.3890) Medical optics instrumentation; (220.4610) Optical fabrication; (230.7380) Waveguides, channeled; (260.3060) Infrared
11.  Writing for publication – raising standards at the AMJ 
The Australasian Medical Journal  2011;4(4):225-228.
doi:10.4066/AMJ.2011.783
PMCID: PMC3562901  PMID: 23393514
12.  Endosymbiotic Bacteria in the Parasitic Ciliate Ichthyophthirius multifiliis▿  
Applied and Environmental Microbiology  2009;75(23):7445-7452.
Endosymbiotic bacteria were identified in the parasitic ciliate Ichthyophthirius multifiliis, a common pathogen of freshwater fish. PCR amplification of DNA prepared from two isolates of I. multifiliis, using primers that bind conserved sequences in bacterial 16S rRNA genes, generated an ∼1,460-bp DNA product, which was cloned and sequenced. Sequence analysis demonstrated that 16S rRNA gene sequences from three classes of bacteria were present in the PCR product. These included Alphaproteobacteria (Rickettsiales), Sphingobacteria, and Flavobacterium columnare. DAPI (4′,6-diamidino-2-phenylindole) staining showed endosymbionts dispersed throughout the cytoplasm of trophonts and, in most, but not all theronts. Endosymbionts were observed by transmission electron microscopy in the cytoplasm, surrounded by a prominent, electron-translucent halo characteristic of Rickettsia. Fluorescence in situ hybridization demonstrated that bacteria from the Rickettsiales and Sphingobacteriales classes are endosymbionts of I. multifiliis, found in the cytoplasm, but not in the macronucleus or micronucleus. In contrast, F. columnare was not detected by fluorescence in situ hybridization. It likely adheres to I. multifiliis through association with cilia. The role that endosymbiotic bacteria play in the life history of I. multifiliis is not known.
doi:10.1128/AEM.00850-09
PMCID: PMC2786411  PMID: 19820157
13.  The genome of the simian and human malaria parasite Plasmodium knowlesi 
Nature  2008;455(7214):799-803.
Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the ‘kra’ monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia1,2. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated3, and it has a close phylogenetic relationship to Plasmodium vivax​4, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or ‘hypnozoite’ in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone5) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome4 and other sequenced Plasmodium genomes6-8. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs9, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
doi:10.1038/nature07306
PMCID: PMC2656934  PMID: 18843368
14.  Methodology for constructing guidance 
Journal of Clinical Pathology  2005;58(3):249-253.
Although guidance exists for the use of many laboratory tests in a wide range of clinical situations, this guidance is spread among a range of literature sources, and is often directed at laboratory specialists rather than test users. Individual general practices display large variations in standardised test requesting, yet much of their testing activity involves a relatively small range of tests. This paper describes a methodological approach to review the available evidence and guidance and to extract relevant primary research work to examine a range of testing scenarios in general practice, with the aim of formulating guidance based on the best available evidence or consensus opinions.
doi:10.1136/jcp.2004.018374
PMCID: PMC1770610  PMID: 15735154
appropriateness; best practice; evidence based pathology; multidisciplinary
15.  The contribution of individual and pairwise combinations of SNPs in the APOA1 and APOC3 genes to interindividual HDL-C variability 
Apolipoproteins (apo) A-I and C-III are components of high-density lipoprotein-cholesterol (HDL-C), a quantitative trait negatively correlated with risk of cardiovascular disease (CVD). We analyzed the contribution of individual and pairwise combinations of single nucleotide polymorphisms (SNPs) in the APOA1/APOC3 genes to HDL-C variability to evaluate (1) consistency of published single-SNP studies with our single-SNP analyses; (2) consistency of single-SNP and two-SNP phenotype–genotype relationships across race-, gender-, and geographical location-dependent contexts; and (3) the contribution of single SNPs and pairs of SNPs to variability beyond that explained by plasma apo A-I concentration. We analyzed 45 SNPs in 3,831 young African–American (N=1,858) and European–American (N=1,973) females and males ascertained by the Coronary Artery Risk Development in Young Adults (CARDIA) study. We found three SNPs that significantly impact HDL-C variability in both the literature and the CARDIA sample. Single-SNP analyses identified only one of five significant HDL-C SNP genotype relationships in the CARDIA study that was consistent across all race-, gender-, and geographical location-dependent contexts. The other four were consistent across geographical locations for a particular race–gender context. The portion of total phenotypic variance explained by single-SNP genotypes and genotypes defined by pairs of SNPs was less than 3%, an amount that is miniscule compared to the contribution explained by variability in plasma apo A-I concentration. Our findings illustrate the impact of context-dependence on SNP selection for prediction of CVD risk factor variability.
doi:10.1007/s00109-005-0037-x
PMCID: PMC1698872  PMID: 16705465
APOA1 gene; APOC3 gene; High-density lipoprotein-cholesterol; Cardiovascular disease
16.  Inequalities of primary care microbiology testing between hospital catchment areas 
Journal of Clinical Pathology  2003;56(12):933-936.
Aims: To compare differences in microbiology testing activity between general practices within and between five hospitals in two National Health Service (NHS) regions in England.
Methods: Retrospective capture of standardised microbiology testing activity from the laboratory computer databases. Six equivalent tests were identified and compared. Data were obtained for 174 general practices in eight primary care groups, served by two NHS hospital trusts and three public health laboratories. The total catchment population was 1 180 000 people. Comparative test activities were displayed graphically and differences in median test activity and the hospital activity distributions were examined by the Wilcoxon signed rank test.
Results: Median testing activity differed by 200% (urine) to 800% (wound swabs) between the trusts that performed the highest and the lowest number of tests, and from 300% to 1900% between the top and bottom 10% activity bands of general practices. Large and significant differences were found between the hospitals, irrespective of whether they belonged to the same trust, and irrespective of their geographical location.
Conclusions: Large differences in microbiology testing exist within individual trust catchment areas in primary care, and there are also considerable differences between trusts. These inequalities may also introduce a selection bias into epidemiological and antibiotic resistance surveillance. This indicates a widespread need to examine and deal with the reasons responsible for these differences.
PMCID: PMC1770142  PMID: 14645353
Appropriateness; evidence based medicine; microbiology; primary care
17.  REporting recommendations for tumour MARKer prognostic studies (REMARK) 
British Journal of Cancer  2005;93(4):387-391.
Despite years of research and hundreds of reports on tumour markers in oncology, the number of markers that have emerged as clinically useful is pitifully small. Often initially reported studies of a marker show great promise, but subsequent studies on the same or related markers yield inconsistent conclusions or stand in direct contradiction to the promising results. It is imperative that we attempt to understand the reasons that multiple studies of the same marker lead to differing conclusions. A variety of methodological problems have been cited to explain these discrepancies. Unfortunately, many tumour marker studies have not been reported in a rigorous fashion, and published articles often lack sufficient information to allow adequate assessment of the quality of the study or the generalisability of the study results. The development of guidelines for the reporting of tumour marker studies was a major recommendation of the US National Cancer Institute and the European Organisation for Research and Treatment of Cancer (NCI-EORTC) First International Meeting on Cancer Diagnostics in 2000. Similar to the successful CONSORT initiative for randomised trials and the STARD statement for diagnostic studies, we suggest guidelines to provide relevant information about the study design, preplanned hypotheses, patient and specimen characteristics, assay methods, and statistical analysis methods. In addition, the guidelines suggest helpful presentations of data and important elements to include in discussions. The goal of these guidelines is to encourage transparent and complete reporting so that the relevant information will be available to others to help them to judge the usefulness of the data and understand the context in which the conclusions apply.
doi:10.1038/sj.bjc.6602678
PMCID: PMC2361579  PMID: 16106245
tumour marker; guidelines; REMARK; NCI; EORTC; prognostic
18.  Histological changes in the oesophageal squamous mucosa: correlation with ambulatory 24 hour pH monitoring 
Journal of Clinical Pathology  2003;56(3):205-208.
Aims: To determine the value of squamous mucosal histology in the assessment of patients with gastro-oesophageal reflux symptoms.
Methods: Sixty six patients with reflux symptoms underwent endoscopy with oesophageal biopsy, manometry, and 24 hour oesophageal pH testing. The following histological features were assessed in squamous mucosa: the degree of basal cell hyperplasia, the degree of papillary zone elongation, and the density of neutrophil and eosinophil infiltration. Comparisons were made between the histological findings and the oesophageal function tests.
Results: The correlation between the traditionally accepted histological markers of gastro-oesophageal reflux disease in squamous mucosa and 24 hour pH testing was predominantly negative, with the exception of neutrophil inflammation in the squamous mucosa of patients with complicated reflux disease.
Conclusions: This study was unable to confirm the value of the Ismail-Beigi criteria as histological markers of acid reflux. By inference, biopsy of the oesophageal squamous mucosa is of limited value in the assessment of patients with reflux symptoms.
PMCID: PMC1769910  PMID: 12610100
ambulatory pH monitoring; gastro-oesphageal reflux disease; histology; oesophagitis
19.  Survival Analysis Part IV: Further concepts and methods in survival analysis 
British Journal of Cancer  2003;89(5):781-786.
doi:10.1038/sj.bjc.6601117
PMCID: PMC2394469  PMID: 12942105
survival analysis; missing data; validation; repeated events
20.  Survival Analysis Part III: Multivariate data analysis – choosing a model and assessing its adequacy and fit 
British Journal of Cancer  2003;89(4):605-611.
doi:10.1038/sj.bjc.6601120
PMCID: PMC2376927  PMID: 12915864
survival analysis; Cox model; AFT model; model checking; choice of coavriates; goodness of fit
21.  Survival Analysis Part II: Multivariate data analysis – an introduction to concepts and methods 
British Journal of Cancer  2003;89(3):431-436.
doi:10.1038/sj.bjc.6601119
PMCID: PMC2394368  PMID: 12888808
survival analysis; Cox model; AFT model; model selection
22.  Survival Analysis Part I: Basic concepts and first analyses 
British Journal of Cancer  2003;89(2):232-238.
doi:10.1038/sj.bjc.6601118
PMCID: PMC2394262  PMID: 12865907
survival analysis; statistical methods; Kaplan-Meier
23.  Patterns of gastritis in patients with gastro-oesophageal reflux disease 
Gut  1999;45(6):798-803.
BACKGROUND—The cause of inflammation in cardiac mucosa at the gastro-oesophageal junction (GOJ) is unclear, both gastro-oesophageal reflux disease (GORD) and Helicobacter pylori having been implicated.
AIMS—To describe patterns of gastritis in patients with symptomatic GORD.
METHODS—In 150 patients (126 normally located Z-line, 24 Barrett's oesophagus) with symptoms of GORD, biopsies were taken of the GOJ, corpus, and antrum. Inflammation was assessed using the updated Sydney System.
RESULTS—For the 126 patients with a normally located Z-line, biopsies of the GOJ revealed cardiac mucosa in 96, fundic mucosa in 29, and squamous mucosa in one. Inflammation in glandular mucosa at the GOJ was present in 99/125 specimens (79%), including 87/96 (91%) with cardiac mucosa and 12/29 (41%) with fundic mucosa. Inflammation in fundic mucosa was closely related to H pylori and active inflammation was only seen in its presence. Inflammation in cardiac mucosa was less closely linked to H pylori. When H pylori was present in cardiac mucosa (28/96, 29%) active inflammation was usually present (25/28, 89%). However, active inflammation was also found in 34/68 (50%) cardiac mucosa specimens without H pylori. Overall, 28/87 (32%) biopsies with carditis were colonised with H pylori and 59/87 (68%) were not. In H pylori colonised patients, inflammation was seen throughout the stomach, while in non-colonised patients, it was confined to cardiac mucosa.
CONCLUSIONS—Patients with symptomatic GORD had a high prevalence of carditis. This was of two types, H pylori associated and unassociated. Except on Giemsa staining, the two were morphologically identical, suggesting mediation by a similar immunological mechanism.


Keywords: cardiac mucosa; carditis; gastro- oesophageal junction; gastro-oesophageal reflux; Helicobacter pylori; inflammation
PMCID: PMC1727740  PMID: 10562575
24.  A prognostic model for ovarian cancer 
British Journal of Cancer  2001;85(7):944-952.
About 6000 women in the United Kingdom develop ovarian cancer each year and about two-thirds of the women will die from the disease. Establishing the prognosis of a woman with ovarian cancer is an important part of her evaluation and treatment. Prognostic models and indices in ovarian cancer should be developed using large databases and, ideally, with complete information on both prognostic indicators and long-term outcome. We developed a prognostic model using Cox regression and multiple imputation from 1189 primary cases of epithelial ovarian cancer (with median follow-up of 4.6 years). We found that the significant (P≤ 0.05) prognostic factors for overall survival were age at diagnosis, FIGO stage, grade of tumour, histology (mixed mesodermal, clear cell and endometrioid versus serous papillary), the presence or absence of ascites, albumin, alkaline phosphatase, performance status on the ZUBROD-ECOG-WHO scale, and debulking of the tumour. This model is consistent with other models in the ovarian cancer literature; it has better predictive ability and, after simplification and validation, could be used in clinical practice. http://www.bjcancer.com © 2001 Cancer Research Campaignhttp://www.bjcancer.com
doi:10.1054/bjoc.2001.2030
PMCID: PMC2375096  PMID: 11592763
ovarian cancer; prognostic model; overall survival
25.  Seminal fluid causes temporarily reduced egg hatch in previously mated females. 
In Drosophila, male accessory gland fluid (seminal fluid) has multiple effects on the female's reproductive efficiency. Here, we show the effect of seminal fluid on rate of egg hatch immediately following mating. Singly mated females were remated to two classes of sterile males, one with seminal fluid and one without seminal fluid. Transfer of seminal fluid results in a strong reduction in egg hatch shortly after the mating. Also, it is shown that remating with normal males causes an immediate reduction of egg hatch followed by recovery to normal egg hatch. In all cases, unhatched eggs contained no sperm. These results are consistent with a role for seminal fluid in sperm competition, mediated by incapacitation or inefficient use of resident sperm.
PMCID: PMC1690506  PMID: 10687828

Results 1-25 (101)