Characterisation of glioblastoma sub-populations using mathematical modelling and inference

Glioblastomas (GBMs) are the most aggressive primary brain tumours and have no known cure. Each individual tumour comprises multiple sub-populations of genetically-distinct cells that may respond differently to targeted therapies and may contribute to disappointing clinical trial results. Image-localized biopsy techniques allow multiple biopsies to be taken during surgery and provide information that identifies regions where particular sub-populations occur within an individual GBM, thus providing insight into their regional genetic variability. These sub-populations may also interact with one another in some way; it is important to ascertain the nature of these interactions, as they may have implications for responses to targeted therapies. In this work, we combine genetic information from image-localised biopsies with a mechanistic model of interacting GBM sub-populations to characterise the nature of interactions between two commonly occurring GBM sub-populations, those with EGFR and PDGFRA genes amplified. Firstly, we develop a mathematical model using a PDE-based formalism and explore the dynamics of our model under a variety of interaction types (Chapter 2). Following on from this, we study population levels found across image-localized biopsy data from an initial cohort of patients and compare this to model outputs under competitive, cooperative and neutral interaction assumptions (Chapter 3). We explore other factors affecting the observed simulated sub-populations, such as selection advantages and phylogenetic ordering of mutations, and conduct a sensitivity analysis, as these factors may also contribute to the levels of EGFR and PDGFRA amplified populations observed in biopsy data. The patient dataset is then expanded to include image-localised biopsies from additional patients and we examine the intra- and inter-tumoural heterogeneity in EGFR and PDGFRA amplification observed in this data (Chapter 4). We then proceed to explore the inferability of the model parameters using synthetic datasets. Finally, we perform inference for the patient dataset, where we are able to gain some insights into the dynamics of and nature of interactions between these amplified sub-populations

Characterisation of glioblastoma sub-populations using mathematical modelling and inference

Glioblastomas (GBMs) are the most aggressive primary brain tumours and have no known cure. Each individual tumour comprises multiple sub-populations of genetically-distinct cells that may respond differently to targeted therapies and may contribute to disappointing clinical trial results. Image-localized biopsy techniques allow multiple biopsies to be taken during surgery and provide information that identifies regions where particular sub-populations occur within an individual GBM, thus providing insight into their regional genetic variability. These sub-populations may also interact with one another in some way; it is important to ascertain the nature of these interactions, as they may have implications for responses to targeted therapies. In this work, we combine genetic information from image-localised biopsies with a mechanistic model of interacting GBM sub-populations to characterise the nature of interactions between two commonly occurring GBM sub-populations, those with EGFR and PDGFRA genes amplified. Firstly, we develop a mathematical model using a PDE-based formalism and explore the dynamics of our model under a variety of interaction types (Chapter 2). Following on from this, we study population levels found across image-localized biopsy data from an initial cohort of patients and compare this to model outputs under competitive, cooperative and neutral interaction assumptions (Chapter 3). We explore other factors affecting the observed simulated sub-populations, such as selection advantages and phylogenetic ordering of mutations, and conduct a sensitivity analysis, as these factors may also contribute to the levels of EGFR and PDGFRA amplified populations observed in biopsy data. The patient dataset is then expanded to include image-localised biopsies from additional patients and we examine the intra- and inter-tumoural heterogeneity in EGFR and PDGFRA amplification observed in this data (Chapter 4). We then proceed to explore the inferability of the model parameters using synthetic datasets. Finally, we perform inference for the patient dataset, where we are able to gain some insights into the dynamics of and nature of interactions between these amplified sub-populations

Herschel/HIFI Spectral Mapping of C+^+, CH+^+, and CH in Orion BN/KL: The Prevailing Role of Ultraviolet Irradiation in CH+^+ Formation

The CH$^+$ ion is a key species in the initial steps of interstellar carbon chemistry. Its formation in diverse environments where it is observed is not well understood, however, because the main production pathway is so endothermic (4280 K) that it is unlikely to proceed at the typical temperatures of molecular clouds. We investigation CH$^+$ formation with the first velocity-resolved spectral mapping of the CH$^+$ $J=1-0, 2-1$ rotational transitions, three sets of CH $\Lambda$-doubled triplet lines, $^{12}$C$^+$ and $^{13}$C$^+$, and CH$_3$OH 835~GHz E-symmetry Q branch transitions, obtained with Herschel/HIFI over $\approx$12 arcmin$^2$ centered on the Orion BN/KL source. We present the spatial morphologies and kinematics, cloud boundary conditions, excitation temperatures, column densities, and $^{12}$C$^+$ optical depths. Emission from C$^+$, CH$^+$, and CH is indicated to arise in the diluted gas, outside of the explosive, dense BN/KL outflow. Our models show that UV-irradiation provides favorable conditions for steady-state production of CH$^+$ in this environment. Surprisingly, no spatial or kinematic correspondences of these species are found with H$_2$ S(1) emission tracing shocked gas in the outflow. We propose that C$^+$ is being consumed by rapid production of CO to explain the lack of C$^+$ and CH$^+$ in the outflow, and that fluorescence provides the reservoir of H$_2$ excited to higher ro-vibrational and rotational levels. Hence, in star-forming environments containing sources of shocks and strong UV radiation, a description of CH$^+$ formation and excitation conditions is incomplete without including the important --- possibly dominant --- role of UV irradiation.Comment: Accepted for publication in The Astrophysical Journa

Differences between murine arylamine N-acetyltransferase type 1 and human arylamine N-acetyltransferase type 2 defined by substrate specificity and inhibitor binding

Background: The mouse has three arylamine N-acetyltransferase genes, (MOUSE)Nat1, (MOUSE)Nat2 and (MOUSE)Nat3. These are believed to correspond to (HUMAN)NAT1, (HUMAN)NAT2 and NATP in humans. (MOUSE)Nat3 encodes an enzyme with poor activity and human NATP is a pseudogene. (MOUSE)Nat2 is orthologous to (HUMAN)NAT1 and their corresponding proteins are functionally similar, but the relationship between (MOUSE)Nat1 and (HUMAN)NAT2 is less clear-cut. Methods: To determine whether the (MOUSE)NAT1 and (HUMAN)NAT2 enzymes are functionally equivalent, we expressed and purified (MOUSE)NAT1*1 and analysed its substrate specificity using a panel of arylamines and hydrazines. To understand how specific residues contribute to substrate selectivity, three site-directed mutants of (MOUSE)NAT2*1 were prepared: these were (MOUSE)NAT2_F125S, (MOUSE)NAT2_R127G and (MOUSE)NAT2_R127L. All three exhibited diminished activity towards “(MOUSE)NAT2-specific” arylamines but were more active against hydrazines than (MOUSE)NAT1*1. The inhibitory and colorimetric properties of a selective naphthoquinone inhibitor of (HUMAN)NAT1 and (MOUSE)NAT2 were investigated. Results: Comparing (MOUSE)NAT1*1 with other mammalian NAT enzymes demonstrated that the substrate profiles of (MOUSE)NAT1 and (HUMAN)NAT2 are less similar than previously believed. Three key residues (F125, R127 and Y129) in (HUMAN)NAT1*4 and (MOUSE)NAT2*1 were required for enzyme inhibition and the associated colour change on naphthoquinone binding. In silico modelling of selective ligands into the appropriate NAT active sites further implicated these residues in substrate and inhibitor specificity in mouse and human NAT isoenzymes. Conclusions: Three non-catalytic residues within (HUMAN)NAT1*4 (F125, R127 and Y129) contribute both to substrate recognition and inhibitor binding by participating in distinctive intermolecular interactions and maintaining the steric conformation of the catalytic pocket. These active site residues contribute to the definition of substrate and inhibitor selectivity, an understanding of which is essential for facilitating the design of second generation (HUMAN)NAT1-selective inhibitors for diagnostic, prognostic and therapeutic purposes. In particular, since the expression of (HUMAN)NAT1 is related to the development and progression of oestrogen-receptor-positive breast cancer, these structure-based tools will facilitate the ongoing design of candidate compounds for use in (HUMAN)NAT1-positive breast tumours. </p

ASSISTÊNCIA MÉDICA CULTURAL DOS GUNAS DE KOSKUNA. VERACRUZ. REPÚBLICA DO PANAMÁ

This study uses a qualitative approach, the ethnonursing research method, and it is based on the theory of Cultural Care Diversity and Universality of Madeleine Leininger (1991; 2006).&nbsp; The study was done in the community of Koskuna that is mostly formed, by the Panamanian indigenous group called Gunas.&nbsp; The purpose of this study was to discover, describe and understand the cultural patterns related to health and wellbeing of this group. The key informants were the group of older gunas that founded the community.&nbsp; The number was six, determined by saturation. The general informants were ten, represented by family members, teachers from the community school, and experts on the guna´s culture. For the collection of data, the enablers from the culture care theory were used, and the techniques were recorded interviews and participant observation with systematic registration in field journals. All participants gave informed consent and had autonomy to leave the study if desired. The analysis of data used Leininger´s (1991) phases of analysis. The results revealed 25 patterns of&nbsp;&nbsp; cultural care that were grouped in seven central themes. Two new constructs of culture care were identified in this study: solidarity as a form of group culture care and respect for nature as a cultural care of the environmental context. The conclusions of the study were geared to the nursing modes of decisions and actions, according to the theory of culture care.&nbsp;Este estudio con abordaje cualitativo, utiliza el método de etnoenfermería y se sustenta en la teoría del Cuidado Cultural Diversidad y Universalidad, de Leininger (1991; 2006).&nbsp; Se desarrolla en Koskuna, comunidad conformada en su mayoría, por el grupo cultural indígena panameño Guna. El propósito del estudio era descubrir, describir y entender los patrones culturales relacionados a la salud y bienestar de las gunas. Los informantes claves fueron los pobladores más antiguos de Koskuna, el número fue de seis, determinado por la técnica de saturación.&nbsp; Los informantes generales fueron familiares de los claves, maestros y expertos en la cultura Guna.&nbsp; Su número fue diez. Para la recolección de datos se utilizaron las guías de la teoría, con las técnicas de entrevista a profundidad y registros en diarios de campo.&nbsp; Las consideraciones éticas incluyeron el consentimiento informado y la autonomía de la participación.&nbsp; Para el análisis de datos se utilizó el facilitador de las cuatro fases de análisis de la teoría. Los resultados revelaron 25 patrones culturales del grupo Guna, que se agruparon en siete temas de cuidado cultural.&nbsp; También se descubrieron dos nuevos constructos de cuidado cultural: la solidaridad como cuidado cultural&nbsp; del grupo y el respeto por la&nbsp; naturaleza como cuidado del entorno cultural.&nbsp; Las conclusiones se refieren a los modos de decisión y de acción de Enfermería, determinados, por los patrones culturales identificados.Este estudo qualitativamente abordado utiliza o método de etnoenfermagem de Leininger e é baseado na teoria de Leininger sobre diversidade e universalidade do cuidado cultural (1991; 2006).&nbsp; É desenvolvido em Koskuna, uma comunidade composta principalmente pelo grupo cultural indígena panamenho Guna. O objetivo do estudo foi descobrir, descrever e compreender padrões culturais relacionados à saúde e bem-estar das gunas.&nbsp; Os informantes-chave eram os colonos mais antigos de Koskuna, o número era seis, determinado pela técnica de saturação.&nbsp; Os informantes estavam familiarizados com as chaves, professores e especialistas em cultura Guna.&nbsp; O número deles era dez. Para a coleta de dados, foram utilizados os guias teóricos, com técnicas de entrevista aprofundadas e registros de revistas de campo.&nbsp; As considerações éticas incluíam consentimento informado e autonomia de participação.&nbsp; Utilizou-se o facilitador das quatro fases da análise teórica para análise de dados. Os resultados revelaram 25 padrões culturais do grupo Guna, que foram agrupados em sete temas de cuidado cultural.&nbsp; Também foram descobertas duas novas construções de cuidados culturais: a solidariedade como o cuidado cultural do grupo e o respeito à natureza como cuidado com o meio cultural.&nbsp; As conclusões referem-se aos métodos de tomada de decisão e ação da enfermagem, determinados pelos padrões culturais identificados

The Perceptions on Male Circumcision as a Preventive Measure Against HIV Infection and Considerations in Scaling up of the Services: A Qualitative Study Among Police Officers in Dar es Salaam, Tanzania.

\ud In recent randomized controlled trials, male circumcision has been proven to complement the available biomedical interventions in decreasing HIV transmission from infected women to uninfected men. Consequently, Tanzania is striving to scale-up safe medical male circumcision to reduce HIV transmission. However, there is a need to investigate the perceptions of male circumcision in Tanzania using specific populations. The purpose of the present study was to assess the perceptions of male circumcision in a cohort of police officers that also served as a source of volunteers for a phase I/II HIV vaccine (HIVIS-03) trial in Dar es Salaam, Tanzania. In-depth interviews with 24 men and 10 women were conducted. Content analysis informed by the socio-ecological model was used to analyze the data. Informants perceived male circumcision as a health-promoting practice that may prevent HIV transmission and other sexually transmitted infections. They reported male circumcision promotes sexual pleasure, confidence and hygiene or sexual cleanliness. They added that it is a religious ritual and a cultural practice that enhances the recognition of manhood in the community. However, informants were concerned about the cost involved in male circumcision and cleanliness of instruments used in medical and traditional male circumcision. They also expressed confusion about the shame of undergoing circumcision at an advanced age and pain that could emanate after circumcision. The participants advocated for health policies that promote medical male circumcision at childhood, specifically along with the vaccination program. The perceived benefit of male circumcision as a preventive strategy to HIV and other sexually transmitted infections is important. However, there is a need to ensure that male circumcision is conducted under hygienic conditions. Integrating male circumcision service in the routine childhood vaccination program may increase its coverage at early childhood. The findings from this investigation provide contextual understanding that may assist in scaling-up male circumcision in Tanzania.\u

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands:Study design and baseline characteristics

Purpose There is a critical need for population-based prospective cohort studies because they follow individuals before the onset of disease, allowing for studies that can identify biomarkers and disease-modifying effects, and thereby contributing to systems epidemiology. Participants This paper describes the design and baseline characteristics of an intensively examined subpopulation of the LifeLines cohort in the Netherlands. In this unique subcohort, LifeLines DEEP, we included 1539 participants aged 18 years and older. Findings to date We collected additional blood (n=1387), exhaled air (n=1425) and faecal samples (n=1248), and elicited responses to gastrointestinal health questionnaires (n=1176) for analysis of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels. Here, we provide an overview of the different data layers in LifeLines DEEP and present baseline characteristics of the study population including food intake and quality of life. We also describe how the LifeLines DEEP cohort allows for the detailed investigation of genetic, genomic and metabolic variation for a wide range of phenotypic outcomes. Finally, we examine the determinants of gastrointestinal health, an area of particular interest to us that can be addressed by LifeLines DEEP. Future plans We have established a cohort of which multiple data levels allow for the integrative analysis of populations for translation of this information into biomarkers for disease, and which will offer new insights into disease mechanisms and prevention

Exploration of Piperidinols as Potential Antitubercular Agents

Novel drugs to treat tuberculosis are required and the identification of potential targets is important. Piperidinols have been identified as potential antimycobacterial agents (MIC &lt; 5 μg/mL), which also inhibit mycobacterial arylamine N-acetyltransferase (NAT), an enzyme essential for mycobacterial survival inside macrophages. The NAT inhibition involves a prodrug-like mechanism in which activation leads to the formation of bioactive phenyl vinyl ketone (PVK). The PVK fragment selectively forms an adduct with the cysteine residue in the active site. Time dependent inhibition of the NAT enzyme from Mycobacterium marinum (M. marinum) demonstrates a covalent binding mechanism for all inhibitory piperidinol analogues. The structure activity relationship highlights the importance of halide substitution on the piperidinol benzene ring. The structures of the NAT enzymes from M. marinum and M. tuberculosis, although 74% identical, have different residues in their active site clefts and allow the effects of amino acid substitutions to be assessed in understanding inhibitory potency. In addition, we have used the piperidinol 3-dimensional shape and electrostatic properties to identify two additional distinct chemical scaffolds as inhibitors of NAT. While one of the scaffolds has anti-tubercular activity, both inhibit NAT but through a non-covalent mechanism

Magnetic resonance imaging brain atrophy assessment in primary age-related tauopathy (PART)

Alzheimer disease (AD) is a neurodegenerative disorder characterized pathologically by the accumulation of amyloid-beta (Aβ) plaques and tau neurofibrillary tangles (NFTs). Recently, primary age-related tauopathy (PART) has been described as a new anatomopathological disorder where NFTs are the main feature in the absence of neuritic plaques. However, since PART has mainly been studied in post-mortem patient brains, not much is known about the clinical or neuroimaging characteristics of PART. Here, we studied the clinical brain imaging characteristics of PART focusing on neuroanatomical vulnerability by applying a previously validated multiregion visual atrophy scale. We analysed 26 cases with confirmed PART with paired clinical magnetic resonance imaging (MRI) acquisitions. In this selected cohort we found that upon correcting for the effect of age, there is increased atrophy in the medial temporal region with increasing Braak staging (r = 0.3937, p = 0.0466). Upon controlling for Braak staging effect, predominantly two regions, anterior temporal (r = 0.3638, p = 0.0677) and medial temporal (r = 0.3836, p = 0.053), show a trend for increased atrophy with increasing age. Moreover, anterior temporal lobe atrophy was associated with decreased semantic memory/language (r = - 0.5823, p = 0.0056; and r = - 0.6371, p = 0.0019, respectively), as was medial temporal lobe atrophy (r = - 0.4445, p = 0.0435). Overall, these findings support that PART is associated with medial temporal lobe atrophy and predominantly affects semantic memory/language. These findings highlight that other factors associated with aging and beyond NFTs could be involved in PART pathophysiology.NACC database is funded by NIA/NIH Grant U01 AG016976. NACC data are contributed by the NIA-funded ADCs: P30 AG019610 (PI Eric Reiman, MD), P30 AG013846 (PI Neil Kowall, MD), P30 AG062428–01 (PI James Leverenz, MD) P50 AG008702 (PI Scott Small, MD), P50 AG025688 (PI Allan Levey, MD, PhD), P50 AG047266 (PI Todd Golde, MD, PhD), P30 AG010133 (PI Andrew Saykin, PsyD), P50 AG005146 (PI Marilyn Albert, PhD), P30 AG062421–01 (PI Bradley Hyman, MD, PhD), P30 AG062422–01 (PI Ronald Petersen, MD, PhD), P50 AG005138 (PI Mary Sano, PhD), P30 AG008051 (PI Thomas Wisniewski, MD), P30 AG013854 (PI Robert Vassar, PhD), P30 AG008017 (PI Jeffrey Kaye, MD), P30 AG010161 (PI David Bennett, MD), P50 AG047366 (PI Victor Henderson, MD, MS), P30 AG010129 (PI Charles DeCarli, MD), P50 AG016573 (PI Frank LaFerla, PhD), P30 AG062429–01(PI James Brewer, MD, PhD), P50 AG023501 (PI Bruce Miller, MD), P30 AG035982 (PI Russell Swerdlow, MD), P30 AG028383 (PI Linda Van Eldik, PhD), P30 AG053760 (PI Henry Paulson, MD, PhD), P30 AG010124 (PI John Trojanowski, MD, PhD), P50 AG005133 (PI Oscar Lopez, MD), P50 AG005142 (PI Helena Chui, MD), P30 AG012300 (PI Roger Rosenberg, MD), P30 AG049638 (PI Suzanne Craft, PhD), P50 AG005136 (PI Thomas Grabowski, MD), P30 AG062715–01 (PI Sanjay Asthana, MD, FRCP), P50 AG005681 (PI John Morris, MD), P50 AG047270 (PI Stephen Strittmatter, MD, PhD). NIH grants to JFC (R01AG054008, R01NS095252, R01AG062348, RF1AG060961), the Tau Consortium, and Alzheimer’s Association (NIRG- 469 15-363188

Herschel/HIFI Spectral Mapping of C^+, CH^+, and CH in Orion BN/KL: The Prevailing Role of Ultraviolet Irradiation in CH^+ Formation

The CH^+ ion is a key species in the initial steps of interstellar carbon chemistry. Its formation in diverse environments where it is observed is not well understood, however, because the main production pathway is so endothermic (4280 K) that it is unlikely to proceed at the typical temperatures of molecular clouds. We investigate the formation of this highly reactive molecule with the first velocity-resolved spectral mapping of the CH^+ J = 1−0, 2−1 rotational transitions, three sets of CH Λ-doubled triplet lines, ^(12)C^+ and ^(13)C^+ ^(2)P_(3/2) - ^(2)P_(1/2), and CH_(3)OH 835 GHz E-symmetry Q-branch transitions, obtained with Herschel/HIFI over a region of ≈ 12 arcmin^2 centered on the Orion BN/KL source. We present the spatial morphologies and kinematics, cloud boundary conditions, excitation temperatures, column densities, and ^(12)C^+ optical depths. Emission from all of C^+, CH^+, and CH is indicated to arise in the diluted gas, outside the explosive, dense BN/KL outflow. Our models show that UV irradiation provides favorable conditions for steady-state production of CH^+ in this environment. Surprisingly, no spatial or kinematic correspondences of the observed species are found with H_2 S(1) emission tracing shocked gas in the outflow. We propose that C^+ is being consumed by rapid production of CO to explain the lack of both C^+ and CH^+ in the outflow. Hence, in star-forming environments containing sources of shocks and strong UV radiation, a description of the conditions leading to CH^+ formation and excitation is incomplete without including the important—possibly dominant—role of UV irradiation