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AXIOME: automated exploration of microbial diversity

Michael DJ Lynch, Andre P Masella, Michael W Hall, Andrea K Bartram, Josh D Neufeld
2013 GigaScience  
Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research. Findings: AXIOME streamlines and
more » ... s analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows. Conclusions: AXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.
doi:10.1186/2047-217x-2-3 pmid:23587322 pmcid:PMC3626533 fatcat:h2ksaavj3vbl5b3jfwxhw2pwma

Second Order Minimum Energy Filtering on SE_3 with Nonlinear Measurement Equations [article]

Johannes Berger, Andreas Neufeld, Florian Becker, Frank Lenzen, and Christoph Schnörr
2015 arXiv   pre-print
Accurate camera motion estimation is a fundamental building block for many Computer Vision algorithms. For improved robustness, temporal consistency of translational and rotational camera velocity is often assumed by propagating motion information forward using stochastic filters. Classical stochastic filters, however, use linear approximations for the non-linear observer model and for the non-linear structure of the underlying Lie Group SE_3 and have to approximate the unknown posteriori
more » ... bution. In this paper we employ a non-linear measurement model for the camera motion estimation problem that incorporates multiple observation equations. We solve the underlying filtering problem using a novel Minimum Energy Filter on SE_3 and give explicit expressions for the optimal state variables. Experiments on the challenging KITTI benchmark show that, although a simple motion model is only employed, our approach improves rotational velocity estimation and otherwise is on par with the state-of-the-art.
arXiv:1502.07903v1 fatcat:nns6mn7u6berbcqk4njggxsxf4

What do we know about older adults and HIV? a review of social and behavioral literature

Andrea Sankar, Andrea Nevedal, Stewart Neufeld, Rico Berry, Mark Luborsky
2011 AIDS Care  
The fastest growing segment of the United States HIV population is people aged 50 and older. This heterogeneous group includes people with diverse pathways into HIV positive status in later life, including aging with the disease as well as later life-acquired infections. As people with HIV live into older ages, solving problems of successful secondary prevention and ongoing treatment requires more specific knowledge of the particular aging-related contextual sociocultural, psychosocial, and
more » ... onal factors salient to the situations of persons living with HIV. Greater knowledge of these factors will help solve challenges to reducing psychological burden and promoting health maintenance for people with HIV. Yet, the current literature on aging and HIV remains nascent. To assess the state of knowledge of the sociocultural and behavioral factors associated with aging with HIV, we conducted a systematic critical content review of peerreviewed social and behavioral research on aging and HIV to answer the question, "How have older age, and social, cultural, and behavioral aspects of the intersection of HIV and age been addressed in the literature?" We searched First Search, Proquest, Psych Info, Pub Med, Wilson Select Plus, and World Cat and identified 1549 articles. We then reviewed these to select peerreviewed articles reporting results of research on the social and behavioral aspects of living with HIV at age 50 and older. Fifty-eight publications were identified that met study inclusion criteria. While few publications reported clear age-related differences, there were significant ethnic differences in living with HIV in later life and also differences among older people when groups were defined by mode of transmission. Findings are discussed in light of constructs from gerontology which may contribute to clarifying how later life, life course stage, and psychological development intersect with, influence, and are influenced by HIV disease and long-term antiretroviral therapy use.
doi:10.1080/09540121.2011.564115 pmid:21939401 pmcid:PMC3199226 fatcat:6qgocc555naeteekjrgusf5mk4

PANDAseq: paired-end assembler for illumina sequences

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown, Josh D Neufeld
2012 BMC Bioinformatics  
Availability and Requirements Project name: PANDAseq Project home page: https://github.com/neufeld/ pandaseq Operating system(s): POSIX-compliant (Windows, Linux, and MacOS) Programming language: C Quality  ... 
doi:10.1186/1471-2105-13-31 pmid:22333067 pmcid:PMC3471323 fatcat:ayrjpxs3yjdldbyh7jtqn6o6ta

Organ- and endotheliotropism of Nipah virus infections in vivo and in vitro

james Neufeld, Hana Weingartl, Andrea Maisner
2009 Thrombosis and Haemostasis  
SummaryNipah virus (NiV) is a highly pathogenic paramyxovirus that was first isolated in 1999 during an outbreak in Malaysia. In contrast to other paramyxoviruses NiV infects many mammalian species. Because of its zoonotic potential, the high pathogenicity and the lack of therapeutic treatment, NiV was classified as a biosafety level 4 pathogen. In humans NiV causes a severe acute encephalitis whereas in some animal hosts respiratory symptoms are predominantly observed. Despite the differences
more » ... n the clinical outcome, microvascular endothelial cell damage predominantly underlies the pathological changes in NiV infections in all sus-ceptible host species. NiV generally induces a pronounced vasculitis which is primarily characterised by endothelial cell necrosis and inflammatory cell infiltration. For future developments of specific antiviral therapies or vaccines, a detailed understanding of the molecular basis of NiV pathogenesis is required.This article reviews the current knowledge about natural and experimental infections in different mammals, focusing on the main organ and cell tropism in vivo, and summarises some recent studies in cell culture on the role of ephrin-B2 and -B3 receptors in NiV infection of endothelial cells.
doi:10.1160/th09-05-0310 pmid:19967130 fatcat:x42g3k3agvf6fnjioq4gc53uly

Second-Order Recursive Filtering on the Rigid-Motion Lie Group SE(3) Based on Nonlinear Observations [article]

Johannes Berger, Frank Lenzen, Florian Becker, Andreas Neufeld, Christoph Schnörr
2015 arXiv   pre-print
Camera motion estimation from observed scene features is an important task in image processing to increase the accuracy of many methods, e.g. optical flow and structure-from-motion. Due to the curved geometry of the state space SE(3) and the non-linear relation to the observed optical flow, many recent filtering approaches use a first-order approximation and assume a Gaussian a posteriori distribution or restrict the state to Euclidean geometry. The physical model is usually also limited to
more » ... orm motions. We propose a second-order minimum energy filter with a generalized kinematic model that copes with the full geometry of SE(3) as well as with the nonlinear dependencies between the state space and observations. The derived filter enables reconstructing motions correctly for synthetic and real scenes, e.g. from the KITTI benchmark. Our experiments confirm that the derived minimum energy filter with higher-order state differential equation copes with higher-order kinematics and is also able to minimize model noise. We also show that the proposed filter is superior to state-of-the-art extended Kalman filters on Lie groups in the case of linear observations and that our method reaches the accuracy of modern visual odometry methods.
arXiv:1507.06810v1 fatcat:wvnq3xxuzncx7p6avjbhaz4p4a

Targeted recovery of novel phylogenetic diversity from next-generation sequence data

Michael D J Lynch, Andrea K Bartram, Josh D Neufeld
2012 The ISME Journal  
et al., 2004; Neufeld and Mohn, 2005) .  ...  Amplification and sequencing of ULs Template genomic DNA was extracted from the same Arctic soil (Alert Nunavut, Canada) examined earlier (Neufeld and Mohn, 2005; Neufeld et al., 2008; Bartram et al.,  ... 
doi:10.1038/ismej.2012.50 pmid:22791239 pmcid:PMC3475379 fatcat:i335wzhigbaetaxzmnh75y6umq

A Genetic Screen in Drosophila Reveals Novel Cytoprotective Functions of the Autophagy-Lysosome Pathway

Andrew M. Arsham, Thomas P. Neufeld, Andreas Bergmann
2009 PLoS ONE  
The highly conserved autophagy-lysosome pathway is the primary mechanism for breakdown and recycling of macromolecular and organellar cargo in the eukaryotic cell. Autophagy has recently been implicated in protection against cancer, neurodegeneration, and infection, and interest is increasing in additional roles of autophagy in human health, disease, and aging. To search for novel cytoprotective features of this pathway, we carried out a genetic mosaic screen for mutations causing increased
more » ... somal and/or autophagic activity in the Drosophila melanogaster larval fat body. By combining Drosophila genetics with live-cell imaging of the fluorescent dye LysoTracker Red and fixed-cell imaging of autophagy-specific fluorescent protein markers, the screen was designed to identify essential metazoan genes whose disruption causes increased flux through the autophagy-lysosome pathway. The screen identified a large number of genes associated with the protein synthesis and ER-secretory pathways (e.g. aminoacyl tRNA synthetases, Oligosaccharyl transferase, Sec61a), and with mitochondrial function and dynamics (e.g. Rieske iron-sulfur protein, Dynamin-related protein 1). We also observed that increased lysosomal and autophagic activity were consistently associated with decreased cell size. Our work demonstrates that disruption of the synthesis, transport, folding, or glycosylation of ER-targeted proteins at any of multiple steps leads to autophagy induction. In addition to illuminating cytoprotective features of autophagy in response to cellular damage, this screen establishes a genetic methodology for investigating cell biological phenotypes in live cells, in the context of viable wild type organisms.
doi:10.1371/journal.pone.0006068 pmid:19562034 pmcid:PMC2698153 fatcat:25sspz2irrhozppwfuajcihoeq

Cultural Rationales Guiding Medication Adherence Among African American with HIV/AIDS

Andrea Sankar, Stewart Neufeld, Rico Berry, Mark Luborsky
2011 AIDS Patients Care and STDs  
To date, only modest gains have been achieved in explaining adherence to medical regimens, limiting effective interventions. This is a particularly important issue for African Americans who are disproportionately affected by the HIV epidemic. Few studies have focused on intragroup variation among African Americans in adherence to ART. The aim of this study was to identify and describe the cultural rationales guiding African American patients' formulation and evaluation of adherence. Rationales
more » ... re key features of purposeful human action. In-depth interviews with 80 seropositive African Americans were tape recorded, transcribed, and analyzed. Participant CD4, viral load and medical histories were collected at each data point. Analysis of four waves of panel data identified three types of adherence rationales: Authoritative Knowledge Rationale (AKR; n = 29, 36.3%), Following Doctors' Orders Rationale (DOR; n = 24, 30.0%) and Individualized Adherence Rationale (IAR; n = 27, 33.8%). Differences in mean reported adherence between the rationale groups did not achieve statistical significance. However, the fraction reporting low adherence ( < 70%), although not different by rationale group at the first interview (T1), was significantly higher for the IAR group by the fourth interview (T4). Objective clinical markers (CD4 and viral load) improved over time (from T1 to T4) for AKR and DOR groups, but remained unchanged for the IAR group, yet self-reported adherence declined for all groups over the course of the four interviews.
doi:10.1089/apc.2010.0345 pmid:21777141 pmcid:PMC3192053 fatcat:iukmjgaahbc47jzyj656lt772m

Reading without the left ventral occipito-temporal cortex

Mohamed L. Seghier, Nicholas H. Neufeld, Peter Zeidman, Alex P. Leff, Andrea Mechelli, Arjuna Nagendran, Jane M. Riddoch, Glyn W. Humphreys, Cathy J. Price
2012 Neuropsychologia  
Nicholas Neufeld was supported by a Commonwealth Scholarship.  ...  ., Seghier, Zeidman, Neufeld, Leff, & Price, 2010; Stephan et al., 2010) .  ... 
doi:10.1016/j.neuropsychologia.2012.09.030 pmid:23017598 pmcid:PMC3524457 fatcat:4cxl7jy6ofautallpbla6h66zm

Second Order Minimum Energy Filtering on $${\text {SE}}_{3}$$ with Nonlinear Measurement Equations [chapter]

Johannes Berger, Andreas Neufeld, Florian Becker, Frank Lenzen, Christoph Schnörr
2015 Lecture Notes in Computer Science  
Accurate camera motion estimation is a fundamental building block for many Computer Vision algorithms. For improved robustness, temporal consistency of translational and rotational camera velocity is often assumed by propagating motion information forward using stochastic filters. Classical stochastic filters, however, use linear approximations for the non-linear observer model and for the non-linear structure of the underlying Lie Group SE3 and have to approximate the unknown posteriori
more » ... ution. In this paper we employ a nonlinear measurement model for the camera motion estimation problem that incorporates multiple observation equations. We solve the underlying filtering problem using a novel Minimum Energy Filter on SE3 and give explicit expressions for the optimal state variables. Experiments on the challenging KITTI benchmark show that, although a simple motion model is only employed, our approach improves rotational velocity estimation and otherwise is on par with the state-of-the-art.
doi:10.1007/978-3-319-18461-6_32 fatcat:qszhxqef75aejkfnncchbtcpme

Sero-positive African Americans' Beliefs about Alcohol and Their Impact on Anti-retroviral Adherence

Andrea Sankar, Tracy Wunderlich, Stewart Neufeld, Mark Luborsky
2006 Aids and Behavior  
Alcohol consumption has been associated with HIV disease progression; yet, the nature of this association is poorly understood. This study sought to determine the influence of patient beliefs about alcohol on ART adherence, and elucidate clinician beliefs about drinking and taking ART. Most patients (85%) believed alcohol and ART do not mix. The three alcohol consumption groups, light, moderate, and heavy, differed in their beliefs about drinking and ART with 64% of light and 55% of moderate
more » ... nkers skipping ART when drinking compared to 29% of heavy drinkers. Beliefs were derived from folk models of alcohol-ART interaction. Patients 50 and older were less likely to skip ART when drinking. Alcohol appears to affect adherence through decisions to forgo ART when drinking not through drunken forgetfulness. Furthermore, over onehalf of clinicians believed alcohol and ART should not be taken together. These findings have implications for patient care and physician training.
doi:10.1007/s10461-006-9144-0 pmid:16799842 pmcid:PMC4216565 fatcat:giojebdhmndsxejszamwkafzfi

The importance of incorporating natural thermal variation when evaluating physiological performance in wild species

Andrea J. Morash, Claire Neufeld, Tyson J. MacCormack, Suzanne Currie
2018 Journal of Experimental Biology  
Environmental variability in aquatic ecosystems makes the study of ectotherms complex and challenging. Physiologists have historically overcome this hurdle in the laboratory by using 'average' conditions, representative of the natural environment for any given animal. Temperature, in particular, has widespread impact on the physiology of animals, and it is becoming increasingly important to understand these effects as we face future climate challenges. The majority of research to date has
more » ... d on the expected global average increase in temperature; however, increases in climate variability are predicted to affect animals as much or more than climate warming. Physiological responses associated with the acclimation to a new stable temperature are distinct from those in thermally variable environments. Our goal is to highlight these physiological differences as they relate to both thermal acclimation and the 'fallacy of the average' or Jensen's inequality using theoretical models and novel empirical data. We encourage the use of more realistic thermal environments in experimental design to advance our understanding of these physiological responses such that we can better predict how aquatic animals will respond to future changes in our climate.
doi:10.1242/jeb.164673 pmid:30037965 fatcat:hloimmapozfftfyeexvrravpri

Synthesis of Radioluminescent CaF2:Ln Core, Mesoporous Silica Shell Nanoparticles for Use in X-ray Based Theranostics

Hayden Winter, Megan J. Neufeld, Lydia Makotamo, Conroy Sun, Andrea M. Goforth
2020 Nanomaterials  
X-ray radiotherapy is a common method of treating cancerous tumors or other malignant lesions. The side effects of this treatment, however, can be deleterious to patient quality of life if critical tissues are affected. To potentially lower the effective doses of radiation and negative side-effects, new classes of nanoparticles are being developed to enhance reactive oxygen species production during irradiation. This report presents the synthesis and radiotherapeutic efficacy evaluation of a
more » ... nanoparticle formulation designed for this purpose, composed of a CaF2 core, mesoporous silica shell, and polyethylene glycol coating. The construct was additionally doped with Tb and Eu during the CaF2 core synthesis to prepare nanoparticles (NPs) with X-ray luminescent properties for potential application in fluorescence imaging. The mesoporous silica shell was added to provide the opportunity for small molecule loading, and the polyethylene glycol coating was added to impart aqueous solubility and biocompatibility. The potential of these nanomaterials to act as radiosensitizers for enhancing X-ray radiotherapy was supported by reactive oxygen species generation assays. Further, in vitro experiments indicate biocompatibility and enhanced cellular damage during X-ray radiotherapy.
doi:10.3390/nano10081447 pmid:32722132 fatcat:vqx2anybf5fy3leif62h7wcufq

A case of co-occuring synesthesia, autism, prodigious talent and strong structural brain connectivity

Andreas Riedel, Simon Maier, Kerstin Wenzler, Bernd Feige, Ludger Tebartz van Elst, Sven Bölte, Janina Neufeld
2020 BMC Psychiatry  
Synesthesia is a sensory phenomenon where certain domain-specific stimuli trigger additional sensations of e.g. color or texture. The condition occurs in about 4% of the general population, but is overrepresented in individuals with Autism Spectrum Disorder (ASD), where it might also be associated with the presence of prodigious talents. Here we describe the case of a young transsexual man with Asperger Syndrome, synesthesia and a prodigious talent for foreign language acquisition. In our case,
more » ... not only letters, numbers, spoken words, music, noises, weekdays and months lead to highly consistent, vivid color sensations but also his own and others' emotions, geometric shapes, any mathematical symbol, and letters from an unfamiliar alphabet (Hebrew). These color associations seem to aid categorization, differentiation and storage of information and might thereby contribute to the young man's language acquisition ability. We investigated the young man's structural brain connectivity in comparison to adults with or without ASD, applying global fiber tracking to diffusion-weighted Magnetic Resonance Imaging (MRI) data. The case presented with increased connectivity, especially between regions involved in visual and emotion processing, memory, and higher order associative binding regions. An electroencephalography experiment investigating synesthetic color and shape sensations while listening to music showed a negligible occipital alpha suppression, indicating that these internally generated synesthetic sensations derive from a different brain mechanism than when processing external visual information. Taken together, this case study endorses the notion of a link between synesthesia, prodigious talent and autism, adding to the currently still sparse literature in this field. It provides new insights into the possible manifestations of synesthesia in individuals with ASD and its potential contribution to prodigious talents in people with an otherwise unexceptional cognitive profile. Additionally, this case impressively illustrates how synesthesia can be a key element not only of sensory perception but also social and emotional processing and contributes to existing evidence of increased brain connectivity in association with synesthesia.
doi:10.1186/s12888-020-02722-w pmid:32605557 fatcat:3t6ye2smxveppctrrjs7slksv4
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