Ngoc Anh Tran | Foreign Trade University (original) (raw)

Papers by Ngoc Anh Tran

Université Grenoble Alpes, Dec 8, 2020

Childhood, student, or adolescent, middle-aged, etc. are the short and long journeys of each pers... more Childhood, student, or adolescent, middle-aged, etc. are the short and long journeys of each person's life. In the early stages, people have changed the most, both physically and mentally. In the next stages, the change occurs more slowly but contributes to deepening our sense of life. And, PhDs: the tortuous passage that I have been in for three years. Three-unforgettable-year help a person become more individual, confidant, and especially more human. And I have to sincerely thank some people for what they brought me: First of all, I want to thank my supervisors: Prof. Jean-Claude Lepretre and Dr. Fannie Alloin. Most likely, I'm not their easiest case they've supervised to explain things more complicated than they are, particularly regarding my habit. I am nevertheless pleased with their input and assistance in clarifying my thoughts and words whenever appropriate. During my first year at LEPMI in particular, their inspiring words were extremely helpful when times were tough. Fannie has always been there, she's paid a lot of attention to my job every time and during these three years she's taken the right choice every time. To be more accurate, I have learned a considerable amount of skills in all the fields: how to address a new subject, the working technique, the analysis of data not limited to the outcome that can be obtained at first glance, the ability to carry on having the most from the job. And there may be more to the chart. Thank you above everything, and all the work you poured into my study, with all its facets. I would like to express my deepest appreciation to the Jury that accepted to examine and referee for my thesis. Thank you for all the interesting questions and fruitful comments on this work. I'd also like to extend my gratitude to my erstwhile supervisor: Prof. Le Ngoc Thach and Ass. Prof. Le My Loan Phung that have been belonged to me and gave me helpful and sincere advice since I was a student up to now. I am also grateful to all MIEL team even if they did not directly supervise my thesis from Dr.

Antibiotics, 2021

Bacterial leaf blight, which is caused by Xanthomonas axonopodis pv. allii, annually causes signi... more Bacterial leaf blight, which is caused by Xanthomonas axonopodis pv. allii, annually causes significant yield losses to Welsh onion in many producing countries, including Vietnam. In this study, we isolated and characterized lytic phages Φ16, Φ17A and Φ31, specific to X. axonopodis pv. allii and belonging to a new phage species and genus within the Autographiviridae, from four provinces in the Mekong Delta of Vietnam. Moreover, we evaluated their efficacy for the biocontrol of leaf blight in greenhouse and field conditions. When applying the three highly related phages individually or as a three-phage cocktail at 108 PFU/mL in greenhouse conditions, our results show that treatment with Φ31 alone provides higher disease prevention than the two other phages or the phage cocktail. Furthermore, we compared phage concentrations from 105 to 108 and showed optimal disease control at 107 and 108 PFU/mL. Finally, under field conditions, both phage Φ31 alone and the phage cocktail treatments ...

Hue University Journal of Science: Natural Science, 2020

For the first time, a realistic microscopic calculation for low-energy neutron-nucleus elastic sc... more For the first time, a realistic microscopic calculation for low-energy neutron-nucleus elastic scattering off open-shell nuclei is carried out within the framework of particle-vibration coupling (PVC). In this study, the pairing correlations of the ground state are taken into account. The dependence of the angular distributions on the pairing gaps have been discussed.

Journal of virology, 1997

Retroviral gene transfer is widely used in experimental and human gene therapy applications. We h... more Retroviral gene transfer is widely used in experimental and human gene therapy applications. We have devised a novel method of generating high-titer retroviral producer cell lines based on the P1 bacteriophage recombinase system Cre-loxP. Incorporation of loxP sites flanking a Neo(r)-SVTK cassette in the proviral DNA allows excision of these selectable markers through expression of Cre recombinase after production of a high-titer producer cell line. The resultant producer line contains a single loxP site flanked by the viral long terminal repeats. Retransfection of this line with the Cre expression vector and a plasmid containing a gene of interest flanked by loxP sites allows insertional recombination of the gene into the favorable preexisting site in the genome and the generation of a new line with a titer equivalent to that of the parental producer cell line. The efficiency of the process is sufficient to allow the generation of multiple new producer lines without the addition of...

Background: The under-representation of Vietnamese ethnic groups in existing genetic databases an... more Background: The under-representation of Vietnamese ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in the population. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in Vietnam and many developing countries. Non-invasive prenatal testing (NIPT) data offers an alternative untapped resource to study genetic variations in the Vietnamese population. Results: We analyzed the low-coverage genomes of 2,683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially five pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency...

Journal of mathematical neuroscience, Jan 16, 2018

The Hopfield recurrent neural network is a classical auto-associative model of memory, in which c... more The Hopfield recurrent neural network is a classical auto-associative model of memory, in which collections of symmetrically coupled McCulloch-Pitts binary neurons interact to perform emergent computation. Although previous researchers have explored the potential of this network to solve combinatorial optimization problems or store reoccurring activity patterns as attractors of its deterministic dynamics, a basic open problem is to design a family of Hopfield networks with a number of noise-tolerant memories that grows exponentially with neural population size. Here, we discover such networks by minimizing probability flow, a recently proposed objective for estimating parameters in discrete maximum entropy models. By descending the gradient of the convex probability flow, our networks adapt synaptic weights to achieve robust exponential storage, even when presented with vanishingly small numbers of training patterns. In addition to providing a new set of low-density error-correcting...

SSRN Electronic Journal, 2016

Principal component analysis (PCA) is a widely used dimension reduction tool in the analysis of m... more Principal component analysis (PCA) is a widely used dimension reduction tool in the analysis of many kind of high-dimensional data. It is used in signal processing, mechanical ingeneering, psychometrics, and other fields under different names. It still bears the same mathematical idea: the decomposition of variation of a high dimensional object into uncorrelated factors or components. However, in many of the above applications, one is interested in capturing the tail variables of the data rather than variation around the mean. Such applications include weather related event curves, expected shortfalls, and speeding analysis among others. These are all high dimensional tail objects which one would like to study in a PCA fashion. The tail character though requires to do the dimension reduction in an asymmetric norm rather than the classical L 2-type orthogonal projection. We develop an analogue of PCA in an asymmetric norm. These norms cover both quantiles and expectiles, another tail event measure. The difficulty is that there is no natural basis, no 'principal components', to the k-dimensional subspace found. We propose two definitions of principal components and provide algorithms based on iterative least squares. We prove upper bounds on their convergence times, and compare their performances in a simulation study. We apply the algorithms to a Chinese weather dataset with a view to weather derivative pricing.

Cell reports, May 21, 2016

Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizoph... more Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizophrenia (SZ). We show that microRNA-9 (miR-9) is abundantly expressed in control neural progenitor cells (NPCs) but also significantly downregulated in a subset of SZ NPCs. We observed a strong correlation between miR-9 expression and miR-9 regulatory activity in NPCs as well as between miR-9 levels/activity, neural migration, and diagnosis. Overexpression of miR-9 was sufficient to ameliorate a previously reported neural migration deficit in SZ NPCs, whereas knockdown partially phenocopied aberrant migration in control NPCs. Unexpectedly, proteomic- and RNA sequencing (RNA-seq)-based analysis revealed that these effects were mediated primarily by small changes in expression of indirect miR-9 targets rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes. Together, these data indicate that aberrant levels and activity of miR-9 ...

is an auto-associative, distributive model of neural memory storage and retrieval. A form of erro... more is an auto-associative, distributive model of neural memory storage and retrieval. A form of error-correcting code, the Hopfield network can learn a set of patterns as stable points of the network dynamic, and retrieve them from noisy inputs-thus Hopfield networks are their own decoders. Unlike in coding theory, where the information rate of a good code (in the Shannon sense) is finite but the cost of decoding does not play a role in the rate, the information rate of Hopfield networks trained with state-of-the-art learning algorithms is of the order log(n)/n, a quantity that tends to zero asymptotically with n, the number of neurons in the network. For specially constructed networks, the best information rate currently achieved is of order 1/ √ n. In this work, we design simple binary Hopfield networks that have asymptotically vanishing error rates at an information rate of 1/log(n). These networks can be added as the decoders of any neural code with noisy neurons. As an example, we apply our network to a binary neural decoder of the grid cell code to attain information rate 1/log(n). Hopfield networks | error-correcting codes | information theory | exponential capacity | grid cells | redundant number system

Canadian Oncology Nursing Journal, 2011

The Pivot Nurse in Oncology (PNO) is a health care professional dedicated to providing patients w... more The Pivot Nurse in Oncology (PNO) is a health care professional dedicated to providing patients with cancer and their families with continuing and consistent supportive care throughout the care trajectory. The purpose of this paper is to describe the variation and frequency of nursing interventions delivered by 12 PNOs at our health centre. An administrative analysis over a three-year period revealed a total of 43,906 interventions that were grouped into 10 categories. This analysis provided a description of the intervention frequency and these interventions were further collapsed into the four role functions of the PNO. Coordination/continuity of care and the assessment of needs and symptoms were identified as the dominant practice domains of the PNO in the professional cancer navigator role.

Journal of bacteriology, 2014

We previously reported that the presence of dideoxythymidine (ddT) in the growth medium selective... more We previously reported that the presence of dideoxythymidine (ddT) in the growth medium selectively inhibits the ability of bacteriophage T7 to infect Escherichia coli by inhibiting phage DNA synthese (N. Q. Tran, L. F. Rezende, U. Qimron, C. C. Richardson, and S. Tabor, Proc. Natl. Acad. Sci. U. S. A. 105:9373-9378, 2008, doi:10.1073/pnas.0804164105). In the presence of T7 gene 1.7 protein, ddT is taken up into the E. coli cell and converted to ddTTP. ddTTP is incorporated into DNA as ddTMP by the T7 DNA polymerase, resulting in chain termination. We have identified the pathway by which exogenous ddT is converted to ddTTP. The pathway consists of ddT transport by host nucleoside permeases and phosphorylation to ddTMP by the host thymidine kinase. T7 gene 1.7 protein phosphorylates ddTMP and ddTDP, resulting in ddTTP. A 74-residue peptide of the gene 1.7 protein confers ddT sensitivity to the same extent as the 196-residue wild-type gene 1.7 protein. We also show that cleavage of th...

Nucleic acids research, Jan 10, 2014

Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cel... more Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in different human cells. In this paper, the architectures of the 41 regulatory networks and the distributions of housekeeping and specific regulatory interactions are investigated. The TF regulatory networks of different human cell types demonstrate similar global three-layer (top, core and bottom) hierarchical architectures, which are greatly different from the yeast TF regulatory network. However, they have distinguishable local organizations, as suggested by the fact that wiring patterns of only a few TFs are enough to distinguish cell identities. The TF regulatory network of human embryonic stem cells (hESCs) is dense and enriched with interactions that are unseen in the ne...

Development (Cambridge, England), 2015

Screens in mosaic Drosophila tissues that use chemical mutagenesis have identified many regulator... more Screens in mosaic Drosophila tissues that use chemical mutagenesis have identified many regulators of growth and patterning. Many of the mutant phenotypes observed were contingent upon the presence of both wild-type and mutant cells in the same tissue. More recently, large collections of RNAi lines or cDNAs expressed under Gal4/UAS control have been used to alter gene expression uniformly in specific tissues. However, these newer approaches are not easily combined with the efficient generation of genetic mosaics. The CoinFLP system described here enables mosaic screens in the context of gene knockdown or overexpression by automatically generating a reliable ratio of mutant to wild-type tissue in a developmentally controlled manner. CoinFLP-Gal4 generates mosaic tissues composed of clones of which only a subset expresses Gal4. CoinFLP-LexGAD/Gal4 generates tissues composed of clones that express either Gal4 or LexGAD, thus allowing the study of interactions between different types of...

Proceedings of the 36th international ACM SIGIR conference on Research and development in information retrieval, 2013

As the volumes of AI problems involving human knowledge are likely to soar, crowdsourcing has bec... more As the volumes of AI problems involving human knowledge are likely to soar, crowdsourcing has become essential in a wide range of worldwide web applications. One of the biggest challenges of crowdsourcing is aggregating the answers collected from crowd workers; and thus, many aggregate techniques have been proposed. However, given a new application, it is difficult for users to choose the best-suited technique as well as appropriate parameter values since each of these techniques has distinct performance characteristics depending on various factors (e.g. worker expertise, question difficulty). In this paper, we develop a benchmarking tool that allows to (i) simulate the crowd and (ii) evaluate aggregate techniques in different aspects (accuracy, sensitivity to spammers, etc.). We believe that this tool will be able to serve as a practical guideline for both researchers and software developers. While researchers can use our tool to assess existing or new techniques, developers can reuse its components to reduce the development complexity.

Plant Signaling & Behavior, 2011

Schizophrenia Bulletin, 2012

although schizophrenia affects a number of brain regions and produces a range of clinical symptom... more although schizophrenia affects a number of brain regions and produces a range of clinical symptoms, we believe its origins lie at the level of single neurons and simple networks. owing to this, as well as to its high degree of heritability, we hypothesize that schizophrenia is amenable to cell-based studies in vitro. Using induced pluripotent stem cell-derived neurons and/or fibroblast-induced neurons, a limitless quantity of live human neurons can now be generated from patient skin biopsies. We predict that cell-based studies will ultimately contribute to our understanding of the molecular and cellular underpinnings of this debilitating disorder.

Review of Quantitative Finance and Accounting, 2010

Proceedings of the National Academy of Sciences, 2008

Bacteriophage T7 DNA polymerase efficiently incorporates dideoxynucleotides into DNA, resulting i... more Bacteriophage T7 DNA polymerase efficiently incorporates dideoxynucleotides into DNA, resulting in chain termination. Dideoxythymidine (ddT) present in the medium at levels not toxic to Escherichia coli inhibits phage T7. We isolated 95 T7 phage mutants that were resistant to ddT. All contained a mutation in T7 gene 1.7 , a nonessential gene of unknown function. When gene 1.7 was expressed from a plasmid, T7 phage resistant to ddT still arose; analysis of 36 of these mutants revealed that all had a single mutation in gene 5 , which encodes T7 DNA polymerase. This mutation changes tyrosine-526 to phenylalanine, which is known to increase dramatically the ability of T7 DNA polymerase to discriminate against dideoxynucleotides. DNA synthesis in cells infected with wild-type T7 phage was inhibited by ddT, suggesting that it resulted in chain termination of DNA synthesis in the presence of gene 1.7 protein. Overexpression of gene 1.7 from a plasmid rendered E. coli cells sensitive to ddT...

Nature, 2011

Schizophrenia (SCZD) is a debilitating neurological disorder with a worldwide prevalence of 1%; t... more Schizophrenia (SCZD) is a debilitating neurological disorder with a worldwide prevalence of 1%; there is a strong genetic component, with an estimated heritability of 80-85% 1. Though postmortem studies have revealed reduced brain volume, cell size, spine density and abnormal neural distribution in the prefrontal cortex and hippocampus of SCZD brain tissue 2 and neuropharmacological studies have implicated dopaminergic, glutamatergic and GABAergic activity in SCZD 3 , the cell types affected in SCZD and the molecular mechanisms underlying the disease state remain unclear. To elucidate the cellular and molecular defects of SCZD, we directly reprogrammed fibroblasts from SCZD patients into human induced pluripotent stem cells (hiPSCs) and subsequently differentiated these disorder-specific hiPSCs into neurons (SI Fig. 1). SCZD hiPSC neurons showed diminished neuronal connectivity in conjunction with decreased neurite number, PSD95-protein levels and glutamate receptor expression. Gene expression profiles of SCZD hiPSC neurons identified altered expression of many components of the cAMP and WNT signaling pathways. Key cellular and molecular elements of the SCZD phenotype were ameliorated following treatment of SCZD hiPSC neurons with the antipsychotic Loxapine. To date, hiPSC neuronal pathology has only been demonstrated in diseases characterized by both the loss of function of a single gene product and rapid disease progression in early childhood 4-6. We now report hiPSC neuronal phenotypes and gene expression changes associated with SCZD, a complex genetic psychiatric disorder (SI Table 1).

Université Grenoble Alpes, Dec 8, 2020

Childhood, student, or adolescent, middle-aged, etc. are the short and long journeys of each pers... more Childhood, student, or adolescent, middle-aged, etc. are the short and long journeys of each person's life. In the early stages, people have changed the most, both physically and mentally. In the next stages, the change occurs more slowly but contributes to deepening our sense of life. And, PhDs: the tortuous passage that I have been in for three years. Three-unforgettable-year help a person become more individual, confidant, and especially more human. And I have to sincerely thank some people for what they brought me: First of all, I want to thank my supervisors: Prof. Jean-Claude Lepretre and Dr. Fannie Alloin. Most likely, I'm not their easiest case they've supervised to explain things more complicated than they are, particularly regarding my habit. I am nevertheless pleased with their input and assistance in clarifying my thoughts and words whenever appropriate. During my first year at LEPMI in particular, their inspiring words were extremely helpful when times were tough. Fannie has always been there, she's paid a lot of attention to my job every time and during these three years she's taken the right choice every time. To be more accurate, I have learned a considerable amount of skills in all the fields: how to address a new subject, the working technique, the analysis of data not limited to the outcome that can be obtained at first glance, the ability to carry on having the most from the job. And there may be more to the chart. Thank you above everything, and all the work you poured into my study, with all its facets. I would like to express my deepest appreciation to the Jury that accepted to examine and referee for my thesis. Thank you for all the interesting questions and fruitful comments on this work. I'd also like to extend my gratitude to my erstwhile supervisor: Prof. Le Ngoc Thach and Ass. Prof. Le My Loan Phung that have been belonged to me and gave me helpful and sincere advice since I was a student up to now. I am also grateful to all MIEL team even if they did not directly supervise my thesis from Dr.

Antibiotics, 2021

Bacterial leaf blight, which is caused by Xanthomonas axonopodis pv. allii, annually causes signi... more Bacterial leaf blight, which is caused by Xanthomonas axonopodis pv. allii, annually causes significant yield losses to Welsh onion in many producing countries, including Vietnam. In this study, we isolated and characterized lytic phages Φ16, Φ17A and Φ31, specific to X. axonopodis pv. allii and belonging to a new phage species and genus within the Autographiviridae, from four provinces in the Mekong Delta of Vietnam. Moreover, we evaluated their efficacy for the biocontrol of leaf blight in greenhouse and field conditions. When applying the three highly related phages individually or as a three-phage cocktail at 108 PFU/mL in greenhouse conditions, our results show that treatment with Φ31 alone provides higher disease prevention than the two other phages or the phage cocktail. Furthermore, we compared phage concentrations from 105 to 108 and showed optimal disease control at 107 and 108 PFU/mL. Finally, under field conditions, both phage Φ31 alone and the phage cocktail treatments ...

Hue University Journal of Science: Natural Science, 2020

For the first time, a realistic microscopic calculation for low-energy neutron-nucleus elastic sc... more For the first time, a realistic microscopic calculation for low-energy neutron-nucleus elastic scattering off open-shell nuclei is carried out within the framework of particle-vibration coupling (PVC). In this study, the pairing correlations of the ground state are taken into account. The dependence of the angular distributions on the pairing gaps have been discussed.

Journal of virology, 1997

Retroviral gene transfer is widely used in experimental and human gene therapy applications. We h... more Retroviral gene transfer is widely used in experimental and human gene therapy applications. We have devised a novel method of generating high-titer retroviral producer cell lines based on the P1 bacteriophage recombinase system Cre-loxP. Incorporation of loxP sites flanking a Neo(r)-SVTK cassette in the proviral DNA allows excision of these selectable markers through expression of Cre recombinase after production of a high-titer producer cell line. The resultant producer line contains a single loxP site flanked by the viral long terminal repeats. Retransfection of this line with the Cre expression vector and a plasmid containing a gene of interest flanked by loxP sites allows insertional recombination of the gene into the favorable preexisting site in the genome and the generation of a new line with a titer equivalent to that of the parental producer cell line. The efficiency of the process is sufficient to allow the generation of multiple new producer lines without the addition of...

Background: The under-representation of Vietnamese ethnic groups in existing genetic databases an... more Background: The under-representation of Vietnamese ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in the population. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in Vietnam and many developing countries. Non-invasive prenatal testing (NIPT) data offers an alternative untapped resource to study genetic variations in the Vietnamese population. Results: We analyzed the low-coverage genomes of 2,683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially five pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency...

Journal of mathematical neuroscience, Jan 16, 2018

The Hopfield recurrent neural network is a classical auto-associative model of memory, in which c... more The Hopfield recurrent neural network is a classical auto-associative model of memory, in which collections of symmetrically coupled McCulloch-Pitts binary neurons interact to perform emergent computation. Although previous researchers have explored the potential of this network to solve combinatorial optimization problems or store reoccurring activity patterns as attractors of its deterministic dynamics, a basic open problem is to design a family of Hopfield networks with a number of noise-tolerant memories that grows exponentially with neural population size. Here, we discover such networks by minimizing probability flow, a recently proposed objective for estimating parameters in discrete maximum entropy models. By descending the gradient of the convex probability flow, our networks adapt synaptic weights to achieve robust exponential storage, even when presented with vanishingly small numbers of training patterns. In addition to providing a new set of low-density error-correcting...

SSRN Electronic Journal, 2016

Principal component analysis (PCA) is a widely used dimension reduction tool in the analysis of m... more Principal component analysis (PCA) is a widely used dimension reduction tool in the analysis of many kind of high-dimensional data. It is used in signal processing, mechanical ingeneering, psychometrics, and other fields under different names. It still bears the same mathematical idea: the decomposition of variation of a high dimensional object into uncorrelated factors or components. However, in many of the above applications, one is interested in capturing the tail variables of the data rather than variation around the mean. Such applications include weather related event curves, expected shortfalls, and speeding analysis among others. These are all high dimensional tail objects which one would like to study in a PCA fashion. The tail character though requires to do the dimension reduction in an asymmetric norm rather than the classical L 2-type orthogonal projection. We develop an analogue of PCA in an asymmetric norm. These norms cover both quantiles and expectiles, another tail event measure. The difficulty is that there is no natural basis, no 'principal components', to the k-dimensional subspace found. We propose two definitions of principal components and provide algorithms based on iterative least squares. We prove upper bounds on their convergence times, and compare their performances in a simulation study. We apply the algorithms to a Chinese weather dataset with a view to weather derivative pricing.

Cell reports, May 21, 2016

Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizoph... more Converging evidence indicates that microRNAs (miRNAs) may contribute to disease risk for schizophrenia (SZ). We show that microRNA-9 (miR-9) is abundantly expressed in control neural progenitor cells (NPCs) but also significantly downregulated in a subset of SZ NPCs. We observed a strong correlation between miR-9 expression and miR-9 regulatory activity in NPCs as well as between miR-9 levels/activity, neural migration, and diagnosis. Overexpression of miR-9 was sufficient to ameliorate a previously reported neural migration deficit in SZ NPCs, whereas knockdown partially phenocopied aberrant migration in control NPCs. Unexpectedly, proteomic- and RNA sequencing (RNA-seq)-based analysis revealed that these effects were mediated primarily by small changes in expression of indirect miR-9 targets rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes. Together, these data indicate that aberrant levels and activity of miR-9 ...

is an auto-associative, distributive model of neural memory storage and retrieval. A form of erro... more is an auto-associative, distributive model of neural memory storage and retrieval. A form of error-correcting code, the Hopfield network can learn a set of patterns as stable points of the network dynamic, and retrieve them from noisy inputs-thus Hopfield networks are their own decoders. Unlike in coding theory, where the information rate of a good code (in the Shannon sense) is finite but the cost of decoding does not play a role in the rate, the information rate of Hopfield networks trained with state-of-the-art learning algorithms is of the order log(n)/n, a quantity that tends to zero asymptotically with n, the number of neurons in the network. For specially constructed networks, the best information rate currently achieved is of order 1/ √ n. In this work, we design simple binary Hopfield networks that have asymptotically vanishing error rates at an information rate of 1/log(n). These networks can be added as the decoders of any neural code with noisy neurons. As an example, we apply our network to a binary neural decoder of the grid cell code to attain information rate 1/log(n). Hopfield networks | error-correcting codes | information theory | exponential capacity | grid cells | redundant number system

Canadian Oncology Nursing Journal, 2011

The Pivot Nurse in Oncology (PNO) is a health care professional dedicated to providing patients w... more The Pivot Nurse in Oncology (PNO) is a health care professional dedicated to providing patients with cancer and their families with continuing and consistent supportive care throughout the care trajectory. The purpose of this paper is to describe the variation and frequency of nursing interventions delivered by 12 PNOs at our health centre. An administrative analysis over a three-year period revealed a total of 43,906 interventions that were grouped into 10 categories. This analysis provided a description of the intervention frequency and these interventions were further collapsed into the four role functions of the PNO. Coordination/continuity of care and the assessment of needs and symptoms were identified as the dominant practice domains of the PNO in the professional cancer navigator role.

Journal of bacteriology, 2014

We previously reported that the presence of dideoxythymidine (ddT) in the growth medium selective... more We previously reported that the presence of dideoxythymidine (ddT) in the growth medium selectively inhibits the ability of bacteriophage T7 to infect Escherichia coli by inhibiting phage DNA synthese (N. Q. Tran, L. F. Rezende, U. Qimron, C. C. Richardson, and S. Tabor, Proc. Natl. Acad. Sci. U. S. A. 105:9373-9378, 2008, doi:10.1073/pnas.0804164105). In the presence of T7 gene 1.7 protein, ddT is taken up into the E. coli cell and converted to ddTTP. ddTTP is incorporated into DNA as ddTMP by the T7 DNA polymerase, resulting in chain termination. We have identified the pathway by which exogenous ddT is converted to ddTTP. The pathway consists of ddT transport by host nucleoside permeases and phosphorylation to ddTMP by the host thymidine kinase. T7 gene 1.7 protein phosphorylates ddTMP and ddTDP, resulting in ddTTP. A 74-residue peptide of the gene 1.7 protein confers ddT sensitivity to the same extent as the 196-residue wild-type gene 1.7 protein. We also show that cleavage of th...

Nucleic acids research, Jan 10, 2014

Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cel... more Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in different human cells. In this paper, the architectures of the 41 regulatory networks and the distributions of housekeeping and specific regulatory interactions are investigated. The TF regulatory networks of different human cell types demonstrate similar global three-layer (top, core and bottom) hierarchical architectures, which are greatly different from the yeast TF regulatory network. However, they have distinguishable local organizations, as suggested by the fact that wiring patterns of only a few TFs are enough to distinguish cell identities. The TF regulatory network of human embryonic stem cells (hESCs) is dense and enriched with interactions that are unseen in the ne...

Development (Cambridge, England), 2015

Screens in mosaic Drosophila tissues that use chemical mutagenesis have identified many regulator... more Screens in mosaic Drosophila tissues that use chemical mutagenesis have identified many regulators of growth and patterning. Many of the mutant phenotypes observed were contingent upon the presence of both wild-type and mutant cells in the same tissue. More recently, large collections of RNAi lines or cDNAs expressed under Gal4/UAS control have been used to alter gene expression uniformly in specific tissues. However, these newer approaches are not easily combined with the efficient generation of genetic mosaics. The CoinFLP system described here enables mosaic screens in the context of gene knockdown or overexpression by automatically generating a reliable ratio of mutant to wild-type tissue in a developmentally controlled manner. CoinFLP-Gal4 generates mosaic tissues composed of clones of which only a subset expresses Gal4. CoinFLP-LexGAD/Gal4 generates tissues composed of clones that express either Gal4 or LexGAD, thus allowing the study of interactions between different types of...

Proceedings of the 36th international ACM SIGIR conference on Research and development in information retrieval, 2013

As the volumes of AI problems involving human knowledge are likely to soar, crowdsourcing has bec... more As the volumes of AI problems involving human knowledge are likely to soar, crowdsourcing has become essential in a wide range of worldwide web applications. One of the biggest challenges of crowdsourcing is aggregating the answers collected from crowd workers; and thus, many aggregate techniques have been proposed. However, given a new application, it is difficult for users to choose the best-suited technique as well as appropriate parameter values since each of these techniques has distinct performance characteristics depending on various factors (e.g. worker expertise, question difficulty). In this paper, we develop a benchmarking tool that allows to (i) simulate the crowd and (ii) evaluate aggregate techniques in different aspects (accuracy, sensitivity to spammers, etc.). We believe that this tool will be able to serve as a practical guideline for both researchers and software developers. While researchers can use our tool to assess existing or new techniques, developers can reuse its components to reduce the development complexity.

Plant Signaling & Behavior, 2011

Schizophrenia Bulletin, 2012

although schizophrenia affects a number of brain regions and produces a range of clinical symptom... more although schizophrenia affects a number of brain regions and produces a range of clinical symptoms, we believe its origins lie at the level of single neurons and simple networks. owing to this, as well as to its high degree of heritability, we hypothesize that schizophrenia is amenable to cell-based studies in vitro. Using induced pluripotent stem cell-derived neurons and/or fibroblast-induced neurons, a limitless quantity of live human neurons can now be generated from patient skin biopsies. We predict that cell-based studies will ultimately contribute to our understanding of the molecular and cellular underpinnings of this debilitating disorder.

Review of Quantitative Finance and Accounting, 2010

Proceedings of the National Academy of Sciences, 2008

Bacteriophage T7 DNA polymerase efficiently incorporates dideoxynucleotides into DNA, resulting i... more Bacteriophage T7 DNA polymerase efficiently incorporates dideoxynucleotides into DNA, resulting in chain termination. Dideoxythymidine (ddT) present in the medium at levels not toxic to Escherichia coli inhibits phage T7. We isolated 95 T7 phage mutants that were resistant to ddT. All contained a mutation in T7 gene 1.7 , a nonessential gene of unknown function. When gene 1.7 was expressed from a plasmid, T7 phage resistant to ddT still arose; analysis of 36 of these mutants revealed that all had a single mutation in gene 5 , which encodes T7 DNA polymerase. This mutation changes tyrosine-526 to phenylalanine, which is known to increase dramatically the ability of T7 DNA polymerase to discriminate against dideoxynucleotides. DNA synthesis in cells infected with wild-type T7 phage was inhibited by ddT, suggesting that it resulted in chain termination of DNA synthesis in the presence of gene 1.7 protein. Overexpression of gene 1.7 from a plasmid rendered E. coli cells sensitive to ddT...

Nature, 2011

Schizophrenia (SCZD) is a debilitating neurological disorder with a worldwide prevalence of 1%; t... more Schizophrenia (SCZD) is a debilitating neurological disorder with a worldwide prevalence of 1%; there is a strong genetic component, with an estimated heritability of 80-85% 1. Though postmortem studies have revealed reduced brain volume, cell size, spine density and abnormal neural distribution in the prefrontal cortex and hippocampus of SCZD brain tissue 2 and neuropharmacological studies have implicated dopaminergic, glutamatergic and GABAergic activity in SCZD 3 , the cell types affected in SCZD and the molecular mechanisms underlying the disease state remain unclear. To elucidate the cellular and molecular defects of SCZD, we directly reprogrammed fibroblasts from SCZD patients into human induced pluripotent stem cells (hiPSCs) and subsequently differentiated these disorder-specific hiPSCs into neurons (SI Fig. 1). SCZD hiPSC neurons showed diminished neuronal connectivity in conjunction with decreased neurite number, PSD95-protein levels and glutamate receptor expression. Gene expression profiles of SCZD hiPSC neurons identified altered expression of many components of the cAMP and WNT signaling pathways. Key cellular and molecular elements of the SCZD phenotype were ameliorated following treatment of SCZD hiPSC neurons with the antipsychotic Loxapine. To date, hiPSC neuronal pathology has only been demonstrated in diseases characterized by both the loss of function of a single gene product and rapid disease progression in early childhood 4-6. We now report hiPSC neuronal phenotypes and gene expression changes associated with SCZD, a complex genetic psychiatric disorder (SI Table 1).