Microbe-induced activation of inflammatory cytokine response in human cells

Human body is in continuous contact with microbes. Although many microbes are harmless or beneficial for humans, pathogenic microbes possess a threat to wellbeing. Antimicrobial protection is provided by the immune system, which can be functionally divided into two parts, namely innate and adaptive immunity. The key players of the innate immunity are phagocytic white blood cells such as neutrophils, monocytes, macrophages and dendritic cells (DCs), which constantly monitor the blood and peripheral tissues. These cells are armed for rapid activation upon microbial contact since they express a variety of microbe-recognizing receptors. Macrophages and DCs also act as antigen presenting cells (APCs) and play an important role in the development of adaptive immunity. The development of adaptive immunity requires intimate cooperation between APCs and T lymphocytes and results in microbe-specific immune responses. Moreover, adaptive immunity generates immunological memory, which rapidly and efficiently protects the host from reinfection. Properly functioning immune system requires efficient communication between cells. Cytokines are proteins, which mediate intercellular communication together with direct cell-cell contacts. Immune cells produce inflammatory cytokines rapidly following microbial contact. Inflammatory cytokines modulate the development of local immune response by binding to cell surface receptors, which results in the activation of intracellular signalling and modulates target cell gene expression. One class of inflammatory cytokines chemokines has a major role in regulating cellular traffic. Locally produced inflammatory chemokines guide the recruitment of effector cells to the site of inflammation during microbial infection. In this study two key questions were addressed. First, the ability of pathogenic and non-pathogenic Gram-positive bacteria to activate inflammatory cytokine and chemokine production in different human APCs was compared. In these studies macrophages and DCs were stimulated with pathogenic Steptococcus pyogenes or non-pathogenic Lactobacillus rhamnosus. The second aim of this thesis work was to analyze the role of pro-inflammatory cytokines in the regulation of microbe-induced chemokine production. In these studies bacteria-stimulated macrophages and influenza A virus-infected lung epithelial cells were used as model systems. The results of this study show that although macrophages and DCs share several common antimicrobial functions, these cells have significantly distinct responses against pathogenic and non-pathogenic Gram-positive bacteria. Macrophages were activated in a nearly similar fashion by pathogenic S. pyogenes and non-pathogenic L. rhamnosus. Both bacteria induced the production of similar core set of inflammatory chemokines consisting of several CC-class chemokines and CXCL8. These chemokines attract monocytes, neutrophils, dendritic cells and T cells. Thus, the results suggest that bacteria-activated macrophages efficiently recruit other effector cells to the site of inflammation. Moreover, macrophages seem to be activated by all bacteria irrespective of their pathogenicity. DCs, in contrast, were efficiently activated only by pathogenic S. pyogenes, which induced DC maturation and production of several inflammatory cytokines and chemokines. In contrast, L. rhamnosus-stimulated DCs matured only partially and, most importantly, these cells did not produce inflammatory cytokines or chemokines. L. rhamnosus-stimulated DCs had a phenotype of "semi-mature" DCs and this type of DCs have been suggested to enhance tolerogenic adaptive immune responses. Since DCs have an essential role in the development of adaptive immune response the results suggest that, in contrast to macrophages, DCs may be able to discriminate between pathogenic and non-pathogenic bacteria and thus mount appropriate inflammatory or tolerogenic adaptive immune response depending on the microbe in question. The results of this study also show that pro-inflammatory cytokines can contribute to microbe-induced chemokine production at multiple levels. S. pyogenes-induced type I interferon (IFN) was found to enhance the production of certain inflammatory chemokines in macrophages during bacterial stimulation. Thus, bacteria-induced chemokine production is regulated by direct (microbe-induced) and indirect (pro-inflammatory cytokine-induced) mechanisms during inflammation. In epithelial cells IFN- and tumor necrosis factor- (TNF-) were found to enhance the expression of PRRs and components of cellular signal transduction machinery. Pre-treatment of epithelial cells with these cytokines prior to virus infection resulted in markedly enhanced chemokine response compared to untreated cells. In conclusion, the results obtained from this study show that pro-inflammatory cytokines can enhance microbe-induced chemokine production during microbial infection by providing a positive feedback loop. In addition, pro-inflammatory cytokines can render normally low-responding cells to high chemokine producers via enhancement of microbial detection and signal transduction.

Systems between information and knowledge : In a memory management model of an extended enterprise

The research question of this thesis was how knowledge can be managed with information systems. Information systems can support but not replace knowledge management. Systems can mainly store epistemic organisational knowledge included in content, and process data and information. Certain value can be achieved by adding communication technology to systems. All communication, however, can not be managed. A new layer between communication and manageable information was named as knowformation. Knowledge management literature was surveyed, together with information species from philosophy, physics, communication theory, and information system science. Positivism, post-positivism, and critical theory were studied, but knowformation in extended organisational memory seemed to be socially constructed. A memory management model of an extended enterprise (M3.exe) and knowformation concept were findings from iterative case studies, covering data, information and knowledge management systems. The cases varied from groups towards extended organisation. Systems were investigated, and administrators, users (knowledge workers) and managers interviewed. The model building required alternative sets of data, information and knowledge, instead of using the traditional pyramid. Also the explicit-tacit dichotomy was reconsidered. As human knowledge is the final aim of all data and information in the systems, the distinction between management of information vs. management of people was harmonised. Information systems were classified as the core of organisational memory. The content of the systems is in practice between communication and presentation. Firstly, the epistemic criterion of knowledge is not required neither in the knowledge management literature, nor from the content of the systems. Secondly, systems deal mostly with containers, and the knowledge management literature with applied knowledge. Also the construction of reality based on the system content and communication supports the knowformation concept. Knowformation belongs to memory management model of an extended enterprise (M3.exe) that is divided into horizontal and vertical key dimensions. Vertically, processes deal with content that can be managed, whereas communication can be supported, mainly by infrastructure. Horizontally, the right hand side of the model contains systems, and the left hand side content, which should be independent from each other. A strategy based on the model was defined.

RAPID HUMAN ACTION RECOGNITION IN H.264/AVC COMPRESSED DOMAIN FOR VIDEO SURVEILLANCE

This paper discusses a novel high-speed approach for human action recognition in H. 264/AVC compressed domain. The proposed algorithm utilizes cues from quantization parameters and motion vectors extracted from the compressed video sequence for feature extraction and further classification using Support Vector Machines (SVM). The ultimate goal of our work is to portray a much faster algorithm than pixel domain counterparts, with comparable accuracy, utilizing only the sparse information from compressed video. Partial decoding rules out the complexity of full decoding, and minimizes computational load and memory usage, which can effect in reduced hardware utilization and fast recognition results. The proposed approach can handle illumination changes, scale, and appearance variations, and is robust in outdoor as well as indoor testing scenarios. We have tested our method on two benchmark action datasets and achieved more than 85% accuracy. The proposed algorithm classifies actions with speed (>2000 fps) approximately 100 times more than existing state-of-the-art pixel-domain algorithms.

A study on fear memory retrieval and REM sleep in maternal separation and isolation stressed rats

As rapid brain development occurs during the neonatal period, environmental manipulation during this period may have a significant impact on sleep and memory functions. Moreover, rapid eye movement (REM) sleep plays an important role in integrating new information with the previously stored emotional experience. Hence, the impact of early maternal separation and isolation stress (MS) during the stress hyporesponsive period (SHRP) on fear memory retention and sleep in rats were studied. The neonatal rats were subjected to maternal separation and isolation stress during postnatal days 5-7 (6 h daily/3 d). Polysomnographic recordings and differential fear conditioning was carried out in two different sets of rats aged 2 months. The neuronal replay during REM sleep was analyzed using different parameters. MS rats showed increased time in REM stage and total sleep period also increased. MS rats showed fear generalization with increased fear memory retention than normal control (NC). The detailed analysis of the local field potentials across different time periods of REM sleep showed increased theta oscillations in the hippocampus, amygdala and cortical circuits. Our findings suggest that stress during SHRP has sensitized the hippocampus amygdala cortical loops which could be due to increased release of corticosterone that generally occurs during REM sleep. These rats when subjected to fear conditioning exhibit increased fear memory and increased, fear generalization. The development of helplessness, anxiety and sleep changes in human patients, thus, could be related to the reduced thermal, tactile and social stimulation during SHRP on brain plasticity and fear memory functions. (C) 2014 Elsevier B.V. All rights reserved.

Human action recognition in H.264/AVC compressed domain using meta-cognitive radial basis function network

In this paper, we propose a H.264/AVC compressed domain human action recognition system with projection based metacognitive learning classifier (PBL-McRBFN). The features are extracted from the quantization parameters and the motion vectors of the compressed video stream for a time window and used as input to the classifier. Since compressed domain analysis is done with noisy, sparse compression parameters, it is a huge challenge to achieve performance comparable to pixel domain analysis. On the positive side, compressed domain allows rapid analysis of videos compared to pixel level analysis. The classification results are analyzed for different values of Group of Pictures (GOP) parameter, time window including full videos. The functional relationship between the features and action labels are established using PBL-McRBFN with a cognitive and meta-cognitive component. The cognitive component is a radial basis function, while the meta-cognitive component employs self-regulation to achieve better performance in subject independent action recognition task. The proposed approach is faster and shows comparable performance with respect to the state-of-the-art pixel domain counterparts. It employs partial decoding, which rules out the complexity of full decoding, and minimizes computational load and memory usage. This results in reduced hardware utilization and increased speed of classification. The results are compared with two benchmark datasets and show more than 90% accuracy using the PBL-McRBFN. The performance for various GOP parameters and group of frames are obtained with twenty random trials and compared with other well-known classifiers in machine learning literature. (C) 2015 Elsevier B.V. All rights reserved.

Compressed domain human action recognition in H.264/AVC video streams

This paper discusses a novel high-speed approach for human action recognition in H.264/AVC compressed domain. The proposed algorithm utilizes cues from quantization parameters and motion vectors extracted from the compressed video sequence for feature extraction and further classification using Support Vector Machines (SVM). The ultimate goal of the proposed work is to portray a much faster algorithm than pixel domain counterparts, with comparable accuracy, utilizing only the sparse information from compressed video. Partial decoding rules out the complexity of full decoding, and minimizes computational load and memory usage, which can result in reduced hardware utilization and faster recognition results. The proposed approach can handle illumination changes, scale, and appearance variations, and is robust to outdoor as well as indoor testing scenarios. We have evaluated the performance of the proposed method on two benchmark action datasets and achieved more than 85 % accuracy. The proposed algorithm classifies actions with speed (> 2,000 fps) approximately 100 times faster than existing state-of-the-art pixel-domain algorithms.

Biochemical and Behavioral Evaluation of Human MAPT Mutations in Transgenic Drosophila melanogaster

Mutations in the human microtubule-associated protein tau (hMAPT) gene including R406W and V337M result in autosomal dominant neurodegenerative disorder. These mutations lead to hyperphosphorylation and aggregation of Tau protein which is a known genetic factor underlying development of Alzheimer's disease (AD). In the present study, transgenic Drosophila models of AD expressing wild-type and mutant forms of hMAPT exhibit a progressive neurodegeneration which was manifested in the form of early death and impairment of cognitive ability. Moreover, they were also found to have significantly decreased activity of neurotransmitter enzymes accompanied by decreased cellular endogenous antioxidant profile. The extent of neurodegeneration, memory impairment, and biochemical profiles was different in the tau transgenic strains which indicate multiple molecular and cellular responses underlie each particular form of hMAPT.

Birth Weight, Working Memory and Epigenetic Signatures in IGF2 and Related Genes: A MZ Twin Study

Neurodevelopmental disruptions caused by obstetric complications play a role in the etiology of several phenotypes associated with neuropsychiatric diseases and cognitive dysfunctions. Importantly, it has been noticed that epigenetic processes occurring early in life may mediate these associations. Here, DNA methylation signatures at IGF2 (insulin-like growth factor 2) and IGF2BP1-3 (IGF2-binding proteins 1-3) were examined in a sample consisting of 34 adult monozygotic (MZ) twins informative for obstetric complications and cognitive performance. Multivariate linear regression analysis of twin data was implemented to test for associations between methylation levels and both birth weight (BW) and adult working memory (WM) performance. Familial and unique environmental factors underlying these potential relationships were evaluated. A link was detected between DNA methylation levels of two CpG sites in the IGF2BP1 gene and both BW and adult WM performance. The BW-IGF2BP1 methylation association seemed due to non-shared environmental factors influencing BW, whereas the WM-IGF2BP1 methylation relationship seemed mediated by both genes and environment. Our data is in agreement with previous evidence indicating that DNA methylation status may be related to prenatal stress and later neurocognitive phenotypes. While former reports independently detected associations between DNA methylation and either BW or WM, current results suggest that these relationships are not confounded by each other.

Recent origin of a hominoid-specific splice form of neuropsin, a gene involved in learning and memory

Neuropsin is a secreted-type serine protease involved in learning and memory. The type II splice form of neuropsin is abundantly expressed in the human brain but not in the mouse brain. We sequenced the type II-spliced region of neuropsin gene in humans and representative nonhuman primate species. Our comparative sequence analysis showed that only the hominoid species (humans and apes) have the intact open reading frame of the type II splice form, indicating that the type II neuropsin originated recently in the primate lineage about 18 MYA. Expression analysis using RT-PCR detected abundant expression of the type II form in the frontal lobe of the adult human brain, but no expression was detected in the brains of lesser apes and Old World monkeys, indicating that the type II form of neuropsin only became functional in recent time, and it might contribute to the progressive change of cognitive abilities during primate evolution.

Increasing top-down suppression from prefrontal cortex facilitates tactile working memory

Navigated transcranial magnetic stimulation (TMS) combined with diffusion-weighted magnetic resonance imaging (DW-MRI) and tractography allows investigating functional anatomy of the human brain with high precision. Here we demonstrate that working memory (WM) processing of tactile temporal information is facilitated by delivering a single TMS pulse to the middle frontal gyrus (MFG) during memory maintenance. Facilitation was obtained only with a TMS pulse applied to a location of the MFG with anatomical connectivity to the primary somatosensory cortex (S1). TMS improved tactile WM also when distractive tactile stimuli interfered with memory maintenance. Moreover, TMS to the same MFG site attenuated somatosensory evoked responses (SEPs). The results suggest that the TMS-induced memory improvement is explained by increased top-down suppression of interfering sensory processing in S1 via the MFG-S1 link. These results demonstrate an anatomical and functional network that is involved in maintenance of tactile temporal WM. (C) 2009 Elsevier Inc. All rights reserved.

Variability in encoding precision accounts for visual short-term memory limitations.

It is commonly believed that visual short-term memory (VSTM) consists of a fixed number of "slots" in which items can be stored. An alternative theory in which memory resource is a continuous quantity distributed over all items seems to be refuted by the appearance of guessing in human responses. Here, we introduce a model in which resource is not only continuous but also variable across items and trials, causing random fluctuations in encoding precision. We tested this model against previous models using two VSTM paradigms and two feature dimensions. Our model accurately accounts for all aspects of the data, including apparent guessing, and outperforms slot models in formal model comparison. At the neural level, variability in precision might correspond to variability in neural population gain and doubly stochastic stimulus representation. Our results suggest that VSTM resource is continuous and variable rather than discrete and fixed and might explain why subjective experience of VSTM is not all or none.

Contingency awareness in human aversive conditioning involves the middle frontal gyrus.

In contrast to the wealth of data describing the neural mechanisms underlying classical conditioning, we know remarkably little about the mechanisms involved in acquisition of explicit contingency awareness. Subjects variably acquire contingency awareness in classical conditioning paradigms, in which they are able to describe the temporal relationship between a conditioned cue and its outcome. Previous studies have implicated the hippocampus and prefrontal cortex in the acquisition of explicit knowledge, although their specific roles remain unclear. We used functional magnetic resonance imaging to track the trial-by-trial acquisition of explicit knowledge in a concurrent trace and delay conditioning paradigm. We show that activity in bilateral middle frontal gyrus and parahippocampal gyrus correlates with the accuracy of explicit contingency awareness on each trial. In contrast, amygdala activation correlates with conditioned responses indexed by skin conductance responses (SCRs). These results demonstrate that brain regions known to be involved in other aspects of learning and memory also play a specific role, reflecting on each trial the acquisition and representation of contingency awareness.

A time-varying controllable fault-tolerant field associative memory model and its simulation

A time-varying controllable fault-tolerant field associative memory model and the realization algorithms are proposed. On the one hand, this model simulates the time-dependent changeability character of the fault-tolerant field of human brain's associative memory. On the other hand, fault-tolerant fields of the memory samples of the model can be controlled, and we can design proper fault-tolerant fields for memory samples at different time according to the essentiality of memory samples. Moreover, the model has realized the nonlinear association of infinite value pattern from n dimension space to m dimension space. And the fault-tolerant fields of the memory samples are full of the whole real space R-n. The simulation shows that the model has the above characters and the speed of associative memory about the model is faster.

A river of memory: landscape, narrative and identity in the Lee Valley, Co. Cork, Ireland

In moments of rapid social changes, as has been witnessed in Ireland in the last decade, the conditions through which people engage with their localities though memory, individually and collectively, remains an important cultural issue with key implications for questions of heritage, preservation and civic identity. In recent decades, cultural geographers have argued that landscape is more than just a view or a static text of something symbolic. The emphasis seems to be on landscape as a dynamic cultural process – an ever-evolving process being constructed and re-constructed. Hence, landscape seems to be a highly complex term that carries many different meanings. Material, form, relationships or actions have different meanings in different settings. Drawing upon recent and continuing scholarly debates in cultural landscapes and collective memory, this thesis sets out to examine the generation of collective memory and how it is employed as a cultural tool in the production of memory in the landscape. More specifically, the research considers the relationships between landscape and memory, investigating the ways in which places are produced, appropriated, experienced, sensed, acknowledged, imagined, yearned for, appropriated, re-appropriated, contested and identified with. A polyvocal-bricoleur approach aims to get below the surface of a cultural landscape, inject historical research and temporal depth into cultural landscape studies and instil a genuine sense of inclusivity of a wide variety of voices (role of monuments and rituals and voices of people) from the past and present. The polyvocal-bricoleur approach inspires a mixed method methodology approach to fieldsites through archival research, fieldwork and filmed interviews. Using a mixture of mini-vignettes of place narratives in the River Lee valley in the south of Ireland, the thesis explores a number of questions on the fluid nature of narrative in representing the story and role of the landscape in memory-making. The case studies in the Lee Valley are harnessed to investigate the role of the above questions/ themes/ debates in the act of memory making at sites ranging from an Irish War of Independence memorial to the River Lee’s hydroelectric scheme to the valley’s key religious pilgrimage site. The thesis investigates the idea that that the process of landscape extends not only across space but also across time – that the concept of historical continuity and the individual and collective human engagement and experience of this continuity are central to the processes of remembering on the landscape. In addition the thesis debates the idea that the production of landscape is conditioned by several social frames of memory – that individuals remember according to several social frames that give emphasis to different aspects of the reality of human experience. The thesis also reflects on how the process of landscape is represented by those who re-produce its narratives in various media.

Analysis of memory B cell responses and isolation of novel monoclonal antibodies with neutralizing breadth from HIV-1-infected individuals.

BACKGROUND: The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. METHODS AND FINDINGS: We immortalized IgG(+) memory B cells from individuals infected with diverse clades of HIV-1 and selected on the basis of plasma neutralization profiles that were cross-clade and relatively potent. Culture supernatants were screened using various recombinant forms of the envelope glycoproteins (Env) in multiple parallel assays. We isolated 58 mAbs that were mapped to different Env surfaces, most of which showed neutralizing activity. One mAb in particular (HJ16) specific for a novel epitope proximal to the CD4 binding site on gp120 selectively neutralized a multi-clade panel of Tier-2 HIV-1 pseudoviruses, and demonstrated reactivity that was comparable in breadth, but distinct in neutralization specificity, to that of the other CD4 binding site-specific neutralizing mAb b12. A second mAb (HGN194) bound a conserved epitope in the V3 crown and neutralized all Tier-1 and a proportion of Tier-2 pseudoviruses tested, irrespective of clade. A third mAb (HK20) with broad neutralizing activity, particularly as a Fab fragment, recognized a highly conserved epitope in the HR-1 region of gp41, but showed striking assay-dependent selectivity in its activity. CONCLUSIONS: This study reveals that by using appropriate screening methods, a large proportion of memory B cells can be isolated that produce mAbs with HIV-1 neutralizing activity. Three of these mAbs show unusual breadth of neutralization and therefore add to the current panel of HIV-1 neutralizing antibodies with potential for passive protection and template-based vaccine design.