Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth

Co-infections alter the host immune response but how the systemic and local processes at the site of infection interact is still unclear. The majority of studies on co-infections concentrate on one of the infecting species, an immune function or group of cells and often focus on the initial phase of the infection. Here, we used a combination of experiments and mathematical modelling to investigate the network of immune responses against single and co-infections with the respiratory bacterium Bordetella bronchiseptica and the gastrointestinal helminth Trichostrongylus retortaeformis. Our goal was to identify representative mediators and functions that could capture the essence of the host immune response as a whole, and to assess how their relative contribution dynamically changed over time and between single and co-infected individuals. Network-based discrete dynamic models of single infections were built using current knowledge of bacterial and helminth immunology; the two single infection models were combined into a co-infection model that was then verified by our empirical findings. Simulations showed that a T helper cell mediated antibody and neutrophil response led to phagocytosis and clearance of B. bronchiseptica from the lungs. This was consistent in single and co-infection with no significant delay induced by the helminth. In contrast, T. retortaeformis intensity decreased faster when co-infected with the bacterium. Simulations suggested that the robust recruitment of neutrophils in the co-infection, added to the activation of IgG and eosinophil driven reduction of larvae, which also played an important role in single infection, contributed to this fast clearance. Perturbation analysis of the models, through the knockout of individual nodes (immune cells), identified the cells critical to parasite persistence and clearance both in single and co-infections. Our integrated approach captured the within-host immuno-dynamics of bacteria-helminth infection and identified key components that can be crucial for explaining individual variability between single and co-infections in natural populations.
The use of storytelling to make sense of painful life events : implications for clinical practice in counselling psychology

The aim of this study is to explore how individuals with an acquired facial disfigurement (FD), following a traumatic accident or illness, psychologically reconstruct themselves using a narrative analysis. Whilst previous studies on visible difference have employed both quantitative and qualitative based methodologies, there is only a handful of research in the psychological literature that specifically explores the subjective experience of people with facial cancer and facial trauma. In particular, there is a lack of attention on how this population reconstruct their internal world and make sense of their FD. Narrative analysis was used as a way of gaining an insight into the ways that these individuals reconstruct themselves and make meaning of their disfigurement. Thus, a sample size of seven individuals who had acquired a disfigurement either as a result of an accident or facial/oral cancer took part. Participants were interviewed using semi-structured interviews. Findings revealed the following narrative genres: 'the outsider', 'the helpless prisoner', and 'the wounded survivor'. In the genre of 'the outsider', participants presented themselves as vulnerable and submissive protagonists who were humiliated, persecuted, and ostracised from the rest of society. The genre of 'the outsider' demonstrates how the consequences of living with a FD and of being a constant victim of social disgrace can leave a profound impact upon one's sense of self and identity. In the genre of 'the helpless prisoner' protagonists shared their stories of living a restricted life and their stories were characterised by stagnation, helplessness, and a sense of isolation. Finally, in the genre of 'the wounded survivor', protagonists portrayed their lives as a series of challenges that provided them with an opportunity for growth, acceptance, and compassion. The findings of this study are put in the context of counselling psychology and clinical implications are discussed.
Improved Efficiency in the Analysis of Phased Mission Systems With Multiple Failure Mode Components

Systems often operate in phased missions where their reliability structure varies over a set of consecutive time periods, known as phases. The reliability of a phased mission is defined as the probability that all phases in the mission are completed without failure. While the Binary Decision Diagram (BDD) method has been shown to be the most efficient solution for measuring the reliability of phased missions with non-repairable components with mutually exclusive failure modes, the existing BDD based methods are still unable to analyze large systems without considerable computational expense. This paper introduces a new BDD based method that is shown to provide improved efficiency and accuracy in the repeat analysis of this type of phased mission.
Methods for Emulation of Multi-core CPU Performance

When validating or evaluating real distributed applications, it is useful to be able to test the application in a large range of environments. In that context, emulation of CPU performance enables researchers to investigate how the performance of the application is affected by the performance of the participating CPUs. Using a homogeneous cluster of fast multi-core nodes, it is therefore possible to evaluate how an application would behave on a heterogeneous set of nodes, with varying performance and number of cores. In this paper, three new methods for the emulation of CPU performance in the multi-core case are proposed: Fracas, CPU-Gov, and CPU-Hogs. Fracas relies on smart configuration of the Linux scheduler to achieve the desired emulation, CPU-Gov leverages the hardware CPU frequency scaling, and CPU-Hogs is a multi-core implementation of a CPU burner. These methods are compared and evaluated together with existing methods, with a set of micro-benchmarks, and show significant improvements over state-of-the-art solutions.
Data Handover Scheme with Weighted Mean N for Lifetime Enhancement in Wireless Sensor Networks

Wireless Sensor Networks being limited energy source, it must function in energy efficient manner to increase the net lifetime of the network i.e. gathering more information for a longer period from the area sensed [1]. Because of limited battery charge, bandwidth and nodes in the transmission range direct communication between sensing nodes to the sink is not a optimal solution for both bandwidth and energy point of view. While the LEACH protocol [2] is used as randomizing cluster heads for equal energy dissemination, the PEGASIS protocol [3] uses a chain of cluster heads participating in different rounds for transmitting data to the base station. As the base station can locate at any distances from the individual nodes, in spite of randomization and chain of cluster heads formation, each node actually dissipates a different amount of energy during its turn of transmission to the base station. DHS takes out this energy difference by data handover in specific cycles through suitable node pairing. But the main limitation of this scheme is its inapplicability to networks with large number of nodes due to the huge amount of computations, in LCMs as proposed in [6], to be carried out for determining the cycle in which a particular pair of nodes should execute a handover. This might time as well as energy consuming. Also, the expanse of self-energy in handover depending on the distance between participating nodes will become considerable if too many handovers take place. In this paper, we propose DHS-with-mean, according to which, all the nodes handover in the same mean cycle, thereby eliminating LCMs, and reducing the complexity of the computations remarkably. Also, we have proposed half DHS with mean, in which not all but only 50% of the nodes execute handovers. Finally, we have proposed 10% DHS-we have experimented with the percentage of nodes participating in handover and have found 10% to be the optimal percentage of nodes to be participating in handover for achieving the maximum network lifetime. Extensive simulations show half DHS gives on the average 3.15%, 5.52%, 3.6% and 6.03% improvement in network lifetime over and above the 10%, 12%, 17%, and 20% improvement achieved by DWeMen alone on PEGASIS, the binary model, LEACH and the direct scheme respectively. Moreover, 10% DHS achieves a further 3.15% and 4.88% improvement over half DHS, in case of PEGASIS and binary model respectively. It thus presents a near optimal solution for equal energy dissipation enhancing network lifetime, for any number of nodes
Improved Heuristics for Partitioned Multiprocessor Scheduling Based on Rate-Monotonic Small-Tasks

Graphics processing units (GPUs) are becoming increasingly important in today’s platforms as their increased generality allows for them to be used as powerful co-processors. In previous work, we have found that GPUs may be integrated into real-time systems through the treatment of GPUs as shared resources, allocated to real-time tasks through mutual exclusion locking protocols. In this paper, we present an optimal k-exclusion locking protocol for globally-scheduled job-level static-priority (JLSP) systems. This protocol may be used to manage a pool of GPU resources in such systems.
Genome-Wide and Species-Wide In Silico Screening for Intragenic MicroRNAs in Human, Mouse and Chicken

MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) involved in regulation of gene expression. Intragenic miRNAs, especially those exhibiting a high degree of evolutionary conservation, have been shown to be coordinately regulated and/or expressed with their host genes, either with synergistic or antagonistic correlation patterns. However, the degree of cross-species conservation of miRNA/host gene co-location is not known and co-expression information is incomplete and fragmented among several studies. Using the genomic resources (miRBase and Ensembl) we performed a genome-wide in silico screening (GWISS) for miRNA/host gene pairs in three well-annotated vertebrate species: human, mouse, and chicken. Approximately half of currently annotated miRNA genes resided within host genes: 53.0% (849/1,600) in human, 48.8% (418/855) in mouse, and 42.0% (210/499) in chicken, which we present in a central publicly available Catalog of intragenic miRNAs (http://www.integratomics-time.com/miR-host/catalog). The miRNA genes resided within either protein-coding or ncRNA genes, which include long intergenic ncRNAs (lincRNAs) and small nucleolar RNAs (snoRNAs). Twenty-seven miRNA genes were found to be located within the same host genes in all three species and the data integration from literature and databases showed that most (26/27) have been found to be co-expressed. Particularly interesting are miRNA genes located within genes encoding for miRNA silencing machinery (DGCR8, DICER1, and SND1 in human and Cnot3, Gdcr8, Eif4e, Tnrc6b, and Xpo5 in mouse). We furthermore discuss a potential for phenotype misattribution of miRNA host gene polymorphism or gene modification studies due to possible collateral effects on miRNAs hosted within them. In conclusion, the catalog of intragenic miRNAs and identified 27 miRNA/host gene pairs with cross-species conserved co-location, co-expression, and potential co-regulation, provide excellent candidates for further functional annotation of intragenic miRNAs in health and disease.
The IST METRA project

This article summarizes the main achievements of the Multi-Element Transmit and Receive Antennas (METRA) Project, an IST research and technological development project carried out between January 2000 and June 2001 by Universitat Politecnica de Catalunya, the Center for Personkommunikation of Aalborg University, Nokia Networks, Nokia Mobile Phones, and Vodafone Group Research and Development. The main objective of METRA was the performance evaluation of multi-antenna terminals in combination with adaptive antennas at the base station in UMTS communication systems. A MIMO channel sounder was developed that provided realistic multi-antenna channel measurements. Using these measured data, stochastic channel models were developed and properly validated. These models were also evaluated in order to estimate their corresponding channel capacity. Different MIMO configurations and processing schemes were developed for both the FDD and TDD modes of UTRA, and their link performance was assessed. Performance evaluation was completed by system simulations that illustrated the benefits of MIMO configurations to the network operator. Implementation cost vs. performance improvement was also covered by the project, including the base station and terminal manufacturer and network operator viewpoints. Finally, significant standards contributions were generated by the project and presented to the pertinent 3GPP working groups.
The Effect of One Bout Endurance And Acute Exercise on HSP 70 in Female

Introduction Excessive exercise will damage in peripheral leukocytes. The moderate stress in form of regular exercise/training may have protective effects against damage. Up-regulation complex regulation of repair systems such as heat shock proteins (HSP70) are seen in response to training and exercise. Modulation of the repair response may be mechanisms by which exercise can beneficially influence our health. The aim of this study was to examine the effect of two types training (endurance and acute) on HSP70 expression. Methodology 20 training female taking part in the intervention volunteered to give blood samples. Subjects were divided two groups, endurance training: with mean age of 23.1±1.4 years, height 159±4.13 cm and weight 59±1.3 Kg. and acute training: with mean age of 21.4±1.8 years, height 161±1.43 cm and weight 57±3.2 Kg. Blood samples were collected from the left hand anticubital vein before and immediately after exercise.Then plasma HSP 70 was analyzed. Data are reported as means ± standard error (SE). Student\'s paired t test and ANOVA was used to assess differences within groups (baseline and after follow-up). Results HSP70 expressions were measured before and after one bout endurance and acute training. Endurance and acute training increased significantly HSP70. These findings demonstrate that prolonged and exhaustion training can induce enhancement of HSP70 expression. Conclusion and discussion. The data presented show that human skeletal muscle responds to the stress of a single period of aerobic and acute exercise by up regulating expression of HSP70. This Proteins are cytoprotective. In addition, an increased content of HSP70 will facilitate any cellular remodeling, which is known to occur after unaccustomed exercise. So the metabolic changes caused by exercise are similar to induce stress protein synthesis. Physical exercise can elevate core temperature and muscle temperatures. It is possible the HSP 70 response to exercise in relation to the tissue assayed (skeletal muscle, lymphocyte, venous, arterial serum). The expression pattern of HSP70 due to training status may be attributed to adaptive mechanisms. The differences observed when HSP70 in the present study may be related to the mode of exercise and the amount of protein damage associated wit the exercise.
Fault-tolerant Routing based on Routing Capabilities in a Hyper-Star Graph

A hyper-star graphHS(n,k) provides a promising topology for interconnection networks of parallel processing systems because it inherits the advantages of a hypercube and a star graph. In this paper, wefocuson fault-tolerant routing in anHS(n,k) graphwith faulty nodes andproposean algorithm to establish a fault-free path between a pair of non-faulty nodes. The algorithm uses limited global information called routing capabilities. Though routing capabilities were originally invented for a hypercube, we extend their notion so that they can be applied to an HS(n,k) graph, which is asymmetric. We have proved that the time complexity to calculate routing capabilities with respect to all the distances at each node isO(n2). In addition, we present the results of a computer experiment to verify that our algorithm attains high reachability to the destination nodes.
Obsessive-compulsive symptoms in Parkinson's disease

To systematically investigate obsessive-compulsive traits in Parkinson's disease, patients were administered the Maudsley obsessional-compulsive inventory (MOCI) and a modification of the Leyton obsessional inventory (LOI) to a sample of non-demented and non-depressed patients with Parkinson's disease. Patients with severe Parkinson's disease showed more obsessive traits than normal controls in MOCI and LOI total scores, and in the “checking”, “doubting”, and “cleaning” subscales of the MOCI. By contrast, patients with mild disease did not differ from controls. A significant correlation was found between severity and duration of illness and MOCI total score. These results support the involvement of basal ganglia in obsessive-compulsive symptomatology. As patients with mild Parkinson's disease did not differ from controls, obsessive-compulsive disorder does not seem to be directly related to the initial nigrostriatal dopaminergic deficiency which causes clinical Parkinson's disease symptomatology. The appearance of obsessive symptoms could be related to the subset of neurochemical changes taking place at the level of the basal ganglia circuitry as disease progresses.
Geometric Complexity Theory: Introduction

These are lectures notes for the introductory graduate courses on geometric complexity theory (GCT) in the computer science department, the university of Chicago. Part I consists of the lecture notes for the course given by the first author in the spring quarter, 2007. It gives introduction to the basic structure of GCT. Part II consists of the lecture notes for the course given by the second author in the spring quarter, 2003. It gives introduction to invariant theory with a view towards GCT. No background in algebraic geometry or representation theory is assumed. These lecture notes in conjunction with the article \cite{GCTflip1}, which describes in detail the basic plan of GCT based on the principle called the flip, should provide a high level picture of GCT assuming familiarity with only basic notions of algebra, such as groups, rings, fields etc.
The Experimental Manipulation of Visual Cortex

The visual cortex is part of the occipital cortex that makes up the primary and secondary visual areas [1,2]. In the primary visual areas of rodents, as in other isocortical areas, two main neuronal types are present: inhibitory interneurons and projecting neurons [3,4]. The inhibitory interneurons belong to several GABAergic subpopulations, while the projection neurons are excitatory pyramidal neurons that are classically distributed in 5 layers, each of which is associated with a preferential projection area [3,4]. Accordingly, the pyramidal neurons of layers II, III and IV give rise to corticocortical connections, while those of layers V and VI project to subcortical structures. In the primary visual cortex pyramidal neurons of layer V project to superficial collicular layers and they give rise to collaterals that project to the pontine nuclei.
Three-capital approach to the study of young people who excel in vocational occupations: A case of WorldSkills competitors and entrepreneurship

This paper examines the entrepreneurial inclinations of young people who achieved excellence in vocational occupations. We propose a three-capital approach to the study of entrepreneurship. Relying on the existing theories and original qualitative and quantitative data analyses, findings from interviews with 30 entrepreneurial and 10 non-entrepreneurial WorldSkills competitors show that psychological capital, social capital and human capital can be combined to explore how young people who excel in vocational occupations develop entrepreneurial mindsets. We show that training for and participation in the largest vocational skills event globally - WorldSkills competition - develops selected aspects of three capitals. However, we also discover that the entrepreneurial motivation precedes competitors' involvement with WorldSkills.
SOC and SOH estimation for Li-ion batteries based on an equivalent hydraulic model. Part I: SOC and surface concentration estimation

Accurate state-of-charge (SOC) and state-of-health (SOH) estimation is critical to ensure a reliable battery-management system (BMS). This problem is addressed here by resorting to a grey box battery model based on the so-called equivalent hydraulic model (EHM). It allows taking into account in a simple way the difference between bulk concentration and critical surface concentration (CSC) at the anode, which turns out to be significant. The dynamic model is coupled with an output equation based on the Butler-Volmer equation, and the state and parameter of the resulting nonlinear dynamic system are estimated through an extended Kalman filter (EKF). Sufficient conditions for the stability of the EKF are analysed. Finally, the results show that the method provides accurate SOC and CSC. It is shown to outperform two recently proposed approaches for CSC estimation in the considered simulation study. The CSC estimate is used in the companion paper in order to estimate the diffusion coefficient of lithium through the electrode and hence deduce a SOH indicator.
Ualitative Ase E*

We describe an envisionment-based qualitative simulation program. The program implements part of an axiomatic, first order theory that has been developed to represent and reason about space and time. Topological information from the modelled domain is expressed as sets of distinct topological relations holding between sets of objects. These form the qualitative states in the underlying theory and simulation. Processes in the theory are represented as paths in the envisionment tree. The algorithm is illustrated with an example of a simulation of phagocytosis and exocytosis two processes used by unicellular organisms for garnering food and expelling waste material respectively.