Miracle-dz/UniFAR-FTUs huggingface dataset:
miRNA array screening reveals cooperative MGMT-regulation between miR-181d-5p and miR-409-3p in glioblastoma

The levels of expression of O6-methylguanine-DNA methyltransferase (MGMT) are relevant in predicting the response to the alkylating chemotherapy in patients affected by glioblastoma. MGMT promoter methylation and the published MGMT regulating microRNAs (miRNAs) do not completely explain the expression pattern of MGMT in clinical glioblastoma specimens. Here we used a genome-wide microarray-based approach to identify MGMT regulating miRNAs. Our screen unveiled three novel MGMT regulating miRNAs, miR-127-3p, miR-409-3p, and miR-124-3p, in addition to the previously identified miR-181d-5p. Transfection of these three novel miRNAs into the T98G glioblastoma cell line suppressed MGMT mRNA and protein expression. However, their MGMT- suppressive effects are 30–50% relative that seen with miR-181d-5p transfection. In silico analyses of The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) revealed that miR-181d-5p is the only miRNA that consistently exhibited inverse correlation with MGMT mRNA expression. However, statistical models incorporating both miR-181d-5p and miR-409-3p expression better predict MGMT expression relative to models involving either miRNA alone. Our results confirmed miR-181d-5p as the key MGMT-regulating miRNA. Other MGMT regulating miRNAs, including the miR-409-3p identified in this report, modify the effect of miR-181d-5p on MGMT expression. MGMT expression is, thus, regulated by cooperative interaction between key MGMT-regulating miRNAs.
From Models to Crop Species: Caveats and Solutions for Translational Metabolomics

Although plant metabolomics is largely carried out on Arabidopsis it is essentially genome-independent, and thus potentially applicable to a wide range of species. However, transfer between species, or even between different tissues of the same species, is not facile. This is because the reliability of protocols for harvesting, handling and analysis depends on the biological features and chemical composition of the plant tissue. In parallel with the diversification of model species it is important to establish good handling and analytic practice, in order to augment computational comparisons between tissues and species. Liquid chromatography–mass spectrometry (LC–MS)-based metabolomics is one of the powerful approaches for metabolite profiling. By using a combination of different extraction methods, separation columns, and ion detection, a very wide range of metabolites can be analyzed. However, its application requires careful attention to exclude potential pitfalls, including artifactual changes in metabolite levels during sample preparation under variations of light or temperature and analytic errors due to ion suppression. Here we provide case studies with two different LC–MS-based metabolomics platforms and four species (Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum, and Oryza sativa) that illustrate how such dangers can be detected and circumvented.
A mobile agent approach for global database constraint checking

Integrity constraints are valuable tools for enforcing consistency of data in a database. Global integrity constraints ensure integrity and consistency of data spanning multiple databases. In this paper, we propose a general framework of a mobile agent based approach for checking global constraints. An insert/update/delete initiated on single site, say <i>S</i><sub>1</sub> may cause the violation of a global constraint. The check for such violation involves accessing related data from multiple sites, say <i>S</i><sub>2</sub>. <i>S</i><sub>n</sub>. <i>Constraint Checker</i> on site <i>S</i><sub>1</sub> generates sub constraint checks on sites <i>S</i><sub>2</sub>. <i>S</i><sub>n</sub> and sends multiple remote agents, <i>rmagent</i><sub>2</sub>. <i>rmagent</i><sub>n</sub> to sites <i>S</i><sub>2</sub>. <i>S</i><sub>n</sub> respectively for checking the sub constraints. These remote agents carry with them data processing code to be executed at remote sites. <i>Constraint Checker</i> gathers results from the remote agents and decides if any constraint is violated. The constraint checking mechanism is much faster as the sub constraint checks are executed in parallel.
APPLICATION-TRANSPARENT ERROR-RECOVERY TECHNIQUES FOR MULTICOMPUTERS †

We describe and compare error recovery techniques for restoring a valid system state in large ‘‘general-purpose’’ multicomputers following component failures. The techniques discussed are application-transparent, i.e., they do not require application processes to be aware of the fault tolerance characteristics of the system. These techniques are based on checkpointing and rollback: process states are periodically saved to stable storage and are restored from stable storage in the event of a hardware failure. We divide existing recovery schemes into two classes: Message Logging and Coordinated Checkpointing, describe several techniques in each class, and present the advantages and limitations of the schemes when used to provide fault tolerance for large multicomputers. I. Introduction
Dynamiceuticals: The Next Stage in Personalized Medicine

The surge in the interest in personalized medicine necessitates a corresponding rational approach for implementing such individualized therapies. Dynamiceuticals represents a natural extension of the Pharmaceutical and Electroceutical fields, where the precise determination of the dynamical regimes of the pathophysiology will guide to devise therapies that ameliorate the pathology in a well-controlled manner, thus being precisely tailored toward the implementation of individualized medicine. This approach foretells to lessen side-effects and achieve superior efficacy as compared with current trial-and-error or open-loop strategies. But does the current state of knowledge and technology allow this scheme to offer what it claims?
Molecular and cellular neurocardiology: development, and cellular and molecular adaptations to heart disease

The nervous system and cardiovascular system develop in concert and are functionally interconnected in both health and disease. This white paper focuses on the cellular and molecular mechanisms that underlie neural–cardiac interactions during development, during normal physiological function in the mature system, and during pathological remodelling in cardiovascular disease. The content on each subject was contributed by experts, and we hope that this will provide a useful resource for newcomers to neurocardiology as well as aficionados.
Empowering Women

Development agencies have increasingly regarded ‘empowerment’ as an essential objective to improve the well-being of marginalised women in India. The perceived success of self-help group (SHG) programmes in this project has encouraged their widespread application across India, becoming the primary mechanism to empower women. However, this success has often been assumed rather than proven, with evaluations generally lacking a conceptualisation of empowerment based on theoretical understandings of power relations. This article aims to overcome this by evaluating the potential of SHG programmes through the reduction of internal, institutional and social constraints that prevent the marginalised from pursuing their interests. An analysis of the ‘normative’ model of SHG programmes, and its actual application shows that while SHG programmes have the potential to empower women, this is often not realised through the persistence of ‘top-down’ approaches in implementation. SHG programmes are further limited in their ability to transform social relations due to their apparent insistence that the marginalised are the only legitimate actors in their own empowerment. Rather than argue for the discontinuation of SHG programmes in India, their potential to empower women can be increased through a ‘bottom-up’ orientation in implementation, while recognising that in and of themselves SHG programmes cannot reduce all the constraints preventing the pursuit of interests.
Assessing Clients' Progress Through a Permanency Planning Program

Abstract Eighty-five HIV-positive mothers were tracked in a descriptive analysis of progress through a nonprofit organization's program of legal and mental health services designed to assist ill parents in making a permanency plan for their children after the parent's death. Data on service utilization was analyzed using a Hierarchical Classes (HICLAS) analysis, which uncovered an interpretable pattern of services that clearly distinguished basic (e.g., intake), legal, and clinical services. From the HICLAS output we created an index of progress: [no services] < [basic services only] < [basic + legal services] < [basic + legal + clinical] services. An index of mood was constructed from staff ratings of clients during home visits. Multiple regression analyses revealed that the number of different moods observed in a client was positively correlated with progress. Number of moods was also positively correlated with positive outcome, that is formulating a legal permanency plan and/or transferring care of the child to a new caregiver. Mediation analyses suggested that number of observed moods influences progress, which in turn increases the likelihood of a positive outcome. A second study replicated the prediction of mood on progress in a group of new caregivers who were not mothers.
A Hybrid Representational Proposal for Narrative Concepts: A Case Study on Character Roles

In this paper we propose the adoption of a hybrid approach to the computational representation of narrative concepts, combining prototype-based and ontology-based representations. In particular we focus on the notion of narrative roles. Inspired by the characterization provided by the TvTropes wiki, where narrative devices are discussed across old and new media, we provide a representation of roles based on the integration of a set of typicality-based semantic dimensions (represented by using the Conceptual Spaces framework) with their corresponding classical characterization in terms of necessary and sufficient conditions (represented in terms of Formal Ontologies).
Purification and partial characterization of a new enveloped RNA virus (Berne virus).

In Berne (Switzerland), a virus was isolated from a horse which was found to be serologically unrelated to known equine viruses. Its growth was unaffected by iododeoxyuridine and it was inactivated by organic solvents. A purification procedure involving ammonium sulphate precipitation and sucrose gradient equilibrium centrifugation was developed and viral activities were monitored using infectivity and enzyme-linked immunosorbent assays. Purified virions of density 1.16 g/ml were shown by negative staining electron microscopy to be roughly spherical and to measure 120 to 140 nm in diameter; projections (peplomers, about 20 nm long) were identified on the virion surface. In thin sections, an envelope and an elongated core structure could be distinguished. The core, measuring about 23 nm across and 104 nm in length, appears to assume a rod-, crescent- or open ring-shape within the envelope. It has a tubular structure and shows a transverse striation (periodicity 4.5 nm). Binding at the plasma membrane was observed. Berne virus is considered as a representative of a hitherto undefined family of widespread animal viruses serologically related to recent bovine isolates in Ames, Iowa (U.S.A.) and Lyon (France).
An inversion algorithm to compute blocking probabilities in loss networks with state-dependent rates

The algorithm developed in Choudhury et al. (1994) for computing (exact) steady-state blocking probabilities for each class in product-form loss networks is extended to cover general state-dependent arrival and service rates. This generalization allows to consider, for the first time, a wide variety of buffered and unbuffered resource-sharing models with non-Poisson traffic, as may arise with overflows in the context of alternative routing. As before, the authors consider noncomplete-sharing policies involving upper-limit and guaranteed-minimum bounds for the different classes, but in the present paper both bounds are discussed simultaneously. These bounds are important for providing different grades of service with protection against overloads by other classes. The algorithm is based on numerically inverting the generating function of the normalization constant, which is derived in the present paper. Major features of the algorithm are: dimension reduction by elimination of nonbinding resources and by conditional decomposition based on special structure, an effective scaling algorithm to control errors in the inversion, efficient treatment of multiple classes with identical parameters and truncation of large sums. The authors show that the computational complexity of the inversion approach is usually significantly lower than the alternative recursive approach. >
Face processing in high‐functioning adolescents with autism: Evidence for weak central coherence

Seventeen adolescents with autism and seventeen typically developing children, matched for chronological age, were tested in a whole versus part paradigm in which participants matched a face target either to a complete face or to a face feature. Previous studies showed an accuracy advantage in whole‐face matching, indicating a holistic processing advantage for adults (Donnelly & Davidoff, 1999). It has been suggested that individuals with autism have difficulty in holistic processing, however the extent to which this difficulty may be moderated by attentional cues is uncertain. The present study included a condition that cued participants to the relevant face feature for matching. In the comparison group, the cue did not moderate the whole‐face matching advantage. In the participants with autism, cueing generated a whole‐face advantage, while uncued stimuli showed no difference between whole face and feature matching. This suggests that a lack of holistic processing in face processing, which is associated with individuals with autism, can be moderated with cueing. The implications for weak central coherence theory are discussed.
Long-term pulse stimulation and recording in an accelerated neuromorphic system

Accelerated neuromorphic systems allow for fast emulation of spiking neural networks. In these systems, the transmission and handling of pulse events is a demanding task due to the required high bandwidth. In this demonstration, we show the pulse handling in the BrainScaleS waferscale system, which is a large-scale system of this kind. The acceleration of the system requires independent experiment control by dedicated high-speed FPGA network nodes. These nodes release pre-stored stimulus pulses from a playback memory and record neural activity to a trace memory. The external DDR2 memory employed for this task on each FPGA board can hold up to 5 · 108 pulse events, enabling long-term experiments. In this work, we use a fast execution of long emulation times for fine-grained characterization of neuromorphic neurons and small spiking networks. Our results point to the main benefit of accelerated neuromorphic hardware systems, making emulations of long-term experiments feasible, e.g. for learning or behavioural studies.
Noradrenergic and cholinergic modulation of olfactory bulb sensory processing

Neuromodulation in sensory perception serves important functions such as regulation of signal to noise ratio, attention, and modulation of learning and memory. Neuromodulators in specific sensory areas often have highly similar cellular, but distinct behavioral effects. To address this issue, we here review the function and role of two neuromodulators, acetylcholine (Ach) and noradrenaline (NE) for olfactory sensory processing in the adult main olfactory bulb. We first describe specific bulbar sensory computations, review cellular effects of each modulator and then address their specific roles in bulbar sensory processing. We finally put these data in a behavioral and computational perspective.
PaperMaker: validation of biomedical scientific publications

Motivation: The automatic analysis of scientific literature can support authors in writing their manuscripts. Implementation: PaperMaker is a novel IT solution that receives a scientific manuscript via a Web interface, automatically analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It analyses the proper use of acronyms and their definitions, and the use of specialized terminology. It provides Gene Ontology (GO) and Medline Subject Headings (MeSH) categorization of text passages, the retrieval of relevant publications from public scientific literature repositories, and the identification of missing or unused references. Result: The author receives a summary of findings, the manuscript in its corrected form and a digital abstract containing the GO and MeSH annotations in the NLM/PubMed format. Availability: http://www.ebi.ac.uk/Rebholz-srv/PaperMaker Contact: rebholz@ebi.ac.uk
Mutual Needs and Wishes of Cancer Patients and Their family Caregivers During the Last Week of Life

The last week of life represents an important time for people dying of cancer and their families. To explore the needs and wishes of patients and their caregivers during the last week of life at home, a descriptive phenomenological study was undertaken in a home care facility located in the northeast of Italy. A purposeful sample of participants affected by advanced cancer was included. For each included patient, a family member assuming the role of principal caregiver was also included. A total of 11 dyads (22 people) were selected and interviewed on a weekly basis. A series of qualitative, semistructured interviews was conducted. Each conversation was intended to provide researchers with an overview of the patient’s and family caregiver’s needs and wishes. The last interview conducted before the patient died was selected and considered for the analysis performed by researchers independently, who then worked closely together for theme triangulations. Needs and wishes in the last week of life were focused on four main themes: (a) Remaining attached to my life (“I wish I was doing things like I used to”); (b) Detaching myself from life, immediately (“I wish this Calvary were over”); (c) Dealing with the dying process (“Waiting in fear”); and (d) Starting to think of life without each other (“Unshared worries”). In order to improve personalized care in the last week of life, nurses are encouraged to assess both patient and caregiver needs and wishes, as well as their reciprocal influence and correspondence, to identify each patient–caregiver unit’s unique holistic care priorities.
The `Event as Event' and the `Event as News': The Significance of `Consonance' for Media Effects Research

In 1970 Halloran, Elliott and Murdock published Demonstrations and Communications which, due to its methodological design, represents a pioneering study in modern mass communication research. The authors were able to demonstrate similarity among the various media's reporting of an anti-Vietnam demonstration in London and that the actual `event as event' was completely different in nature from the `event as news'. Recent studies show that when reporting is consonant the mass media have a considerable influence on society. The media have particular influence over the subjects discussed in a society, the aspects of and criteria on a topic which are considered important and the climate of opinion which the population perceives as prevailing on a given subject.
Disturbance Observer-Based Robust Control of Free-Floating Space Manipulators

A disturbance observer-based control scheme is proposed for free-floating space manipulator with nonlinear dynamics derived using the virtual manipulator approach. The derived dynamic equation uses only link angles as generalized coordinates, which is suitable for the controller design in joint space. Since joint coupling, model uncertainties in robot dynamics are treated as lumped disturbances, a disturbance observer is developed at each joint of degree-of-freedom space manipulator to decouple and simplify the controller design. Simulation results of a six-link space manipulator show that the proposed scheme achieves superior performance, especially when large external disturbances are present.
The State, Rural Environments, and Globalisation: ‘Action at a Distance’ via the Australian Landcare Program

Contrary to the suggestion that transnational capital has largely subsumed the agency of Australian governments and farmers in shaping rural environments, in this paper I argue that new, often indirect, forms of action have developed within the context of globalisation and neoliberalism. These may be described as forms of ‘action at a distance’, oriented towards shaping both the environment within which people make decisions and the ways in which they are likely to respond to that environment. Since 1989, the National Landcare Program has mobilised around 30% of farm businesses to participate in community Landcare groups based on principles of self-help, cooperation, and localised action. This has initiated a new phase of negotiation over the delimitation of objects of governance, and facilitated the deployment of novel forms of state influence. Of particular importance have been technologies of knowledge that promote the further intensification of agriculture as environmentally rational and responsible, a trend reinforced by the vast bulk of neoliberal agricultural policy. Although neoliberal policy and local Landcare action appear contradictory, they do appear consistent with the self-understandings of Australian farmers as independent and self-reliant—understandings that render more direct forms of state intervention problematic. It thus remains to be seen how profoundly Landcare will reshape rural landscapes.
Factors affecting the social status of Australian young adults

Relationships between social groups-defined by ethnicity, gender, and social status-environment and school-outcome measures from 2 earlier studies (Marjoribanks, 1991, 1995), and young adults' social status were examined in a 3rd study, using the same sample of research participants. Data were collected from 21-year-old Australians of Anglo-Australian, Greek, and Southern Italian descent. The results of the present study and those of the 2 earlier studies suggest that social groups, defined by ethnicity, gender, and social status, exhibit significant differences in the learning environments and school-related outcomes of children and adolescents and that social-group variations in young adults' social status can be attributed to group differences in earlier environments and school outcomes.