Miracle-dz/UniFAR-FTUs huggingface dataset:
Recurrent rhinovirus infections in a child with inherited MDA5 deficiency

MDA5 is a cytosolic sensor of double-stranded RNA (ds)RNA including viral byproducts and intermediates. We studied a child with life-threatening, recurrent respiratory tract infections, caused by viruses including human rhinovirus (HRV), influenza virus, and respiratory syncytial virus (RSV). We identified in her a homozygous missense mutation in IFIH1 that encodes MDA5. Mutant MDA5 was expressed but did not recognize the synthetic MDA5 agonist/(ds)RNA mimic polyinosinic-polycytidylic acid. When overexpressed, mutant MDA5 failed to drive luciferase activity from the IFNB1 promoter or promoters containing ISRE or NF-&kgr;B sequence motifs. In respiratory epithelial cells or fibroblasts, wild-type but not knockdown of MDA5 restricted HRV infection while increasing IFN-stimulated gene expression and IFN-&bgr;/&lgr;. However, wild-type MDA5 did not restrict influenza virus or RSV replication. Moreover, nasal epithelial cells from the patient, or fibroblasts gene-edited to express mutant MDA5, showed increased replication of HRV but not influenza or RSV. Thus, human MDA5 deficiency is a novel inborn error of innate and/or intrinsic immunity that causes impaired (ds)RNA sensing, reduced IFN induction, and susceptibility to the common cold virus.
Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility index quantify differences within backbone flexibility, whereas changes in the cooperativity correlation quantify differences within pairwise mechanical couplings. Regardless of metric, the same general conclusions are drawn. That is, small structural perturbations introduced by single point mutations have a frequent and pronounced affect on lysozyme flexibility that can extend over long distances. Specifically, an appreciable change occurs in backbone flexibility for 48% of the residues, and a change in cooperativity occurs in 42% of residue pairs. The average distance from mutation to a site with a change in flexibility is 17–20 Å. Interestingly, the frequency and scale of the changes within single point mutant structures are generally larger than those observed in the hen egg white lysozyme (HEWL) ortholog, which shares 61% sequence identity with human lysozyme. For example, point mutations often lead to substantial flexibility increases within the β-subdomain, which is consistent with experimental results indicating that it is the nucleation site for amyloid formation. However, β-subdomain flexibility within the human and HEWL orthologs is more similar despite the lowered sequence identity. These results suggest compensating mutations in HEWL reestablish desired properties.
Techniques for Selecting and Manipulating Object in Virtual Environment Based on 3-DOF Trackers and Data Glove

We design and implement virtual object selection and manipulation in VE using 3-DOF trackers and data glove, including ray-casting technique using 1 tracker and 1 data glove and go-go technique using 2 trackers and 1 data glove. The cost of these techniques is reduced because they both do not need the 6-DOF tracker that must be operated in a well-prepared environment. User can grab and release virtual object by simple movement of hand and the interaction is more natural since the mouse is replaced by data glove.
The Human Genome Project--an overview.

The human genome sequence will underpin human biology and medicine in the next century, providing a single, essential reference to all genetic information. The international program to determine the complete DNA sequence (3,000 million bases) is well underway. As of January 2000, 50% of the sequence is available in the public domain. A comprehensive working draft is expected this year, and the entire sequence is projected to be finished in 2003. DNA sequencing is carried out on mapped, overlapping bacterial clones of 150-200 kb. The working draft comprises assembled unfinished sequence and is released immediately in the public domain. The draft sequence of each clone is then completed, by closing any remaining gaps and resolving any ambiguities, before the entire sequence is checked, annotated, and submitted to the public databases. The sequence of each clone is finished to an accuracy of >99.99%. The availability of a reference sequence of the genome provides the basis for studying the nature of sequence variation, particularly single nucleotide polymorphisms (SNPs), in human populations. SNP typing is a powerful tool for genetic analysis, and will enable us to uncover the association of loci at specific sites in the genome with many disease traits. SNPs occur at a frequency of approximately 1 SNP/kb throughout the genome when the sequence of any two individuals is compared. Programs to detect and map SNPs in the human genome are underway with the aim of establishing a SNP map of the genome during the next two years. The human genome sequence will provide a complete description of all the genes. Annotation of the sequence with the gene structures is achieved by a combination of computational analysis (predictive and homology-based) and experimental confirmation by cDNA sequencing. Detecting homologies between newly defined gene products and proteins of known function helps to postulate biochemical functions for them, which can then be tested. Establishing the association of specific genes with disease phenotypes by mutation screening, particularly for monogenic disorders, provides further assistance in defining the functions of some gene products, as well as helping to establish the cause of the disease. As our knowledge of gene sequences and sequence variation in populations increases, we will pinpoint more and more of the genes and proteins that are important in common, complex diseases. A more detailed understanding of the function of the human genome will be achieved as we identify sequences that control gene expression. Given the availability of gene sequences, the expression status of genes in particular tissues can be monitored in parallel. By comparing corresponding genomic sequences in different species (for example: man, mouse, chicken, and zebrafish), regions that have been highly conserved during evolution can be identified, many of which reflect conserved functions such as gene regulation. These approaches promise to greatly accelerate our interpretation of the human genome sequence.
From surface to intracellular non-invasive nanoscale study of living cells impairments

Among the enduring challenges in nanoscience, subsurface characterization of living cells holds major stakes. Developments in nanometrology for soft matter thriving on the sensitivity and high resolution benefits of atomic force microscopy have enabled detection of subsurface structures at the nanoscale. However, measurements in liquid environments remain complex, in particular in the subsurface domain. Here we introduce liquid-mode synthesizing atomic force microscopy (l-MSAFM) to study both the inner structures and the chemically induced intracellular impairments of living cells. Specifically, we visualize the intracellular stress effects of glyphosate on living keratinocytes skin cells. This new approach, l-MSAFM, for nanoscale imaging of living cell in their physiological environment or in presence of a chemical stress agent could resolve the loss of inner structures induced by glyphosate, the main component of a well-known pesticide (RoundUp™). This firsthand ability to monitor the cell’s inner response to external stimuli non-destructively and in liquid, has the potential to unveil critical nanoscale mechanisms of life science.
On a continuous-state population-size-dependent branching process and its extinction

A continuous-state population-size-dependent branching process { X t } is a modification of the Jiřina process. We prove that such a process arises as the limit of a sequence of suitably scaled population-size-dependent branching processes with discrete states. The extinction problem for the population X t is discussed, and the limit distribution of X t / t obtained when X t tends to infinity.
Absence of postural muscle synergies for balance following spinal cord transection 5 6 7

30 31 Although cats that have been spinalized can also be trained to stand and step with full 32 weight support, directionally-appropriate long-latency responses to perturbations are impaired, 33 suggesting that these behaviors are mediated by distinct neural mechanisms. However, it remains 34 unclear whether these responses reflect an attenuated postural response using the appropriate 35 muscular coordination patterns for balance, or are due to fundamentally different neural 36 mechanisms such as increased muscular co-contraction, or short-latency stretch responses. Here 37 we used muscle synergy analysis on previously collected data to identify whether there are 38 changes in the spatial organization of muscle activity for balance within an animal following 39 spinalization. We hypothesized that the modular organization of muscle activity for balance 40 control is disrupted by spinal cord transection. In each of 4 animals, muscle synergies were 41 extracted from postural muscle activity both before and after spinalization using non-negative 42 matrix factorization. Muscle synergy number was reduced post-spinalization in 3 animals, and 43 increased in 1 animal. However, muscle synergy structure was greatly altered post-spinalization 44 with reduced direction tuning, suggesting little consistent organization of muscle activity. 45 Further, muscle synergy recruitment was correlated to subsequent force production in the intact 46 but not spinalized condition. Our results demonstrate that the modular structure of sensorimotor 47 feedback responses for balance control are severely disrupted post-spinalization, suggesting that 48 the muscle synergies for balance control are not accessible by spinal circuits alone. Moreover, 49 we demonstrate that spinal mechanisms underlying weight support are distinct from brainstem 50 mechanisms underlying directional balance control. 51
Hybrid genetic-ant colony algorithm based job scheduling method research of arc welding robot

Research of job scheduling methods of arc welding robot is focused in this paper. The job scheduling of arc welding robot is considered as a Traveling-salesman-Problem. Welding job scheduling is modeled and relevant job scheduling optimization methods are designed. Genetic algorithm and ant colony algorithm are applied to robot welding job scheduling first. Then, based on the characteristics of both algorithms, hybrid genetic ant colony algorithm is designed to improve optimization performance. With simulated weldment as the subject, genetic algorithm, ant colony algorithm and hybrid genetic ant colony algorithm are analyzed and compared by simulation. Validity of above methods is verified.
New Pragmatism and Old Europe

Pragmatism has become a vital force in contemporary intellectual life. There are a number of reasons for this, of which four are especially notable. First, whereas early critical theorists tended to be hostile to American pragmatism, contemporary critical theory is steeped in the pragmatic tradition. This is especially the case for Jürgen Habermas, whose earlier work on philosophy of science, as well as his recent writings on communicative rationality and discourse ethics draw heavily on the work of Charles S. Peirce (Habermas, 1984, 1987, 1996, 1998; Aboulafia et al., 2001). Second, the renewed interest in G.H. Mead has been one that attempts to put Mead in his intellectual context. Whereas interpreters like Blumer used to construct a presentist reading of Mead (Mead as a precursor of symbolic interactionism and opponent of structural-functionalism), more recently the tendency has been to demonstrate the extent to which Mead was embedded in the pragmatic tradition of the time (e.g. Aboulafia, 1991, 2001; Cook, 1993; Joas, 1985). Not surprisingly, some of those scholars have also tried to study the relevance of other pragmatists for social theory (e.g. Joas, 1993, 1996). Third, Richard Rorty has embraced John Dewey’s pragmatism as a source of inspiration for his anti-foundationalist philosophy. Rorty’s reliance on Dewey was not as obvious in his path-breaking Philosophy and the Mirror of Nature (1980), but Rorty has been acknowledging the influence ever since the publication of Consequences of Pragmatism (e.g. Rorty, 1982, 1998, 1999). Hence Rorty’s influence, for instance in literary theory, went hand in hand with a growing interest in the tradition of pragmatism. Fourth, in opposition to the non-foundational and non-representational dimensions of pragmatism, critical realism has also sparked a renewed interest in Peirce whose reflections on abduction are at the centre of the realist notion of scientific explanation (Archer et al., 1998; Creaven, 2001; Cruickshank, 2003; Danemark, 2002; Joseph, 2002; Outhwaite, 1987). The aim of this special issue is to discuss the role of pragmatism in social and European Journal of Social Theory 7(3): 267–274
What is in a Rumour: Combined Visual Analysis of Rumour Flow and User Activity

Due to the rapid propagation of rumours in Online Social Networks (OSNs), identifying and understanding characteristic patterns, evolution and user behaviours behind this activity is essential. Yet, there are few tools that can support analysing rumours and activities of players in their propagation. In this paper we propose a visual analysis approach to explore rumour components and life cycles as well as their association with user actions. The approach is realized by the implementation of a prototype system, called RumourFlow. Our framework designs, adopts and implements multiple visualizations and modeling tools that are integrated to reveal rumour contents and participants' activity, both within a rumour and across different rumours. The approach supports analysts in drawing hypotheses regarding rumour propagation. This paper presents the various models, algorithms and visualizations employed for rumour strength, rumour contents, user participation, as well as the core role of the visualizations in studying this phenomenon. The effectiveness of the approach is illustrated by a use case highlighting relevant insight into rumour spreading, most of which could not otherwise be observed.
Hybrid Operational Space Control for Compliant Legged Systems

This paper introduces the concept of hybrid operational space control, a method that unifies kinematic tracking of individual joints with an inverse dynamics task space controller for the remainder of the robot. The proposed control strategy allows for a hierarchical task decomposition while simultaneously regulating the inner forces between the contact points. At the same time it improves fast tracking for compliant systems by means of appropriate low level position controllers. Introducing StarlETH, a compliant quadrupedal robot, the applicability of the controller and the hardware is demonstrated in realtime simulations and hardware experiments. We perform static walking in challenging terrain and show how the controller can combine precise and fast position control with robust and compliant interaction with the environment.
Crusading Journalism: Changing Public Attitudes and Policy-Making Agendas

INVESTIGATIVE reporting is a costly and trendy enterprise used by publishers and broadcasters to build their audiences. Researchers studying mass media influence on the salience of issues before the public-their "agenda-setting" function-seldom have studied this controversial form of reporting. Nonetheless, agenda-setting research is growing, and with it the question of the strength of the causal relationship between media content and public opinion. The methodologies and the findings vary from study to study, with the agenda-setting effects demonstrated both in broadcast and print media. (See literature review by Roberts and Bachen, 1981.)
Economic shocks , conflict and the slave trade

Suppression of the slave trade after 1807 increased the incidence of conflict between Africans. We use geo-coded data on African conflicts to uncover a discontinuous increase in conflict after 1807 in areas affected by the slave trade. In West Africa, the slave trade declined. This empowered interests that rivaled existing authorities, and political leaders resorted to violence in order to maintain their influence. In West-Central and South-East Africa, slave exports increased after 1807 and were produced through violence. We validate our explanation using Southwestern Nigeria and Eastern South Africa as examples.
Joint Hebrew Segmentation and Parsing using a PCFGLA Lattice Parser

We experiment with extending a lattice parsing methodology for parsing Hebrew (Goldberg and Tsarfaty, 2008; Golderg et al., 2009) to make use of a stronger syntactic model: the PCFG-LA Berkeley Parser. We show that the methodology is very effective: using a small training set of about 5500 trees, we construct a parser which parses and segments unsegmented Hebrew text with an F-score of almost 80%, an error reduction of over 20% over the best previous result for this task. This result indicates that lattice parsing with the Berkeley parser is an effective methodology for parsing over uncertain inputs.
Generating living theory and understanding in action research studies

The paper explains how individuals can generate their living theories from action research as explanations for their educational influences in learning. The epistemological significance of these explanations is explored in terms of the energy and values that are expressed in explanatory principles of learning in enquiries of the kind, `How do I improve what I am doing? '. Limitations in the expression of the meanings of these explanatory principles through words on pages of printed text are overcome from a perspective of inclusionality and in multi-media explanations that focus on the embodied knowledges of action researchers. These explanations can be accessed through the live URLs provided in the article. Evidence that the explanations of educational influences in learning from Whitehead's educational research programme have been used by others is provided from the masters and doctoral degrees of other living theory action researchers.
Viral Pneumonias in Forensic Autopsies: Evaluation and Classification of Histopathologic Changes With Microbiologic Correlation

AbstractLower respiratory infections are commonly due to viruses and are the third largest cause of death. Respiratory tract viruses have a tendency to target the specific regions in the lung and can harm the host via direct effect of the virus and the host's inflammatory response. In this study, relationships between morphologic changes in the lung and the viral agent type isolated in the lung by the polymerase chain reaction technique were investigated. This study was performed retrospectively at 113 autopsy cases in the Council of Forensic Medicine in Istanbul. Slides from the lung tissues diagnosed as interstitial pneumonia and detected viral agent in polymerase chain reaction were evaluated and reviewed under light microscope by 2 pathologists simultaneously according to predetermined bronchiolar, alveolar, and interstitial findings. Alveolar findings were detected in 108 cases (95.6%), whereas interstitial and bronchiolar findings were detected in 91 (80.5%) and 38 (33.6%) cases, respectively. Intra-alveolar edema was the most common alveolar finding. Some findings such as multinucleated syncytial cells and smudge cells can aid the search for etiologic agent. Interstitial inflammation was the most common histopathologic finding in the lung in viral infections and the most prominent clue to viral infections in the lung histopathologically without discrimination of viral agent type.
Social adjustment in depressed patients treated with venlafaxine and amitriptyline

Social dysfunction is often associated with depressive disorders and its evaluation is an important measure of treatment outcome. The aim of this study was to assess the effect of two treatments, venlafaxine and amitriptyline, on the social functioning of depressed patients. Twenty-eight outpatients, meeting criteria for recurrent or single major depressive episodes, took part in a double-blind, 8-week trial with amitriptyline or venlafaxine (maximum of 150 mg/day) and were assessed by the Self-Report Social Adjustment Scale (SAS-SR) before and at the end of treatment. The scale was also applied to a carefully selected non-psychiatric sample. Both drugs showed the same efficacy on a clinical scale, but venlafaxine improved social functioning more than amitriptyline as only venlafaxine-treated patients reached SAS-SR values estimated for normal subjects. This effect might be linked to the higher rate of side-effects observed with amitriptyline.
Controllable electrosprayed nanoparticles for quantitative characterization and exposure protocol

Accurate size profiling on the physical sizes of aqueous nanoparticles and molecules may be affected by various factors such as the particle aggregation or the small molecular sizes. Thus, a nanoparticle exposure chamber system was constructed in which the aqueous nanoparticles are electrosprayed and dispersed into a controllable manner prior to be determined on their size distribution and concentration. The sizes determined by our system on polystyrene nanobeads are in good accordance with dynamic light scattering (DLS) and TEM. The system was further used to measure the physical sizes of bovine serum albumin (BSA), blue dextran and hybrid nanoparticles whose sizes are not easily measured with either DLS or TEM. In addition to serving as a complementary tool on the size and concentration measurements of nanoparticles, this system can also be used as a quantitative exposure protocol for airborne nanoparticles with defined nanoparticle sizes and concentrations.
Converging Networks and Clashing Stories: South Africa's Agricultural Biotechnology Debate

The debate over agricultural biotechnology in South Africa is not only polarized, but also complicated by the increasingly blurry boundaries of food governance. This was particularly apparent during the World Summit on Sustainable Development (WSSD), held in Johannesburg in August 2002. This article explores how the politics and policies surrounding genetic modification (GM) in South Africa have taken shape within a range of overlapping transnational networks of information, advocacy, regulation, and resource exchange. Drawing on fieldwork conducted before and during the summit, it examines how South African actors identify with and draw on these networks, but also express concerns and aspirations defined by more localized experiences and conditions. It observes how South Africa has come to be seen as a pivotal site for the future of GM farming and food across the whole of the African continent.