Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting human blood viscosity in silico

The viscosity of blood has long been used as an indicator in the understanding and treatment of disease, and the advent of modern viscometers allows its measurement with ever-improving clinical convenience. However, these advances have not been matched by theoretical developments that can yield a quantitative understanding of blood’s microrheology and its possible connection to relevant biomolecules (e.g., fibrinogen). Using coarse-grained molecular dynamics and two different red blood cell models, we accurately predict the dependence of blood viscosity on shear rate and hematocrit. We explicitly represent cell–cell interactions and identify the types and sizes of reversible rouleaux structures that yield a tremendous increase of blood viscosity at low shear rates. We also present the first quantitative estimates of the magnitude of adhesive forces between red cells. In addition, our simulations support the hypothesis, previously deduced from experiments, of yield stress as an indicator of cell aggregation. This non-Newtonian behavior is analyzed and related to the suspension’s microstructure, deformation, and dynamics of single red blood cells. The most complex cell dynamics occurs in the intermediate shear rate regime, where individual cells experience severe deformation and transient folded conformations. The generality of these cell models together with single-cell measurements points to the future prediction of blood-viscosity anomalies and the corresponding microstructures associated with various diseases (e.g., malaria, AIDS, and diabetes mellitus). The models can easily be adapted to tune the properties of a much wider class of complex fluids including capsule and vesicle suspensions.
Conformable and scalable tactile sensor skin for curved surfaces

We present the design and realization of a conformable tactile sensor skin (patent pending). The skin is organized as a network of self-contained modules consisting of tiny pressure-sensitive elements which communicate through a serial bus. By adding or removing modules it is possible to adjust the area covered by the skin as well as the number (and density) of tactile elements. The skin is therefore highly modular and thus intrinsically scalable. Moreover, because the substrate on which the modules are mounted is sufficiently pliable to be folded and stiff enough to be cut, it is possible to freely distribute the individual tactile elements. A tactile skin composed of multiple modules can also be installed on curved surfaces. Due to their easy configurability we call our sensors "cut-and-paste tactile sensors. " We describe a prototype implementation of the skin on a humanoid robot
Online Visual Analytics of Text Streams

We present an online visual analytics approach to helping users explore and understand hierarchical topic evolution in high-volume text streams. The key idea behind this approach is to identify representative topics in incoming documents and align them with the existing representative topics that they immediately follow (in time). To this end, we learn a set of streaming tree cuts from topic trees based on user-selected focus nodes. A dynamic Bayesian network model has been developed to derive the tree cuts in the incoming topic trees to balance the fitness of each tree cut and the smoothness between adjacent tree cuts. By connecting the corresponding topics at different times, we are able to provide an overview of the evolving hierarchical topics. A sedimentation-based visualization has been designed to enable the interactive analysis of streaming text data from global patterns to local details. We evaluated our method on real-world datasets and the results are generally favorable.
Mobile ad hoc networking: an essential technology for pervasive computing

In the near future, a pervasive computing environment can be expected based on the recent progress and advances in computing and communication technologies. The next generation of mobile communications will include both prestigious infrastructured wireless networks and novel infrastructureless mobile ad hoc networks (MANETs). A MANET is a collection of wireless nodes that can dynamically form a network to exchange information without using any pre-existing fixed network infrastructure. The special features of MANET bring this technology great opportunities together with severe challenges. This paper describes the fundamental problems of ad hoc networking by giving its related research background and including the concept, features, status and applications of MANET. Some of the technical challenges MANET poses are also presented, based on which the paper points out some of the key research issues for ad hoc networking technology that are expected to promote development and accelerate commercial applications. Special attention is paid to network layer routing strategy of MANET and key research issues include new X-cast routing algorithms, security and reliability schemes, QoS model and mechanisms for interworking with outside IP networks.
SASqPCR: Robust and Rapid Analysis of RT-qPCR Data in SAS

Reverse transcription quantitative real-time PCR (RT-qPCR) is a key method for measurement of relative gene expression. Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization. Currently no computer program for RT-qPCR data analysis is suitable for analytical optimization and user-controllable customization based on data quality, experimental design as well as specific research aims. Here I introduce an all-in-one computer program, SASqPCR, for robust and rapid analysis of RT-qPCR data in SAS. This program has multiple macros for assessment of PCR efficiencies, validation of reference genes, optimization of data normalizers, normalization of confounding variations across samples, and statistical comparison of target gene expression in parallel samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. In addition, it is highly automatic and functionally extendable. Thus users are the actual decision-makers controlling RT-qPCR data analyses. SASqPCR and its tutorial are freely available at http://code.google. com/p/sasqpcr/downloads/list.
Visualization of Large Chemical Databases with Application to Drug Design

This paper reviews our recent studies on the visualization of chemical database and its application in drug design at the molecular and cellular levels. It sketches the background of computer-aided drug design, and gives the mathematical formulations of fundamental database computational problems. Solutions of these problems rely on multivariate nonlinear optimization, combinatorial optimization, numerical linear algebra, and multivariate statistical analysis. This paper presents a fast algorithm for visualizing large chemical databases as a flrst step in solving the chemical database analysis problems. The algorithm is a novel combination of the singular value decomposition and principal component analysis techniques with the truncatedNewton minimization method (TNPACK) based on the classic distance geometry approach. Numerical experiments to real chemical databases show that our visualization algorithm has great potential in aiding the generation of drug candidates or the optimization of bioactive compounds.
A Multilevel CMOS–MEMS Design Methodology Based on Response Surface Models

We have developed a novel methodology to design systems composed of complementary metal-oxide-semiconductor (CMOS) and microelectromechanical systems (MEMS) parts. This multiscale methodology combines bottom-up modeling and top-down design-space exploration through the following steps: 1) In bottom-up modeling, characteristics of CMOS circuits and MEMS structures are accurately simulated at the circuit and MEMS device level; 2) on the basis of the results of a statistical regression method, these characteristics are abstracted into individual response surface models (RSMs), each with a set of coefficients of design parameters; 3) the models are mathematically connected to describe an elemental unit comprising CMOS and MEMS components; 4) the characteristics of the whole system of elemental units are abstracted into another RSM to cover the system performance; and 5) in top-down design-space exploration, the system requirements are connected to a set of design parameters for the CMOS circuits and MEMS structures by utilizing the RSMs in the reverse direction. To verify the concept, our design methodology was applied to a CMOS-MEMS fingerprint sensor.
A Panorama of Software Architectures in Game Development

As video games evolve into richer and more sophisticated products, the software driving those games become more complex. One of the research areas offered by Software Engineering to cope with this complexity, while reducing risks and improving software quality, is Software Architecture. The purpose of this paper is to present an overview of possibly all work having investigated, established and used software architectures for the development of video games. For this, a Systematic Mapping was conducted. The achieved results show an increasing, however still mild, interest in the exploration of software architectures for the development of video games, and lays out lines of research that can be explored. KeywordsSoftware Architecture; Game Development; Video Game; Computer Game; Systematic Mapping
Mutant Prion Protein Expression Is Associated with an Alteration of the Rab GDP Dissociation Inhibitor α (GDI)/Rab11 Pathway*

The prion protein (PrP) is a glycosylphosphatidylinositol-anchored membrane glycoprotein that plays a vital role in prion diseases, a class of fatal neurodegenerative disorders of humans and animals. Approximately 20% of human prion diseases display autosomal dominant inheritance and are linked to mutations in the PrP gene on chromosome 20. PrP mutations are thought to favor the conformational conversion of PrP into a misfolded isoform that causes disease by an unknown mechanism. The PrP mutation D178N/Met-129 is linked to fatal familial insomnia, which causes severe sleep abnormalities and autonomic dysfunction. We showed by immunoelectron microscopy that this mutant PrP accumulates abnormally in the endoplasmic reticulum and Golgi of transfected neuroblastoma N2a cells. To investigate the impact of intracellular PrP accumulation on cellular homeostasis, we did a two-dimensional gel-based differential proteomics analysis. We used wide range immobilized pH gradient strips, pH 4–7 and 6–11, to analyze a large number of proteins. We found changes in proteins involved in energy metabolism, redox regulation, and vesicular transport. Rab GDP dissociation inhibitor α (GDI) was one of the proteins that changed most. GDI regulates vesicular protein trafficking by acting on the activity of several Rab proteins. We found a specific reduction in the level of functional Rab11 in mutant PrP-expressing cells associated with impaired post-Golgi trafficking. Our data are consistent with a model by which mutant PrP induces overexpression of GDI, activating a cytotoxic feedback loop that leads to protein accumulation in the secretory pathway.
Towards unsupervised training of the classifier-based speech translator

Concept classiﬁcation has been proven to be a useful translation method for speech-to-speech translation applications. However, preparing training data for classiﬁer is a cumbersome task for human annotators. An unsupervised training method is introduced here that is based on utterance clustering. A technique to measure the distance between two utterances, based on the concepts they express, along with an appropriate clustering method has been adapted.
Sound and extensible renaming for java

Descriptive names are crucial to understand code. However, good names are notoriously hard to choose and manually changing a globally visible name can be a maintenance nightmare. Hence, tool support for automated renaming is an essential aid for developers and widely supported by popular development environments. This work improves on two limitations in current refactoring tools: too weak preconditions that lead to unsoundness where names do not bind to the correct declarations after renaming, and too strong preconditions that prevent renaming of certain programs. We identify two main reasons for unsoundness: complex name lookup rules make it hard to define sufficient preconditions, and new language features require additional preconditions. We alleviate both problems by presenting a novel extensible technique for creating symbolic names that are guaranteed to bind to a desired entity in a particular context by inverting lookup functions. The inverted lookup functions can then be tailored to create qualified names where otherwise a conflict would occur, allowing the refactoring to proceed and improve on the problem with too strong preconditions. We have implemented renaming for Java as an extension to the JastAdd Extensible Java Compiler and integrated it in Eclipse. We show examples for which other refactoring engines have too weak preconditions, as well as examples where our approach succeeds in renaming entities by inserting qualifications. To validate the extensibility of the approach we have implemented renaming support for Java 5 and AspectJ like inter-type declarations as modular extensions to the initial Java 1.4 refactoring engine. The renaming engine is only a few thousand lines of code including extensions and performance is on par with industrial strength refactoring tools.
Comparison of Robot-Assisted Reaching to Free Reaching in Promoting Recovery From Chronic Stroke

Recent studies have suggested that physical rehabilitation performed with robotic devices can enhance arm movement recovery following stroke. In these studies, the robotic devices mechanically assisted arm movement as the patient attempted to move. Although this “robotic active assist” technique has shown promise, a key question remains unanswered: is the mechanical assistance provided by the robots necessary, or is it primarily the repetitive movement attempts by the patients that stimulate recovery? We are using a novel robotic device called the Assisted Rehabilitation and Measurement (ARM) Guide to investigate this question. To date, ten subjects have completed twenty-four therapy sessions over an eight-week period, randomized to either a robot exercise group (N = 6) or non-robotic exercise group (N = 4). For the robot exercise group, the ARM Guide mechanically assisted in reaching to a series of targets. For the non-robotic group, the subjects performed unassisted, unrestrained reaching exercises to the same targets for the same number of repetitions as the ARM Guide group. All subjects have been evaluated using a set of clinical and biomechanical measures of arm movement. The ten subjects tested so far have shown improvement in the measures after completion of both exercise programs. However, the amount of improvement has been comparable for the robot and free reaching groups. Although the subject numbers are currently insufficient to draw a definitive conclusion, these results are suggestive that the repetitive movement attempts by the patient, rather than the active assistance from the ARM Guide, are the primary stimuli to recovery.
Physiological Role of Gap-Junctional Hemichannels: Extracellular Calcium-Dependent Isosmotic Volume Regulation

Hemichannels in the overlapping regions of apposing cells plasma membranes join to form gap junctions and provide an intercellular communication pathway. Hemichannels are also present in the nonjunctional regions of individual cells and their activity is gated by several agents, including calcium. However, their physiological roles are unknown. Using techniques of atomic force microscopy (AFM), fluorescent dye uptake assay, and laser confocal immunofluorescence imaging, we have examined the extracellular calcium-dependent modulation of cell volume. In response to a change in the extracellular physiological calcium concentration (1.8 to ≤1.6 mM) in an otherwise isosmotic condition, real-time AFM imaging revealed a significant and reversible increase in the volume of cells expressing gap-junctional proteins (connexins). Volume change did not occur in cells that were not expressing connexins. However, after the transient or stable transfection of connexin43, volume change did occur. The volume increase was accompanied by cytochalasin D-sensitive higher cell stiffness, which helped maintain cell integrity. These cellular physical changes were prevented by gap-junctional blockers, oleamide and β-glycyrrhetinic acid, or were reversed by returning extracellular calcium to the normal level. We conclude that nongap-junctional hemichannels regulate cell volume in response to the change in extracellular physiological calcium in an otherwise isosmotic situation.
Performance comparison of two route optimisation schemes for AODV in MANETs

In this study, we extend performance evaluation of two different 'route optimisation' schemes proposed in Bilgin and Khan 2010 and Bilgin et al. 2010, with new performance metrics like normalised energy consumption, packet delivery fraction, average end-to-end delay, and average connection lifetime. In addition, we provide performance comparison of this two schemes against each other with pure AODV as a reference. The compared schemes are implemented as extension of AODV in ns-2 packet level network simulator. The first scheme, called 1-hop shrink, periodically checks if there is any shortcut i.e., direct connection between two endpoints of each successive and overlapped triplet of nodes along active routes. On the other hand, the second scheme, called multi-hop shrink, periodically checks if there is a shortcut between any two nodes on a route by broadcasting a special packet starting from at the third node on active connections.
Distributed WRBG Matching Approach for Multiflow Two-Way D2D Networks

Device-to-device (D2D) communication has great potential to improve spectrum efficiency and offload traffic for cellular networks. In this paper, we focus on a multiflow two-way D2D network with decode-and-forward (DF) relays, coexisting with OFDMA cellular network. The spectrum sharing and relay selection are considered to minimize the outage probability of the device in D2D networks. The induced problem is a complicated probabilistic integral programming. A novel weighted random bipartite graph (WRBG)-based minimum weight maximum matching (MWMM) approach will be proposed in this paper. To offload not only the traffic but also the signaling and computation overhead, the improved min-sum algorithm will be applied to find the MWMM in the distributed manner with only polynomial complexity. The proposed approach enjoys an advantage that the close-form approximation formulas for optimal outage probability and diversity-multiplexing tradeoff can be derived by analyzing the properties of MWMM on WRBG. Both the theoretical derivations and simulation results will illustrate that the proposed approach for multiflow two-way D2D networks achieves the same performance as single-flow two-way D2D systems. Therefore, the distributed WRBG matching approach yields not only a practical distributed algorithm, but also a simple and elegant theoretical framework for multiflow two-way D2D networks.
Experimental validation of a CFRP laminated/fabric hybrid layout for retrofitting and repairing timber beams

ABSTRACT This paper proposes a new hybrid layout to retrofit and repair timber beams by means of carbon composite material. It is based on the combination of a carbon laminate strip attached on the tension side, and a carbon fabric discontinuously wrapping the timber element. This layout has been experimentally validated by means of a study involving large-scale timber beams with many years in service. Results demonstrate not only that the bending load capacity of the broken beams can be totally recovered, but that it may even be increased by 70% with respect to the non-broken ones.
Mobile Escape Analysis for occam-pi

Escape analysis is the process of discovering boundaries of dynamically al- located objects in programming languages. For object-orientedlanguages such as C++ and Java, this analysis leads to an understanding of which program objects interact directly, as well as what objects hold references to other ob jects. Such information can be used to help verify the correctness of an implementation with respect to its design, or provide information to a run-time system about which objects can be allocated on the stack (because they do not 'escape' the method in which th ey are declared). For existing object-oriented languages, this analysis is typi cally made difficult by aliasing endemic to the language, and is further complicated by inheritance and polymorphism. In contrast, the occam-π programming language is a process-orientedlanguage, with systems built from layered networks of communicating concurrent processes. The lan- guage has a strong relationship with the CSP process algebra, that can be used to reason formally about the correctness of occam-π programs. This paper presents early work on a compositional escape analysis technique for mobiles in the occam-π programming language, in a style not dissimilar to existing CSP analyses. The primary aim is to discover the boundaries of mobiles within the communication graph, and to determine whether or not they escape any particular pro- cess or network of processes. The technique is demonstrated by analysing some typ- ical occam-π processes and networks, giving a formal understanding of their mobile escape behaviour.
Meisetz and the birth of the KRAB motif

The largest family of transcription factors in mammals is of Cys(2)His(2) zinc finger-proteins, each with an NH(2)-terminal KRAB motif. Extensive expansions of this family have occurred in separate mammalian lineages, with approximately 400 such genes known in the human genome. Despite their widespread occurrence, the evolutionary provenance of the KRAB motif is unclear since previously it has not been found outside of the tetrapod vertebrates. Here, we show that homologues of the histone methyltransferase Meisetz are present within the sea urchin (Strongylocentrotus purpuratus) genome. Sea urchin and mammalian Meisetz sequences each contain an N-terminal KRAB motif, which thereby establishes an early origin of the KRAB motif prior to the divergence of echinoderm and chordate lineages. Finally, we present evidence that KRAB motifs derive from a novel family of KRI (KRAB Interior) motifs that were present in the last common ancestor of animals, plants and fungi.
Double‐blind placebo‐controlled study of sublingual immunotherapy with house dust mite extract (D. pt.) in children

Safety and efficacy of sublingual (sublingual‐swallow) immunotherapy (IT) with house dust mite extract were evaluated in 30 children (6 ‐ 152/3 years of age) over the first 12 months of an ongoing study. The cumulative dose was 570 μg Der p I (five times that administered with subcutaneous therapy). Safety: One patient on active treatment dropped out after 8 weeks because of a subjective feeling of severe weakness, questionably induced by the therapy. Five patients on active therapy and one patient on placebo reported minor local side effects. Efficacy: Pulmonary symptoms were reduced after 12 months in actively treated asthmatics, but this was not consistent with the lack of improvement in bronchial reactivity, skin sensitivity and specific IgG and IgG4 against D. pt. in this group. In patients with rhinitis nasal sensitivity was reduced in the placebo group without concomitant improvement in the nasal symptom score. Specific IgE (D. pt. and D. f.) in creased significantly more in the active treatment group after 3 and 12 months. We conclude that sublingual IT over 12 months with the fivefold Der p 1 dose of subcutaneous IT was well tolerated, but there was no consistent clinical or immunological benefit compared to placebo.