Miracle-dz/UniFAR-FTUs huggingface dataset:
From pointer systems to counter systems using shape analysis

We aim at checking safety properties on systems manipulating dynamic linked lists. First we prove that every pointer system is bisimilar to an effectively constructible counter system. We then deduce a two-step analysis procedure. We first build an over-approximation of the reachability set of the pointer system. If this overapproximation is too coarse to conclude, we then extract from it a bisimilar counter system which is analyzed via efficient symbolic techniques developed for general counter systems.
Dynamic scanning force microscopy investigation of nanostructured spiral-like domains in Langmuir–Blodgett monolayers

The advantages/limitations obtained by working in dynamic scanning force microscopy (DSFM) at different levels of tip/sample interaction forces (from the net attractive to the hard repulsive regime) are experimentally shown by imaging monolayers containing novel fibre-like supramolecular nanostructures wrapped up in spiral-like domains. The structures have been obtained by using the Langmuir–Blodgett technique and transferring onto mica monolayers of quercetin-3-O-palmitate molecules mixed with a fraction of about 25% of dimyristoylphosphatidylcholine. The measurements in the attractive regime allowed us to reveal morphological features of the supramolecular structures that cannot be demonstrated by the conventional repulsive regime. In particular, by attractive dynamic scanning force microscopy (DSFMA) the height of the fibre-like structures was a factor of two to three higher and peculiar nano-ruptures along the wrapped fibres have been observed. The influence of the tip/sample contact interaction was investigated by recording images in hard tapping and successively imaging the same region in DSFMA as well as by comparing the images in DSFMA with those obtained in negative lift mode force modulation microscopy, phase imaging and friction force microscopy.
Microfluidic Lab-On-A-Chip for Chemical and Biological Analysis and Discovery

Introduction Micromachining Methods Micromachining of Silicon Micromachining of Glass Micromachining of Fused Quartz (or Fused Silica) Micromachining of Polymeric Chips Metal Patterning World-to-Chip Interface Microfluidic Flow Liquid Pumping Methods Microfluidic Flow Control Sample Introduction Electrokinetic Injection Hydrodynamic Injection Other Sample Injection Methods Sample Pre-concentration Sample Stacking Extraction Porous Membrane Other Pre-concentration Methods Separation Gas Chromatography (GC) Capillary Electrophoresis (CE) Chromatographic Separations Coupled Separations Detection Methods Optical Detection Methods Electrochemical (EC) Detection Mass Spectrometry (MS) Other Detection Methods Applications to Cellular/Particle Analysis Retention of Cells and Particles Studies of Cells in a Flow Other Cell Operations Applications to Nucleic Acids Analysis Nucleic Acids Extraction and Purification Nucleic Acids Amplification DNA Hybridization Other Nucleic Acid Applications Applications to Protein Analysis Immunoassay Protein Separation Enzymatic Assays Appendix Problem Sets Introduction Micromachining Microfluidic Flow Sample Introduction Sample Preconcentration Separation Detection Cellular Analysis Nucleic Acid Analysis Protein Analysis References Glossary
Memory overbooking and dynamic control of Xen virtual machines in consolidated environments

The newly emergent cloud computing environments host hundreds to thousands of services on a shared resource pool. The sharing is enhanced by virtualization technologies allowing multiple services to run in different virtual machines (VMs) on a single physical node. Resource overbooking allows more services with time-varying demands to be consolidated reducing operational costs. In the past, researchers have studied dynamic control mechanisms for allocating CPU to virtual machines, when CPU is overbooked with respect to the sum of the peak demands from all the VMs. However, runtime re-allocation of memory among multiple VMs has not been widely studied, except on VMware platforms. In this paper, we present a case study where feedback control is used for dynamic memory allocation to Xen virtual machines in a consolidated environment. We illustrate how memory behaves differently from CPU in terms of its relationship to application-level performance, such as response times. We have built a prototype of a joint resource control system for allocating both CPU and memory resources to co-located VMs in real time. Experimental results show that our solution allows all the hosted applications to achieve the desired performance in spite of their time-varying CPU and memory demands, whereas a solution without memory control incurs significant service level violations.
Influence of Controlled Cooling in Bimodal Scaffold Fabrication Using Polymers with Different Melting Temperatures

The combination of different materials and capabilities to manufacture at several scales open new possibilities in scaffold design for bone regeneration. This work is focused on bimodal scaffolds that combine polylactic acid (PLA) melt extruded strands with polycaprolactone (PCL) electrospun fibers. This type of bimodal scaffold offers better mechanical properties, compared to the use of PCL for the extruded strands, and provides potential a means for controlled drug and/or growth factor delivery through the electrospun fibers. The technologies of fused deposition modeling (FDM) and electrospinning were combined to create 3D bimodal constructs. The system uses a controlled cooling system allowing the combination of polymers with different melting temperatures to generate integrated scaffold architecture. The thermoplastic polymers used in the FDM process enhance the mechanical properties of the bimodal scaffold and control the pore structure. Integrated layers of electrospun microfibers induce an increase of the surface area for cell culture purposes, as well as potential in situ controlled drug and/or growth factor delivery. The proposed bimodal scaffolds (PLA extruded strands and PCL electrospun fibers) show appropriate morphology and better mechanical properties when compared to the use of PCL extruded strands. On average, bimodal scaffolds with overall dimensions of 30 × 30 × 2.4 mm3 (strand diameter of 0.5 mm, strand stepover of 2.5 mm, pore size of 2 mm, and layer height of 0.3 mm) showed scaffold stiffness of 23.73 MPa and compression strength of 3.85 MPa. A cytotoxicity assay based human fibroblasts showed viability of the scaffold materials.
Automatic method for sharp feature extraction from 3D data of man-made objects

A novel algorithm is proposed for extracting sharp features automatically from scanned 3D data of man-made CAD-like objects. The input of our method consists of a mesh or an unstructured point cloud that is captured on the object surface. First, the vector between a given point and the centroid of its neighborhood at a given scale is projected on the normal vector and called the ‘projected distance’ at this point. This projected distance is calculated for every data point. In a second stage, Otsu's method is applied to the histogram of the projected distances in order to select the optimal threshold value, which is used to detect potential sharp features at a single scale. These two stages are applied iteratively with the other incremental scales. Finally, points recorded as potential features at every scale are marked as valid sharp features. The method has many advantages over existing methods such as intrinsic simplicity, automatic selection of threshold value, accurate and robust detection of sharp features on various objects. To demonstrate the robustness of the method, it is applied on both synthetic and real 3D data of point clouds and meshes with different noise levels.
Function and X-Ray crystal structure of Escherichia coli YfdE

Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is 30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT) expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively) that appear to encode substrate specificity.
Monte Carlo Methods and Bayesian Computation : MCMC

Markov chain Monte Carlo (MCMC) methods use computer simulation of Markov chains in the parameter space. The Markov chains are defined in such a way that the posterior distribution in the given statistical inference problem is the asymptotic distribution. This allows to use ergodic averages to approximate the desired posterior expectations. Several standard approaches to define such Markov chains exist, including Gibbs sampling, Metropolis-Hastings and reversible jump. Using these algorithms it is possible to implement posterior simulation in essentially any problem which allow pointwise evaluation of the prior distribution and likelihood function.
Characterization of Metamaterial Transmission Lines with Coupled Resonators Through Parameter Extraction

Since resonant-type metamaterial transmission lines were proposed (Martin et al., 2003), this kind of transmission lines have been of significant importance in the development of new and innovative microwave devices. The small size and novel characteristics of these transmission lines based on sub-wavelength resonators allows the miniaturization and improvement of existing devices (Bonache et al., 2006a, 2006b; Gil et al., 2007a, 2007b), as well as the design of components with new functionalities (Siso et al., 2008, 2009). Due to the complicated layouts that these designs usually involve, having an accurate equivalent circuit model is an important assist during the design process. Besides, the application of parameter extraction methods (Bonache et al., 2006c) to obtain the values of the electrical parameters of the circuit model makes possible the characterization of both the transmission line and, therefore, the microwave device. The circuit models and parameter extraction methods presented in this chapter have been widely verified and their accuracy permits even their application for automatic layout generation based on space mapping techniques (Selga et al., 2010), which is a large and useful advance in the design of such structures.
Discovery and Preclinical Characterization of Novel Small Molecule TRK and ROS1 Tyrosine Kinase Inhibitors for the Treatment of Cancer and Inflammation

Receptor tyrosine kinases (RTKs), in response to their growth factor ligands, phosphorylate and activate downstream signals important for physiological development and pathological transformation. Increased expression, activating mutations and rearrangement fusions of RTKs lead to cancer, inflammation, pain, neurodegenerative diseases, and other disorders. Activation or over-expression of ALK, ROS1, TRK (A, B, and C), and RET are associated with oncogenic phenotypes of their respective tissues, making them attractive therapeutic targets. Cancer cDNA array studies demonstrated over-expression of TRK-A and ROS1 in a variety of cancers, compared to their respective normal tissue controls. We synthesized a library of small molecules that inhibit the above indicated RTKs with picomolar to nanomolar potency. The lead molecule GTx-186 inhibited RTK-dependent cancer cell and tumor growth. In vitro and in vivo growth of TRK-A-dependent IMR-32 neuroblastoma cells and ROS1-overexpressing NIH3T3 cells were inhibited by GTx-186. GTx-186 also inhibited inflammatory signals mediated by NFκB, AP-1, and TRK-A and potently reduced atopic dermatitis and air-pouch inflammation in mice and rats. Moreover, GTx-186 effectively inhibited ALK phosphorylation and ALK-dependent cancer cell growth. Collectively, the RTK inhibitor GTx-186 has a unique kinase profile with potential to treat cancer, inflammation, and neuropathic pain.
Understanding how appraisal of doctors produces its effects: a realist review protocol

Introduction UK doctors are now required to participate in revalidation to maintain their licence to practise. Appraisal is a fundamental component of revalidation. However, objective evidence of appraisal changing doctors’ behaviour and directly resulting in improved patient care is limited. In particular, it is not clear how the process of appraisal is supposed to change doctors’ behaviour and improve clinical performance. The aim of this research is to understand how and why appraisal of doctors is supposed to produce its effect. Methods and analysis Realist review is a theory-driven interpretive approach to evidence synthesis. It applies realist logic of inquiry to produce an explanatory analysis of an intervention that is, what works, for whom, in what circumstances, in what respects. Using a realist review approach, an initial programme theory of appraisal will be developed by consulting with key stakeholders in doctors’ appraisal in expert panels (ethical approval is not required), and by searching the literature to identify relevant existing theories. The search strategy will have a number of phases including a combination of: (1) electronic database searching, for example, EMBASE, MEDLINE, the Cochrane Library, ASSIA, (2) ‘cited by’ articles search, (3) citation searching, (4) contacting authors and (5) grey literature searching. The search for evidence will be iteratively extended and refocused as the review progresses. Studies will be included based on their ability to provide data that enable testing of the programme theory. Data extraction will be conducted, for example, by note taking and annotation at different review stages as is consistent with the realist approach. The evidence will be synthesised using realist logic to interrogate the final programme theory of the impact of appraisal on doctors’ performance. The synthesis results will be written up according to RAMESES guidelines and disseminated through peer-reviewed publication and presentations. Trial registration number The protocol is registered with PROSPERO 2014:CRD42014007092.
An overview of a probabilistic tracker for multiple cooperative tracking agents

An overview of a probabilistic cooperative tracking approach is presented in this paper. First, a new tutorial-like detailed explanation of the condensation algorithm by Isard and Blake, (1998) is described. Then we apply the probabilistic tracker to track an object (easily extendable to multiple objects) according to multiple degrees of freedom of the cameras that are able to pan, tilt and zoom. To increase the robustness of the tracking system we extend the one camera tracking method to multiple camera case and each camera is considered as an agent that can communicate with a central unit or it can act based on its own decision. Each camera will gain a level of reliability during the tracking that is used in probabilistic tracking method to improve the performance
Bioavailability, distribution and clearance of tracheally instilled, gavaged or injected cerium dioxide nanoparticles and ionic cerium

Cerium oxide nanoparticles (NPs) have wide commercial applications. Understanding their fate in the body is fundamental to toxicological evaluations. We compared bioavailability, tissue distribution, clearance and excretion of radioactive 141Ce after intratracheal instillation (IT), gavage, or intravenous (IV) injection of neutron-activated 141CeO2 NPs and 141CeCl3 (ionic 141Ce) in Wistar Han rats. First, we evaluated pulmonary responses to IT-instilled CeO2 NPs and CeCl3 and observed dose-dependent inflammatory effects. Then, groups of rats were IT-instilled with 1 mg kg−1 of 141CeO2 NPs or 0.1 mg kg−1 141CeCl3. Sequential analyses of lungs over 28 days showed slow lung clearance of 141CeO2 NPs (half-life = ~140 days) and of ionic 141Ce (half-life = ~55 days). However, less than 1% and 6% of instilled 141Ce was measured in selected extrapulmonary organs in 141CeO2 NPs and ionic 141Ce groups, respectively. Following gavage (5 mg kg−1), nearly 100% of both test materials was excreted in the feces. Since detected 141Ce activity in tissues could be in nanoparticulate or dissolved form, we also compared the 141Ce tissue distribution post-IV injection with the IT and gavage data. Both IV-injected ionic 141CeCl3 and 141CeO2 NPs were predominantly retained in the liver, bone and spleen, all organs that typically remove circulating particles. We conclude that nanoceria is slowly cleared from the lungs but has minimal extrapulmonary accumulation. Potential risks from prolonged pulmonary retention need further investigation. Risk from ingested nanoceria is likely far lower due to very low absorption and rapid elimination of ceria not absorbed from the gastrointestinal tract.
CHEMICAL REACTIONS OF GLASS CULLET USED AS CEMENT COMPONENT

The recovery of container glass (cullet) for recycling can often lead to the generation of surplus quantities of the material. The pozzolanicity of finely ground glass cullet (GGC) can be exploited by using it as a cement component in concrete. This paper examines two of the chemical reactions most significant to this mode of use, namely, the pozzolanic reaction and the potentially deleterious alkali–silica reaction. Although the presence of GGC has little effect on the reactions of portland cement, larger quantities of calcium silicate hydrate gel are formed, which are thought to contain quantities of sodium. Blends containing the largest quantities of calcium silicate hydrate gel also displayed the highest strengths. Expansion due to alkali–silica reaction of mortars containing GGC is reduced relative to controls. This can be understood when it is considered that the pozzolanic and alkali–silica reactions are chemically identical. The fine cullet particles have a high surface area and, hence, favor the rapid pozzolanic rate of reaction over the slower alkali–silica reaction rate.
Discovering Visual Hierarchy through Unsupervised Learning

1 Introduction: We present a method for discovering visual hierarchy in a set of images. Automatically grouping and organizing images has applications for personal use where personal photographs can be arranged as overexposed or underexposed, urban or rural landscape, closeups or family gatherings (lots of people etc) besides various other useful hierarchies. This also has applications in the educational/research domain where it would be interesting and maybe useful to find out if a large dataset as the ImageNet [1] can be arranged in other interesting hierarchies. Effective hierarchies allow for efficient searching of images and better image recommendations (i.e. other images similar to a certain image of interest).
Diagnosis and Management of Bleeding Disorder in a Child

Children with symptoms of bleeding and bruising are commonly seen in clinical practice. Primary care providers should be able to decide when and whether evaluation for bleeding disorder is warranted. This decision depends on one’s index of suspicion for bleeding disorder based on history, physical examination, and screening laboratory investigations. Knowledge of the hemostatic physiology is essential to be able to order appropriate laboratory investigations and their accurate interpretation. Prothrombin time (PT), activated partial thromboplastin time (aPTT), and blood platelet concentration constitute the initial diagnostic work up of any bleeding disorder. Abnormality in any of these parameters in a child with excessive bleeding should lead to presumptive diagnosis of bleeding disorder and trigger referral to a hematologist for confirmation and definitive treatment. Awareness of basic treatment principles for management of bleeding/clotting disorders may prepare the provider to develop appropriate management plans, especially in a life threatening situation.
On Binary Methods

∗partially supported by NSF grant CCR-9121778 and NSF grant CCR-9424123. Internet:kim@cs.williams. edu †Internet: luca@src.dec.com. ‡Internet: castagna@dmi.ens. fr §Jonathan Eifrig, Scott Smith, Valery Trifonov. Contact Scott Smith. Research partially supported by NSF grant CCR-9301340 and AFOSR grant F49620-93-1-0169. Internet: scott@cs.jhu. edu. ¶partially supported by NSF grants CCR-9108654 and CCR9593168. Internet: leavens@cs.iastate. edu. ‖Internet: benjamin.pierce@cl.cam. ac.uk c © John Wiley & Sons, Inc.
Two-photon fluorescence and confocal video microscopy of in-vivo human skin

We present a system for in-vivo skin imaging consisting of a two-photon fluorescence and a confocal reflectance video microscope. The two devices share one microscope objective, but have separate light sources, detectors, scan-units and control electronics. This makes it possible to image a region of the skin using the two different modalities, while exploiting the specific advantages of each method. In the images we clearly distinguish several skin layers, i.e., stratum corneum, viable epidermis, basal layer and upper dermis. Close to the skin surface individual keratinocytes in the stratum corneum are visible with the two-photon microscope, while in reflectance images the texture is much more uniform. Slightly deeper in the skin the smooth cellular structure of the epidermis becomes visible for both imaging modalities. Below the basal layer, which marks the boundary between epidermis and the dermis, fibrous structure appears which can be attributed to capillary vessels and dermal collagen. We use the combined imaging device for studying the effect of occlusion on human skin. From the fluorescence images we observe swelling of the stratum corneum, while the reflectance microscope shows changes in the scattering properties due to hydration. We show that by combining two microscopes in one we can obtain images that contain complementary information, thereby enhancing the potential for each individual modality.