Miracle-dz/UniFAR-FTUs huggingface dataset:
Alignment and integration of complex networks by hypergraph-based spectral clustering

Complex networks possess a rich, multiscale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction, or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.
Heterogeneity of natural Foxp3+ T cells: A committed regulatory T-cell lineage and an uncommitted minor population retaining plasticity

Natural regulatory T cells (Treg) represent a distinct lineage of T lymphocytes committed to suppressive functions, and expression of the transcription factor Foxp3 is thought to identify this lineage specifically. Here we report that, whereas the majority of natural CD4+Foxp3+ T cells maintain stable Foxp3 expression after adoptive transfer to lymphopenic or lymphoreplete recipients, a minor fraction enriched within the CD25− subset actually lose it. Some of those Foxp3− T cells adopt effector helper T cell (Th) functions, whereas some retain “memory” of previous Foxp3 expression, reacquiring Foxp3 upon activation. This minority “unstable” population exhibits flexible responses to cytokine signals, relying on transforming growth factor-β to maintain Foxp3 expression and responding to other cytokines by differentiating into effector Th in vitro. In contrast, CD4+Foxp3+CD25high T cells are resistant to such conversion to effector Th even after many rounds of cell division. These results demonstrate that natural Foxp3+ T cells are a heterogeneous population consisting of a committed Treg lineage and an uncommitted subpopulation with developmental plasticity.
Planar Reachability in Linear Space and Constant Time

We show how to represent a planar digraph in linear space so that reach ability queries can be answered in constant time. The data structure can be constructed in linear time. This representation of reach ability is thus optimal in both time and space, and has optimal construction time. The previous best solution used O(n log n) space for constant query time [Thorup FOCS'01].
A Novel Surface Plasmon Resonance Biosensor for the Rapid Detection of Botulinum Neurotoxins

Botulinum neurotoxins (BoNTs) are Category A agents on the NIAID (National Institute of Allergy and Infectious Diseases) priority pathogen list owing to their extreme toxicity and the relative ease of production. These deadly toxins, in minute quantities (estimated human i.v. lethal dose LD50 of 1–2 ng/kg body weight), cause fatal flaccid paralysis by blocking neurotransmitter release. The current gold standard detection method, the mouse-bioassay, often takes days to confirm botulism. Furthermore, there are no effective antidotes known to reverse the symptoms of botulism, and as a result, patients with severe botulism often require meticulous care during the prolonged paralytic illness. To combat potential bio-terrorism incidents of botulinum neurotoxins, their rapid detection is paramount. Surface plasmon resonance (SPR) is a very sensitive technique to examine bio-molecular interactions. The label-free, real-time analysis, with high sensitivity and low sample consumption makes this technology particularly suitable for detection of the toxin. In this study, we demonstrated the feasibility in an assay with a newly designed SPR instrument for the rapid detection of botulinum neurotoxins. The LOD (limit of detection) of the Newton Photonics (NP) SPR based assay is 6.76 pg/mL for Botulinum Neurotoxin type A Light Chain (BoNT/A LC). We established that the detection sensitivity of the system is comparable to the traditional mouse LD50 bioassay in BoNT/A using this SPR technology.
Octamerization Enables Soluble CD46 Receptor To Neutralize Measles Virus In Vitro and In Vivo

ABSTRACT A chimeric fusion protein encompassing the CD46 ectodomain linked to the C-terminal part of the C4b binding protein (C4bp) α chain (sCD46-C4bpα) was produced in eukaryotic cells. This protein, secreted as a disulfide-linked homo-octamer, was recognized by a panel of anti-CD46 antibodies with varying avidities. Unlike monomeric sCD46, the octameric sCD46-C4bpα protein was devoid of complement regulatory activity. However, sCD46-C4bpα was able to bind to the measles virus hemagglutinin protein expressed on murine cells with a higher avidity than soluble monomeric sCD46. Moreover, the octameric sCD46-C4bpα protein was significantly more efficient than monomeric sCD46 in inhibiting virus binding to CD46, in blocking virus induced cell-cell fusion, and in neutralizing measles virus in vitro. In addition, the octameric sCD46-C4bpα protein, but not the monomeric sCD46, fully protected CD46 transgenic mice against a lethal intracranial measles virus challenge.
Orthogonal polynomials for refinable linear functionals

A refinable linear functional is one that can be expressed as a convex combination and defined by a finite number of mask coefficients of certain stretched and shifted replicas of itself. The notion generalizes an integral weighted by a refinable function. The key to calculating a Gaussian quadrature formula for such a functional is to find the three-term recursion coefficients for the polynomials orthogonal with respect to that functional. We show how to obtain the recursion coefficients by using only the mask coefficients, and without the aid of modified moments. Our result implies the existence of the corresponding refinable functional whenever the mask coefficients are nonnegative, even when the same mask does not define a refinable function. The algorithm requires O(n 2 ) rational operations and, thus, can in principle deliver exact results. Numerical evidence suggests that it is also effective in floating-point arithmetic.
Outage probability of multi-code DS-CDMA with linear interference suppression

We examine the outage probability of a multi-code DS-CDMA system with minimum mean squared error (MMSE) linear interference suppression. Multi-code DS-CDMA allows different information rates by varying the number of spreading codes assigned to each user. Power control is used to achieve a set of target signal-to-interference-plus-noise ratios (SINRs), and an outage occurs if a user must increase the transmitted power above a maximum power limit. To compete the outage probability, we derive an accurate approximation for the variance of received SINR over the user population assuming MMSE detection with short spreading codes. Outage probability is then shown as a function of the number of codes assigned to each user. For a fixed outage probability, our results show that a multi-code scheme can provide approximately 2 dB gain in SINR relative to the corresponding single-code (variable processing gain) scheme.
Process analytical technology (PAT) for biopharmaceuticals

Process analytical technology (PAT), the regulatory initiative for building in quality to pharmaceutical manufacturing, has a great potential for improving biopharmaceutical production. The recommended analytical tools for building in quality, multivariate data analysis, mechanistic modeling, novel models for interpretation of systems biology data and new sensor technologies for cellular states, are instrumental in exploiting this potential. Industrial biopharmaceutical production has gradually become dependent on large-scale processes using sensitive mammalian cell cultures. This further emphasizes the need for improved PAT solutions. We summarize recent progress in this area based on an expert workshop held at the 8(th) European Symposium on Biochemical Engineering Sciences (Bologna, 2010), and highlight new opportunities for exploiting PAT when applied in biopharmaceutical production. We conclude with recommendations for advancing PAT applications in the biopharmaceutical industry.
Tissue Transglutaminase, Not Lysyl Oxidase, Dominates Early Calcium-Dependent Remodeling of Fibroblast-Populated Collagen Lattices

Cell-populated collagen gels have provided significant insight into the cellular contractile mechanisms and cell-matrix interactions that are necessary for compacting and remodeling extant matrix. Nevertheless, little research has been devoted towards determining how cells entrench these deformations that contribute to establishing a preferred mechanical state. To this end, we examined the roles of two covalent matrix cross-linkers, i.e. tissue transglutaminase and lysyl oxidase, during global remodeling of the free-floating fibroblast-populated collagen lattice. Inhibition of tissue transglutaminase resulted in a reduced rate of compaction compared to controls during early remodeling (up to 2 days). In contrast, inhibition of lysyl oxidase did not alter the early compaction of these lattices, but it reduced the compaction after 2 days of culture. Acute inhibition of different contractile mechanisms suggested further that calcium-dependent contractility may have dominated during the initial remodeling of the collagen lattice before giving way to calcium-independent contractility at later times. In summary, these findings suggest that early remodeling of the free-floating collagen lattice is facilitated by calcium-dependent cell contraction while entrenchment is dominated by a tissue transglutaminase-mediated cross-linking of the extant matrix. As remodeling continues, however, lysyl oxidase increases its contribution, perhaps by consolidating de novo collagen fibrils into fibers to continue the remodeling while the cells transition to a more sustained, calcium-independent contractility. These results promise to influence future tissue engineering studies as well as computational simulations aimed at understanding matrix remodeling in complex in vivo situations.
AD in Fortran, Part 1: Design

We propose extensions to Fortran which integrate forward and reverse Automatic Differentiation (AD) directly into the programming model. Irrespective of implementation technology, embedding AD constructs directly into the language extends the reach and convenience of AD while allowing abstraction of concepts of interest to scientific-computing practice, such as root finding, optimization, and finding equilibria of continuous games. Multiple different subprograms for these tasks can share common interfaces, regardless of whether and how they use AD internally. A programmer can maximize a function F by calling a library maximizer, XSTAR=ARGMAX(F,X0), which internally constructs derivatives of F by AD, without having to learn how to use any particular AD tool. We illustrate the utility of these extensions by example: programs become much more concise and closer to traditional mathematical notation. A companion paper describes how these extensions can be implemented by a program that generates input to existing Fortran-based AD tools.
Demonstration of a Domain-Specic Language Debugging Framework

This demonstration presents a debugging framework that targets domain-specic languages (DSLs). The DSL Debugging Framework (DDF) generates debuggers automatically from DSL grammar specications. The debugging concern is weaved into a base grammar in an aspect-oriented style. DDF was used to generate debuggers for three dierent types of DSLs (imperative, declarative, and hybrid) that are translated into a General Purpose Language (GPL), such as Java. The demonstration will show how debugging concerns are weaved into the base grammar of a hybrid DSL to generate a debugger. The generated debugger will be demonstrated on a DSL for describing GUIs.
Application of ant colony optimization for the risk management of wind damage in forest planning

Ant colony optimization (ACO) is still quite a new technique and seldom used in the field of forest planning compared to other heuristics such as simulated annealing and genetic algorithms. This work was aimed at evaluating the suitability of ACO for optimizing the clear-cut patterns of a forest landscape when aiming at simultaneously minimizing the risk of wind damage and maintaining sustainable and even flow of periodical harvests. For this purpose, the ACO was first revised and the algorithm was coded using the Visual Basic Application of the ArcGIS software. Thereafter, the performance of the modified ACO was demonstrated in a forest located in central Finland using a 30-year planning period. Its performance was compared to simulated annealing and a genetic algorithm. The revised ACO performed logically since the objective function value was improving and the algorithm was converging during the optimization process. The solutions maintained a quite even periodical harvesting timber while minimizing the risk of wind damage. Implementing the solution would result in smooth landscape in terms of stand height after the 30-year planning period. The algorithm is quite sensitive to the parameters controlling pheromone updating and schedule selecting. It is comparable in solution quality to simulated annealing and genetic algorithms.
Segmentation of vessels through supervised classification in wide-field retina images of infants with Retinopathy of Prematurity

The earliest signs of Retinopathy of Prematurity (ROP) are tortuosity and dilation of retinal vessels, both considered of primary importance for the diagnosis and the follow-up of the disease. However, an accepted computerized system for their quantitative measurement is still missing. Vessel segmentation algorithms designed for adults' fundus images do not work well in infants' fundus images. In order to provide an accurate segmentation of the infant's retina vascularity we propose a supervised classification approach. The extracted feature set comprises multi-scales vesselness and texture features. Their combination allows the discrimination both between vessels and background, and between choroidal and retinal vessels. In order to reduce the computational complexity, the most useful subset of features to be fed to the classifier is determined employing a wrapper greedy forward-selection method. The performance of the proposed method is assessed by cross-validation on a dataset of 20 images acquired with a RetCam fundus camera. Average accuracy and Matthews' correlation coefficient are respectively 0.97 and 0.67 with respect to manual ground truth reference.
Evolving Optimized Forward and Reverse Transforms using Genetic Algorithms on a Supercomputer

The use of digital images is increasing all the time in personal digital photography, medical imaging, and fingerprint image databases. The goal of this research is to improve the image quality of a given compressed digital image while maintaining the same file size of the image. Wavelet based image compression is improved upon by using Genetic Algorithms on a supercomputer to evolve transforms that have better image quality after image compression.
Early [(11)C]Flumazenil/H(2)O positron emission tomography predicts irreversible ischemic cortical damage in stroke patients receiving acute thrombolytic therapy.

BACKGROUND AND PURPOSE Central benzodiazepine receptor ligands, such as [(11)C]flumazenil (FMZ), are markers of neuronal integrity and therefore might be useful in the differentiation of functionally and morphologically damaged tissue early in ischemic stroke. We sought to assess the value of a benzodiazepine receptor ligand for the early identification of irreversible ischemic damage to cortical areas that cannot benefit from reperfusion. METHODS Eleven patients (7 male, 4 female, aged 52 to 75 years) with acute, hemispheric ischemic stroke were treated with alteplase (recombinant tissue plasminogen activator; 0.9 mg/kg according to National Institute of Neurological Disorders and Stroke protocol) within 3 hours of onset of symptoms. At the beginning of thrombolysis, cortical cerebral blood flow ([(15)O]H(2)O) and FMZ binding were assessed by positron emission tomography (PET). Those early PET findings were related to the change in neurological deficit (National Institutes of Health Stroke Scale) and to the extent of cortical damage on MRI or CT 3 weeks after the stroke. RESULTS Hypoperfusion was observed in all cases, and in 8 patients the values were below critical thresholds estimated at 12 mL/100 g per minute, comprising 1 to 174 cm(3) of cortical tissue. Substantial reperfusion was seen in most of these regions 24 hours after thrombolysis. In 4 cases, distinct areas of decreased FMZ binding were detected. Those patients suffered permanent lesions in cortical areas corresponding to their FMZ defects (112 versus 146, 3 versus 3, 2 versus 1, and 128 versus 136 cm(3)). In the other patients no morphological defects were detected on MRI or CT, although blood flow was critically decreased in areas ranging in size up to 78 cm(3) before thrombolysis. CONCLUSIONS These findings suggest that imaging of benzodiazepine receptors by FMZ PET distinguishes between irreversibly damaged and viable penumbra tissue early after acute stroke.
A hybrid PAPR reduction scheme for OFDM using SLM with clipping at the transmitter, and sparse reconstruction at the receiver

This paper presents a technique to handle the problem of high peak-to-average power ratio (PAPR) in orthogonal frequency-division multiplexing (OFDM) systems. The presented scheme is a combination of two well-known techniques, namely selected mapping (SLM) and clipping. In contrast to other hybrid schemes, where the mentioned techniques are performed consecutively, we integrate the clipping procedure in the SLM algorithm. This yields an additional PAPR reduction compared to the serial combination. Further, the clipping strategies are considered with focus on receiver-side peak reconstruction using methods provided by the theory of Compressed Sensing. Knowledge on the clipping strategies at the receiver yields an additional gain in peak reconstruction and reduces the bit error probability of the transmission. Simulation results verify the performance of the presented scheme.
Localized spectro-temporal features for automatic speech recognition

Recent results from physiological and psychoacoustic studies indicate that spectrally and temporally localized time-frequency envelope patterns form a relevant basis of auditory perception. This motivates new approaches to feature extraction for automatic speech recognition (ASR) which utilize two-dimensional spectro-temporal modulation ﬁlters. The paper provides a mo-tivation and a brief overview on the work related to Localized Spectro-Temporal Features (LSTF). It further focuses on the Gabor feature approach, where a feature selection scheme is applied to automatically obtain a suitable set of Gabor-type features for a given task. The optimized feature sets are examined in ASR experiments with respect to robustness and their statistical properties are analyzed.
Low-cost and Faster Tracking Systems Using Core-sets for Pose-Estimation

How can a \$20 toy quadcopter hover using a weak "Internet of Things" mini-board and a web-cam? In the pose-estimation problem we need to rotate a set of $n$ marker (points) and choose one of their n! permutations, so that the sum of squared corresponding distances to another ordered set of $n$ markers is minimized. A popular heuristic for this problem is ICP. We prove that \emph{every} set has a weighted subset (core-set) of constant size (independent of $n$), such that computing the optimal orientation of the small core-set would yield \emph{exactly} the same result as using the full set of $n$ markers. A deterministic algorithm for computing this core-set in $O(n)$ time is provided, using the Caratheodory Theorem from computational geometry. We developed a system that enables low-cost and real-time tracking by computing this core-set on the cloud in one thread, and uses the last computed core-set locally in a parallel thread. Our experimental results show how these core-sets can boost the tracking time and quality for large and even small sets of both IR and RGB markers on a toy quadcopter. Open source code for the system and algorithm is provided
Fundamental aspects of Pickering emulsion stabilisation

Much research has been carried out in recent years on Pickering emulsions, but understanding of the underlying physics requires considerable strengthening. This thesis seeks to address several fundamental aspects by presenting the results of recent experimental work. This work has focused on a model oil-in-water emulsion system stabilised by fluorescent colloidal silica particles and using a mixture of dodecane and isopropyl myristate as the oil phase. The phase behaviour of the particle dispersions has been altered using sodium chloride and sodium iodide, whilst sodium hydroxide and hydrochloric acid have been used to adjust the pH of samples. Comparisons are also made to emulsions stabilised by commercially available fumed silica. Conventionally, it was assumed that a weakly flocculating particle dispersion is required in order to generate a stable Pickering emulsion. It is shown in this work, however, that in some circumstances a weakly flocculating dispersion leads to the least stable emulsion. It is therefore argued that a more nuanced view of Pickering stabilisation is required, taking into account the factors affecting whether particles will adsorb to the interface during emulsification. Very recently it has begun to be suspected that Pickering emulsions sometimes aggregate due to the sharing of particles between two droplets, an effect known as bridging. In this thesis it is also shown that particle bridges can form in Pickering emulsions at high shear, and that they can subsequently be broken by low shear or by modifying the particle wettability. For the first time, electron microscopy has been used to provide direct evidence of droplets sharing particles. A simple theoretical model is developed, based on collisions between partially coated droplets, which captures the trends observed experimentally. It is argued that particle bridging may have been overlooked in the literature, and that the shear history of emulsions is a crucial determinant of subsequent behaviour.
Field emission effects of nitrogenated carbon nanotubes on chlorination and oxidation

With reference to our recent reports [Appl. Phys. Lett. 90, 192107 (2007); Appl. Phys. Lett. 91, 202102 (2007)] about the electronic structure of chlorine treated and oxygen-plasma treated nitrogenatcd carbon nanotubes (N-CNTs), here we studied the electron field emission effects on chlorination (N-CNT:Cl) and oxidation (N-CNT:O) of N-CNT. A high current density (J) of 15.0 mA/cm(2) has been achieved on chlorination, whereas low J of 0.0052 mA/cm(2) is observed on oxidation compared to J=1.3 mA/cm(2) for untreated N-CNT at an applied electric field E-A of similar to 1.9 V/mu m. The turn-on electric field (E-TO) was similar to 0.875. The 1.25 V/mu m was achieved for N-CNT:C1 and N-CNT:O, respectively, with respect to E-TO= 1.0 V/mu n for untreated one. These findings are due to the formation of different bonds with carbon and nitrogen in the N-CNT during the process of chlorine (oxygen)-plasma treatment by the charge transfer, or else that changes the density of free charge carriers and hence enhances (reduces) the field emission properties of N-CNTs:C1 (N-CNTs:O). (C) 2008 American Institute of Physics. [DOI: 10. 1063/1.2981090]