Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune Antibodies and Helminth Products Drive CXCR2-Dependent Macrophage-Myofibroblast Crosstalk to Promote Intestinal Repair

Helminth parasites can cause considerable damage when migrating through host tissues, thus making rapid tissue repair imperative to prevent bleeding and bacterial dissemination particularly during enteric infection. However, how protective type 2 responses targeted against these tissue-disruptive multicellular parasites might contribute to homeostatic wound healing in the intestine has remained unclear. Here, we observed that mice lacking antibodies (Aid-/-) or activating Fc receptors (Fcrg-/-) displayed impaired intestinal repair following infection with the murine helminth Heligmosomoides polygyrus bakeri (Hpb), whilst transfer of immune serum could partially restore chemokine production and rescue wound healing in Aid-/- mice. Impaired healing was associated with a reduced expression of CXCR2 ligands (CXCL2/3) by macrophages (MΦ) and myofibroblasts (MF) within intestinal lesions. Whilst antibodies and helminths together triggered CXCL2 production by MΦ in vitro via surface FcR engagement, chemokine secretion by intestinal MF was elicited by helminths directly via Fcrg-chain/dectin2 signaling. Blockade of CXCR2 during Hpb challenge infection reproduced the delayed wound repair observed in helminth infected Aid-/- and Fcrg-/- mice. Finally, conditioned media from human MΦ stimulated with infective larvae of the helminth Ascaris suum together with immune serum, promoted CXCR2-dependent scratch wound closure by human MF in vitro. Collectively our findings suggest that helminths and antibodies instruct a chemokine driven MΦ-MF crosstalk to promote intestinal repair, a capacity that may be harnessed in clinical settings of impaired wound healing.
High-temperature brazing of molybdenum to 12Cr18Ni10Ti steel with the CTEMET 1301 rapidly quenched nickel brazing alloy

Abstract Extensive studies are being carried out to develop a divertor (Divertor: a device in a thermonuclear reactor, intended for receiving of particle flows and radiation from the periphery of the plasma column. It is the most heavily loaded part of the reactor chamber surfaces with energy fluxes.) for tokamaks with a container for supplying liquid metal to the reception surface, with the construction of actual structures with high reliability and long service life. In this case, it is necessary to develop methods for joining dissimilar materials. In the transition section, molybdenum and steel (12Cr18Ni10Ti) pipes are joined by brazing. In this work, the method of producing a strong, heat resisting and hermetic joint between molybdenum and 12Cr18Ni10Ti corrosion-resisting steel is developed. Brazing is carried out using a paste based on CTEMET-1301 brazing alloy. The method of assembling the components in order to produce optimum gaps in brazing resulting in the homogeneous brazed joint without the formation of a brittle eutectic interlayer is developed. The brazed specimens were tested for heat resistance, leak tightness and service life at the given load. All the specimens withstood the tests. The mechanical properties of the brazed joints were determined by measuring the microhardness of the region of the welded joint and by shear tests. The results show that the strength characteristics depend strongly on the size of the gap between the brazed components. For the specimens assembled with the optimum gap the ultimatum shear strength was 500 ± 50 MPa.
On-chip Frequency Comb Generation at Visible Wavelengths via Simultaneous Second-and Third-order Optical Nonlinearities References and Links

Microresonator-based frequency comb generation at or near visible wavelengths would enable applications in precise optical clocks, frequency metrology, and biomedical imaging. Comb generation in the visible has been limited by strong material dispersion and loss at short wavelengths, and only very narrowband comb generation has reached below 800 nm. We use the second-order optical nonlinearity in an integrated high-Q silicon nitride ring resonator cavity to convert a near-infrared frequency comb into the visible range. We simultaneously demonstrate parametric frequency comb generation in the near-infrared, second-harmonic generation, and sum-frequency generation. We measure 17 comb lines converted to visible wavelengths extending to 765 nm. Towards an accurate frequency standard at 778 nm using a laser diode stabilized on a hyperfine component of the doppler-free two-photon transitions in rubidium, " Opt. Tailored anomalous group-velocity dispersion in silicon channel waveguides, " Opt.
Efficient Algorithms for Routing Interchangeable Terminals

This paper presents new algorithms for routing two rows of interchangeable terminals across a 2-layer channel. The number of horizontal tracks required for routing is significantly reduced by simply interchanging terminals in each cell. Savings up to one-third of horizontal tracks or more are achieved by interchanging terminals. The Deutsch Difficult Example is used as a test routing problem. The number of horizontal segments per net is limited to one, no "doglegs. " The program is coded in Pascal and implemented on a VAX-11/780 computer.
Recommending adaptive changes for framework evolution

In the course of a framework's evolution, changes ranging from a simple refactoring to a complete rearchitecture can break client programs. Finding suitable replacements for framework elements that were accessed by a client program and deleted as part of the framework's evolution can be a challenging task. We present a recommendation system, SemDiff, that suggests adaptations to client programs by analyzing how a framework adapts to its own changes. In a study of the evolution of the Eclipse JDT framework and three client programs, our approach recommended relevant adaptive changes with a high level of precision, and detected non-trivial changes typically undiscovered by current refactoring detection techniques.
Java code patterns for Petri net based behavioral models

CNet is a component-based conception for graphically designing modular, concurrent, and distributed control systems based on Petri nets. CNet components can be considered an alternative to IEC 61499 functions blocks. The elements forming the components' interfaces are derived from a special class of colored Petri nets, called PNet. A mapping of these interface definitions to Java language constructs has been proposed and published. In this paper we present Java code patterns that implement the behavior of the PNet language elements. These code patterns allow the automatic code generation of CNet component descriptions preserving the event-discrete and concurrent character of the Petri net representation. The concepts are explained and demonstrated using CNet/PNet, but they may be generalized and applied to other design conceptions like IEC 61499 or UML activity diagrams.
Abstraction based solution of complex attainability problems for decomposable continuous plants

The focus of the present paper is systems of nonlinear continuous sub-plants that share a common input but are otherwise coupled only through the specification of a control problem, possibly including state constraints. Examples include cart-pole systems and collision avoidance problems involving multiple vehicles. We propose a method that uses finite state models for solving highly complex continuous attainability problems. We first prove that finite state models, also called discrete abstractions, of the overall plant may be obtained as products of abstractions of sub-plants. The latter, which we call factors, may be determined quickly and concurrently. We also modify a state-of-the-art algorithm for the discrete, auxiliary attainability problems that arise, to work directly with the set of factors and prove that the asymptotic computational complexity of the modified algorithm matches that of the original one. In practice, the latter will often be much slower since the representation of the abstraction of the overall plant on a computer is likely to require an excessive amount of memory. Practicability of our method is demonstrated by successfully designing discrete controllers that globally stabilize decomposable nonlinear continuous plants whose overall finite state models would include millions of states and billions of transitions. Working with the factors instead, problem data fit into main memory of a customary personal computer, and computations take only minutes.
Spatial and temporal variability across life's hierarchies in the terrestrial Antarctic

Antarctica and its surrounding islands lie at one extreme of global variation in diversity. Typically, these regions are characterized as being species poor and having simple food webs. Here, we show that terrestrial systems in the region are nonetheless characterized by substantial spatial and temporal variations at virtually all of the levels of the genealogical and ecological hierarchies which have been thoroughly investigated. Spatial variation at the individual and population levels has been documented in a variety of genetic studies, and in mosses it appears that UV-B radiation might be responsible for within-clump mutagenesis. At the species level, modern molecular methods have revealed considerable endemism of the Antarctic biota, questioning ideas that small organisms are likely to be ubiquitous and the taxa to which they belong species poor. At the biogeographic level, much of the relatively small ice-free area of Antarctica remains unsurveyed making analyses difficult. Nonetheless, it is clear that a major biogeographic discontinuity separates the Antarctic Peninsula and continental Antarctica, here named the ‘Gressitt Line’. Across the Southern Ocean islands, patterns are clearer, and energy availability is an important correlate of indigenous and exotic species richness, while human visitor numbers explain much of the variation in the latter too. Temporal variation at the individual level has much to do with phenotypic plasticity, and considerable life-history and physiological plasticity seems to be a characteristic of Antarctic terrestrial species. Environmental unpredictability is an important driver of this trait and has significantly influenced life histories across the region and probably throughout much of the temperate Southern Hemisphere. Rapid climate change-related alterations in the range and abundance of several Antarctic and sub-Antarctic populations have taken place over the past several decades. In many sub-Antarctic locations, these have been exacerbated by direct and indirect effects of invasive alien species. Interactions between climate change and invasion seem set to become one of the most significant conservation problems in the Antarctic. We conclude that despite the substantial body of work on the terrestrial biodiversity of the Antarctic, investigations of interactions between hierarchical levels remain scarce. Moreover, little of the available information is being integrated into terrestrial conservation planning, which lags far behind in this region by comparison with most others.
Evaluating The Quality of Generated Playlists Based on Hand-Crafted Samples

The automated generation of playlists represents a particular type of the music recommendation problem with two special characteristics. First, the tracks of the list are usually consumed immediately at recommendation time; second, tracks are listened to mostly in consecutive order so that the sequence of the recommended tracks can be relevant. A number of different approaches for playlist generation have been proposed in the literature. In this paper, we review the existing core approaches to playlist generation, discuss aspects of appropriate offline evaluation designs and report the results of a comparative evaluation based on different data sets. Based on the insights from these experiments, we propose a comparably simple and computationally tractable new baseline algorithm for future comparisons, which is based on track popularity and artist information and is competitive with more sophisticated techniques in our evaluation settings.
Numerical methods for linear complementarity problems in physics-based animation

This course provides an introduction to the definition of linear complementarity problems (LCPs) and outlines the derivation of a toolbox of numerical methods. It also presents a small convergence study on the methods to illustrate their numerical properties. The course is a good introduction to implementing numerical methods, because it includes tips and tricks for implementation based on considerable practical experience.
A simple continuous excitation model for parametric vocoding

We describe a continuous-pitch parametric vocoder suitable for speech coding and statistical text to speech synthesis. The spectral model is based on linear prediction. We show that glottal modelling techniques from recent literature can be cherry-picked to produce an excitation signal with properties known to be useful in the above application areas. We further show that the continuous pitch paradigm can be extended to glottal modelling. The resulting vocoder yields synthetic speech that is generally better than without glottal modelling; it has been used in a parametric speech coding application, and is freely available.
Weaker Regularity Conditions and Sparse Recovery in High-Dimensional Regression

Regularity conditions play a pivotal role for sparse recovery in high-dimensional regression. In this paper, we present a weaker regularity condition and further discuss the relationships with other regularity conditions, such as restricted eigenvalue condition. We study the behavior of our new condition for design matrices with independent random columns uniformly drawn on the unit sphere. Moreover, the present paper shows that, under a sparsity scenario, the Lasso estimator and Dantzig selector exhibit similar behavior. Based on both methods, we derive, in parallel, more precise bounds for the estimation loss and the prediction risk in the linear regression model when the number of variables can be much larger than the sample size.
Effect of reinforcement gradient on creep response in FG composite cylinders

The paper investigates the effect of varying reinforcement gradation index (m) on steady state creep behaviour of thick walled cylinder made of functionally graded composite under internal and external pressure. The SiCp reinforcement in the cylinder is assumed to vary radially according to the power law function with reinforcement gradation index (m). The distribution of SiCp reinforcement is uniform for m=0, increasing for m>0 and decreasing m<0 along the radial direction. The creep behavior of the composite is described by Norton’s Power law. The results obtained for FG cylinder are compared with those estimated for a uniform composite cylinder. The study reveals that for the radial stress in cylinder decreases throughout when the SiCp reinforcement content is decreasing (m<0) along the radius in the FGM cylinder. Upon imposing SiCp gradient, for non-linearly decreasing reinforcement content along the radius, in the composite cylinder, the tangential stress increases near the inner radius but decreases toward the outer radius. Unlike stresses, the tangential and radial strain rates in the composite cylinder reduce over the entire radius when the SiCp reinforcement content is decreasing (m<0) along the radius in the FGM cylinder.
Extracellular Blockade of K+ Channels by Tea

TEA is a classical blocker of K+ channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue at Shaker position 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992. Neuron. 8:483–491). The data suggest that TEA interacts simultaneously with the aromatic residues of the four monomers. The determination of the 3-D structure of the KcsA channel using X-ray crystallography (Doyle, D.A., J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998. Science. 280:69–77) has raised some issues that remain currently unresolved concerning the interpretation of these observations. In particular, the center of the Tyr82 side chains in KcsA (corresponding to position 449 in Shaker) forms a square of 11.8-Å side, a distance which is too large to allow simultaneous interactions of a TEA molecule with the four aromatic side chains. In this paper, the external blockade by TEA is explored by molecular dynamics simulations of an atomic model of KcsA in an explicit phospholipid bilayer with aqueous salt solution. It is observed, in qualitative accord with the experimental results, that TEA is stable when bound to the external side of the wild-type KcsA channel (with Tyr82), but is unstable when bound to a mutant channel in which the tyrosine residue has been substituted by a threonine. The free energy profile of TEA relative to the pore is calculated using umbrella sampling simulations to characterize quantitatively the extracellular blockade. It is found, in remarkable agreement with the experiment, that the TEA is more stably bound by 2.3 kcal/mol to the channel with four tyrosine residues. In the case of the wild-type KcsA channel, TEA (which has the shape of a flattened oblate spheroid) acts as an ideal plug blocking the pore. In contrast, it is considerably more off-centered and tilted in the case of the mutant channel. The enhanced stability conferred by the tyrosine residues does not arise from Π–cation interactions, but appears to be due to differences in the hydration structure of the TEA. Finally, it is shown that the experimentally observed voltage dependence of TEA block, which is traditionally interpreted in terms of the physical position of the TEA along the axis of the pore, must arise indirectly via coupling with the ions in the pore.
One‐ and two‐body decomposable Poisson‐Boltzmann methods for protein design calculations

Successfully modeling electrostatic interactions is one of the key factors required for the computational design of proteins with desired physical, chemical, and biological properties. In this paper, we present formulations of the finite difference Poisson‐Boltzmann (FDPB) model that are pairwise decomposable by side chain. These methods use reduced representations of the protein structure based on the backbone and one or two side chains in order to approximate the dielectric environment in and around the protein. For the desolvation of polar side chains, the two‐body model has a 0.64 kcal/mol RMSD compared to FDPB calculations performed using the full representation of the protein structure. Screened Coulombic interaction energies between side chains are approximated with an RMSD of 0.13 kcal/mol. The methods presented here are compatible with the computational demands of protein design calculations and produce energies that are very similar to the results of traditional FDPB calculations.
The KEGG resource for deciphering the genome

A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome. ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.
Large semilattices of breadth three

A 1984 problem of S.Z. Ditor asks whether there exists a lattice of cardinality @ 2, with zero, in which every principal ideal is finite and every element has at most three lower covers. We prove that the existence of such a lattice follows from either one of two axioms that are known to be independent of ZFC, namely (1) Martin's Axiom restricted to collections of @ 1 dense subsets in posets of precaliber @ 1, (2) the existence of a gap-1 morass. In particular, the existence of such a lattice is consistent with ZFC, while the non-existence of such a lattice implies that ! 2 is inaccessible in the constructible universe. We also prove that for each regular uncountable cardinaland each positive integer n, there exists a (_ ,0)-semilattice L of cardinality � +n and breadth n+1 in which every principal ideal has less thanelements.
Analysis of RPE morphometry in human eyes

Purpose To describe the RPE morphometry of healthy human eyes regarding age and topographic location using modern computational methods with high accuracy and objectivity. We tested whether there were regional and age-related differences in RPE cell area and shape. Methods Human cadaver donor eyes of varying ages were dissected, and the RPE flatmounts were immunostained for F-actin with AF635-phalloidin, nuclei stained with propidium iodide, and imaged with confocal microscopy. Image analysis was performed using ImageJ (NIH) and CellProfiler software. Quantitative parameters, including cell density, cell area, polygonality of cells, number of neighboring cells, and measures of cell shape, were obtained from these analyses to characterize individual and groups of RPE cells. Measurements were taken from selected areas spanning the length of the temporal retina through the macula and the mid-periphery to the far periphery. Results Nineteen eyes from 14 Caucasian donors of varying ages ranging from 29 to 80 years were used. Along a horizontal nasal to temporal meridian, there were differences in several cell shape and size characteristics. Generally, the cell area and shape was relatively constant and regular except in the far periphery. In the outer third of the retina, the cell area and shape differed from the inner two-thirds statistically significantly. In the macula and the far periphery, an overall decreasing trend in RPE cell density, percent hexagonal cells, and form factor was observed with increasing age. We also found a trend toward increasing cell area and eccentricity with age in the macula and the far periphery. When individuals were divided into two age groups, <60 years and ≥60 years, there was a higher cell density, lower cell area, lower eccentricity, and higher form factor in the younger group in the macula and the far periphery (p<0.05 for all measurements). No statistically significant differences in RPE morphometry between age groups were found in the mid-periphery. Conclusions Human cadaver RPE cells differ mainly in area and shape in the outer one third compared to the inner two-thirds of the temporal retina. RPE cells become less dense and larger, lose their typical hexagonal shape, and become more oval with increasing age.