Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of telocytes in skeletal muscle interstitium: implication for muscle regeneration

Skeletal muscle interstitium is crucial for regulation of blood flow, passage of substances from capillaries to myocytes and muscle regeneration. We show here, probably, for the first time, the presence of telocytes (TCs), a peculiar type of interstitial (stromal) cells, in rat, mouse and human skeletal muscle. TC features include (as already described in other tissues) a small cell body and very long and thin cell prolongations—telopodes (Tps) with moniliform appearance, dichotomous branching and 3D‐network distribution. Transmission electron microscopy (TEM) revealed close vicinity of Tps with nerve endings, capillaries, satellite cells and myocytes, suggesting a TC role in intercellular signalling (via shed vesicles or exosomes). In situ immunolabelling showed that skeletal muscle TCs express c‐kit, caveolin‐1 and secrete VEGF. The same phenotypic profile was demonstrated in cell cultures. These markers and TEM data differentiate TCs from both satellite cells (e.g. TCs are Pax7 negative) and fibroblasts (which are c‐kit negative). We also described non‐satellite (resident) progenitor cell niche. In culture, TCs (but not satellite cells) emerge from muscle explants and form networks suggesting a key role in muscle regeneration and repair, at least after trauma.
The Nociceptin/Orphanin FQ Receptor Antagonist UFP-101 Reduces Microvascular Inflammation to Lipopolysaccharide In Vivo

Microvascular inflammation occurs during sepsis and the endogenous opioid-like peptide nociceptin/orphanin FQ (N/OFQ) is known to regulate inflammation. This study aimed to determine the inflammatory role of N/OFQ and its receptor NOP (ORL1) within the microcirculation, along with anti-inflammatory effects of the NOP antagonist UFP-101 (University of Ferrara Peptide-101) in an animal model of sepsis (endotoxemia). Male Wistar rats (220 to 300 g) were administered lipopolysaccharide (LPS) for 24 h (-24 h, 1 mg kg-1; -2 h, 1 mg kg-1 i.v., tail vein). They were then either anesthetised for observation of the mesenteric microcirculation using fluorescent in vivo microscopy, or isolated arterioles (~200 µm) were studied in vitro with pressure myography. 200 nM kg-1 fluorescently labelled N/OFQ (FITC-N/OFQ, i.a., mesenteric artery) bound to specific sites on the microvascular endothelium in vivo, indicating sparse distribution of NOP receptors. In vitro, arterioles (~200 µm) dilated to intraluminal N/OFQ (10-5M) (32.6 + 8.4%) and this response was exaggerated with LPS (62.0 +7.9%, p=0.031). In vivo, LPS induced macromolecular leak of FITC-BSA (0.02 g kg-1 i.v.) (LPS: 95.3 (86.7 to 97.9)%, p=0.043) from post-capillary venules (<40 µm) and increased leukocyte rolling as endotoxemia progressed (p=0.027), both being reduced by 150 nmol kg-1 UFP-101 (i.v., jugular vein). Firstly, the rat mesenteric microcirculation expresses NOP receptors and secondly, NOP function (ability to induce dilation) is enhanced with LPS. UFP-101 also reduced microvascular inflammation to endotoxemia in vivo. Hence inhibition of the microvascular N/OFQ-NOP pathway may have therapeutic potential during sepsis and warrants further investigation.
Evaluation of a New Vasculature by High Resolution Light Microscopy: Primo Vessel and Node

The primo vascular system is composed of nodes and vessels. The bundle of sub-vessels of the promo vessel is laid into an external jacket composed of endothelial cells. The node is heterogeneous in nature, composed of twisted sub-vessel bundles that fill up nearly the entire node volume. The enlarged sub-vessel inside the node harbors microcells that express stem cells and stem cells niche markers. We conclude that these microcells are progenitors of multipotent stem cells and the nodes serve as the stem cell niches outside the bone marrow.
Block Krylov subspace methods for shifted systems with different right-hand sides

We present some new techniques for solving a family (or a sequence of families) of linear systems in which the coefficient matrices differ only by a scalar multiple of the identity (shifted systems). Our goal is to develop methods for shifted systems which have fewer restrictions usually associated with such methods (e.g., all residuals needing to be collinear). The systems are parameterized by i,
Tuning-free step-size adaptation

Incremental learning algorithms based on gradient descent are effective and popular in online supervised learning, reinforcement learning, signal processing, and many other application areas. An oft-noted drawback of these algorithms is that they include a step-size parameter that needs to be tuned for best performance, which may require manual intervention and significant domain knowledge or additional data. In many cases, an entire vector of step-size parameters (e.g., one for each input feature) needs to be tuned in order to attain the best performance of the algorithm. To address this, several methods have been proposed for adapting step sizes online. For example, Sutton's IDBD method can find the best vector step size for the LMS algorithm, and Schraudolph's ELK1 method, an extension of IDBD to neural networks, has proven effective on large applications, such as 3D hand tracking. However, to date all such step-size adaptation methods have included a tunable step-size parameter of their own, which we call the meta-step-size parameter. In this paper we show that the performance of existing step-size adaptation methods are strongly dependent on the choice of their meta-step-size parameter and that their meta-step-size parameter cannot be set reliably in a problem-independent way. We introduce a series of modifications and normalizations to the IDBD method that together eliminate the need to tune the meta-step-size parameter to the particular problem. We show that the resulting overall algorithm, called Autostep, performs as well or better than the existing step-size adaptation methods on a number of idealized and robot prediction problems and does not require any tuning of its meta-step-size parameter. The ideas behind Autostep are not restricted to the IDBD method and the same principles are potentially applicable to other incremental learning settings, such as reinforcement learning.
A Tutorial on Automated Text Categorisation

The automated categorisation (or classification) of texts into topical categories has a long history, dating back at least to 1960. Until the late ’80s, the dominant approach to the problem involved knowledge-engineering automatic categorisers, i.e. manually building a set of rules encoding expert knowledge on how to classify documents. In the ’90s, with the booming production and availability of on-line documents, automated text categorisation has witnessed an increased and renewed interest. A newer paradigm based on machine learning has superseded the previous approach. Within this paradigm, a general inductive process automatically builds a classifier by “learning”, from a set of previously classified documents, the characteristics of one or more categories; the advantages are a very good effectiveness, a considerable savings in terms of expert manpower, and domain independence. In this tutorial we look at the main approaches that have been taken towards automatic text categorisation within the general machine learning paradigm. Issues of document indexing, classifier construction, and classifier evaluation, will be touched upon. 1 A definition of the text categorisation task Document categorisation (or classification) may be seen as the task of determining an assignment of a value from {0,1} to each entry of the decision matrix d1 . dj . dn c1 a11 . a1j . a1n . ci ai1 . aij . ain . cm am1 . amj . amn where C = {c1, . , cm} is a set of pre-defined categories, and D = {d1, . , dn} is a set of documents to be categorised (sometimes called “requests”). A value of 1 for aij is interpreted as a decision to file dj under ci, while a value of 0 is interpreted as a decision not to file dj under ci. Fundamental to the understanding of this task are two observations: • the categories are just symbolic labels. No additional knowledge of their “meaning” is available to help in the process of building the categoriser; in particular, this means that the “text” constituting the label (e.g. Sports in a news categorisation task) cannot be used; • the attribution of documents to categories should, in general, be attributed on the basis of the content of the documents, and not on the basis of metadata (e.g. publication date,
Influences of CO2 Laser, FKL Laser, and Mechanical Cutting on the Magnetic Properties of Electrical Steel Sheets

The degrading influence of different cutting techniques on the magnetic behavior of electrical steel sheets has been well recognized. However, more research is needed to understand how the influences of different cutting techniques compare, notably with respect to laser versus mechanical cutting and for different materials. This paper addresses the influences of CO2 laser cutting, FKL laser cutting, and mechanical cutting on the magnetization characteristics and specific losses of electrical steel sheets determined by Epstein frame measurements on rectangular samples and by the measurements of stator lamination stacks. Experimental results based on three different materials commonly used with electric machines and investigated at different frequencies are provided.
Lung computed tomography density distribution in a porcine model of one-lung ventilation.

BACKGROUND One-lung ventilation (OLV) exposes the dependent lung to increased mechanical stress which may affect the postoperative course. This study evaluates regional pulmonary gas/tissue distribution in a porcine model of OLV. METHODS Nine anaesthetized and mechanically ventilated (V(T)=10 ml kg(-1), FI(O(2))=0.40, PEEP=5 cm H(2)O) pigs were studied. After lung separation by an endobronchial blocker, lateral thoracotomy and OLV were performed in six pigs. Three animals served as controls. Static end-expiratory and end-inspiratory spiral computed tomography (CT) scans were done before, during, and after OLV and at corresponding times in controls. CT images were analysed by defined regions of interest and summarized voxels were classified by defined lung X-ray density intervals (atelectasis, poorly aerated, normally aerated, and overaerated). RESULTS Dependent lungs contained poorly aerated regions and atelectasis with a significant tidal recruitment during conventional two-lung ventilation (TLV) before OLV (expiration vs inspiration: atelectasis 29% vs 14%; poorly aerated 66% vs 44%; normally aerated 4% vs 41% of the dependent lung volume, P<0.05). During OLV (V(T)=10 ml kg(-1)), cyclic recruitment was increased. The density spectrum of the ventilated lung changed from consolidation to aeration (expiration vs inspiration: atelectasis 10% vs 2%; poorly aerated 71% vs 18%; normally aerated 19% vs 79%, P<0.05). After OLV, increased aeration remained with less atelectasis and poorly aerated regions. Lung density distribution in the non-dependent lung of OLV pigs was unaltered after the period of complete lung collapse. CONCLUSIONS Cyclic tidal recruitment during OLV in pigs was associated with a persistent increase of aeration in the dependent lung.
Research directions in data wrangling: Visualizations and transformations for usable and credible data

In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of ‘data wrangling’ often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration arelongstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.
Contribution of Personality, Job Strain, and Occupational Self-Efficacy to Job Satisfaction in Different Occupational Contexts

Using a large sample of employed adults (N = 1,714) living in Switzerland, this study investigates the relationship between the five-factor model of personality dimensions and job satisfaction, considering the role of job strain as defined by Karasek’s job demand–control model and occupational self-efficacy. These relationships were assessed both within the overall sample of employed and specific occupational groups. The analyses on the overall sample show an effect of neuroticism and extraversion on job satisfaction. Furthermore, job strain and occupational self-efficacy are related to job satisfaction. The effect of neuroticism is partly mediated by job strain and occupational self-efficacy, while extraversion and conscientiousness have an indirect effect through occupational self-efficacy. When we consider the occupational groups, the results highlight differences between the groups showing variability in the relationship between personality, job strain and occupational self-efficacy, and their effects on job satisfaction.
Energy- and Cost-Efficiency Analysis of ARM-Based Clusters

General-purpose computing domain has experienced strategy transfer from scale-up to scale-out in the past decade. In this paper, we take a step further to analyze ARM-processor based cluster against Intel X86 workstation, from both energy-efficiency and cost-efficiency perspectives. Three applications are selected and evaluated to represent diversified applications, including Web server throughput, in-memory database, and video transcoding. Through detailed measurements, we make the observations that the energy-efficiency ratio of the ARM cluster against the Intel workstation varies from 2.6-9.5 in in-memory database, to approximately 1.3 in Web server application, and 1.21 in video transcoding. We also find out that for the Intel processor that adopts dynamic voltage and frequency scaling (DVFS) techniques, the power consumption is not linear with the CPU utilization level. The maximum energy saving achievable from DVFS is 20%. Finally, by utilizing a monthly cost model of data centers, we conclude that ARM cluster based data centers are feasible, and are advantageous in computationally lightweight applications, e.g. in-memory database and network-bounded Web applications. The cost advantage of ARM cluster diminishes progressively for computation-intensive applications, i.e. dynamic Web server application and video transcoding, because the number of ARM processors needed to provide comparable performance increases.
Atomic Carbon in Arp 220

We present detections of the 3P1-3P0 fine-structure line of neutral carbon and of the J=3-2 rotational line of carbon monoxide in the ultraluminous infrared galaxy Arp 220, obtained at the Caltech Submillimeter Observatory. C I emission in Arp 220 is found to be at the expected level in relation to the strong far-infrared (FIR) dust emission and to the CO emission, whereas the C II emission seen by the Infrared Space Observatory long-wavelength spectrometer is very weak. The C I data confirm the presence of a large mass of molecular gas in the nucleus of Arp 220, corresponding to a high extinction in the visible (Av=1000). For this galaxy, the total cooling due to atomic carbon is comparable to the total cooling due to carbon monoxide. We use the observed C I/CO (1-0) and CO (3-2)/CO (1-0) emissivity ratios, together with the photon-dominated region models, to infer an average gas density of n(H2) ≈ 104 cm−3. We estimate the UV radiation field in this galaxy from the FIR continuum, and independently from hydrogen recombination lines, to be about a factor of 40,000 larger than in the solar vicinity (G0=4×104). The relative weakness of the C II fine-structure line is explained by the large gas density, the exceptionally strong UV field, and the large dust opacity. C II emission from high-redshift analogs of Arp 220 may not be as easy to detect as had been anticipated. However, both CO and C I lines will still be strong emitters.
The Role of Inertial Sensitivity in Motor Planning

To achieve a given motor task a single trajectory must be chosen from the infinite set of possibilities consistent with the task. To investigate such motor planning in a natural environment, we examined the kinematics of reaching movements made around a visual obstacle in three-dimensional space. Within each session, the start and end points of the movement were uniformly varied around the obstacle. However, the distribution of the near points, where the paths came closest to the obstacle, showed a strong anisotropy, clustering at the poles of a preferred axis through the center of the obstacle. The preferred axes for movements made with the left and right arms were mirror symmetric about the midsagittal plane, suggesting that the anisotropy stems from intrinsic properties of the arm rather than extrinsic visual factors. One account of these results is a sensitivity model of motor planning, in which the movement path is skewed so that when the hand passes closest to the obstacle, the arm is in a configuration that is least sensitive to perturbations that might cause collision. To test this idea, we measured the mobility ellipse of the arm. The mobility minor axis represents the direction in which the hand is most inertially stable to a force perturbation. In agreement with the sensitivity model, the mobility minor axis was not significantly different from the preferred near point axis. The results suggest that the sensitivity of the arm to perturbations, as determined by its inertial stability, is taken into account in the planning process.
A new approach to Cholesky-based covariance regularization in high dimensions

In this paper we propose a new regression interpretation of the Cholesky factor of the covariance matrix, as opposed to the well-known regression interpretation of the Cholesky factor of the inverse covariance, which leads to a new class of regularized covariance estimators suitable for high-dimensional problems. Regularizing the Cholesky factor of the covariance via this regression interpretation always results in a positive definite estimator. In particular, one can obtain a positive definite banded estimator of the covariance matrix at the same computational cost as the popular banded estimator of Bickel & Levina (2008b), which is not guaranteed to be positive definite. We also establish theoretical connections between banding Cholesky factors of the covariance matrix and its inverse and constrained maximum likelihood estimation under the banding constraint, and compare the numerical performance of several methods in simulations and on a sonar data example. Copyright 2010, Oxford University Press.
Perturbation of Lytic and Latent Gammaherpesvirus Infection in the Absence of the Inhibitory Receptor CEACAM1

Control of gammaherpesvirus infections requires a complex, well orchestrated immune response regulated by positive and negative co-signaling molecules. While the impact of co-stimulatory molecules has been addressed in various studies, the role of co-inhibitory receptors has not been tested. The ITIM-bearing CEACAM1 is an inhibitory receptor expressed by a variety of immune cells, including B, T and NK cells. Using Ceacam1−/− mice, we analyzed the in vivo function of CEACAM1 during acute and latent murine gammaherpesvirus 68 (MHV-68) infection. During acute lytic replication, we observed lower virus titers in the lungs of Ceacam1−/− mice than in WT mice. In contrast, during latency amplification, Ceacam1−/− mice displayed increased splenomegaly and a higher latent viral load in the spleen. Analysis of the immune response revealed increased virus-specific antibody levels in Ceacam1−/− mice, while the magnitude of the T cell-mediated antiviral immune response was reduced. These findings suggest that inhibitory receptors can modulate the efficacy of immune responses against gammaherpesvirus infections.
Nonorthogonal Joint Diagonalization by Combining Givens and Hyperbolic Rotations

A new algorithm for computing the nonorthogonal joint diagonalization of a set of matrices is proposed for independent component analysis and blind source separation applications. This algorithm is an extension of the Jacobi-like algorithm first proposed in the joint approximate diagonalization of eigenmatrices (JADE) method for orthogonal joint diagonalization. The improvement consists mainly in computing a mixing matrix of determinant one and columns of equal norm instead of an orthogonal mixing matrix. This target matrix is constructed iteratively by successive multiplications of not only Givens rotations but also hyperbolic rotations and diagonal matrices. The algorithm performance, evaluated on synthetic data, compares favorably with existing methods in terms of speed of convergence and complexity.
The Final Frontier of pH and the Undiscovered Country Beyond

The comparison of volumes of cells and subcellular structures with the pH values reported for them leads to a conflict with the definition of the pH scale. The pH scale is based on the ionic product of water, K w = [H+]×[OH−]. We used K w [in a reversed way] to calculate the number of undissociated H2O molecules required by this equilibrium constant to yield at least one of its daughter ions, H+ or OH− at a given pH. In this way we obtained a formula that relates pH to the minimal volume VpH required to provide a physical meaning to K w, (where N A is Avogadro’s number). For example, at pH 7 (neutral at 25°C) VpH = 16.6 aL. Any deviation from neutral pH results in a larger VpH value. Our results indicate that many subcellular structures, including coated vesicles and lysosomes, are too small to contain free H+ ions at equilibrium, thus the definition of pH based on K w is no longer valid. Larger subcellular structures, such as mitochondria, apparently contain only a few free H+ ions. These results indicate that pH fails to describe intracellular conditions, and that water appears to be dissociated too weakly to provide free H+ ions as a general source for biochemical reactions. Consequences of this finding are discussed.