Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Protein Expression in Two Cholangiocarcinoma Cell Lines Undergoing Formation of Multicellular Tumor Spheroids In Vitro

Epithelial-to-Mesenchymal Transition (EMT) is relevant in malignant growth and frequently correlates with worsening disease progression due to its implications in metastases and resistance to therapeutic interventions. Although EMT is known to occur in several types of solid tumors, the information concerning tumors arising from the epithelia of the bile tract is still limited. In order to approach the problem of EMT in cholangiocarcinoma, we decided to investigate the changes in protein expression occurring in two cell lines under conditions leading to growth as adherent monolayers or to formation of multicellular tumor spheroids (MCTS), which are considered culture models that better mimic the growth characteristics of in-vivo solid tumors. In our system, changes in phenotypes occur with only a decrease in transmembrane E-cadherin and vimentin expression, minor changes in the transglutaminase protein/activity but with significant differences in the proteome profiles, with declining and increasing expression in 6 and in 16 proteins identified by mass spectrometry. The arising protein patterns were analyzed based on canonical pathways and network analysis. These results suggest that significant metabolic rearrangements occur during the conversion of cholangiocarcinomas cells to the MCTS phenotype, which most likely affect the carbohydrate metabolism, protein folding, cytoskeletal activity, and tissue sensitivity to oxygen.
Neuronal Activity in Rat Barrel Cortex Underlying Texture Discrimination

Rats and mice palpate objects with their whiskers to generate tactile sensations. This form of active sensing endows the animals with the capacity for fast and accurate texture discrimination. The present work is aimed at understanding the nature of the underlying cortical signals. We recorded neuronal activity from barrel cortex while rats used their whiskers to discriminate between rough and smooth textures. On whisker contact with either texture, firing rate increased by a factor of two to ten. Average firing rate was significantly higher for rough than for smooth textures, and we therefore propose firing rate as the fundamental coding mechanism. The rat, however, cannot take an average across trials, but must make an immediate decision using the signals generated on each trial. To estimate single-trial signals, we calculated the mutual information between stimulus and firing rate in the time window leading to the rat's observed choice. Activity during the last 75 ms before choice transmitted the most informative signal; in this window, neuronal clusters carried, on average, 0.03 bits of information about the stimulus on trials in which the rat's behavioral response was correct. To understand how cortical activity guides behavior, we examined responses in incorrect trials and found that, in contrast to correct trials, neuronal firing rate was higher for smooth than for rough textures. Analysis of high-speed films suggested that the inappropriate signal on incorrect trials was due, at least in part, to nonoptimal whisker contact. In conclusion, these data suggest that barrel cortex firing rate on each trial leads directly to the animal's judgment of texture.
A TLM-BASED NETWORK-ON-CHIP PERFORMANCE EVALUATION FRAMEWORK

The variety of interconnection structures presently nowadays for SoC (System-on-Chip), bus and networkson-Chip NoCs, each of them with a wide set of setup parameters, provides a huge amount of design alternatives. Although the interconnection structure is a key SoC component, there are few design tools in order to set the appropriate configuration parameters for a given application at the firsts stages of the SoC design. The present study aims to enhance the SoC communication platform design area, when a Networkon-Chip NoC is used. The novelty of this work is the performance evaluation of different NoC configuration at firsts stages of the SoC design flow (SystemC TLM). For evaluating the NoC a monitoring process was carried on. Our approach employed a set of metrics for NoC to elucidate the global and inner NoC behavior under a wide variety of traffic conditions.
Lie algebroid structures on a class of affine bundles

We introduce the notion of a Lie algebroid structure on an affine bundle whose base manifold is fibered over R. It is argued that this is the framework which one needs for coming to a time-dependent generalization of the theory of Lagrangian systems on Lie algebroids. An extensive discussion is given of a way one can think of forms acting on sections of the affine bundle. It is further shown that the affine Lie algebroid structure gives rise to a coboundary operator on such forms. The concept of admissible curves and dynamical systems whose integral curves are admissible brings an associated affine bundle into the picture, on which one can define in a natural way a prolongation of the original affine Lie algebroid structure.
A voltage-dependent persistent sodium current in mammalian hippocampal neurons

Currents generated by depolarizing voltage pulses were recorded in neurons from the pyramidal cell layer of the CA1 region of rat or guinea pig hippocampus with single electrode voltage-clamp or tight- seal whole-cell voltage-clamp techniques. In neurons in situ in slices, and in dissociated neurons, subtraction of currents generated by identical depolarizing voltage pulses before and after exposure to tetrodotoxin revealed a small, persistent current after the transient current. These currents could also be recorded directly in dissociated neurons in which other ionic currents were effectively suppressed. It was concluded that the persistent current was carried by sodium ions because it was blocked by TTX, decreased in amplitude when extracellular sodium concentration was reduced, and was not blocked by cadmium. The amplitude of the persistent sodium current varied with clamp potential, being detectable at potentials as negative as -70 mV and reaching a maximum at approximately -40 mV. The maximum amplitude at -40 mV in 21 cells in slices was -0.34 +/- 0.05 nA (mean +/- 1 SEM) and -0.21 +/- 0.05 nA in 10 dissociated neurons. Persistent sodium conductance increased sigmoidally with a potential between -70 and -30 mV and could be fitted with the Boltzmann equation, g = gmax/(1 + exp[(V' - V)/k)]). The average gmax was 7.8 +/- 1.1 nS in the 21 neurons in slices and 4.4 +/- 1.6 nS in the 10 dissociated cells that had lost their processes indicating that the channels responsible are probably most densely aggregated on or close to the soma. The half- maximum conductance occurred close to -50 mV, both in neurons in slices and in dissociated neurons, and the slope factor (k) was 5-9 mV. The persistent sodium current was much more resistant to inactivation by depolarization than the transient current and could be recorded at greater than 50% of its normal amplitude when the transient current was completely inactivated. Because the persistent sodium current activates at potentials close to the resting membrane potential and is very resistant to inactivation, it probably plays an important role in the repetitive firing of action potentials caused by prolonged depolarizations such as those that occur during barrages of synaptic inputs into these cells.
Precise Characterization of the Penumbra Revealed by MRI: A Modified Photothrombotic Stroke Model Study

Aims To precisely characterize the penumbra by MRI based on a modified photothrombotic stroke mouse model. Methods The proximal middle cerebral artery was occluded by a convenient laser system in conjunction with an intravenous injection of Rose Bengal in mice. And the suture MCAO model was performed in seven mice as a comparison of the reproducibility. One hour after occlusion, the penumbra was defined in six random photothrombotic stroke mice by mismatch between perfusion-weighted imaging and the apparent diffusion coefficient map on a home-made workstation. After imaging, three random mice of them were chosen to perform the reperfusion surgery. And the other three mice were sacrificed to stain for several potential penumbra markers, such as c-fos and heart shock protein 90. In the remaining mice, the evolution of the lesions was detected on the apparent diffusion coefficient map, diffusion-weighted imaging and T2-weighted imaging at 1, 3, 6, 12 and 24 hours. After evaluating the neurological deficit scores, the brains were sectioned and stained by triphenyltetrazolium chloride and Nissl. Results The mice subjected to photothrombosis showed significant behavioral deficits. One hour after occlusion, the low perfusion areas on the perfusion-weighted imaging interlaced with the hypointense areas on the apparent diffusion coefficient map, demonstrating that the penumbra was located both surrounding and inside the lesions. This phenomenon was subsequently confirmed by the c-fos and heart shock protein 90 staining. The final T2-weighted images of the mice subjected to the reperfusion surgery were also consistent with the penumbra images at one hour. At early stages, the lesions were clearly identified on the apparent diffusion coefficient map; the volumes of the lesions on the diffusion-weighted imaging and T2-weighted imaging did not reach a maximum until 12 hours. The coefficient of variation (CV) of the final lesions in the photothrombotic stroke mice was 21.7% (0.08 of 0.37) on T2-weighted imaging and 27.8% (0.10 of 0.35) on triphenyltetrazolium chloride, representing a high reproducibility (n = 7). While the CV of the lesions in the MCAO stroke mice was only 70% (0.24 of 0.34, n = 4). Conclusions This study has provided a precise imaging definition of the penumbra based on a reproducible photothrombotic stroke mouse model.
Kernel-function Based Algorithms for Semidefinite Optimization

Recently, Y.Q. Bai, M. El Ghami and C. Roos [3] introduced a new class of so-called eligible kernel functions which are defined by some simple conditions. The authors designed primal-dual interiorpoint methods for linear optimization (LO) based on eligible kernel functions and simplified the analysis of these methods considerably. In this paper we consider the semidefinite optimization (SDO) problem and we generalize the aforementioned results for LO to SDO. The iteration bounds obtained are analogous to the results in [3] for LO.
Guest Editorial : Advances in Cloud Computing

The possibility to migrate a virtual server from one physical computer in a cloud to another physical computer in the same cloud is important in order to obtain a balanced load. In order to facilitate live migration of virtual servers, one needs to provide large shared storage systems that are accessible for all the physical servers that are used in the cloud. Distributed storage systems offer reliable and cost-effective storage of large amounts of data and such storage systems will be used in future Cloud Computing. We have evaluated four large distributed storage systems. Two of these use Distributed Hash Tables (DHTs) in order to keep track of how data is distributed, and two systems use multicasting to access the stored data. We measure the read/write/delete performance, as well as the recovery time when a storage node goes down. The evaluations are done on the same hardware, consisting of 24 storage nodes and a total storage capacity of 768 TB of data. These evaluations show that the multicast approach outperforms the DHT approach.
Enhanced Gaussian Mixture Model for Indoor Positioning Accuracy

Received Signal Strength Indicator (RSSI) is used in indoor positioning for measuring object distance to the base station. However, acquiring accurate RSSI values is challenging because wireless interference factors, such as multipath decline interference, make RSSI values of the same object fluctuate over time. Therefore, instead of a single RSSI, RSSI acquisition will collect a set of RSSI values from which the most moderate RSSI is derived. For this purpose, we propose an Enhanced Gaussian Mixture Model (EGMM) to derive a more precise RSSI for improving indoor positioning accuracy. EGMM enhances Gaussian Mixture Model (GMM) by applying Akaike information criterion (AIC) to determine the best K value for GMM to divide RSSI values into K sets representing signals from different paths. Then, EGMM identifies the most appropriate set of RSSI values to derive a more precise RSSI and thus improves the accuracy of indoor positioning. Our EGMM solution performs well in an open indoor space. The experiment is conducted with iBeacon devices, and the average error distance of EGMM is about 64% of those generated by existing Gaussian filtering. The average positioning error of EGMM is about 0.48 meter, which is adequate to indoor positioning accuracy.
Dynamic Bandwidth Allocation Based on Online Traffic Prediction for Real-Time MPEG-4 Video Streams

The distinct characteristics of variable bit rate (VBR) video traffic and its quality of service (QoS) constraints have posed a unique challenge on network resource allocation and management for future integrated networks. Dynamic bandwidth allocation attempts to adaptively allocate resources to capture the burstiness of VBR video traffic, and therefore could potentially increase network utilization substantially while still satisfying the desired QoS requirements. We focus on prediction-based dynamic bandwidth allocation. In this context, the multiresolution learning neural-network-based traffic predictor is rigorously examined. A well-known-heuristic based approach RED-VBR scheme is used as a baseline for performance evaluation. Simulations using real-world MPEG-4 VBR video traces are conducted, and a comprehensive performance metrics is presented. In addition, a new concept of renegotiation control is introduced and a novel renegotiation control algorithm based on binary exponential backoff (BEB) is proposed to efficiently reduce renegotiation frequency.
A dual threshold calculating method for fiber's edge extraction

In the fiber cross-sectional image analysis system, correctly detecting fiber's edge is critical for fiber geometric feature extraction and further fiber identification. In this paper, a dual threshold calculating method is proposed to obtain accurate and continuous fiber edge, as well as to control the image noise. After eliminating the non-uniform illumination in the fiber image, the low threshold is calculated based on the statistics histogram of the standard deviation of pixels' gray level in the image. And then the high threshold is computed by bisection algorithm combined with the low threshold. After tracing and denoising algorithm, the fiber wall that can correctly describe fiber's contour is detected. The pseudo edges and dual edges detected by traditional algorithms are eliminated, and image noise is well reduced. The experimental result shows that the proposed dual threshold selection algorithm is simple, convenient and efficient to extract fiber edge from fiber cross-sectional image.
Selenium-Substituted Hydroxyapatite/Biodegradable Polymer/Pamidronate Combined Scaffold for the Therapy of Bone Tumour

The present study evaluated a new concept of combined scaffolds as a promising bone replacement material for patients with a bone tumour or bone metastasis. The scaffolds were composed of hydroxyapatite doped with selenium ions and a biodegradable polymer (linear or branched), and contained an active substance—bisphosphonate. For this purpose, a series of biodegradable polyesters were synthesized through a ring-opening polymerization of ε-caprolactone or d,l-lactide in the presence of 2-hydroxyethyl methacrylate (HEMA) or hyperbranched 2,2-bis(hydroxymethyl)propionic acid polyester-16-hydroxyl (bis-MPA) initiators, substances often used in the synthesis of medical materials. The polymers were obtained with a high yield and a number-average molecular weight up to 45,300 (g/mol). The combined scaffolds were then manufactured by a direct compression of pre-synthesized hydroxyapatite doped with selenite or selenate ions, obtained polymer and pamidronate as a model drug. It was found that the kinetic release of the drug from the scaffolds tested in vitro under physiological conditions is strongly dependent on the physicochemical properties and average molecular weight of the polymers. Furthermore, there was good correlation with the hydrolytic biodegradation results of the scaffolds fabricated without drug. The preliminary findings suggest that the fabricated combined scaffolds could be effectively used for the sustained delivery of bioactive molecules at bone defect sites.
POWERFUL H2 EMISSION AND STAR FORMATION ON THE INTERACTING GALAXY SYSTEM Arp 143: OBSERVATIONS WITH SPITZER AND GALEX

We present new mid-infrared (IR; 5–35 μm) and ultraviolet (1539–2316 Å) observations of the interacting galaxy system Arp 143 (NGC 2444/2445) from the Spitzer Space Telescope and Galaxy Evolution Explorer. In this system, the central nucleus of NGC 2445 is surrounded by knots of massive star formation in a ringlike structure. We find unusually strong emission from warm H2 associated with an expanding shock wave between the nucleus and the western knots. At this ridge, the flux ratio between H2 and polycyclic aromatic hydrocarbon (PAH) emission is nearly ten times higher than in the nucleus. Arp 143 is one of the most extreme cases known in that regard. From our multiwavelength data, we derive a narrow age range of the star forming knots between 2 Myr and 7.5 Myr, suggesting that the ring of knots was formed almost simultaneously in response to the shock wave traced by the H2 emission. However, the knots can be further subdivided into two age groups: those with an age of 2–4 Myr (knots A, C, E, and F), which are associated with 8 μm emission from PAHs, and those with an age of 7–8 Myr (knots D and G), which show little or no 8 μm emission shells surrounding them. We attribute this finding to an aging effect of the massive clusters which, after about 6 Myr, no longer excite the PAHs surrounding the knots.
Dye-interleaved nanocomposite: Indigo carmine and methyl orange in the lamella of zinc-aluminium-layered double hydroxide

Layered organic-inorganic hybrid nanocomposite, containing an organic dye in an inorganic interlayer was prepared using indigo carmine (IC) and methyl orange (OM) as a guest in Zn2-Al layered double hydroxide (LDH) inorganic host by a ion exchange , with [Zn2-Al-Cl] LDH in aqueous solution. The affinity of the LDH with the dyes was studied as a function of contact time, initial pH of the solutions and initial dye concentration. It was found that 8h is enough time for the equilibrium state to be reached in IC and OM adsorption. IC and OM retention was independent of the initial pH. The adsorption isotherm of IC and OM, described by the Langmuir model, is of L-type. Powder X-ray diffractogram shows that the basal spacing of the Zn2-Al layered double hydroxide with Chloride as intergallery anion [Zn2-Al-Cl] expanded from 0.78 nm to 2.22 nm for the Zn2-Al layered double hydroxide-IC layered organic-inorganic hybrid nanocomposite [Zn2-Al-IC] and 2.4 nm for the Zn2-Al layered double hydroxide-OM layered organic-inorganic hybrid nanocomposite [Zn2-Al-OM].
ESTIMATION OF THE NOISE VARIANCE FROM THE BACKGROUND HISTOGRAM MODE OF AN MR IMAGE

In the literature, many methods are available for estimation of the variance of the noise in magnetic resonance (MR) images. A commonly used method, based on the maximum of the background mode of the histogram, is revisited and a new, robust and easy to use method is presented based on maximum likelihood (ML) estimation. Both methods are evaluated in terms of accuracy and precision using simulated MR data. It is shown that the newly proposed method outperforms the commonly used method in terms of mean-squared-error.
Impaired Cerebrovascular Reactivity With Steal Phenomenon Is Associated With Increased Diffusion in White Matter of Patients With Moyamoya Disease

Background and Purpose— Reduced cerebrovascular reactivity (CVR) with steal phenomenon is an independent predictor for stroke and may indicate tissue exposed to episodic low-grade ischemia. The apparent diffusion coefficient (ADC) calculated using diffusion-weighted MRI is effective in characterizing focal brain ischemia and subtle structural changes in normal-appearing white matter (WM). We hypothesized that regions of steal phenomenon are associated with increased ADC in normal-appearing WM of patients with Moyamoya disease. Methods— Twenty-two patients with unilateral CVR impairment secondary to Moyamoya disease and 12 healthy control subjects underwent diffusion-weighted MRI and functional MRI mapping of the cerebrovascular response to hypercapnia. Parametric maps of ADC and CVR were calculated, coregistered, and segmented using automated image processing methods. ADC of normal-appearing WM was compared between hemispheres, and between WM with negative CVR (ie, steal phenomenon) and WM with positive CVR. Results— In patients, ADC of normal-appearing WM was elevated in the hemisphere ipsilateral to the CVR impairment compared with the contralateral hemisphere (P<0.005) and in WM with negative CVR compared with WM with positive CVR (P<0.001). WM in regions of steal phenomenon within the affected hemisphere had higher ADC than homologous contralateral WM (P<0.005). In control subjects, negative CVR in WM was not associated with elevated ADC. Conclusions— Regions of steal phenomenon are spatially correlated with elevated ADC in normal-appearing WM of patients with Moyamoya disease. This structural abnormality may reflect low-grade ischemic injury after exhaustion of the cerebrovascular reserve capacity.
On Selecting the Right Optimizations for Virtual Machine Migration

To reduce the migration time of a virtual machine and network traffic generated during migration, existing works have proposed a number of optimizations to pre-copy live migration. These optimizations are delta compression, page skip, deduplication, and data compression. The cost-benefit analysis of these optimizations may preclude the use of certain optimizations in specific scenarios. However, no study has compared the performance & cost of these optimizations, and identified the impact of application behaviour on performance gain. Hence, it is not clear for a given migration scenario and an application, what is the best optimization that one must employ? In this paper, we present a comprehensive empirical study using a large number of workloads to provide recommendations on selection of optimizations for pre-copy live migration. The empirical study reveals that page skip is an important optimization as it reduces network traffic by 20% with negligible additional CPU cost. Data compression yields impressive gains in reducing network traffic (37%) but at the cost of a significant increase in CPU consumption (5×). De-duplication needs to be applied with utmost care as the increase in CPU utilization might outweigh the benefits considerably. The combination of page skip and data compression works the best across workloads and results in a significant reduction in network traffic (40%).
Revised Estimates for the Number of Human and Bacteria Cells in the Body

We critically revisit the “common knowledge” that bacteria outnumber human cells by a ratio of at least 10:1 in the human body. We found the total number of bacteria in the “reference man” to be 3.9·1013, with an uncertainty (SEM) of 25%, and a variation over the population (CV) of 52%. For human cells we identify the dominant role of the hematopoietic lineage to the total count of body cells (≈90%), and revise past estimates to reach a total of 3.0·1013 human cells in the 70 kg “reference man” with 2% uncertainty and 14% CV. Our analysis updates the widely-cited 10:1 ratio, showing that the number of bacteria in our bodies is actually of the same order as the number of human cells. Indeed, the numbers are similar enough that each defecation event may flip the ratio to favor human cells over bacteria.