Miracle-dz/UniFAR-FTUs huggingface dataset:
Multidimensional long‐term time‐lapse microscopy of in vitro peripheral nerve regeneration

In order to test the effectiveness of a new advanced time‐lapse microscopy imaging and image processing and analysis system, and to do quantitative and qualitative temporal analyses of in vitro peripheral nerve regeneration, long‐term time‐lapse imaging of cultures of mouse dorsal root ganglia (DRGs) was performed. DRGs were placed in a Petri dish, covered with collagen gel, their attached peripheral nerves were cut in the middle, creating a gap, and the dish was filled with culture medium. Six preparations were kept on the time‐lapse imaging system, which provides a suitable incubation environment and enables to capture images from multiple coordinates at x,y,z axes at desired time intervals for 13 days. In general, the time‐lapse imaging system proved quite stable and efficient, although some improvements are certainly required. Two main components of peripheral nerve regeneration, outgrowth of axons and activities of resident cells, were examined. Axons started to grow during the first hour of incubation with a 16.5 μm/h rate and showed the slowest rates (0.7 μm/h) on days 8 and 9, after which they resumed higher speeds again. The first cell came out of the proximal end of the cut nerve on the second day and it was a Schwann cell (SC), which was the prominent cell type in the preparations throughout the experiment. SCs were higher in number (83.15% of all cells) but slower in migration (3.4 vs. 7.3 μm/h, P < 0.001) than other cells. Other observed characteristics of axonal outgrowth and cellular activity and interactions between axons and the cells are discussed. Microsc. Res. Tech. 64:228–242, 2004. © 2004 Wiley‐Liss, Inc.
Unfavorable hormonal, metabolic, and inflammatory alterations persist after menopause in women with PCOS.

CONTEXT Women with polycystic ovary syndrome (PCOS) are known to suffer from hyperandrogenism and impaired glucose tolerance, as well as chronic inflammation, exposing them to an increased risk of cardiovascular diseases. However, the degree to which these hormonal and metabolic alterations persist after menopause (MP) is not well documented. OBJECTIVE Our objective was to explore whether adverse metabolic and hormonal alterations persist after MP in women with PCOS. DESIGN We conducted a cross-sectional university hospital-based study. PATIENTS AND INTERVENTIONS Twenty-one pre-MP (n = 10) and post-MP (n = 11) women diagnosed with PCOS were compared with 29 healthy controls (pre-MP, n = 11; post-MP, n = 18). Two-hour oral glucose tolerance tests were performed, and ovarian steroid secretion capacity was assessed (human chorionic gonadotropin tests). Areas under the curves (AUC) were calculated. RESULTS Both pre-MP and post-MP women with PCOS had increased insulin response in oral glucose tolerance tests (AUC(ins) pre-MP = 6733.7 vs. 3382.9; post-MP = 9732.1 vs. 3265.3) and were more insulin resistant than controls. Androgen secretion capacity was increased before and after MP in PCOS (AUC of androstenedione; pre-MP: 1218.4 vs. 853.2; post-MP: 1000.0 vs. 531.3). High-sensitivity C-reactive protein remained elevated after MP in PCOS (pre-MP: 1.3 vs. 0.7; post-MP: 1.4 vs. 0.9 mg/liter). Adjustment for body mass index did not alter the results except for glucose metabolism. CONCLUSIONS The results indicate that impaired glucose metabolism, enhanced ovarian androgen secretion, and chronic inflammation observed in pre-MP women with PCOS persist after menopausal transition emphasizing life-long health risks related to this syndrome.
Environmental species sorting dominates forest-bird community assembly across scales.

Environmental species sorting and dispersal are seen as key factors in community assembly, but their relative importance and scale dependence remain uncertain, as the extent to which communities are consistently assembled throughout their biomes. To address these issues, we analysed bird metacommunity structure in a 1200-km(2) forested landscape (Istranca Forests) in Turkish Thrace at the margin of the Western Palaearctic (WP) temperate-forest biome. First, we used spatial regressions and Mantel tests to assess the relative importance of environmental and spatial factors as drivers of local species richness and composition within the metacommunity. Second, we analysed species' abundance-occupancy relationship across the metacommunity and used null models to assess whether occupancy is determined by species' environmental niches. Third, we used generalized linear models to test for links between species' metacommunity-wide occupancy and their broader WP regional populations and assessed whether these links are consistent with environmental species sorting. There was strong environmental control on local species richness and composition patterns within the metacommunity, but non-environmental spatial factors had also an important joint role. Null model analyses on randomized communities showed that species' occupancy across the metacommunity was strongly determined by species' environmental niches, with occupancy being related to niche position marginality. Species' metacommunity-wide occupancy correlated with their local abundance as well as with their range size and total abundance for the whole WP, suggesting that the same assembly mechanisms act consistently across local to regional scales. A species specialization index that was estimated by bird species' habitat use across France, incorporating both niche position and breadth, was significantly related to species' occupancy and abundance at both metacommunity and WP regional scales. Hence, the same niche-related assembly mechanisms appear to act consistently across the WP region. Overall, our results suggest that the structure of the Istranca Forest' bird metacommunity was predominantly controlled by environmental species sorting in a manner consistent with the broader WP region. However, variability in local community structure was also linked to purely spatial factors, albeit more weakly.
Non-canonical translation in RNA viruses

Viral protein synthesis is completely dependent upon the translational machinery of the host cell. However, many RNA virus transcripts have marked structural differences from cellular mRNAs that preclude canonical translation initiation, such as the absence of a 5′ cap structure or the presence of highly structured 5′UTRs containing replication and/or packaging signals. Furthermore, whilst the great majority of cellular mRNAs are apparently monocistronic, RNA viruses must often express multiple proteins from their mRNAs. In addition, RNA viruses have very compact genomes and are under intense selective pressure to optimize usage of the available sequence space. Together, these features have driven the evolution of a plethora of non-canonical translational mechanisms in RNA viruses that help them to meet these challenges. Here, we review the mechanisms utilized by RNA viruses of eukaryotes, focusing on internal ribosome entry, leaky scanning, non-AUG initiation, ribosome shunting, reinitiation, ribosomal frameshifting and stop-codon readthrough. The review will highlight recently discovered examples of unusual translational strategies, besides revisiting some classical cases.
CNN based approach for activity recognition using a wrist-worn accelerometer

In recent years, significant advancements have taken place in human activity recognition using various machine learning approaches. However, feature engineering have dominated conventional methods involving the difficult process of optimal feature selection. This problem has been mitigated by using a novel methodology based on deep learning framework which automatically extracts the useful features and reduces the computational cost. As a proof of concept, we have attempted to design a generalized model for recognition of three fundamental movements of the human forearm performed in daily life where data is collected from four different subjects using a single wrist worn accelerometer sensor. The validation of the proposed model is done with different pre-processing and noisy data condition which is evaluated using three possible methods. The results show that our proposed methodology achieves an average recognition rate of 99.8% as opposed to conventional methods based on K-means clustering, linear discriminant analysis and support vector machine.
Adiabatic Effectiveness Measurements of Endwall Film-Cooling for a First Stage Vane

In gas turbine development, the direction has been towards higher turbine inlet temperatures to increase the work output and thermal efficiency. This extreme environment can significantly impact component life. One means of preventing component burnout in the turbine is to effectively use film-cooling whereby coolant is extracted from the compressor and injected through component surfaces. One such surface is the endwall of the first stage nozzle guide vane. This paper presents measurements of two endwall film-cooling hole patterns combined with cooling from a flush slot that simulates leakage flow between the combustor and turbine sections. Adiabatic effectiveness measurements showed the slot flow adequately cooled portions of the endwall. Measurements also showed two very difficult regions to cool including the leading edge and pressure side-endwall junction. As the momentum flux ratios were increased for the film-cooling jets in the stagnation region, the coolant was shown to impact the vane and wash down onto the endwall surface. Along the pressure side of the vane in the upstream portion of the passage, the jets were shown to separate from the surface rather than penetrate to the pressure surface. In the downstream portion of the passage, the jets along the pressure side of the vane were shown to impact the vane thereby eliminating any uncooled regions at the junction. The measurements were also combined with computations to show the importance of considering the trajectory of the flow in the near-wall region, which can be highly influenced by slot leakage flows.Copyright © 2004 by ASME
PPARγ Activation: A Potential Treatment For Pulmonary Hypertension

Pharmacological activation of the transcription factor PPARγ affects the expression of key genes involved in the development of pulmonary hypertension (PH), subsequently has a variety of beneficial effects in the vasculature, and hence might be a powerful treatment of PH. The pathobiology of pulmonary arterial hypertension (PAH) involves multiple molecular pathways and environmental modifiers and is characterized by progressive obliteration of pulmonary arterioles, leading to increased pulmonary vascular resistance (PVR), right heart failure, and death in ≈40 to 60% of patients 5 years after diagnosis. There is emerging evidence that many key genes involved in PAH development are targets of the insulin-sensitizing transcription factor peroxisome proliferator–activated receptor γ (PPARγ), and that pharmacological PPARγ activation would lead to their beneficial induction or repression and subsequent antiproliferative, anti-inflammatory, proapoptotic, and direct vasodilatory effects in the vasculature. PPARγ acts downstream of bone morphogenetic protein receptor II (BMP-RII), which is the cell surface receptor that is mutated or dysfunctional in many forms of PAH. Because our recent clinical observations indicate that insulin resistance may be an environmental risk factor or disease modifier (“second hit”), we suggest that PPARγ-activating agents might be beneficial in the future treatment of both insulin-resistant and insulin-sensitive PAH patients with or without BMP-RII mutations.
Hybrid control for a class of underactuated mechanical systems

This paper considers a stabilizing hybrid scheme to control a class of underactuated mechanical systems. The hybrid controller consists of a collection of state feedback controllers plus a discrete-event supervisor. When the continuous-state hits a switching boundary, a new controller is applied to the plant. Lyapunov theory is used to determine the switching boundaries and to guarantee the stability of the closed-loop hybrid system. This approach is applied to the well-known swing up and balancing control problem of the inverted pendulum.
The CoMIRVA Toolkit for Visualizing Music-Related Data

We present CoMIRVA, which is an abbreviation for Collection of Music Information Retrieval and Visualization Applications. CoMIRVA is a Java framework and toolkit for information retrieval and visualization. It is licensed under the GNU GPL and can be downloaded from http://www.cp. jku.at/comirva/. At the moment, the main functionalities include music information retrieval, web retrieval, and visualization of the extracted information. In this paper, we focus on the visualization aspects of CoMIRVA. Since many of the information retrieval functions are intended to be applied to problems of the field of music information retrieval (MIR), we demonstrate the functions using data like similarity matrices of music artists gained by analyzing artist-related web pages. CoMIRVA is continuously being extended. Currently, it supports the following visualization techniques: Self-Organizing Map, Smoothed Data Histogram, Circled Bars, Circled Fans, Probabilistic Network, Continuous Similarity Ring, Sunburst, and Music Description Map. Since space is limited, we can only present a selected number of these in this paper. As one key feature of CoMIRVA is its easy extensibility, we further elaborate on how CoMIRVA was used for creating a novel user interface to digital music repositories.
On Achieving the Shortest-Path Routing in 2-D Meshes

In this paper, we present a fully distributed process to collect and distribute the minimal connected component (MCC) fault information so that the shortest-path between the source and the destination can always be found in the corresponding information-based routing via routing decisions at each intermediate node. Considering the communication cost in the above information distribution, a more practical implementation is provided with only a low number of nodes along the boundary lines involved in the information propagation. The experimental results show the substantial improvement of our approach in terms of the success rate in finding the shortest-path and the average path length.
Video Surveillance Systems - A Survey

Video surveillance is increasing significance approach as organizations seek to safe guard physical and capital assets. At the same time, the necessity to observe more people, places, and things coupled with a desire to pull out more useful information from video data is motivating new demands for scalability, capabilities, and capacity. These demands are exceeding the facilities of traditional analog video surveillance approaches. Providentially, digital video surveillance solutions derived from different data mining techniques are providing new ways of collecting, analyzing, and recording colossal amounts of video data. This paper addresses some of the approaches for video surveillance systems.
Towards a smart glove: Arousal recognition based on textile Electrodermal Response

This paper investigates the possibility of using Electrodermal Response, acquired by a sensing fabric glove with embedded textile electrodes, as reliable means for emotion recognition. Here, all the essential steps for an automatic recognition system are described, from the recording of physiological data set to a feature-based multiclass classification. Data were collected from 35 healthy volunteers during arousal elicitation by means of International Affective Picture System (IAPS) pictures. Experimental results show high discrimination after twenty steps of cross validation.
Integrating Pattern-Based and Distributional Similarity Methods for Lexical Entailment Acquisition

This paper addresses the problem of acquiring lexical semantic relationships, applied to the lexical entailment relation. Our main contribution is a novel conceptual integration between the two distinct acquisition paradigms for lexical relations - the pattern-based and the distributional similarity approaches. The integrated method exploits mutual complementary information of the two approaches to obtain candidate relations and informative characterizing features. Then, a small size training set is used to construct a more accurate supervised classifier, showing significant increase in both recall and precision over the original approaches.
Interfacial recognition of human prostate-specific antigen by immobilized monoclonal antibody: effects of solution conditions and surface chemistry

The specific recognition between monoclonal antibody (anti-human prostate-specific antigen, anti-hPSA) and its antigen (human prostate-specific antigen, hPSA) has promising applications in prostate cancer diagnostics and other biosensor applications. However, because of steric constraints associated with interfacial packing and molecular orientations, the binding efficiency is often very low. In this study, spectroscopic ellipsometry and neutron reflection have been used to investigate how solution pH, salt concentration and surface chemistry affect antibody adsorption and subsequent antigen binding. The adsorbed amount of antibody was found to vary with pH and the maximum adsorption occurred between pH 5 and 6, close to the isoelectric point of the antibody. By contrast, the highest antigen binding efficiency occurred close to the neutral pH. Increasing the ionic strength reduced antibody adsorbed amount at the silica–water interface but had little effect on antigen binding. Further studies of antibody adsorption on hydrophobic C8 (octyltrimethoxysilane) surface and chemical attachment of antibody on (3-mercaptopropyl)trimethoxysilane/4-maleimidobutyric acid N-hydroxysuccinimide ester-modified surface have also been undertaken. It was found that on all surfaces studied, the antibody predominantly adopted the ‘flat on’ orientation, and antigen-binding capabilities were comparable. The results indicate that antibody immobilization via appropriate physical adsorption can replace elaborate interfacial molecular engineering involving complex covalent attachments.
Iterative suppression of Co-Channel Interference

Co-Channel Interference (CCI) is one of the major bottlenecks in the performance of today's densely planned wireless cellular systems. A receiver equipped with multiple receive antennas and sufficient computational budget typically exploits the spatial dimension and iterative processing between the detector and the channel decoder to suppress this interference. In this paper, we propose modifications in the standard iterative turbo processing based CCI suppression to especially boost the receiver performance in a dominant CCI scenario. Performance gains of 3-5 dB are shown to be achieved over the conventional iterative approaches for an LTE uplink system.
Stability analysis and control design of a class of event based control systems

Event Based Control (EBC) provides a reduction of mean control rates, which is an important advantage in control systems, specially when network environment gets involved. For this reason, the study of design methodologies for EBC systems that met desired specifications regarding stability and performance issues are a valuable research field. This work presents a control design process applied to a class of EBC systems using LMIs, including stability issues on the light of Asynchronous Dynamical System theory. The application of the proposed methodology is presented by an example, showing good performance in simulation results.
The role of Fas-Fas ligand-mediated apoptosis in autoimmune lacrimal gland disease in MRL/MpJ mice.

PURPOSE MRL/MpJ mice spontaneously develop lacrimal gland inflammation and are a model for the human disorder Sjögren's syndrome. MRL/MpJ-lpr/lpr (MRL/lpr) and MRL/Mp-+/+ (MRL/+) mice are congenic substrains, which differ only by a single autosomal recessive gene, the lpr mutation. This mutation results in defective Fas protein, defective lymphocytic apoptosis, and accelerated autoimmune lacrimal gland disease in MRL/lpr mice. We evaluated apoptosis in the lacrimal glands of MRL/lpr and MRL/+ mice. METHODS Inflammatory cells in the lacrimal glands of MRL/lpr and MRL/+ mice were evaluated for apoptosis with TUNEL staining and Fas and Fas ligand expression with immunohistochemistry. RESULTS MRL/lpr mice had a greater percentage of the lacrimal gland replaced by inflammatory infiltrate (30.3% +/- 7.0%) than did MRL/+ mice (13.0% +/- 3.0%, P = 0.02). However, similar amounts of lymphocytic apoptosis were present in the lacrimal glands of MRL/lpr and MRL/+ mice. The mean number of apoptotic cells per unit area of inflammation was 23.8 +/- 2.4 in MRL/lpr mice and 24.6 +/- 6.0 in MRL/+ mice (P = 0.91). Fas expression was absent on lymphocytes in MRL/lpr mice but was present on lymphocytes in MRL/+ mice. Fas ligand expression was present on epithelial structures in both substrains. CONCLUSIONS The accelerated lacrimal gland disease inflammation in MRL/lpr mice does not appear to be due to decreased apoptosis in the microenvironment of the lacrimal gland of MRL/lpr mice. It appears that in MRL/lpr mice there is defective extrathymic lymphoid apoptosis, permitting a relatively greater expansion of autoreactive T cells, which subsequently invade the lacrimal gland.
Treasury Auctions : What Do the Recent Models and Results Tell Us ?

One of the most important auction markets in the world today is that of U.S. Treasury securities; approximately $2 trillion worth of Treasury securities was auctioned in 1995. As in other auctions, a set of rules determines how bids are used to determine prices; this set of rules makes up the format of the Treasury auction. A long-standing debate (dating back to the early 1960s) has centered on the selection of an appropriate auction format for various Treasury securities, one that would be least subject to possible manipulations by any individual trader or a cartel and also result in the highest possible revenues for the Treasury. 1 This debate received fresh impetus after the infamous May 1991 auction for two-year Treasury notes, which led to a squeeze in the available supply of these securities in the postauction, or secondary, market. At this auction Salomon Brothers, one of the biggest primary dealers, grossly violated the maximum amount of the note that it could buy (U.S. Treasury 1992). As a result, the two-year notes started trading at abnormal premiums in the secondary market. In other words, following the auction , the secondary market for the two-year notes suddenly became very illiquid. An illiquid secondary market could not only increase the Treasury's cost of financing in subsequent auctions but is also detrimental to the Federal Reserve's ability to carry out its open market operations in the most efficient manner. An understanding of the various auction formats and what they entail for the Treasury's cost of financing, squeezes, and market liquidity is important to all participants of the Treasury auction market and, to some extent, everyone interested in Treasury securities. The nature of Treasury auctions differs from many other types of auctions. Most consist of the sale of a single good that is not traded before or after the auction. These auctions have been the subject of considerable study. In contrast, in a Treasury auction, multiple units of the same good are auctioned, and the auction is preceded by trading in a forward market, in which one can