Miracle-dz/UniFAR-FTUs huggingface dataset:
Status of mitochondria in living human fibroblasts during growth and senescence in vitro: use of the laser dye rhodamine 123

Rhodamine 123, a fluorescent laser dye that is selectively taken up into mitochondria of living cells, was used to examine mitochondrial morphology in early-passage (young), late-passage (old), and progeric human fibroblasts. Mitochondria were readily visualized in all cell types during growth (mid-log) and confluent stages. In all cell strains at confluence, mitochondria became shorter, more randomly aligned, and developed a higher proportion of bead-like forms. Treatment of cells for six days with Tevenel, a chloramphenicol analog that inhibits mitochondrial protein synthesis, brought about a marked depletion of mitochondria and a diffuse background fluorescence. Cyanide produced a rapid release of preloaded mitochondrial fluorescence followed by detachment and killing of cells. Colcemid caused a random coiling and fragmentation of mitochondria particularly in the confluent stage. No gross differences were discernible in mitochondria of the three cell strains in mid-log and confluent states or after these treatments. Butanol-extractable fluorescence after loading with rhodamine 123 was lower in all cell strains in confluent compared to mid-log stages. At confluence all three cell strains had similar rhodamine contents at zero-time and after washout up to 24 h. At the mid-log stage, young cells contained more rhodamine initially and lost it more rapidly than old or progeria cells, in that order. The data indicate no gross derangement in the morphology or number of mitochondria in old and progeria fibroblasts but there is a reduction of protonmotive force evident in these cells at the mid-log stage that may be growth limiting.
Overview of excelsior JET, a high performance alternative to java virtual machines

This paper describes the architecture of Excelsior JET, a Java optimizing environment based upon ahead-of-time compilation of Java bytecode to platform-specific (native) code. Advantages of static compilation originate from the possibility of employing powerful resource-expensive optimizations resulting in much better code quality than in the case of dynamic (just-in-time) complation implemented in contemporary Java Virtual Machines (JVMs). Moreover, a noticeable innovation of JET is the Mixed Compilation Model that allows a compiled program to load classes dynamically as the Java Language Specification requires. Along with a highly optimizing compiler, JET includes a scalable run-time system that provides effective memory management with garbage collection, threading, etc. The experimental results presented in the paper were obtained on a variety of benchmarks and real-world Java applications. Tested against two most popular JVMs (Sun HotSpot and IBM JIT), programs optimized by JET demonstrated better performance and lower resource demand in most cases.
The Pseudomonas aeruginosa Proteome during Anaerobic Growth

ABSTRACT Isotope-coded affinity tag analysis and two-dimensional gel electrophoresis followed by tandem mass spectrometry were used to identify Pseudomonas aeruginosa proteins expressed during anaerobic growth. Out of the 617 proteins identified, 158 were changed in abundance during anaerobic growth compared to during aerobic growth, including proteins whose increased expression was expected based on their role in anaerobic metabolism. These results form the basis for future analyses of alterations in bacterial protein content during growth in various environments, including the cystic fibrosis airway.
Practical and methodological challenges in designing and conducting human-robot interaction studies

Human-robot interaction is a rapidly growing research area which more and more roboticists and computer scientists are moving into. Publications on work resulting from such studies rarely consider in detail the practical and methodological problems encountered. This paper aims to highlight and critically discuss such problems involved in conducting human-robot interaction studies. We provide some examples by discussing our experiences of running two trials that involved humans and robots physically interacting in a common space. Our discussion emphasises the need to take safety requirements into account, and minimise the risk of physical harm to human subjects. Ethical considerations are considered, which are often within a formal or legal framework depending on the host country or institution. We also discuss future improvements for features of our trials and make suggestions as to how to overcome the challenges we encountered. We hope that the lessons learnt will be used to improve future human-robot interaction trials.
Marking the counterfactual: ERP evidence for pragmatic processing of German subjunctives

Counterfactual conditionals are frequently used in language to express potentially valid reasoning from factually false suppositions. Counterfactuals provide two pieces of information: their literal meaning expresses a suppositional dependency between an antecedent (If the dice had been rigged…) and a consequent (… then the game would have been unfair). Their second, backgrounded meaning refers to the opposite state of affairs and suggests that, in fact, the dice were not rigged and the game was fair. Counterfactual antecedents are particularly intriguing because they set up a counterfactual world which is known to be false, but which is nevertheless kept to when evaluating the conditional's consequent. In the last years several event-related potential (ERP) studies have targeted the processing of counterfactual consequents, yet counterfactual antecedents have remained unstudied. We present an EEG/ERP investigation which employed German conditionals to compare subjunctive mood (which marks counterfactuality) with indicative mood at the critical point of mood disambiguation via auxiliary introduction in the conditional's antecedent. Conditional sentences were presented visually one word at a time. Participants completed an acceptability judgment and probe detection task which was not related to the critical manipulation of linguistic mood. ERPs at the point of mood disambiguation in the antecedent were compared between indicative and subjunctive. Our main finding is a transient negative deflection in frontal regions for subjunctive compared to indicative mood in a time-window of 450–600 ms. We discuss this novel finding in respect to working memory requirements for rule application and increased referential processing demands for the representation of counterfactuals' dual meaning. Our result suggests that the counterfactually implied dual meaning is processed without any delay at the earliest point where counterfactuality is marked by subjunctive mood.
The Iterative Bayesian Model Averaging Algorithm for Survival Analysis: an Improved Method for Gene Selection and Survival Analysis on Microarray Data

Survival analysis is a supervised learning technique that in the context of microarray data is most frequently used to identify genes whose expression levels are correlated with patient survival prognosis. Survival analysis is generally applied to diseased samples for the purpose of analyzing time to event, where the event can be any milestone of interest (e.g., metastases, relapse, or death). Typically, the interest is in identifying genes that are predictive of a patient’s chances for survival. In such cases, both the accuracy of the prediction and the number of genes necessary to obtain a given accuracy is important. In particular, methods that select a small number of relevant genes and provide accurate patient risk assessment can aid in the development of simpler diagnostic tests. In addition, methods that adopt a weighted average approach over multiple models have the potential to provide more accurate predictions than methods that do not take model uncertainty into consideration. To this end, we developed the iterative Bayesian Model Averaging (BMA) method for gene selection and survival analysis on microarray data [1]. Typical gene selection and survival analysis procedures ignore model uncertainty and use a single set of relevant genes (model) to predict patient risk. BMA is a multivariate technique that takes the interaction of variables (typically genes) and model uncertainty into account. In addition, the output of BMA contains posterior probabilities for each prediction, which can be useful in assessing the correctness of a given prognosis.
Extreme Clonality in Lymphoblastoid Cell Lines with Implications for Allele Specific Expression Analyses

Lymphoblastoid cell lines (LCL) are being actively and extensively used to examine the expression of specific genes and genome-wide expression profiles, including allele specific expression assays. However, it has recently been shown that approximately 10% of human genes exhibit random patterns of monoallelic expression within single clones of LCLs. Consequently allelic imbalance studies could be significantly compromised if bulk populations of donor cells are clonal, or near clonal. Here, using X chromosome inactivation as a readout, we confirm and quantify widespread near monoclonality in two independent sets of cell lines. Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays.
A Power-Efficient Reconfigurable Output-Capacitor-Less Low-Drop-Out Regulator for Low-Power Analog Sensing Front-End

A power efficient reconfigurable output-capacitor-less (OCL) low-drop-out (LDO) voltage regulator for low-power analog sensing front-end is proposed in this paper. This LDO consists of a floating-gate <bold><italic>n</italic></bold> MOS pass transistor, an adaptively biased error amplifier, and capacitive circuits for voltage reference generation and for feedback sensing. The error amplifier adopts a class-AB input differential pair and an adaptively biased regulated cascode topology to improve transient response under the stringent constraint of low quiescent current consumption. The reference voltage is implemented by programming charges on capacitors without employing a bandgap circuit. A prototype chip is designed and fabricated in a 0.35 <inline-formula> <tex-math notation="LaTeX">$\mu\text{m}$</tex-math></inline-formula> CMOS process to demonstrate the reconfigurability and to validate the performance. The output voltage can be programmed in continuum in the range of 1.2 V to 2.5 V with measured temperature coefficients less than 45 <inline-formula> <tex-math notation="LaTeX">$\text{ppm}/^{\circ}\text{C}$</tex-math></inline-formula>. The maximum load current is designed to be 1 mA with output voltage drop less than 0.1%. With programmable quiescent current levels less than 1 <inline-formula> <tex-math notation="LaTeX">$\mu\text{A}$</tex-math></inline-formula>, the current efficiency is higher than 99.9%. From measurements, the line regulation is 0.17 mV/V or <inline-formula> <tex-math notation="LaTeX">$-$</tex-math></inline-formula> 75 dB. The designed OCL LDO remains stable with maximum output load capacitance up to 1 nF under the zero load condition.
Efficacy of gaseous nitric oxide in the treatment of skin and soft tissue infections

Bacterial burden significantly interferes with the healing process in chronic ulcers. Nitric oxide (NO) plays a key role in regulating skin's response to infection and wound healing. In previous studies, we demonstrated that exogenous NO gas (gNO) at 200 parts per million (ppm) exhibits potent antimicrobial effects against a representative range of pathogens. The aim of the present study is to explore the antimicrobial properties of gNO in vivo and to determine skin cells' sensitivity to the cytotoxic effects of gNO. To test gNO's antimicrobial effects, full‐thickness wounds were infected with Staphylococcus aureus on the dorsal skin surface of New Zealand White rabbit and treated with 200 ppm gNO for 8 hours/day for 3 consecutive days. Significant reduction in wound bacterial content was observed in the presence of gNO. In a separate experiment, primary cultures of human fibroblasts, keratinocytes, and endothelial cells were established to test gNO's cytotoxicity in the skin. Methyl thiazolyl tetrazolium proliferation assays demonstrated that human skin cells, unlike bacterial cells, exhibited significant resistance toward gNO cytotoxicity. In vitro migration studies on keratinocytes and endothelial cells revealed that gNO treatment does not seem to interfere with reepithelialization and angiogenesis during the process of wound healing. Following 24 hours of gNO treatment, fibroblasts expressed significantly higher levels of procollagen and, to a lesser degree, a decrease in matrix metalloproteinase ‐1 mRNA. In conclusion, the present study provides evidence for the potential application of high doses of gNO as an antimicrobial agent for the treatment of infection in chronic nonhealing ulcers or burn patients, without compromising the viability, and function of skin cells.
Performance of cold sprayed Ni‐20Cr and Ni‐50Cr coatings on SA 516 steel in actual industrial environment of a coal fired boiler

Power plants are one of the major industries suffering from severe erosion–corrosion (E‐C) problems resulting in substantial losses. One way of tackling this problem is by the use of thermal spray coatings. In the current investigation a new emerging technique i.e. cold spray coating process was used to deposit Ni‐20Cr and Ni‐50Cr powder on SA 516 (grade 70) boiler steel. The bare as well as the coated steels were subjected to cyclic experimental studies, in the superheater zone of a coal fired boiler. Weight change, thickness loss, XRD, FE‐SEM/EDS and X‐ray mapping techniques were used to analyse the eroded‐corroded specimens. The uncoated steel showed weight gain after exposure in the actual boiler environment, whereas, for the coated steels there was initial weight loss followed by negligible weight change. Based upon thickness loss data the cold‐sprayed Ni‐50Cr coating was found to provide better E‐C resistance than the Ni‐20Cr coating.
A Job Scheduling Method Based on Expected Probability of Completion of Voting in Volunteer Computing

This paper addresses the problem of job scheduling in volunteer computing (VC) systems where each computation job is replicated and distributed to multiple participants (workers) to remove incorrect results. In the job scheduling of VC, the number of assigned workers to complete a job is an important factor for the system performance, however, it cannot be fixed because some of the workers may not return results in real VC. We propose a job scheduling method which considers the expected probability of completion (EPC) for each job based on the worker's history information. The key idea of the proposed method is to assign jobs so that EPC is always greater than a specified value (SPC). By setting SPC as a reasonable value, any job in the proposed method can be completed without excess allocations, which leads to the higher performance of VC systems. Simulation results show that the performance of the proposed method is up to 5 times higher than that of the conventional method, while keeping the error rate lower than a required value.
Detection of TiO2 nanoparticles in cells by flow cytometry

Evaluation of the potential hazard of man‐made nanomaterials has been hampered by a limited ability to observe and measure nanoparticles in cells. In this study, different concentrations of TiO2 nanoparticles were suspended in cell culture medium. The suspension was then sonicated and characterized by dynamic light scattering and microscopy. Cultured human‐derived retinal pigment epithelial cells (ARPE‐19) were incubated with TiO2 nanoparticles at 0, 0.1, 0.3, 1, 3, 10, and 30 μg/ml for 24 hours. Cellular reactions to nanoparticles were evaluated using flow cytometry and dark field microscopy. A FACSCalibur™ flow cytometer was used to measure changes in light scatter after nanoparticle incubation. Both the side scatter and forward scatter changed substantially in response to the TiO2. From 0.1 to 30 μg/ml TiO2, the side scatter increased sequentially while the forward scatter decreased, presumably due to substantial light reflection by the TiO2 particles. Based on the parameters of morphology and the calcein‐AM/propidium iodide viability assay, TiO2 concentrations below 30 μg/ml TiO2 caused minimal cytotoxicity. Microscopic analysis was done on the same cells using an E‐800 Nikon microscope containing a xenon light source and special dark field objectives. At the lowest concentrations of TiO2 (0.1–0.3 μg/ml), the flow cytometer could detect as few as 5–10 nanoparticles per cell due to intense light scattering by TiO2. Rings of concentrated nanoparticles were observed around the nuclei in the vicinity of the endoplasmic reticulum at higher concentrations. These data suggest that the uptake of nanoparticles within cells can be monitored with flow cytometry and confirmed by dark field microscopy. This approach may help fulfill a critical need for the scientific community to assess the relationship between nanoparticle dose and cellular toxicity Such experiments could potentially be performed more quickly and easily using the flow cytometer to measure both nanoparticle uptake and cellular health. Published 2010 Wiley‐Liss, Inc.
Clustering Based Automatic Refactorings Identification

The aim of this paper is to approach the problem of improving the design of an object oriented software system, by identifying the appropriate refactorings. It is well known that improving the quality of software systems design is an important issue during the evolution of object oriented software systems. This improvement can be achieved by refactoring the software system in order to improve its internal structure, but without altering the external behavior of the code. In this paper we introduce a hierarchical divisive clustering algorithm for automatic identification of refactorings that improve the internal structure of a software system. We evaluate our approach using JHotDraw case study and a real software system, emphasizing its advantages in comparison with existing similar approaches.
An extrapolation method applied to a constitutive material model to recalculate creep fatigue experiments

The cyclic behaviour of steam turbine components is currently a key issue in terms of the discontinuity in the power supply from regenerative energy systems like wind-mills. These systems call for a combined and flexible use of conventional steam power plants. The influence on fatigue behaviour with superimposed creep on lifetime of large plant components is still unknown. Fatigue loading of such components is induced by temperature transients during start-up and shut-down processes. This requires an anisothermal inspection of the thermo-mechanical fatigue (TMF) loading at design. Hence a viscoplastic constitutive material model of type Chaboche was adapted to a 10%Cr forged steel. As a verification of the constitutive material model, uniaxial and biaxial TMF experiments were performed. These experiments were derived from a temperature cycle on the surface of a turbine rotor during a hot start. In order to recalculate deformation and to estimate lifetime the constitutive material model was implemented in a FEM application. The constitutive material model of type Chaboche introduced here demonstrates the applicability for the recalculation of multiaxial deformation with implicit evolution of damage under service-type conditions. Further efforts are necessary for the investigation of innovative parameter identification methods and routines for the extrapolation of the inner variables of the constitutive material model under cyclic loading. INTRODUCTION High temperature transients at start-up and shut-down processes lead to multiaxial strains and stresses at the heated surface of rotors (Figure 1a). The difference between the surface temperature and the average core temperature causes compression strains during the start-up (Figure 1b), while at shut-down tension strains occur. At stationary service condition of the turbine temperature equibalance usually leads to tension stresses which relax during long hold times. Notches in component structure lead to superimposed plastic strains and contribute to a decrease of lifetime.
Nano-liposome-based target toxicity machine: an alternative/complementary approach in atopic diseases

Abstract Despite using lots of progression in hypersensitivity, it is not yet a cure. Current treatment for allergy focuses on two approaches, including treats only the symptoms of allergy by utilizing drugs and the other is desensitization therapy (immunotherapy), which involves administration of specific allergens. The main obstacle to hypersensitivity permanent treatment is the IgE producing subclass of B-lymphocytes which is the source of IgE- producing in hypersensitive patients. Removal of these lymphocytes causes noticeable reduction in the levels of IgE and allergic responses significantly. In this paper, we proposed a novel complementary approach, which we have called the “nano-liposomes-based target toxicity machine (NBTTM)”, which controls hypersensitivity by removing the IgE producing B-lymphocytes. In this regard, our proposed nano-liposomes (pollen allergens/Aptamer/SCFV/MIP loaded lipid bilayer enclosing toxin interior) will be able to bind to any IgE markers in the lymphatic circulation. The nano-liposomes will bind to the IgE + atopic B cells and cause cell death by internalizing into B cells.
Strain and mechanical behavior measurements of soft tissues with digital speckle method

Soft tissues of human and animals are composite, typically being made up of the collagen and elastin fibres with high water contents. The strain measurement in soft tissues has proven to be a difficult task. Digital Speckle Method, an optical measurement method combining with computer image processing technique, has many advantages like full-field, non-contact and high measuring accuracy. Two main techniques, the Digital Speckle Correlation Method (DSCM) and Electric Speckle Pattern Interferometry (ESPI), have been developed and applied on many aspects. Using these two methods, the strain measurements caused by the continual deformation of soft tissues under pure tensile loading are completed and presented in this paper. Experiments are performed under the conditions of constant temperature and necessitate humidity with smart sensor. After capture a series of speckle patterns in continual time period, the displacement and strain distribution of soft tissues can be obtained by two improved techniques (Improved DSCM and Time-Sequence ESPI). Thus, the tensile modulus and Poisson ratio of soft tissues will be extracted.
CD14 cooperates with complement receptor 3 to mediate MyD88-independent phagocytosis of Borrelia burgdorferi

Phagocytosis of Borrelia burgdorferi, the causative agent of Lyme disease, is a poorly understood process, despite its importance during the host immune response to infection. B. burgdorferi has been shown to bind to different receptors on the surface of phagocytic cells, including the β2 integrin, complement receptor 3 (CR3). However, whether these receptors mediate the phagocytosis of the spirochete remains unknown. We now demonstrate that CR3 mediates the phagocytosis of the spirochete by murine macrophages and human monocytes. Interaction of B. burgdorferi with the integrin is not sufficient, however, to internalize the spirochete; phagocytosis requires the interaction of CR3 with the GPI-anchored protein, CD14, independently of TLR/MyD88-induced or inside-out signals. Interestingly, the absence of CR3 leads to marked increases in the production of TNF in vitro and in vivo, despite reduced spirochetal uptake. Furthermore, the absence of CR3 during infection with B. burgdorferi results in the inefficient control of bacterial burdens in the heart and increased Lyme carditis. Overall, our data identify CR3 as a MyD88-independent phagocytic receptor for B. burgdorferi that also participates in the modulation of the proinflammatory output of macrophages. These data also establish a unique mechanism of CR3-mediated phagocytosis that requires the direct cooperation of GPI-anchored proteins.