Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation and Co‐Ordination of Nuclear Gene Expression During Mitochondrial Biogenesis

Biogenesis of mitochondria is happening constantly due to the physiological and developmental situation of a cell. As mitochondrial biogenesis is a complex process producing about 20 % of cellular protein, the expression of the 1000 genes involved is expected to be coordinated and regulated tightly. The variety of physiological stimuli and differentiation states lead to the idea of a complex network connecting many different regulatory pathways. By analysing nuclear encoded mitochondrial genes some of the factors involved in the regulation and coordination of mitochondrial gene expression were identified. These factors include general transcription factors such as Sp1 or YY1, as well as transcription factors specific for mitochondrial genes like the nuclear respiratory factors NRF1 and 2. An important control function linked to the physiological situation of a cell is triggered by hormones such as steroid and thyroid hormones. Even cell type‐specific regulatory proteins like the myogenin transcription factor family have a strong influence on some mitochondrial genes in the specific cellular background. The regulatory function of most of these proteins can be modulated and enhanced by the coactivators PGC‐1α and β and PRC. Although regulatory pathways have been characterized in more detail in recent years, no regulation mechanism has been shown to work on all analysed mitochondrial genes, and the general concept of mitochondrial regulation still remains unclear.
Hepatitis C virus RNA quantitation and degradation studies in whole blood samples in vitro

Hepatitis C virus (HCV) qualitative and quantitative polymerase chain reaction (PCR) tests have evolved from specialist research tools into tests that are widely used in routine clinical practice. Clinical therapeutic decisions are based on HCV RNA titre; hence if the result is inaccurate, patients may be given, or alternatively denied, treatment inappropriately. Little data exist on the effect of environmental conditions on HCV RNA titre after blood has been taken from the patient.1–3 We therefore decided to evaluate the variation in HCV RNA titre after whole blood samples were taken from patients, to determine whether time at room temperature, temperature variation and blood collection systems affect the result obtained by the clinician. Patients were recruited to the study from the liver clinic at the John Hunter Hospital …
Dimensions of Organizational Agility in the Software and IT Service Industry: Insights from an Empirical Investigation

Agility has increasingly gained attention in the software and IT services industry over the last years and academia put a heavy emphasis on research about agile software development methods. However, an organization does not only comprise development teams, and research often lacks an organizational perspective on agility. Presently, we have no consensus about what constitutes an “agile organization”. Hence, in this study, I identify the structure behind the concept of organizational agility using an exploratory research approach. I conducted a survey among organizations in the software and IT service industry and performed an, exploratory factor analysis and a cluster analysis (based on the variables). The results show that one can describe organizational agility using six interrelated factors that one can further aggregate into the three basic dimensions of “agility prerequisites”, “agility of people”, and “structures enhancing agility”. The identified structure is a first step toward a common understanding of organizational agility and helps to guide further research activities while simultaneously supporting practitioners in assessing the agility of their organizations.
Controllability and matchings in random bipartite graphs

Motivated by an application in controllability we consider maximum matchings in random bipartite graphs G = (A,B). First we analyse Karp–Sipser’s algorithm to determine the asymptotic size of maximum matchings in random bipartite graphs with a fixed degree distribution. We then allow an adversary to delete one edge adjacent to every vertex in A in the more restricted model where each vertex in A chooses d neighbours uniformly at random from B.
Cloning and insertional inactivation of Streptomyces argillaceus genes involved in the earliest steps of biosynthesis of the sugar moieties of the antitumor polyketide mithramycin

Two genes (mtmD and mtmE) were cloned and sequenced from the mithramycin producer Streptomyces argillaceus. Comparison with proteins in databases and enzymatic assays after expression in Escherichia coli showed that they encode a glucose-1-phosphate:TTP thymidylyl transferase and a TDP-D-glucose 4,6-dehydratase, respectively. The mtmD gene was inactivated by gene replacement, generating a nonproducing mutant that accumulates a tetracyclic compound designated premithramycinone. The identification of premithramycinone reveals new aspects of the mithramycin biosynthetic pathway and suggests that at least some glycosylations occur before breakage of the fourth ring.
Image formation by a general optical system. 2: Computing methods.

Angle and height variables, akin to the paraxial variables for the marginal and pupil (principal) rays in an axially symmetric system, are introduced. These give simple forms of opening and closing formulas for ray tracing, which are always determinate and of good accuracy. Preliminary ray tracing establishes the pupil periphery and base ray for any given object point, and thence the principal azimuths around the base ray are determined. For cases where the object and/or image surfaces are curved, formulas are given for the necessary coordinate transformations from the base systems used for ray tracing to the local and canonical coordinate systems used for aberration and image assessment calculations. Generalized numerical apertures are used for the two principal azimuths for any object image point, formulas for which, and also for the two corresponding principal magnifications, are given.
Evaluating aerial vessel detector in multiple maritime surveillance scenarios

In this paper we present an autonomous detection approach for airborne surveillance in maritime scenarios. This approach is robust to sun glare, waves and scale variation. Additionally, we introduce a new metric to evaluate detection and tracking results that is more adequate for these scenarios. The proposed detection method is evaluated using videos from different monitoring missions and its results are compared with a state-of-the-art neural network. This comparison is done using a traditional and the proposed evaluation metric.
Design and experiment of a rectifying antenna for 900 MHz wireless power transmission

A new rectenna with a loop antenna and a designed rectifier by commercial Schottky diode has been developed. The used doubler rectifier provides optimum output DC voltage of 1.54 V as well as 47 % RF-DC conversion efficiency is achieved when 0 dBm RF power is received at 925 MHz. The rectifier has good impedance matching with the loop antenna corresponding to its optimum frequency response.
Registration of Functional Data Using Fisher-Rao Metric

We introduce a novel geometric framework for separating the phase and the amplitude variability in functional data of the type frequently studied in growth curve analysis. This framework uses the Fisher-Rao Riemannian metric to derive a proper distance on the quotient space of functions modulo the time-warping group. A convenient square-root velocity function (SRVF) representation transforms the Fisher-Rao metric into the standard $\ltwo$ metric, simplifying the computations. This distance is then used to define a Karcher mean template and warp the individual functions to align them with the Karcher mean template. The strength of this framework is demonstrated by deriving a consistent estimator of a signal observed under random warping, scaling, and vertical translation. These ideas are demonstrated using both simulated and real data from different application domains: the Berkeley growth study, handwritten signature curves, neuroscience spike trains, and gene expression signals. The proposed method is empirically shown to be be superior in performance to several recently published methods for functional alignment.
Role for Matrix Metalloproteinase-2 in Oxidized Low-Density Lipoprotein–Induced Activation of the Sphingomyelin/Ceramide Pathway and Smooth Muscle Cell Proliferation

Background—Oxidized LDLs (oxLDLs) and matrix metalloproteinases (MMPs) are present in atherosclerotic lesions. OxLDLs activate various signaling pathways potentially involved in atherogenesis. OxLDLs induce smooth muscle cell (SMC) proliferation mediated by the activation of the sphingomyelin/ceramide pathway and tyrosine kinase receptors. MMPs are also able to induce SMC migration and proliferation in addition to extracellular matrix degradation. The present study was designed to investigate whether MMPs play a role in the mitogenic effect of oxLDLs. Methods and Results—OxLDLs induce the release of activated MMP-2 in SMC culture medium. MMP-2 was identified by its 65-kDa gelatinase activity on zymography and by using specific blocking antibodies and MMP-2−/− cells. MMP inhibitors (batimastat and Ro28-2653) and the blocking antibodies anti–MMP-2 and anti–membrane type 1-MMP inhibited the oxLDL-induced sphingomyelin/ceramide pathway activation and subsequent activation of ERK1/2 and DNA synthesis but did not inhibit the oxLDL-induced epidermal growth factor receptor and platelet-derived growth factor receptor activation. Exogenously added activated MMP-2 or membrane type 1-MMP-1 triggered the activation of both sphingomyelin/ceramide and ERK1/2 pathways and DNA synthesis. Conversely, suppression of MMP-2 expression in MMP-2−/− cells or in SMCs treated by small-interference RNA also blocked both sphingomyelin/ceramide signaling and DNA synthesis. Conclusions—Together, these data demonstrate that MMP-2 plays a pivotal role in oxLDL-induced activation of the sphingomyelin/ceramide signaling pathway and subsequent SMC proliferation. These pathways may constitute a potential therapeutic target for modulating the oxLDL-induced proliferation of SMCs in atherosclerosis or restenosis.
Probabilistic Forecasting and Bayesian Data Assimilation

In this book the authors describe the principles and methods behind probabilistic forecasting and Bayesian data assimilation. Instead of focusing on particular application areas, the authors adopt a general dynamical systems approach, with a profusion of low-dimensional, discrete-time numerical examples designed to build intuition about the subject. Part I explains the mathematical framework of ensemble-based probabilistic forecasting and uncertainty quantification. Part II is devoted to Bayesian filtering algorithms, from classical data assimilation algorithms such as the Kalman filter, variational techniques, and sequential Monte Carlo methods, through to more recent developments such as the ensemble Kalman filter and ensemble transform filters. The McKean approach to sequential filtering in combination with coupling of measures serves as a unifying mathematical framework throughout Part II. Assuming only some basic familiarity with probability, this book is an ideal introduction for graduate students in applied mathematics, computer science, engineering, geoscience and other emerging application areas.
Reproduction of the FC/DFC units in nucleoli

ABSTRACT The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units, loci of rDNA transcription and early RNA processing. In the present study we followed cell cycle related changes of these units in 2 human sarcoma derived cell lines with stable expression of RFP-PCNA (the sliding clamp protein) and GFP-RPA43 (a subunit of RNA polymerase I, pol I) or GFP-fibrillarin. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60–80%. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis, but become again active in the postmitotic daughter cells.
INTEGRATION OF GIS AND BIM FOR INDOOR GEOVISUAL ANALYTICS

This paper presents an endeavour of integration of GIS (Geographical Information System) and BIM (Building Information Modelling) for indoor geovisual analytics. The merits of two types of technologies, GIS and BIM are firstly analysed in the context of indoor environment. GIS has well-developed capabilities of spatial analysis such as network analysis, while BIM has the advantages for indoor 3D modelling and dynamic simulation. This paper firstly investigates the important aspects for integrating GIS and BIM. Different data standards and formats such as the IFC (Industry Foundation Classes) and GML (Geography Markup Language) are discussed. Their merits and limitations in data transformation between GIS and BIM are analysed in terms of semantic and geometric information. An optimized approach for data exchange between GIS and BIM datasets is then proposed. After that, a strategy of using BIM for 3D indoor modelling, GIS for spatial analysis, and BIM again for visualization and dynamic simulation of the analysis results is presented. Based on the developments, this paper selects a typical problem, optimized indoor emergency evacuation, to demonstrate the integration of GIS and BIM for indoor geovisual analytics. The block Z of the Hong Kong Polytechnic University is selected as a test site. Detailed indoor and outdoor 3D models of the block Z are created using a BIM software Revit. The 3D models are transferred to a GIS software ArcGIS to carry out spatial analysis. Optimized evacuation plans considering dynamic constraints are generated based on network analysis in ArcGIS assuming there is a fire accident inside the building. The analysis results are then transferred back to BIM software for visualization and dynamic simulation. The developed methods and results are of significance to facilitate future development of GIS and BIM integrated solutions in various applications.
Journal policy on research funded by the tobacco industry

As editors of the BMJ , Heart , Thorax and BMJ Open , we have decided that the journals will no longer consider for publication any study that is partly or wholly funded by the tobacco industry. Our new policy is consistent with those of other journals including PLoS Medicine , PLoS One , PLoS Biology ;1 Journal of Health Psychology ;2 journals published by the American Thoracic Society;3 and the BMJ 's own Tobacco Control. 4 Critics may argue—as many did when journals stopped publishing cigarette advertisements—that publishing such research does not constitute endorsing its findings and that, as long as funding sources are fully disclosed, readers can consider that information and make up their own minds about the quality of the work. Peer review should prevail, goes this line of thinking: it's not the editor's job to make these kinds of judgments. However, this view ignores the growing body of evidence that biases and research misconduct are often impossible …
Creatine transporter and mitochondrial creatine kinase protein content in myopathies

Total creatine or phosphocreatine, or both, are reduced in the skeletal muscle of patients with inflammatory myopathy, mitochondrial myopathy, and muscular dystrophy/congenital myopathy. We used Western blotting techniques to measure skeletal muscle creatine transporter protein and sarcomeric mitochondrial creatine kinase (mtCK) protein content in patients with inflammatory myopathy (N = 8), mitochondrial myopathy (N = 5), muscular dystrophy (N = 7), and congenital myopathy (N = 3), as compared to a control group without a neuromuscular diagnosis (N = 8). Creatine transporter protein content was lower for all groups compared to control subjects (P < 0.05; P < 0.01 for congenital myopathy). Mitochondrial CK (mtCK) was lower for inflammatory myopathy (P < 0.05), higher for mitochondrial myopathy (P < 0.05), not different for muscular dystrophy, and markedly lower for the congenital myopathy group (P < 0.01), compared to control subjects. Together, these data suggest that the reduction in total creatine or phosphocreatine in patients with certain myopathies is correlated with creatine transporter and not mtCK protein content. This further supports the belief that creatine monohydrate supplementation may benefit patients with low muscle creatine stores, although the reduction in creatine transporter protein may have implications for dosing. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 682–688, 2001
5kV/200ns Pulsed Power Switch based on a SiC-JFET Super Cascode

In many pulse power applications there is a trend to modulators based on semiconductor technology. For these modulators high voltage and high current semiconductor switches are required in order to achieve a high pulsed power. Therefore, often high power IGBT modules or IGCT devices are used. Since these devices are based on bipolar technology the switching speed is limited and the switching losses are higher. In contrast to bipolar devices unipolar ones (e.g. SiC JFETs) basically offer a better switching performance. Moreover, these devices enable high blocking voltages in case large bandgap materials as SiC are used. At the moment SiC JFET devices with a blocking voltage of 1.5 kV per JFET are available. Alternatively, the operating voltage could be increased by connecting N JFETs and a low voltage MOSFET in series resulting in a Super Cascode switch with a blocking voltage N-times higher than the blocking voltage of a single JFET. In order to evaluate the achievable switching speed of the Super Cascode and its applicability in solid state modulators, the performance of such a SiC switch is examined in this paper. Furthermore, the performance of the Super Cascode is compared with 4.5 kV IGBTs made by Powerex, which are mounted in a special low inductive housing for minimising the rise and fall times.
Global ethics and virtual worlds: Ensuring functional integrity in transnational research studies

For more than three decades, research ethics in the biomedical and behavioral sciences, in the U.S. and beyond, has been guided by policies and standards derived from the Belmont Report. Although they have been adapted and revised over time, the underlying guidelines have limited applicability to the challenges of today's research environment, especially because of the influence of modern communications and information technologies and their ubiquitous presence across varied, and often incompatible, legal regimes and social norms. This paper examines a number of issues in this research context, with particular stress on the challenges posed by transnational experimental projects in virtual worlds and social networks. Several key aspects of the Menlo Report - a 2011 update to the Belmont Report - are also discussed. Consideration is given to a more rational and coordinated approach to managing ethics observance in multiple jurisdictions, with special attention on guidelines for the conduct of transnational research in and on virtual environments and online social network systems.
Feline musculoskeletal pain index: responsiveness and testing of criterion validity.

BACKGROUND Progress in establishing if therapies provide relief to cats with degenerative joint disease (DJD)-associated pain is hampered by a lack of validated owner-administered assessment methods. HYPOTHESIS That an appropriately developed subjective owner-completed instrument (Feline Musculoskeletal Pain Index-FMPI) to assess DJD-associated impairment would have responsiveness and criterion validity. ANIMALS Twenty-five client-owned cats with DJD-associated pain. METHODS FMPI responsiveness (ability to detect the effect of an analgesic treatment) and validity (correlation with an objective measure) were explored through a stratified, randomized, double blinded, placebo-controlled, crossover 10-week clinical study. Meloxicam was administered to effect pain relief. A linear mixed model, backward stepwise regression, and Pearson correlations were used to assess responsiveness and criterion validity with the assumption that the NSAID would increase activity. RESULTS Positive responses of cats to placebo (P = .0001) and meloxicam treatment (P = .0004) were detected; however, the instrument did not detect any difference between placebo and meloxicam (linear mixed model), even for the high impairment cases. Percent meloxicam target dose administered, temperament, and total baseline FMPI score were covariates that most affected FMPI scores. Controlling for significant covariates, most positive effects were seen for placebo treatment. Positive treatment effects on activity were detected, but only for the cases designated as most highly impaired. CONCLUSIONS AND CLINICAL IMPORTANCE Neither responsiveness nor criterion validity were detected by the inclusion criteria for cases in this study. The data suggest that further work is indicated to understand factors affecting activity in cats to optimize inclusion criteria.
Avian infectious bronchitis--virus distribution in tissues of chicks.

The virus of infectious bronchitis (IB) multiplies primarily in the respiratory tract; little is known about its presence in other organs. Fabricant and Levine (1) reported the presence of virus in eggs during active infection and for 36 days thereafter. Winterfield and Hitchner (5) isolated IB virus from kidneys. The main purpose of this study was to determine what tissues were invaded by IB virus of low and high embryo-passage levels, to estimate the concentration of virus in the tissues, and to determine whether different serological types of avian bronchitis virus would yield similar results.
C-Type Lectin Receptors Differentially Induce Th17 Cells and Vaccine Immunity to the Endemic Mycosis of North America

Vaccine immunity to the endemic mycoses of North America requires Th17 cells, but the pattern recognition receptors and signaling pathways that drive these protective responses have not been defined. We show that C-type lectin receptors exert divergent contributions to the development of antifungal Th17 cells and vaccine resistance against Blastomyces dermatitidis, Histoplasma capsulatum, and Coccidioides posadasii. Acquired immunity to B. dermatitidis requires Dectin-2, whereas vaccination against H. capsulatum and C. posadasii infection depends on innate sensing by Dectin-1 and Dectin-2, but not Mincle. Tracking Ag-specific T cells in vivo established that the Card9 signaling pathway acts indispensably and exclusively on differentiation of Th17 cells, while leaving intact their activation, proliferation, survival, and migration. Whereas Card9 signaling is essential, C-type lectin receptors offer distinct and divergent contributions to vaccine immunity against these endemic fungal pathogens. Our work provides new insight into innate immune mechanisms that drive vaccine immunity and Th17 cells.