Miracle-dz/UniFAR-FTUs huggingface dataset:
An Oxidized Purine Nucleoside Triphosphatase, MTH1, Suppresses Cell Death Caused by Oxidative Stress*

MTH1 hydrolyzes oxidized purine nucleoside triphosphates such as 8-oxo-2′-deoxyguanosine 5′-triphosphate (8-oxo-dGTP) and 2-hydroxy-2′-deoxyadenosine 5′-triphosphate (2-OH-dATP) and thus protects cells from damage caused by their misincorporation into DNA. In the present study, we established MTH1-null mouse embryo fibroblasts that were highly susceptible to cell dysfunction and death caused by exposure to H2O2, with morphological features of pyknosis and electron-dense deposits accumulated in mitochondria. The cell death observed was independent of both poly(ADP-ribose) polymerase and caspases. A high performance liquid chromatography tandem mass spectrometry analysis and immunofluorescence microscopy revealed a continuous accumulation of 8-oxo-guanine both in nuclear and mitochondrial DNA after exposure to H2O2. All of the H2O2-induced alterations observed in MTH1-null mouse embryo fibroblasts were effectively suppressed by the expression of wild type human MTH1 (hMTH1), whereas they were only partially suppressed by the expression of mutant hMTH1 defective in either 8-oxo-dGTPase or 2-OH-dATPase activity. Human MTH1 thus protects cells from H2O2-induced cell dysfunction and death by hydrolyzing oxidized purine nucleotides including 8-oxo-dGTP and 2-OH-dATP, and these alterations may be partly attributed to a mitochondrial dysfunction.
Titanium Implants for Bone-anchored Hearing Aids - Host Reaction

In a series of 31 prospectively followed patients equipped with bone-anchored hearing aids (BAHA), 7 titanium implants (19.4%) were lost in 6 patients after a median of 42 months (range: 27-78 months), often after visible resorption of bone around the superficial part of the implant. Expressed in a sample life table, no implants were lost during the first 2 years. After 3-4 years, the success rate dropped to about 85% and after 6-7 years to about 75%. Research that aims to define the factors which influence the extrusion rate is needed.
System-level design models and implementation techniques

Electronic systems need to accommodate rapidly changing product specifications and to reduce design costs together with design turn-around time. To be able to reuse part of previous designs and to be able to include new functionality rapidly, system designers tend to use microcontrollers and digital signal processors (DSPs) as much as possible. For performance reasons they may be forced to design special purpose hardware, but even then there is a strong motivation toward the reuse of parts already designed. This trend will change the industrial landscape and will make the trade and assembly of intellectual properties (IPs) embodied in layouts, RTL designs, and software programs indispensable. We believe that system design should be based on the use of one or more formal models to describe the behavior of the system at a high level of abstraction, before a decision on its decomposition into hardware and software components is taken. Design should then be based on a sequence consisting of the initial functional design (i.e. specifying what the system is intended to do) and its analysis, the mapping of such functional description, into an architecture, and the consequent performance evaluation. The final implementation of the system should be made using automatic synthesis as much as possible from this high level of abstraction, to ensure implementations that are "correct by construction". Validation (through simulation or verification) should be done at the highest possible levels of abstraction.
Autoantibodies, complement and type I interferon as biomarkers for personalized medicine in SLE

Systemic lupus erythematosus (SLE) can be a mysterious disease, presenting with extremely divergent clinical phenotypes. Already, biomarkers are very helpful tools for diagnosis, assessment and monitoring of disease activity, differential diagnosis of clinical manifestations, prediction of the disease course and stratified therapy, and they hold the key to personalized medicine in SLE. We summarize the clinical information that can only be supplied by autoantibodies, complement components and interferon biomarkers in this diverse disease.
EH domain proteins Pan1p and End3p are components of a complex that plays a dual role in organization of the cortical actin cytoskeleton and endocytosis in Saccharomyces cerevisiae

Several proteins from diverse organisms have been shown to share a region of sequence homology with the mammalian epidermal growth factor receptor tyrosine kinase substrate Eps15. Included in this new protein family, termed EH domain proteins, are two yeast proteins, Pan1p and End3p. We have shown previously that Pan1p is required for normal organization of the actin cytoskeleton and that it associates with the actin patches on the cell cortex. End3p has been shown by others to be an important factor in the process of endocytosis. End3p is also known to be required for the organization of the actin cytoskeleton. Here we report that Pan1p and End3p act as a complex in vivo. Using the pan1-4 mutant which we isolated and characterized previously, the END3 gene was identified as a suppressor of pan1-4 when overexpressed. Suppression of the pan1-4 mutation by multicopy END3 required the presence of the mutant Pan1p protein. Coimmunoprecipitation and two-hybrid protein interaction experiments indicated that Pan1p and End3p associate with each other. The localization of Pan1p to the cortical actin cytoskeleton became weakened in the end3 mutant at the permissive temperature and undetectable at the restrictive temperature, suggesting that End3p may be important for proper localization of Pan1p to the cortical actin cytoskeleton. The finding that the pan1-4 mutant was defective in endocytosis as severely as the end3 mutant under nonpermissive conditions supports the notion that the association between Pan1p and End3p is of physiological relevance. Together with results of earlier reports, these results provide strong evidence suggesting that Pan1p and End3p are the components of a complex that has essential functions in both the organization of cell membrane-associated actin cytoskeleton and the process of endocytosis.
Lie group analysis of non-linear dynamic of micro structures under electrostatic field

This paper presents an analytical solution of nonlinear differential equation of micro-structures subjected to electro- static fields. The constitutive equation of such a model is a second order differential equation (ODE). The problem is solved when the assumption of linear deflection is considered. However, deflection of micro cantilevers in practical applications is non- linear. Moreover, the constitutive ODE is stiff and various numerical algorithms used to solve it yield non-consistent numerical solutions. A deduction order method - Lie group symmetry is employed to reduce the order of the ODE. Although the resulting first order ODE has no symmetry that would guarantee an explicit close form solution, it enables an analytical formulation for the no-damping assumption only. The restoring force term in the first order ODE reveals the pull-in voltage as expressed in classical MEMS textbooks. It is shown that the numerical solution for the second order ODE and the reduced first order ODE are same. Finding any symmetry other than translation, scaling or rotation will enable the reduction of the first order ODE and thus, the formulation of an analytical solution to this highly non-linear problem.
X exceptionalism in Caenorhabditis speciation

Speciation genetics research in diverse organisms shows the X‐chromosome to be exceptional in how it contributes to “rules” of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X‐chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large‐X effect hypothesis. Studies to date implicate improper chromatin regulation of the X‐chromosome by small RNA pathways as integral to hybrid male dysfunction. Sexual transitions in reproductive mode to self‐fertilizing hermaphroditism inject distinctive molecular evolutionary features into the speciation process for some species. Caenorhabditis also provides unique opportunities for analysis in a system with XO sex determination that lacks a Y‐chromosome, sex chromosome‐dependent sperm competition differences and mechanisms of gametic isolation, exceptional accessibility to the development process and rapid experimental evolution. As genetic analysis of reproductive isolation matures with investigation of multiple pairs of Caenorhabditis species and new species discovery, nematodes will provide a powerful complement to more established study organisms for deciphering the genetic basis of and rules to speciation.
Knowledge discovery method based on data mining for marine propulsion system

Modern vessels have comprehensive platform management capability that allow them to achieve unprecedented levels of operational effectiveness and contribute to crew reduction. The focus of this paper is to address a new knowledge discovery method based on data mining to support the task activities for integrated management of ship propulsion system. The requirements of management knowledge are analyzed. Data mining algorithm is put forward to identify the related useful running mode knowledge of marine propulsion system. This new method which based on data mining would enhance the capability of knowledge based management for marine propulsion system.
A Comparison of Perceptual Ratings and Computed Audio Features

The backbone of most music information retrieval systems is the features extracted from audio. There is an abundance of features suggested in previous studies ranging from low-level spectral properties to high-level semantic descriptions. These features often attempt to model different perceptual aspects. However, few studies have verified if the extracted features correspond to the assumed perceptual concepts. To investigate this we selected a set of features (or musical factors) from previous psychology studies. Subjects rated nine features and two emotion scales using a set of ringtone examples. Related audio features were extracted using existing toolboxes and compared with the perceptual ratings. The results indicate that there was a high agreement among the judges for most of the perceptual scales. The emotion ratings energy and valence could be well estimated by the perceptual features using multiple regression with adj. R = 0.93 and 0.87, respectively. The corresponding audio features could only to a certain degree predict the corresponding perceptual features indicating a need for further development.
THE INFLUENCE OF BODY MASS ON CALCULATION OF POWER DURING LOWER‐BODY RESISTANCE EXERCISES

The objective of this investigation was to examine the influence of body mass in the calculation of power and the subsequent effect on the load-power relationship in the jump squat, squat, and power clean. Twelve Division I male athletes were evaluated on their performance across various intensities in all the 3 lifts. Power output was calculated using 3 separate techniques: (a) including the contribution of body mass in force output (IBM), (b) including the contribution of the mass of body less the mass of the shanks and feet in force output (IBMS), and (c) excluding the contribution of body mass in force output (EBM). Peak power, peak power relative to body mass, and peak force calculated using EBM were significantly (p ≤ 0.05) lower than outputs calculated with IBM and IBMS. The load that maximized power output was unchanged between the 3 techniques in the jump squat (0% 1 repetition maximum [1RM]) and power clean (80% 1RM) but was shifted from 56% (IBM and IBMS) to 71% 1RM (EBM) in the squat. Across all 3 movements, the shape of the load-power curve was affected when derived via the EBM method as a result of the underrepresentation of power output at light loads. This was due to the majority of the load being neglected when the mass of the body was removed from the system mass used in the calculation of force. This study indicates that not only is the actual power output significantly lower when body mass is excluded from the force output of a lower body movement, but the load-power relationship is altered as well. Therefore, it is imperative that the mass of the individual being tested is incorporated into the calculation of force used to determine power output during lower-body movements.
Septal Localization of FtsQ, an Essential Cell Division Protein in Escherichia coli

ABSTRACT Septation in Escherichia coli requires several gene products. One of these, FtsQ, is a simple bitopic membrane protein with a short cytoplasmic N terminus, a membrane-spanning segment, and a periplasmic domain. We have constructed a merodiploid strain that expresses both FtsQ and the fusion protein green fluorescent protein (GFP)-FtsQ from single-copy chromosomal genes. The gfp-ftsQgene complements a null mutation in ftsQ. Fluorescence microscopy revealed that GFP-FtsQ localizes to the division site. Replacing the cytoplasmic and transmembrane domains of FtsQ with alternative membrane anchors did not prevent the localization of the GFP fusion protein, while replacing the periplasmic domain did, suggesting that the periplasmic domain is necessary and sufficient for septal targeting. GFP-FtsQ localization to the septum depended on the cell division proteins FtsZ and FtsA, which are cytoplasmic, but not on FtsL and FtsI, which are bitopic membrane proteins with comparatively large periplasmic domains. In addition, the septal localization of ZipA apparently did not require functional FtsQ. Our results indicate that FtsQ is an intermediate recruit to the division site.
Understanding the shape of the galaxy two-point correlation function at z ~= 1 in the COSMOS field

We investigate how the shape of the galaxy two-point correlation function as measured in the zCOSMOS survey depends on local environment, quantified in terms of the density contrast on scales of 5 h^(−1) Mpc. We show that the flat shape previously observed at redshifts between z= 0.6 and 1 can be explained by this volume being simply 10 per cent overabundant in high-density environments, with respect to a universal density probability distribution function. When galaxies corresponding to the top 10 per cent tail of the distribution are excluded, the measured w_(p)(r_(p)) steepens and becomes indistinguishable from Lambda cold dark matter (ΛCDM) predictions on all scales. This is the same effect recognized by Abbas & Sheth in the Sloan Digital Sky Survey (SDSS) data at z ≃ 0 and explained as a natural consequence of halo–environment correlations in a hierarchical scenario. Galaxies living in high-density regions trace dark matter haloes with typically higher masses, which are more correlated. If the density probability distribution function of the sample is particularly rich in high-density regions because of the variance introduced by its finite size, this produces a distorted two-point correlation function. We argue that this is the dominant effect responsible for the observed ‘peculiar’ clustering in the COSMOS field.
Reovirus guanylyltransferase is L2 gene product lambda 2

Reovirus guanylyltransferase, studied as a covalent enzyme-GMP intermediate, was used to guanylate appropriate acceptor molecules in vitro to produce authentic cap structures. Guanylyltransferase activity was associated with lambda 2, the 140-kilodalton product of the L2 gene segment of reovirus serotypes 1 and 3.
Resource allocation between reproductive phases: the importance of thermal conditions in determining the cost of incubation

Changes in the resources allocated to particular stages of reproduction are expected to influence allocation to, and performance in, subsequent reproductive stages. Experimental manipulation of individual investment patterns provides important evidence that such physiological trade‐offs occur, and can highlight the key environmental variables that influence reproductive costs. By temporarily altering the thermal properties of starling nests, we reduced the energetic demand of first‐clutch incubation, and examined the effect of this manipulation on performance during the same and the subsequent reproductive attempts. Compared with controls, starlings investing less in incubation were more successful in fledging young, and were more likely to hatch all their eggs if a subsequent reproductive attempt was made. Our results show that incubation demands can limit reproductive success, and that resources saved during incubation can be reallocated to later stages of the same reproductive attempt and to future reproductive attempts. This study also shows that small changes in thermal environment can affect breeding success by altering the energetic demands imposed on incubating parents, independently of the effect of temperature on other environmental variables such as food supply.
Updates on Mapping Quantitative Trait Loci Theoretical model for gene-gene , gene-environment , and gene-sex interactions based on congenic-strain analysis of blood pressure in Dahl salt-sensitive rats

Rapp JP. Theoretical model for gene-gene, gene-environment, and gene-sex interactions based on congenic-strain analysis of blood pressure in Dahl salt-sensitive rats. Physiol Genomics 45: 737–750, 2013. First published June 11, 2013; doi:10.1152/physiolgenomics.00046. 2013. — There is a significant literature describing quantitative trait loci (QTL) controlling blood pressure (BP) in the Dahl salt-sensitive (S) rat. In studies to identify the genes underlying BP QTL it has been common practice to place chromosomal segments from low BP strains on the genetic background of the S rat and then reduce the congenic segments by substitution mapping. The present work suggests a model to simulate genetic interactions found using such congenic strains. The QTL are considered to be switches that can be either in series or in parallel represented by the logic operators AND or OR, respectively. The QTL switches can be on/off switches but are also allowed specific leak properties. The QTL switches are represented by a “universal” switch consisting of two molecules binding to form a complex. Genetic inputs enter the model as allelic products of one of the binding molecules and environmental variation (including dietary saltand sex-related differences) enters as an influence on the concentration of the other binding molecule. The pairwise interactions of QTL are very well simulated and fall into recognizable patterns. There is, however, often more than one assumed model to predict a given pattern so that all patterns do not necessarily have a unique solution. Nevertheless, the models obtained provide a framework for placing the QTL in pathways relative to one another. Moreover, based on their leak properties pairs of QTL could be identified in which one QTL may alter the properties of the other QTL.
Computers and Operations Research: A Marriage for Growth

Rapid changes in both hardware and software computer technology pose many challenges to quantitative applications, and especially to operations research. Much of the future success of OR will depend on its ability to meet these challenges by marrying its approaches to computer technology and then using this enhanced capability to reach out to important new problem areas. To support the contention that OR is moving in these directions, as it must, this paper begins by reviewing computing progress to date as it relates to OR. Then it views three facets of the expansion of OR: university enrollments (and those on nonresident aliens in particular), application opportunities, and the dispersion of OR people in large organizations. The paper is an outgrowth of a plenary lecture at the May 1991 TIMS/ORSA meeting in Nashville.
Two's company, three's a crowd: can H2S be the third endogenous gaseous transmitter?

Bearing the public image of a deadly “gas of rotten eggs,” hydrogen sulfide (H2S) can be generated in many types of mammalian cells. Functionally, H2S has been implicated in the induction of hippocampal long‐term potentiation, brain development, and blood pressure regulation. By acting specifically on KATP channels, H2S can hyperpolarize cell membranes, relax smooth muscle cells, or decrease neuronal excitability. The endogenous metabolism and physiological functions of H2S position this gas well in the novel family of endogenous gaseous transmitters, termed “gasotransmitters. ” It is hypothesized that H2S is the third endogenous signaling gasotransmitter, besides nitric oxide and carbon monoxide. This positioning of H2S will open an exciting field‐H2S physiology‐encompassing realization of the interaction of H2S and other gasotransmitters, sulfurating modification of proteins, and the functional role of H2Sin multiple systems. It may shed light on the pathogenesis of many diseases related to the abnormal metabolism of H2S. — Wang, R. Two's company, three's a crowd: can H2S be the third endogenous gaseous transmitter? FASEB J. 16, 1792–1798 (2002)
Involvement of a spliced and defective human foamy virus in the establishment of chronic infection

Human foamy retrovirus (HFV) is found as two proviruses (HFV and delta HFV) which differ by a splice-induced deletion within the bel1 transactivator gene. The defective delta HFV (which lacks a functional Bel1 but harbors an intronless bet gene) is predominantly found in nonlytic infections in vitro as well as in vivo. Here, we show that infection of cell lines stably transduced by delta HFV DNA with the highly lytic HFV leads to chronic infections characterized by an absence of lysis, a balanced ratio of HFV to delta HFV, and a persistent Bet expression accompanied by a shutoff of structural genes. While this system only partially reflects the natural situation, in which target cells are infected by HFV and delta HFV simultaneously, it strongly suggests that delta HFV is a defective interfering retrovirus. Accordingly, previous or concomitant exposure to delta HFV viruses greatly enhances the formation of lysis-resistant clones in culture after HFV infection. The inability of delta HFV proviruses encoding a mutated bet gene to induce chronic infection suggests a role for Bet in this process. Through a specific, splice-induced, genomic deletion, resulting in a switch from Bel1 to Bet expression, the lytic properties of HFV are progressively lost. Such programmed inactivation of a key gene represents a new regulatory mechanism of gene expression in retroviruses.
Homogeneity of Danish Environmental and Clinical Isolates of Shewanella algae

ABSTRACT Danish isolates of Shewanella algae constituted by whole-cell protein profiling a very homogeneous group, and no clear distinction was seen between strains from the marine environment and strains of clinical origin. Although variation between all strains was observed by ribotyping and random amplified polymorphic DNA analysis, no clonal relationship between infective strains was found. From several patients, clonally identical strains of S. algaewere reisolated up to 8 months after the primary isolation, indicating that the same strain may be able to maintain the infection.