Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for recognition and repair of the 3′-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis

Abstract NExo is an enzyme from Neisseria meningitidis that is specialized in the removal of the 3′-phosphate and other 3′-lesions, which are potential blocks for DNA repair. NExo is a highly active DNA 3′-phosphatase, and although it is from the class II AP family it lacks AP endonuclease activity. In contrast, the NExo homologue NApe, lacks 3′-phosphatase activity but is an efficient AP endonuclease. These enzymes act together to protect the meningococcus from DNA damage arising mainly from oxidative stress and spontaneous base loss. In this work, we present crystal structures of the specialized 3′-phosphatase NExo bound to DNA in the presence and absence of a 3′-phosphate lesion. We have outlined the reaction mechanism of NExo, and using point mutations we bring mechanistic insights into the specificity of the 3′-phosphatase activity of NExo. Our data provide further insight into the molecular origins of plasticity in substrate recognition for this class of enzymes. From this we hypothesize that these specialized enzymes lead to enhanced efficiency and accuracy of DNA repair and that this is important for the biological niche occupied by this bacterium.
Inuit Voices on Quality Education in Nunavut: Policy Implications

This paper is based on a research that explored how Inuit community members in Nunavut Territory, Canada, conceptualized quality education in the socio-cultural context of the territory. Data were collected through telephone interviews of 13 Inuit community members in Nunavut and document reviews both of which were conducted in 2010. The data analysis showed that Inuit community members are r gravely concerned with:(1) the low grade twelve graduation rates and high dropout rates in the territory schools;(2) School improvement planning that engages Inuit communities; (3) Integration of school with the larger community; (4) Communicative engagement with parents and other community stakeholders; (5) Culturally relevant school programming and pedagogy; and (6) Culturally appropriate disciplinary methods. In the conclusion, the paper spells out the policy implications of the findings.
Relation between presence‐absence of a visible nucleoid and metabolic activity in bacterioplankton cells

We investigated the report of Zweifel and Hagstriim that only a portion of marine bacteria contain nucleoids -- the DNA-containing regions of procaryotic cells-and that such bacteria correspond to the active or viable fraction of bacterioplankton. In Oregon coastal waters, 21-64% of bacteria had visible nucleoids; numbers of nucleoid-visible (NV) bacteria were greater than numbers of metabolically active bacteria, based on cells with active electron transport systems (ETS) and intact cell membranes. During log growth of a marine isolate, proportions of NV and ETS-active cells approached 100%. In stationary growth phase, the fraction of ETS-active cells decreased rapidly, while that of NV cells remained high for 7 d. When starved cells of the isolate were resupplied with nutrient (50 mg liter-l peptone), total cell number did not increase during the initial 6 h, but the proportion of NV cells increased from 27 to lOO%, and that of ETS-active cells from 6 to 75%. In an analogous experiment with a bacterioplankton assemblage, a similar trend was observed: the number of NV cells doubled during the initial 6 h prior to an increase in total cell counts. These results show that some bacteria without visible nucleoids are capable of becoming NV cells, and thus have DNA in a nucleoid region not detectable with the method used here. Enumeration of bacterioplankton by staining with the fluorochromes acridine orange or 4’,6-diamidino-2phenylidole (DAPI) and then counting via epifluorescence microscopy is one of the most common methods used in aquatic microbiology. Zweifel and Hagstriim (1995) presented evidence that only a fraction of the cells counted with these methods appear to be living bacteria. They based this observation on the presence or absence of a nucleoid-a region packed with condensed DNA in the bacterial cell. The standard direct count method based on DAPI staining of aldehyde-preserved marine bacteria (Porter and Feig 1980) was shown to be nonspecific for DNA; a modification of the method resulted in efficient binding of DAPI to DNA and removal of most nonspecific DAPI staining of other cell components (Zweifel and Hagstrijm 1995). In seawater taken from the Baltic Sea, the North Sea, and the Mediterranean Sea, Zweifel and Hagstriim reported that from 2 to 32% of bacterioplankton appeared to contain nucleoids. They inferred from their results, which included laboratory culture experiments, that cells with nucleoids corresponded to the portion of the bacterial assemblage that is active or viable and that cells without nucleoids were “ghost” cells that did not contain DNA and were therefore incapable of growth.
The Standardized Pressure Injury Prevention Protocol for improving nursing compliance with best practice guidelines

Compliance with international best practice guidelines can effectively prevent most hospital-acquired pressure injuries (HAPIs). (Black 2011, National Pressure Ulcer Advisory Panel 2010, Padula et al. 2016) These guidelines include several nursing interventions that first were introduced in 1992 by the U.S. Agency for Healthcare Research & Quality (AHRQ), and have since been updated by the National Pressure Ulcer Advisory Panel (NPUAP) every 3-5 years. (NPUAP 2014, Panel on the Prediction and Prevention of Pressure Ulcers in Adults 1992. AHCPR Publication No. 91-0047) Following admission, nurses should perform a daily skin check and risk-assessment using a validated risk tool. (Bergstrom 1987, Braden 1994) Patients determined to be high-risk receive additional measures: (a) repositioning every 2-4 hours; (b) managing skin care and incontinence; (c) improving nutrition; (d) using pressure-relieving support surfaces; and (e) reducing friction and shear. (NPUAP 2014, Agency for Healthcare Research and Quality 2011) Many hospitals struggle to incorporate these guidelines into a daily routine given the intense amount of nursing time, costliness to implement, uncertain clinical effectiveness, and competing patient demands and hospital priorities. This article is protected by copyright. All rights reserved.
Dark Energy and Dark Matter Interaction: Kernels of Volterra Type and Coincidence Problem

We study a new exactly solvable model of coupling of the Dark Energy and Dark Matter, in the framework of which the kernel of non-gravitational interaction is presented by the integral Volterra-type operator well-known in the classical theory of fading memory. Exact solutions of this isotropic homogeneous cosmological model were classified with respect to the sign of the discriminant of the cubic characteristic polynomial associated with the key equation of the model. Energy-density scalars of the Dark Energy and Dark Matter, the Hubble function and acceleration parameter are presented explicitly; the scale factor is found in quadratures. Asymptotic analysis of the exact solutions has shown that the Big Rip, Little Rip, Pseudo Rip regimes can be realized with the specific choice of guiding parameters of the model. We show that the Coincidence problem can be solved if we consider the memory effect associated with the interactions in the Dark Sector of the universe.
Insect Glutathione S-Transferases

ABSTRACT Simon J. Yu (1996) Insect glutathione S-transferases. Zoological Studies 35(1): 9-19. Glutathione S­ transferases (GSTs) have been purified from more than 24 insect species, including Lepidoptera, Diptera, Coleoptera, Dictyoptera, and Hymenoptera. These transferases exist in multiple forms; as many as eight isozymes were found in midguts and fat bodies of fall armyworm larvae. Molecular weights of insect GSTs are within the range of 35 000-63 000. They consist of two subunits (homodimers and heterodimers) of molecular weight between 19000 and 35000. Insect GSTs metabolize various electrophilic xenobiotics, including halogenated compounds, nitro compounds, a.i3-unsaturated compounds, isothiocyanates, organo­ thiocyanates, organophosphates, and oxides. At least 55 chemicals have served as substrates for GSTs in insects. GSTs have been induced by numerous xenoblotlcs, including insecticides, drugs, host plants, and allelochemicals in over 21 species of insects. Among these inducers, insecticides (organochlorines), host plants (umbellifers and crucifers), and allelochemicals (furanocoumarins, indoles, and flavonoids) are the most potent inducers of the enzymes. Species differences in enzyme inducibility were observed in Lepidoptera. GST induction in insects was associated with increased GST mRNA levels indicating de novo synthesis of the enzyme. GSTs have been implicated in the resistance to insecticides and allelochemicals in insects. The high GST activity found in insecticide-resistant insects was associated with increased level of specific mRNA.
Microcrystalline silicon solar cells deposited at high rates

Hydrogenated microcrystalline silicon (μc-Si:H) thin-film solar cells were prepared at high rates by very high frequency plasma-enhanced chemical vapor deposition under high working pressure. The influence of deposition parameters on the deposition rate (RD) and the solar cell performance were comprehensively studied in this paper, as well as the structural, optical, and electrical properties of the resulting solar cells. Reactor-geometry adjustment was done to achieve a stable and homogeneous discharge under high pressure. Optimum solar cells are always found close to the transition from microcrystalline to amorphous growth, with a crystallinity of about 60%. At constant silane concentration, an increase in the discharge power did hardly increase the deposition rate, but did increase the crystallinity of the solar cells. This results in a shift of the μc-Si:H∕a-Si:H transition to higher silane concentration, and therefore leads to a higher RD for the optimum cells. On the other hand, an increase in the t.
An optimized blockchain solution for the IBM z14

Blockchain is a technology that has been available for several years and has already had several generations. Multiple implementations exist. In this paper, we describe how one of them, the Hyperledger Fabric, is used today to demonstrate the wide usage of the technology for multiple markets beyond finance and cryptocurrency. The use cases highlight the relevance of security—due to the type of data and the distributed foundation of blockchain—and of system performance to enable the use cases in production. Security and performance are the base for the architecture of blockchain on the IBM LinuxONE systems. The Secure Service Container prevents tampering, and the cryptocard usage hardens the solution—and the performance optimization in the compiler, cryptoinstructions, and large caches provides the performance. These optimizations have been further extended with the IBM z14 beyond previous IBM Z generations. In this paper, we describe how a cluster topology is used to implement a high-availability service that scales dynamically from small networks to large ones using the hot plug capabilities of the IBM LinuxONE systems.
CD200 is a useful marker in the diagnosis of chronic lymphocytic leukemia

The diagnosis of CLL is supported by a typical morphology and immunophenotype and usually does not present difficulties. Nevertheless, some patients with CLL can show an atypical phenotype, this raising the possibility of a lymphoproliferative disorder other than CLL. It has been recently shown that the expression of CD200 could be a rather consistent marker for CLL.
ADVANCED WAVEFORM SIMULATION FOR SEISMIC MONITORING

Earthquake source parameters underpin several aspects of nuclear explosion monitoring. Such aspects are: calibration of moment magnitudes (including coda magnitudes) and magnitude and distance amplitude corrections (MDAC); source depths; discrimination by isotropic moment tensor components; and waveform modeling for structure (including waveform tomography). This project seeks to improve methods for and broaden the applicability of estimating source parameters from broadband waveforms using the Cut-and-Paste (CAP) methodology. The CAP method uses a library of Green’s functions for a one-dimensional (1D, depth-varying) seismic velocity model. The method separates the main arrivals of the regional waveform into 5 windows: Pnl (vertical and radial components), Rayleigh (vertical and radial components) and Love (transverse component). Source parameters are estimated by grid search over strike, dip, rake and depth and seismic moment or equivalently moment magnitude, MW, are adjusted to fit the amplitudes. Key to the CAP method is allowing the synthetic seismograms to shift in time relative to the data in order to account for path-propagation errors (delays) in the 1D seismic velocity model used to compute the Green’s functions. The CAP method has been shown to improve estimates of source parameters, especially when delay and amplitude biases are calibrated using high signal-to-noise data from moderate earthquakes, CAP+. In the last year, we have focused on several tasks: (1) Building a High-Quality Catalog of Earthquake Source Parameters for the Middle East and East Asia. In East Asia we computed source parameters using the CAP method for a set of events studied by Herrmann et al., (2006) using a complete waveform technique. Results indicated excellent agreement with the moment magnitudes in the range 3.5–5.5. Below magnitude 3.5, the scatter increases. For events with more than 2–3 observations at different azimuths, we found good agreement of focal mechanisms. Depths were generally consistent, although differences of up to 10 km were found. These results suggest that CAP modeling provides estimates of source parameters at least as reliable as complete waveform modeling techniques. However, East Asia and the Yellow Sea Korean Paraplatform (YSKP) region studied are relatively laterally homogeneous and may not benefit from the CAP method’s flexibility to shift waveform segments to account for path-dependent model errors. A more challenging region to study is the Middle East where strong variations in sedimentary basin, crustal thickness and crustal and mantle seismic velocities greatly impact regional wave propagation. We applied the CAP method to a set of events in and around Iran and found good agreement between estimated focal mechanisms and those reported by the Global Centroid Moment Tensor (CMT) catalog. We found a possible bias in the moment magnitudes that may be due to the thick low-velocity crust in the Iranian Plateau area.
Shortcomings of the Winkler Model in the Assessment of Sectioned Tunnels under Seismic Loading

A Winkler-type model is often applied in the design of tunnels subject to seismic loading. Since the subgrade stiffness is modelled by disjoint springs, distributed continuously along the tunnel, the model does not account for retroaction via the soil. This may not be a problem in the design of tunnels with a uniform cross section. However, for sectioned tunnels divided into a number of elements, erroneous results may be expected—especially regarding the relative deformations at the joints. In this paper, the results of a Winkler model are compared with a full three-dimensional continuum ﬁnite-element solution, using a planned tunnel at Thessaloniki, Greece, as a case study. The aim of the analysis is to quantify the inaccuracy of the Winkler model in the prediction of damage at a gasket between two tunnel elements.
Democracy in crisis? The declining support for national democracy in European countries, 2007-2011

The Great Recession that started in 2007/2008 has been the worst economic downturn since the crisis of the 1930s in Europe. It led to a major sovereign debt crisis, which is arguably the biggest challenge for the European Union (EU) and its common currency. Not since the 1950s have advanced democracies experienced such a dramatic external imposition of austerity and structural reform policies through inter- or supranational organisations such as the EU and the International Monetary Fund (IMF) or as implicitly requested by international financial markets. Did this massive interference with the room for maneuver of parliaments and governments in many countries erode support for national democracy in the crisis since 2007? Did citizens realise that their national democratic institutions were no longer able to effectively decide on major economic and social policies, on economic and welfare state institutions? And did they react by concluding that this constrained democracy no longer merited further support? These are the questions guiding this article, which compares 26 EU countries in 2007�2011 and re-analyses 78 national surveys. Aggregate data from these surveys is analysed in a time-series cross-section design to examine changes in democratic support at the country level. The hypotheses also are tested at the individual level by estimating a series of cross-classified multilevel logistic regression models. Support for national democracy � operationalised as satisfaction with the way democracy works and as trust in parliament � declined dramatically during the crisis. This was caused both by international organisations and markets interfering with national democratic procedures and by the deteriorating situation of the national economy as perceived by individual citizens.
Simulating the image quality of the human eye using the Zenike polynomials

The visual system of the human eye is a part of the central nervous system by which the human body sees and interprets the information provided by the visible light in order to build a representation of the world around. During the propagations of the light trough the eye medium, the retinal image can be deteriorated by an eye which suffers from diseases and disorders. For retinal images the most important sources of image quality degradation are diffraction and optical aberrations. We simulate the effect of the diffraction on human vision. We present a description of the aberrations and we use the Zernike polynomials to simulate the wavefront aberrations of the eye. We compute the point spread function of an eye and we simulate its effects on the human vision.
Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens

ABSTRACT The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction‐site associated DNA sequencing (RAD‐seq). An F2 resource family was generated by mating Oh‐Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main‐effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome‐wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and ‐0.31 in males and ‐0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD‐seq.
Computation of Fundamental Periods for Moment Frames Using a Hand-Calculated Approach

The second method (known as Method B), specified in the 1997 Uniform Building Code Static Force Procedure, is a rational and accurate approach for finding the fundamental period of a frame. The for- mula used in Method B, however, is not a popular formula because it involves time-consuming computations of frame deflections which usually require the use of computer software. A hand-calculated approach for the computation of frame deflections using a calculator rather than a computer is suggested in this paper in order to turn Method B into a practical method for determining the fundamental periods of low-rise moment frames. The general stiffness matrix of a three-story, three-bay frame presented in this paper is intended to be used as an aid to compute the deflections for any moment frame within three stories in height and within three bays in width. Examples shown in this paper illustrate the step by step procedure for the computation of the fundamental periods of low-rise moment frames using the proposed hand-calculated approach. These examples also demonstrate that the results obtained from the proposed hand-calculated static approach agree with that obtained from the dynamic analysis.
Role of membrane associated molecules in liver fibrosis

The aim of the study was to evaluate the role of membrane associated proteins in tissue formation and remodeling, in normal embryogenesis and in liver disease. Molecules associated with cellular membranes provide a fundamental basis for cellular interactions during development, homeostasis and disease. Similar basic mechanisms play a crucial role in liver disease such as in tissue modeling during embryogenesis. In the first study we investigated the expression of the cell adhesion molecule Rcadherin during formation of muscle and parenchymatous organs in the developing mouse embryo. R-cadherin was expressed during myogenesis in a pattern suggesting that it plays a role in myoblast cell-cell interactions. R-cadherin was also expressed by epithelia. In kidney, the expression pattern was associated with mesenchymal-epithelial interactions. R-cadherin exclusively rescued formation of epithelia and muscle in teratomas derived from E-cadherin null embryonic stem cells. From the results of this study we concluded that R-cadherin plays a role in formation of striated muscle and possibly also of epithelia. In the second study, we evaluated the role of neural cell adhesion molecule (NCAM) in biliary type fibrosis and liver fibrosis due to parenchymatous disease. NCAM knock-out mice had attenuated liver fibrosis after bile duct ligation but not after carbon tetrachloride injections. Furthermore, hepatic stellate cells isolated from N-CAM knock-outs had impaired activation. These results suggest a role of N-CAM in biliary type liver fibrosis. In the third study we studied the distribution of EBP50 in patients with biliary liver disease. EBP50 is a scaffolding protein involved in stabilization of transport proteins at the plasma membrane. EBP50 was normally expressed in hepatocytes and native bile ducts of patients with cystic fibrosis carrying the CFTR mutation F508, primary biliary cirrhosis and primary sclerosing cholangitis. However, EBP50 was delocalized to the basolateral membranes, cytoplasm and nucleus in proliferating cells of the ductular reactions. This finding, together with suppressed proliferation of cultured cholangiocytes when EBP50 is downregulated, suggests that it has a role the in proliferation of biliary epithelial cells in biliary liver disease. Liver fibrosis due to long-term treatment with methotrexate is related to continuous low-grade hepatocellular damage. In the fourth study we evaluated the impact of the risk factors diabetes, over-weight, alcohol and viral hepatitis on development of liver fibrosis in methotrexate treated psoriasis patients. The results showed that patients with over-weight and/or diabetes had significantly higher risk of developing liver fibrosis and cirrhosis, at a lower accumulative dose methotrexate.