Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of the Escherichia coli Mug Protein in the Removal of Uracil and 3,N 4-Ethenocytosine from DNA*

The human thymine-DNA glycosylase has a sequence homolog in Escherichia coli that is described to excise uracils from U·G mismatches (Gallinari, P., and Jiricny, J. (1996)Nature 383, 735–738) and is named mismatched uracil glycosylase (Mug). It has also been described to remove 3,N 4-ethenocytosine (εC) from εC·G mismatches (Saparbaev, M., and Laval, J. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 8508–8513). We used a mug mutant to clarify the role of this protein in DNA repair and mutation avoidance. We find that inactivation of mug has no effect on C to T or 5-methylcytosine to T mutations in E. coli and that this contrasts with the effect of ung defect on C to T mutations and of vsr defect on 5-methylcytosine to T mutations. Even under conditions where it is overproduced in cells, Mug has little effect on the frequency of C to T mutations. Because uracil-DNA glycosylase (Ung) and Vsr are known to repair U·G and T·G mismatches, respectively, we conclude that Mug does not repair U·G or T·G mismatches in vivo. A defect inmug also has little effect on forward mutations, suggesting that Mug does not play a role in avoiding mutations due to endogenous damage to DNA in growing E. coli. Cell-free extracts frommug + ung cells show very little ability to remove uracil from DNA, but can excise εC. The latter activity is missing in extracts from mug cells, suggesting that Mug may be the only enzyme in E. coli that can remove this mutagenic adduct. Thus, the principal role of Mug in E. coli may be to help repair damage to DNA caused by exogenous chemical agents such as chloroacetaldehyde.
Skeleton extraction of 3D objects with radial basis functions

A skeleton is a lower dimensional shape description of an object. The requirements of a skeleton differ with applications. For example, object recognition requires skeletons with primitive shape features to make similarity comparison. On the other hand, surface reconstruction needs skeletons, which contain detailed geometry information to reduce the approximation error in the reconstruction process. Whereas many previous works are concerned about skeleton extraction, most of these methods are sensitive to noise, time consuming, or restricted to specific 3D models. A practical approach for extracting skeletons from general 3D models using radial basis functions (RBFs) is proposed. A skeleton generated with this approach conforms more to the human perception. Given a 3D polygonal model, the vertices are regarded as centers for RBF level set construction. Next, a gradient descent algorithm is applied to each vertex to locate the local maxima in the RBF; the gradient is calculated directly from the partial derivatives of the RBF. Finally, with the inherited connectivity from the original model, local maximum pairs are connected with links driven by the active contour model. The skeletonization process is completed when the potential energy of these links is minimized.
Human conjunctival epithelial cell responses to platelet-activating factor (PAF): signal transduction and release of proinflammatory cytokines

Purpose The aims of the study were to characterize the signal transduction responses to platelet-activating factor (PAF) and to monitor the downstream effects of PAF on the production of proinflammatory cytokines in human conjunctival epithelial cells (HCECs). Methods The generation of inositol phosphates ([3H]IPs) from [3H]phosphoinositide (PI) hydrolysis and the mobilization of intracellular calcium ([Ca2+]i) were evaluated using ion exchange chromatography and Fura-2 fluorescence techniques, respectively. The production of the cytokines (interleukin-6 [IL-6], interleukin-8 [IL-8], and granulocyte macrophage colony-stimulating factor [GM-CSF]) from PAF-stimulated HCECs was quantified using specific ELISA assays. Specific PAF antagonists were used to study the pharmacological aspects of PAF actions in HCECs. Results PAF (100 nM) maximally stimulated PI turnover in HCECs by 2.3±0.02 fold (n=21) above basal levels and with a potency (EC50) of 5.9±1.7 nM (n=4). PAF or its stabilized analog, methyl carbamyl (mc)PAF (EC50=0.8 nM), rapidly mobilized [Ca2+]i, which peaked within 30–60 s and remained elevated for 3 min. PAF (10 nM–1 µM) stimulated the release of the proinflammatory cytokines, IL-6, IL-8, and GM-CSF, 1.4–3.5 fold above basal levels. The effects of PAF (100 nM) on PI turnover and [Ca2+]i were potently antagonized by the PAF antagonists, 1-o-hexadecyl-2-o-acetyl–sn-glycero-3-phospho (N,N,N-trimethyl) hexanolamine (IC50=0.69 µM; Ki=38 nM), methyl 2-(phenylthio)ethyl-1,4-dihydro-2,4,6-trimethyl-pyridine-3,5-dicsrboxylate (PCA-42481; IC50=0.89 µM; Ki=50 nM), rac-3-(N-octadecylcarbomoyl)-2-methoxy) propyl-(2-thiazolioethyl) phosphate (CV-3988; IC50=13 µM; Ki=771 nM), and (+/−)-cis-3,5-dimethyl-2-(3-pyridyl)thiazolidin-4-one HCl (SM-10661; IC50=14 µM; Ki=789 nM [n=3 for each antagonist]). PAF-induced production of IL-6, IL-8, and GM-CSF from HCECs was also blocked by these PAF antagonists (IC50=4.6– 8.6 µM). Conclusions HCECs respond to PAF by generating IPs, mobilizing [Ca2+]i, and then secreting cytokines into the extracellular medium. These results suggest that HCECs may be key target cells for the PAF released from conjunctival mast cells following ocular allergic reactions. Therefore, HCECs in culture represent suitable in vitro models for the investigation of the role of PAF in human ocular allergic and inflammatory diseases and for the discovery of therapeutically useful PAF antagonists.
A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides

Human milk contains approximately 200 complex oligosaccharides believed to stimulate the growth and establishment of a protective microbiota in the infant gut. The lack of scalable analytical techniques has hindered the measurement of bacterial metabolism of these and other complex prebiotic oligosaccharides. An in vitro, multi‐strain, assay capable of measuring kinetics of bacterial growth and detailed oligosaccharide consumption analysis by FTICR‐MS was developed and tested simultaneously on 12 bifidobacterial strains. For quantitative consumption, deuterated and reduced human milk oligosaccharide (HMO) standards were used. A custom software suite developed in house called Glycolyzer was used to process the large amounts of oligosaccharide mass spectra automatically with 13C corrections based on de‐isotoping protocols. High growth on HMOs was characteristic of Bifidobacterium longum biovar infantis strains, which consumed nearly all available substrates, while other bifidobacterial strains tested, B. longum bv. longum, B. adolescentis, B. breve and B. bifidum, showed low or only moderate growth ability. Total oligosaccharide consumption ranged from a high of 87% for B. infantis JCM 7009 to only 12% for B. adolescentis ATCC 15703. A detailed analysis of consumption glycoprofiles indicated strain‐specific capabilities towards differential metabolism of milk oligosaccharides. This method overcomes previous limitations in the quantitative, multi‐strain analysis of bacterial metabolism of HMOs and represents a novel approach towards understanding bacterial consumption of complex prebiotic oligosaccharides.
Multi-speaker articulatory reconstruction based on an eigen articulatory HMM

We present a multi-speaker articulatory reconstruction method based on speaker-independent articulatory features and speaker-dependent features. These features are separated by using a multi-speaker articulatory database. This separation method consists of normalizing palate positions among the speakers and separating multi-speaker articulatory data into a speaker-independent eigen articulatory HMM and a speaker-adaptive matrix by using speaker-adaptive training (SAT). With the proposed method, the average RMS errors of the measured and reconstructed articulatory parameters were 1.35 mm. This result shows that the proposed method makes it possible to control speaker idiosyncrasies in the articulatory parameter domain.
IMIOL: A SYSTEM FOR INDEXING IMAGES BY THEIR SEMANTIC CONTENT BASED ON POSSIBILISTIC FUZZY CLUSTERING AND ADAPTIVE RESONANCE THEORY NEURAL NETWORKS LEARNING

Image databases are becoming large and of potential use in many areas, including medical diagnosis, astronomy, and the Web. These images, if analyzed, can reveal useful and potential information. Image indexing is the process of extracting and modeling the content of the image, the image data relationships, or other patterns not explicitly stored. Done this way, images could be indexed with the extracted knowledge, and thereby searching in these large databases for a particular information or pattern becomes more efficient and more reliable. For example, a medical doctor can search a medical database for already-diagnosed patient images having the same symptoms as the one at hand. Here we present a model for image indexing that bridges the gap between the visual content (or low-level descriptors) and the semantic content (or concepts). In our proposal, an image is modeled as being a set of objects, and each object is modeled with visual and semantics contents. Determination of the distinct objects (or segmentation) of the image is achieved through Possibilistic Fuzzy clustering. Thereafter, the visual content (namely, color, texture, and shape) of each object is computed using image processing techniques. Subsequently, each object is presented to the Concept Object Knowledge Base (COKB) for extraction of the semantic content using shape-based recognition. This knowledge base is constructed via neural learning with Adaptive Resonance Theory networks. Experimentation on standard large image databases reveal a good performance of our model.
Fundamental Results on Base Station Movement Problem for Sensor Networks

The benefits of using mobile base station to prolong sensor network lifetime have been well recognized. However, due to the complexity of the problem (time-dependent network topology and traffic routing), theoretical performance limits and provably optimal algorithms remain difficult to develop. This paper fills this important gap by contributing theoretical results regarding the optimal movement of a mobile base station. Our main result hinges upon two key intermediate results. In the first result, we show that a time-dependent joint base station movement and flow routing problem can be transformed into a location-dependent problem. In the second result, we show that, for (1 − ε) optimality, the infinite possible locations for base station movement can be reduced to a finite set of locations via several constructive steps [i.e., discretization of energy cost through a geometric sequence, division of a disk into a finite number of subareas, and representation of each subarea with a fictitious cost point (FCP)]. Subsequently, for each FCP, we can obtain the best sojourn time for the base station (as well as the corresponding location-dependent flow routing) via a simple linear program. We prove that the proposed solution can guarantee the achieved network lifetime is at least (1 − ε) of the maximum network lifetime, where ε can be made arbitrarily small depending on required precision.
Enhanced resistance of adriamycin-treated MCR-5 lung fibroblasts by increased intracellular glutathione peroxidase and extracellular antioxidants.

Considerable evidence indicates that reactive oxygen species play an etiological role in both cardiotoxicity and the skin necrosis induced by adriamycin (ADM). An increase in glutathione peroxidase activity on addition of selenium to cultured MCR-5 lung fibroblasts was observed; this increase was accompanied by enhanced cellular resistance to ADM toxicity. Moreover, the presence of exogenous antioxidant systems, such as superoxide dismutase, catalase, vitamin E, dimethylsulfoxide, and desferroxamine, an iron chelating agent, resulted in significant protection from ADM-mediated damage.
Contribution of cyclic parthenogenesis and colonization history to population structure in Daphnia

Cyclic parthenogenesis, the alternation of parthenogenetic and sexual reproduction, can lead to a wide scope of population structures, ranging from almost monoclonal to genetically highly diverse populations. In addition, sexual reproduction in aquatic cyclic parthenogens is associated with the production of dormant stages, which both enhance potential gene flow among populations as well as impact local evolutionary rates through the formation of dormant egg banks. Members of the cladoceran genus Daphnia are widely distributed key organisms in freshwater habitats, which mostly exhibit this reproduction mode. We assessed patterns of genetic variation within and among populations in the eurytopic and morphologically variable species Daphnia longispina, using data from both nuclear (13 microsatellite loci) and mitochondrial (partial sequencing of the 12S rRNA gene) markers from a set of populations sampled across Europe. Most populations were characterized by very high clonal diversity, reflecting an important impact of sexual reproduction and low levels of clonal selection. Among‐population genetic differentiation was very high for both nuclear and mitochondrial markers, and no strong pattern of isolation by distance was observed. We also did not observe any substantial genetic differentiation among traditionally recognized morphotypes of D. longispina. Our findings of high levels of within‐population genetic variation combined with high among‐population genetic differentiation are in line with predictions of the monopolization hypothesis, which suggests that in species with rapid population growth and potential for local adaptation, strong priority effects due to monopolization of resources lead to reduced levels of gene flow.
An analytical equation for the oscillation frequency of high-frequency ring oscillators

An analytical equation for the oscillation frequency of a ring oscillator is derived. The derivation is done using a novel method which does not need to find an expression for the delay of each stage. The resulting equation includes the effect of time-varying parasitics. It also includes the effect of the gate resistance, which has a large effect on the oscillation frequency at high frequencies. Measurement results of ring oscillators fabricated in a 0.18-/spl mu/m CMOS process show that the resulting equation has an average error of 8% over a large range of parameter variations.
Educational and behavioural problems in babies of 32–35 weeks gestation

AIM To identify incidence of school and behaviour problems at age 7 years in children born between 32 and 35 weeks gestation, and investigate perinatal risk factors. METHOD The study population consisted of all children born at 32–35 weeks gestation to mothers resident in Oxfordshire in l990. General practitioners, parents, and teachers were asked about health, behaviour, and education by postal questionnaire. Teachers rated children on level of function in six areas using a five point scale. They also completed the Strengths and Difficulties behaviour questionnaire. Perinatal risk factors were identified for children with poor school performance using a univariate and multivariate analysis. RESULTS Teacher responses were obtained for 117 (66%) of the 176 children in the cohort. Twenty nine (25%) required support from a non-teaching assistant, five (4%) had required a statement of special educational needs, and three (3%) were at special school. Poor outcome was reported for 32% in writing, 31% in fine motor skills, 29% in mathematics, 19% in speaking, 21% in reading, and 12% in physical education. On the behaviour questionnaire, 19% of the cohort achieved an abnormal hyperactivity score (population norm 10%). Multivariate analysis showed perinatal variables that remained significant, independent of other variables; they were discharge from the special care baby unit > 36 weeks postconceptional age (odds ratio 4.15; 95% confidence interval 1.43 to 12.05) and male sex (odds ratio 3.88; 95% confidence interval 1.42 to 10.6). CONCLUSION Up to a third of children born between 32 and 35 weeks gestation may have school problems. As there are larger numbers in this gestational category compared with smaller babies, this finding has implications for educational services.
The Two-Edge Connectivity Survivable-Network Design Problem in Planar Graphs

Consider the following problem: given a graph with edge costs and a subset Q of vertices, find a minimum-cost subgraph in which there are two edge-disjoint paths connecting every pair of vertices in Q. The problem is a failure-resilient analog of the Steiner tree problem arising, for example, in telecommunications applications. We study a more general mixed-connectivity formulation, also employed in telecommunications optimization. Given a number (or requirement) r(v) ∈ {0, 1, 2} for each vertex v in the graph, find a minimum-cost subgraph in which there are min {r(u), r(v)} edge-disjoint u-to-v paths for every pair u, v of vertices. We address the problem in planar graphs, considering a popular relaxation in which the solution is allowed to use multiple copies of the input-graph edges (paying separately for each copy). The problem is max SNP-hard in general graphs and strongly NP-hard in planar graphs. We give the first polynomial-time approximation scheme in planar graphs. The running time is O(nlog n). Under the additional restriction that the requirements are only non-zero for vertices on the boundary of a single face of a planar graph, we give a polynomial-time algorithm to find the optimal solution.
A practical vector control algorithm for μ-based induction motor drives using a new space vector current controller

In this paper, a very simple vector control algorithm is proposed for /spl mu/-based induction motor drives. The proposed method controls the motor torque directly and linearly to achieve instantaneous torque response without oscillation. The merits of this control method include its simple architecture and obviating the coordinate transformation. At the same time, a new space vector-based current controller is proposed to serve as a quick response torque controller of the proposed drive system. In addition to the current error, information on the current error derivative is further employed so that one can take more advantages of adding the zero voltage vector for reducing the switching frequency. As a result, the efficiency can be greatly increased. It is seen that through integration of the above two parts, the proposed drive system is very simple to implement and has very good performance. >
Edaphic and microclimatic controls over permafrost response to fire in interior Alaska

Discontinuous permafrost in the North American boreal forest is strongly influenced by the effects of ecological succession on the accumulation of surface organic matter, making permafrost vulnerable to degradation resulting from fire disturbance. To assess factors affecting permafrost degradation after wildfire, we compared vegetation composition and soil properties between recently burned and unburned sites across three soil landscapes (rocky uplands, silty uplands, and sandy lowlands) situated within the Yukon Flats and Yukon-Tanana Uplands in interior Alaska. Mean annual air temperatures at our study sites from 2011 to 2012 were relatively cold (−5.5 ° C) and favorable to permafrost formation. Burning of mature evergreen forests with thick moss covers caused replacement by colonizing species in severely burned areas and recovery of pre-fire understory vegetation in moderately burned areas. Surface organic layer thickness strongly affected thermal regimes and thaw depths. On average, fire caused a five-fold decrease in mean surface organic layer thickness, a doubling of water storage in the active layer, a doubling of thaw depth, an increase in soil temperature at the surface (−0.6 to +2.1 ° C) and at 1 m depth (−1.7 to +0.4 ° C), and a two-fold increase in net soil heat input. Degradation of the upper permafrost occurred at all burned sites, but differences in soil texture and moisture among soil landscapes allowed permafrost to persist beneath the active layer in the silty uplands, whereas a talik of unknown depth developed in the rocky uplands and a thin talik developed in the sandy lowlands. A changing climate and fire regime would undoubtedly influence permafrost in the boreal forest, but the patterns of degradation or stabilization would vary considerably across the discontinuous permafrost zone due to differences in microclimate, successional patterns, and soil characteristics.
How Much Do Focal Infarcts Distort White Matter Lesions and Global Cerebral Atrophy Measures?

Background: White matter lesions (WML) and brain atrophy are important biomarkers in stroke and dementia. Stroke lesions, either acute or old, symptomatic or silent, are common in older people. Such stroke lesions can have similar signals to WML and cerebrospinal fluid (CSF) on magnetic resonance (MR) images, and may be classified accidentally as WML or CSF by MR image processing algorithms, distorting WML and brain atrophy volume from the true volume. We evaluated the effect that acute or old stroke lesions at baseline, and new stroke lesions occurring during follow-up, could have on measurement of WML volume, cerebral atrophy and their longitudinal progression. Methods: We used MR imaging data from patients who had originally presented with acute lacunar or minor cortical ischaemic stroke symptoms, recruited prospectively, who were scanned at baseline and about 3 years later. We measured WML and CSF volumes (ml) semi-automatically. We manually outlined the acute index stroke lesion (ISL), any old stroke lesions present at baseline, and new lesions appearing de novo during follow-up. We compared baseline and follow-up WML volume, cerebral atrophy and their longitudinal progression excluding and including the acute ISL, old and de novo stroke lesions. A non-parametric test (Wilcoxon’s signed rank test) was used to compare the effects. Results: Among 46 patients (mean age 72 years), 33 had an ISL visible on MR imaging (median volume 2.05 ml, IQR 0.88–8.88) and 7 of the 33 had old lacunes at baseline: WML volume was 8.54 ml (IQR 5.86–15.80) excluding versus 10.98 ml (IQR 6.91–24.86) including ISL (p < 0.001). At follow-up, median 39 months later (IQR 30–45), 3 patients had a de novo stroke lesion; total stroke lesion volume had decreased in 11 and increased in 22 patients: WML volume was 12.17 ml (IQR 8.54–19.86) excluding versus 14.79 ml (IQR 10.02–38.03) including total stroke lesions (p < 0.001). Including/excluding lacunes at baseline or follow-up also made small differences. Twenty-two of the 33 patients had tissue loss due to stroke lesions between baseline and follow-up, resulting in a net median brain tissue volume loss (i.e. atrophy) during follow-up of 24.49 ml (IQR 12.87–54.01) excluding versus 24.61 ml (IQR 15.54–54.04) including tissue loss due to stroke lesions (p < 0.001). Including stroke lesions in the WML volume added substantial noise, reduced statistical power, and thus increased sample size estimated for a clinical trial. Conclusions: Failure to exclude even small stroke lesions distorts WML volume, cerebral atrophy and their longitudinal progression measurements. This has important implications for design and sample size calculations for observational studies and randomised trials using WML volume, WML progression or brain atrophy as outcome measures. Improved methods of discriminating between stroke lesions and WML, and between tissue loss due to stroke lesions and true brain atrophy are required.