Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutation and the repair of radiation damage in bacteria.

Early studies of lethal and mutagenic effects of ultraviolet light (UV) in bacteria revealed an unmistakable, but complex, relation between them. The similarity of the action spectra for killing (1) and mutation induction (2), both showing sharp peaks at about 2650 A, suggested absorption by nucleic acids as the initial step in both. The photoreversibility of induced mutations (3, 4) indicated a possible similarity between some premutational UV photoproducts and the photoreversible fraction of the UV damage leading to death. Extensive comparison of dose-effect curves (reviewed in 5), while showing that lethality and mutagenesis usually have similar dose thresholds, made it clear that no simple, universally applicable quantitative relation exists between them. The modifiability of induced mutation frequency by posttreatments not affecting survival (6) reinforced this conclusion. Recent developments in radiation biology prompt the reexamination of mutagenesis as it relates to the production and repair of lethal UV damage. Particularly relevant are the identification of thymine dimer as an important UV photoproduct in the DNA of irradiated bacteria (7); the elucidation of one kind of photoreactivation as an enzymic process (8) involving the monomerization of thymine dimers (9), and the demonstration that the excision of thymine dimers from the DNA is an early step in the dark repair of UV damage in Escherichia coli (10, 11). These insights, as well as recent indications that UV produces dimers of other pyrimidines that may be repaired by similar mechanisms (12), provoke many questions about the possible role of pyrimidine dimers and their repair in the induction of mutations (12, 13). In this discussion, our current knowledge of UV mutagenesis in bacteria will be considered in relation to some of these questions, and the answers will be sought without regard for the historical sequence in which the evidence was obtained. A measure of hindsight may prove of some value in reappraising the bacterial mutation studies of the last decade. An exhaustive review will not be attempted here, and only studies relevant to the particular questions considered will be discussed.
Role of Cellular Cholesterol Metabolism in Vascular Cell Calcification*

Vascular calcification impairs vessel compliance and increases the risk of cardiovascular events. We found previously that liver X receptor agonists, which regulate intracellular cholesterol homeostasis, augment PKA agonist- or high phosphate-induced osteogenic differentiation of vascular smooth muscle cells. Because cholesterol is an integral component of the matrix vesicles that nucleate calcium mineral, we examined the role of cellular cholesterol metabolism in vascular cell mineralization. The results showed that vascular smooth muscle cells isolated from LDL receptor null (Ldlr−/−) mice, which have impaired cholesterol uptake, had lower levels of intracellular cholesterol and less osteogenic differentiation, as indicated by alkaline phosphatase activity and matrix mineralization, compared with WT cells. PKA activation with forskolin acutely induced genes that promote cholesterol uptake (LDL receptor) and biosynthesis (HMG-CoA reductase). In WT cells, inhibition of cholesterol uptake by lipoprotein-deficient serum attenuated forskolin-induced matrix mineralization, which was partially reversed by the addition of cell-permeable cholesterol. Prolonged activation of both uptake and biosynthesis pathways by cotreatment with a liver X receptor agonist further augmented forskolin-induced matrix mineralization. Inhibition of either cholesterol uptake, using Ldlr−/− cells, or of cholesterol biosynthesis, using mevastatin-treated WT cells, failed to inhibit matrix mineralization due to up-regulation of the respective compensatory pathway. Inhibition of both pathways simultaneously using mevastatin-treated Ldlr−/− cells did inhibit forskolin-induced matrix mineralization. Altogether, the results suggest that up-regulation of cholesterol metabolism is essential for matrix mineralization by vascular cells.
Contributing to Public Document Repositories: A Critical Mass Theory Perspective

Public document repositories (PDRs) are valuable resources available on the Internet and are a component of the broader information commons freely accessible to the public. Instances of PDRs include the repository of reviews at Amazon.com and the online encyclopedia at Wikipedia. These repositories are created and sustained by the voluntary contributions of individuals who are not compensated for their inputs. This paper draws on and extends critical mass theory in the context of PDRs. Using data on the reviews written by prolific reviewers at Amazon.com and the text of their personal profiles, we find the critical mass of contributors at the PDR not only to be prolific and contributing high-quality reviews, but also to be among the earliest contributors of reviews on products. Reviewer profiles revealed the presence of multiple self-oriented motives (self expression, personal development, utilitarian motives, and enjoyment) and other-oriented motives (social affiliation, altruism, and reciprocity) for contribution. We find that the quality and quantity of contributions are inversely related and the motives for quantity of contribution are different from those related to the quality of contribution. The study highlights that PDRs are viewed by contributors as social contexts even though making contributions is an individual act that does not involve social interaction.
Contractor selection using fuzzy comparison judgement

A model is proposed for selecting the optimal result of contractor selection under multi criteria environment. Fuzzy comparing judgment is used to tackling the vagueness and uncertainty in choosing significant preferences by decision maker regarding to the subjective opinion. Finally, the model was tested in tender evaluation processes for awarding the most beneficial contractor to perform the construction project.
Development and Field Trial of a Driver Assistance System to Encourage Eco-Driving in Light Commercial Vehicle Fleets

Driver training schemes and eco-driving techniques can reduce fuel consumption by 10%, but their effectiveness depends on the willingness of drivers to change their behavior, and changes may be short lived. Onboard driver assistance systems have been proposed, which encourage driving style improvement. Such systems, when fitted in commercial vehicles, can assume some authority since uneconomical driving styles can be reported to a fleet manager. A driver assistance system has been developed and tried in the field with commercial vehicle drivers. The system aims to reduce fuel consumption by encouraging two behaviors: reduced rates of acceleration, and early upshifting through the gears. Visual feedback is reinforced with audible warnings when the driver makes uneconomical power demands of the engine. Field trials of the system were undertaken in the U.K. using 15 light commercial vehicles, driven by their professional drivers from a range of commercial applications. The trials consisted of two-week baseline data collection, which drivers were not aware of, followed by two weeks of data collection with the system being active. During the trials a total of 39 300 km of trip data were collected, which demonstrated fuel savings of up to 12% and average fuel savings of 7.6%.
Sociocultural Change and Integrative Syntheses in Human Development: Autonomous‐Related Self and Social–Cognitive Competence

Understanding human development in the con- text of socioeconomic-cultural change requires a consid- eration of both the contextual and the global aspects of development that involves an ''integrative synthesis'' of the 2. Such a synthesis may be considered a conceptual model or goal of human development and may be observed in different spheres of development. This article proposes ''autonomous-related self'' and ''cognitive-social competence'' as 2 integrative syntheses that provide insight into adaptations to changing environmental demands and suggests that although they are not ade- quately recognized in psychology, these syntheses can be considered as aspects of optimal development. The article presents the 22-year longitudinal Turkish Early Enrich- ment Project as a case in point that illustrates the rele- vance of these integrative syntheses, as well as how they can be promoted.
Continuous F0 Modeling for HMM Based Statistical Parametric Speech Synthesis

The modeling of fundamental frequency, or F0, in HMM-based speech synthesis is a critical factor in delivering speech which is both natural and accurately conveys all of the many nuances of the message. However, F0 modeling is difficult because F0 values are normally considered to depend on a binary voicing decision such that they are continuous in voiced regions and undefined in unvoiced regions. F0 is therefore a discontinuous function of time. Multi-space probability distribution HMM (MSDHMM) is a widely used solution to this problem. The MSDHMM essentially uses a joint distribution of discrete voicing labels and the discontinuous F0 observations. However, due to the discontinuity assumption, the MSDHMM provides a rather weak F0 trajectory model. In this paper, F0 is viewed as being a continuous function of time and this is achieved by assuming that F0 can be observed within unvoiced regions as well as voiced regions. This provides a continuous F0 data stream which can be modeled by standard HMMs. Voicing labels are modeled either implicitly or explicitly in order to perform voicing classification and a globally tied distribution (GTD) technique is used to achieve robust F0 estimation. Both objective measures and subjective listening tests demonstrate that continuous F0 modeling yields better synthesized F0 trajectories and significant improvements to the naturalness of synthesized speech compared to using the MSDHMM model.
Graph Based Scalable Algorithms with Applications

OF THE DISSERTATION In this thesis, we propose various algorithms for problems arising in nonlinear circuits, nonlinear electromagnetics and data mining. Through the design and implementation of these algorithms, we show that the algorithms developed are scalable. In the first part of the thesis we provide two solutions to the forward problem of finding the steady-state solution of nonlinear RLC circuits subjected to harmonic forcing. The work generalizes and provides a mathematical theory bridging prior work on structured graphs and extending it to random graphs. Both algorithms are shown to be orders of magnitude faster than time stepping. We introduce an inverse problem of maximizing the energy/voltage at certain nodes of the graph without altering the graph structure. By altering the eigenvalues associated with the weighted graph Laplacian of the underlying circuit using a Newton-type algorithm, we solve the inverse problem. Extensive results verify that a majority of random graph circuits are capable of causing amplitude boosts. Next, we connect nonlinear Maxwell’s equations in 2D to the RLC circuit problem. This relationship is achieved by considering the finite volume decomposition of nonlinear Maxwell’s equations. When we consider a discretization of the domain, the dual graph of this discretization provides us with a planar random graph structure very similar to our previous work. Thus, algorithms developed in the previous work become applicable. Using distributed computing, we develop an implementation of one of the algorithms that scales to large-scale problems allowing us to obtain accurate and fast solutions. Simulations are conducted for structured and unstructured meshes, and we verify that the method is first-order in space. Our final application is in the field of supervised learning for regression problems. Regression trees have been used extensively since their introduction and form the basis of several state-of-the-art machine learning methods today. Regression trees minimize the loss criterion (objective function) using a greedy heuristic algorithm. The usual form of the loss criterion is the squared error. While it has been known that minimizing the absolute deviation provides more robust trees in the presence of outliers trees based on absolute loss minimization have been ignored because they were believed to be computationally expensive. We provide the first implementation which has the same algorithmic complexity as compared to trees built with the squared error loss function. Besides computing absolute deviation trees, our algorithm generalizes and can be used as a non-parametric alternative to quantile regression.
Cyclic GMP-activated conductance of retinal photoreceptor cells.

This review examines the ionic conductance that generates the electrical response to light in rods and cones of the vertebrate retina. In visual physiology this conductance is commonly referred to as the light-regulated or light-sensitive conductance. The designation cGMP-activated con­ ductance is perhaps preferable because it is now known to be controlled by guanosine 3',5'-cyclic monophosphate (abbreviated here as cGMP); light modulates the conductance solely by changing the intracellular con­ centration of cGMP. We shall use the different terms for the conductance interchangeably. A review on this channel seems timely in view of the speed of recent progress in understanding its nature and function. The conductance is interesting for several reasons. First, it has physio­ logical properties that are beautifully suited for its role in visual trans­ duction. Second, it is the first ionic channel found whose gating is directly controlled by a cyclic nucleotide. Third, there are indications that the conductance may belong to a new family of ion channels involved in signal
Prolificacy and Its Relationship with Age, Body Weight, Parity, Previous Litter Size and Body Linear Type Traits in Meat-type Goats

Data on age and body weight at breeding, parity, previous litter size, days open and some descriptive body linear traits from 389 meat-type, prolific Black Bengal goats in Tripura State of India, were collected for 3 and 1/2 years (2007 to 2010) and analyzed using logistic regression model. The objectives of the study were i) to evaluate the effect of age and body weight at breeding, parity, previous litter size and days open on litter size of does; and ii) to investigate if body linear type traits influenced litter size in meat-type, prolific goats. The incidence of 68.39% multiple births with a prolificacy rate of 175.07% was recorded. Higher age (>2.69 year), higher parity order (>2.31), more body weight at breeding (>20.5 kg) and larger previous litter size (>1.65) showed an increase likelihood of multiple litter size when compared to single litter size. There was a strong, positive relationship between litter size and various body linear type traits like neck length (>22.78 cm), body length (>54.86 cm), withers height (>48.85 cm), croup height (>50.67 cm), distance between tuber coxae bones (>11.38 cm) and distance between tuber ischii bones (>4.56 cm) for discriminating the goats bearing multiple fetuses from those bearing a single fetus.
The natural history of low‐grade ductal carcinoma in situ of the breast in women treated by biopsy only revealed over 30 years of long‐term follow‐up

Opportunities to study the natural history of ductal carcinoma in situ (DCIS) are rare. A few studies of incompletely excised lesions in the premammographic era now recognized as DCIS have provided critical insights into its proclivity for local recurrence in the original site. At the time the biopsies in the current study were originally examined, small DCIS was not diagnosed and, by default, these women were treated by biopsy only.
Ablation of smooth muscle myosin heavy chain SM2 increases smooth muscle contraction and results in postnatal death in mice

The physiological relevance of smooth muscle myosin isoforms SM1 and SM2 has not been understood. In this study we generated a mouse model specifically deficient in SM2 myosin isoform but expressing SM1, using an exon-specific gene targeting strategy. The SM2 homozygous knockout (SM2−/−) mice died within 30 days after birth, showing pathologies including segmental distention of alimentary tract, retention of urine in renal pelvis, distension of bladder, and the development of end-stage hydronephrosis. In contrast, the heterozygous (SM2+/−) mice appeared normal and reproduced well. In SM2−/− bladder smooth muscle the loss of SM2 myosin was accompanied by a concomitant down-regulation of SM1 and a reduced number of thick filaments. However, muscle strips from SM2−/− bladder showed increased contraction to K+ depolarization or in response to M3 receptor agonist Carbachol. An increase of contraction was also observed in SM2−/− aorta. However, the SM2−/− bladder was associated with unaltered regulatory myosin light chain (MLC20) phosphorylation. Moreover, other contractile proteins, such as α-actin and tropomyosin, were not altered in SM2−/− bladder. Therefore, the loss of SM2 myosin alone could have induced hypercontractility in smooth muscle, suggesting that distinctly from SM1, SM2 may negatively modulate force development during smooth muscle contraction. Also, because SM2−/− mice develop lethal multiorgan dysfunctions, we propose this regulatory property of SM2 is essential for normal contractile activity in postnatal smooth muscle physiology.
Journal of Graph Algorithms and Applications Convex Grid Drawings of Plane Graphs with Rectangular Contours

In a convex drawing of a plane graph, all edges are drawn as straight-line segments without any edge-intersection and all facial cycles are drawn as convex polygons. In a convex grid drawing, all vertices are put on grid points. A plane graph G has a convex drawing if and only if G is internally triconnected, and an internally triconnected plane graph G has a convex grid drawing on an (n − 1) × (n − 1) grid if either G is triconnected or the triconnected component decomposition tree T (G) of G has two or three leaves, where n is the number of vertices in G. In this paper, we show that an internally triconnected plane graph G has a convex grid drawing on a 2n × n 2 grid if T (G) has exactly four leaves. We also present an algorithm to find such a drawing in linear time. Our convex grid drawing has a rectangular contour, while most of the known algorithms produce grid drawings having triangular contours.
On a Regularized Scheme for Approximate Acoustic Cloaking Using Transformation Optics

In this paper, we study approximate cloaking for the Helmholtz equation in three dimensions where the cloaking device is based on transformations which blow up a cylinder of fixed height and small cross section of radius $\varepsilon$ into the cloaked region. Assuming the zero Dirichlet boundary condition is imposed on the boundary of the cloaked region, we show that the degree of visibility is of order $\varepsilon$ as $\varepsilon$ goes to 0. This fact is quite surprising since it is known that the degree of visibility, for the scheme using transformations which blow up a small region of diameter $\varepsilon$ into the cloaked region, is of order $\varepsilon$ in three dimensions and $1/ |\ln \varepsilon|$ in two dimensions. To understand the relation between these contexts, we as well revisit the known estimates and show that the degree of visibility is of order $\varepsilon^{d-1}$ $(d=2,3)$ for the scheme using transformations which blow up a small ball of diameter $\varepsilon$ into the cloaked regio.
Loosely Coupled Architecture for Bio-Network Reverse Engineering

Bio-network reverse engineering is inferring networks of biological entities with given observed data. In biology, our main concern is to find out the systematic architecture of biological entities and their functional role in living organisms. Thus it is very important to provide proper systematic approaches for such reverse engineering for bio-networks. Previously, we developed an information fusion platform for bio-network inference and analysis, named BioCAD. BioCAD pro- vided a good workplace where various network inference and analysis techniques were integrated for user-specific variants of bio-network inference problems. The previous version of BioCAD has a tightly coupled architecture where the integrated usage of provided modules is available only in the form of given workflows. Even though it has provided good workplace for bio-network reverse engineering, there are some limitations in adding new modules and selective usage of provided modules. To overcome such limitations, we are designing and developing BioCAD 2.0 which has a loosely-coupled architecture. We propose our current approach of building new BioCAD 2.0 and BioCAD 2.0 will be a powerful workbench for bio-network reverse engineering.
Investigating selection and reading performance on a mobile phone while walking

More and more people interact with their mobile phone while walking. The presented research analyzes; firstly, the negative effect of walking when considering reading and target selection tasks, such as weaker performance and higher workload. Here, we focused on one-handed interaction with a touch screen whereby the thumb is used as the input device. Secondly, we analyze how these negative effects can be compensated by increasing the text size and the size of the targets to select on the mobile phone. A comparative user study was conducted with 16 participants who performed target acquisition and reading tasks while standing and walking. The results show that whilst performance decreases, cognitive load increases significantly when reading and selecting targets when walking. Furthermore, the results show that the negative effect regarding target selection can be compensated by increasing the target size, but the text reading task did not yield better performance results for a larger text size due to the increased demand for scrolling. These results can be used to inform future designs of mobile user interfaces which might provide a dedicated walking mode.
Prevalence and risk factors of age-related macular degeneration in Korea: the Korea National Health and Nutrition Examination Survey 2010-2011.

PURPOSE To investigate the prevalence and risk factors of age-related macular degeneration (AMD) in the general Korean adult population. METHODS The study involved a nationally representative Korean population from the 2010 to 2011 Korea National Health and Nutrition Examination Survey. A total of 7899 subjects ≥ 40 years old participated in health interviews, physical examinations, and ophthalmologic assessment including fundus photography. RESULTS The overall prevalence of early AMD was estimated at 6.7% (95% confidence interval [CI], 6.1-7.4), and that of late AMD was estimated at 0.7% (95% CI, 0.5-0.9), which included 0.5% prevalence of neovascular AMD and 0.2% prevalence of geographic atrophy. The prevalence rates of early and late AMD among participants aged ≥ 65 years were 16.9% and 1.8%, respectively. Hyperopia was positively associated with the presence of any AMD type (odds ratio [OR], 1.08 for every 1 diopter increase). In multivariate analyses, significant risk factors for the presence of any AMD type were age, serum high-density lipoprotein (HDL) level, serum gamma-glutamyl transferase (GGT) level, and hepatitis B surface antigen (HBsAg) serum positivity (OR, 2.26). The risk factors for late AMD included age, ever-smoking history (OR, 2.18), serum GGT level, and systolic blood pressure. CONCLUSIONS The prevalence of AMD in Korea was similar to the prevalence of pooled Asian and Western populations. Age and serum GGT level were strongly associated with both the presence of any AMD and late AMD. Additionally, serum HDL level, HBsAg serum positivity, ever-smoking history, and systolic blood pressure were identified as risk factors for AMD.