Miracle-dz/UniFAR-FTUs huggingface dataset:
The Frequency of Barred Spiral Galaxies in the Near-Infrared

We have determined the fraction of barred galaxies in the H-band for a statistically well-defined sample of 186 spirals drawn from the Ohio State University Bright Spiral Galaxy Survey. We find 56% of our sample to be strongly barred in the H band while another 16% is weakly barred. Only 27% of our sample is unbarred in the near-infrared. The RC3 and the Carnegie Atlas of Galaxies both classify only about 30% of our sample as strongly barred. Thus strong bars are nearly twice as prevalent in the near-infrared as in the optical. The frequency of genuine optically hidden bars is significant but lower than many claims in the literature: 40% of the galaxies in our sample that are classified as unbarred in the RC3 show evidence for a bar in the H band while the Carnegie Atlas lists this fraction as 66%. Our data reveal no significant trend in bar fraction as a function of morphology in either the optical or H band. Optical surveys of high-redshift galaxies may be strongly biased against finding bars, as bars are increasingly difficult to detect at bluer rest wavelengths.
The expression of recombinant genes in Escherichia coli can be strongly stimulated at the transcript production level by mutating the DNA‐region corresponding to the 5′‐untranslated part of mRNA

Secondary structures and the short Shine–Dalgarno sequence in the 5′‐untranslated region of bacterial mRNAs (UTR) are known to affect gene expression at the level of translation. Here we report the use of random combinatorial DNA sequence libraries to study UTR function, applying the strong, σ32/σ38‐dependent, and positively regulated Pm promoter as a model. All mutations in the libraries are located at least 8 bp downstream of the transcriptional start site. The libraries were screened using the ampicillin‐resistance gene (bla) as reporter, allowing easy identification of UTR mutants that display high levels of expression (up to 20‐fold increase relative to the wild‐type at the protein level). Studies of the two UTR mutants identified by a modified screening procedure showed that their expression is stimulated to a similar extent at both the transcript and protein product levels. For one such mutant a model analysis of the transcription kinetics showed significant evidence of a difference in the transcription rate (about 18‐fold higher than the wild type), while there was no evidence of a difference in transcript stability. The two UTR sequences also stimulated expression from a constitutive σ70‐dependent promoter (P1/Panti‐tet), demonstrating that the UTR at the DNA or RNA level has a hitherto unrecognized role in transcription.
HCV 3a Core Protein Increases Lipid Droplet Cholesteryl Ester Content via a Mechanism Dependent on Sphingolipid Biosynthesis

Hepatitis C virus (HCV) infected patients often develop steatosis and the HCV core protein alone can induce this phenomenon. To gain new insights into the pathways leading to steatosis, we performed lipidomic profiling of HCV core protein expressing-Huh-7 cells and also assessed the lipid profile of purified lipid droplets isolated from HCV 3a core expressing cells. Cholesteryl esters, ceramides and glycosylceramides, but not triglycerides, increased specifically in cells expressing the steatogenic HCV 3a core protein. Accordingly, inhibitors of cholesteryl ester biosynthesis such as statins and acyl-CoA cholesterol acyl transferase inhibitors prevented the increase of cholesteryl ester production and the formation of large lipid droplets in HCV core 3a-expressing cells. Furthermore, inhibition of de novo sphingolipid biosynthesis by myriocin - but not of glycosphingolipid biosynthesis by miglustat - affected both lipid droplet size and cholesteryl ester level. The lipid profile of purified lipid droplets, isolated from HCV 3a core-expressing cells, confirmed the particular increase of cholesteryl ester. Thus, both sphingolipid and cholesteryl ester biosynthesis are affected by the steatogenic core protein of HCV genotype 3a. These results may explain the peculiar lipid profile of HCV-infected patients with steatosis.
Personality Traits in HILDA

Wave 5 was the first time in HILDA that respondents were questioned on their personality character traits. The inclusion of personality in HILDA was based on the Five Factor (Big-Five) Personality Inventory, which is a descriptive model of personality identifying five broad dimensions including Emotional stability, Extraversion, Openness to experience, Agreeableness, and Conscientiousness. This paper will item analyse responses to the 36 personality questions used in Wave 5 to evaluate how well they capture the separate constructs of the Five Factor Personality Inventory, and to assess the reliabilities of each of the scales. In addition, this paper will examine how the HILDA personality scales correlate with other measures available in HILDA, known to be associated with personality. Using a maximum likelihood factor analysis, the items grouped into seven factors, five of which support the Big-Five structure. Subsequent analysis for a five factor solution suggested that the majority of items performed appropriately. The resulting five scales show an adequate degree of internal consistency, good variance and discriminating properties, and normal distributions. The association of the five scales with other measures known to be associated with personality were found, with few exceptions, to be consistent with the literature. The conceptual status of the Big-Five has limited the extent to which certain psychometric properties, such as construct and content validity, can be examined. With this in consideration, we interpret our results as offering an adequate, but not complete, support for the HILDA personality traits inventory and subsequent scales. I strongly recommend the use of the original TDA-40 items, as opposed to the current 36 items, in future waves of HILDA.
Modeling the contact between a rolling sphere and a compliant ground plane

In this paper a complete 3D contact model is presented. This model has nonlinearity in determining both normal and friction forces. A new nonlinear normal force model is introduced and the differences between this new model and previous ones are described. Also, the characteristics of this model are discussed and compared with the classical models and empirical results. For calculating the friction force, a new nonlinear model which is able to calculate presliding displacement and viscous friction is presented. It is shown that this model allows us to keep track of all the energy in the system and therefore, supports an energy audit. Also, the rolling motion of a sphere on a compliant ground plane is simulated, and the results are presented. Rolling motion is an integral part of simulating the general 3D motion of a robot’s foot while in contact with the ground.
Disc Hemorrhages and Their Risk Factors in an Urban South Korean Population

Purpose The aim of this study was to estimate the prevalence of disc hemorrhage (DH) and evaluate its related risk factors in an urban South Korean population. Methods This retrospective cross-sectional study included subjects who underwent health screening at the Health Screening Center of Kangbuk Samsung Hospital from August 2012 to July 2013. All fundus photographs were first reviewed by two ophthalmologists and then by two glaucoma specialists and one retina specialist to determine the presence of DHs. In addition to fundus photographs, each participant completed systemic examination as well as sociodemographic and behavioral questionnaires. Results Fundus photographs were available for 164,029/168,044 (97.61%) subjects 20 years and older. The prevalence of DH was 226/164,029 (0.14%; 95% confidence interval, 0.12 to 0.16) per subject. A large proportion (61.5%) of eyes with DH had localized wedge-shaped retinal nerve fiber layer defects indicative of glaucoma. There was also a slight increase in DH prevalence with age, but no other statistically significant associations were found. Conclusions The prevalence of DH was 0.14% in urban South Korean subjects 20 years and older. Older age and the presence of glaucomatous retinal nerve fiber layer defects were associated with higher prevalence of DH. These findings suggest that the presence of a DH in an eye implies a high likelihood of glaucoma, although its absence does not indicate that glaucoma is absent.
Predictive coding, precision and synchrony

Abstract Gotts, Chow and Martin provide a very nice review of repetition priming and suppression that reaches a compelling conclusion—we need to look more closely at synchronization in learning and priming. Indeed, current modeling work focuses on this issue—namely, the dynamic causal modeling of electrophysiological responses to address the role of synchrony in Bayesian explaining away. This commentary revisits the nature and relationships among the four theories in Gotts et al. and nuances some of their empirical predictions. In particular, I emphasize precision or uncertainty in predictive coding as a unifying consideration.
EXPLORING THE EFFECTS OF TOOTH WEAR ON FUNCTIONAL MORPHOLOGY: A PRELIMINARY STUDY USING DENTAL TOPOGRAPHIC ANALYSIS

Mammalian tooth form reflects the material properties of foods. Much research has focused on relationships between aspects of dental morphology and diet. Understanding these relationships allows us to infer feeding adaptations from the teeth of fossil forms. Most such studies have focused on unworn (rather than worn) teeth because these are easier to characterize and compare among species. Nevertheless, tooth shape changes with wear, and most fossil teeth are worn. How does wear affect functional efficiency? Can dental morphology of worn teeth be used to infer diets of fossil species? The study described here presents a new way to examine the shapes of worn teeth so that we may begin to answer these important questions. Geographic information systems (GIS) were used to model teeth as topographic landscapes. A laser scanner generated a digital elevation model of the occlusal surface, and slope, angularity, surface area, relief, and modal aspect of each cusp, and other variables were quantified. Data on worn gorilla molars are given as an example. Although some aspects of morphology (e.g., surface area, occlusal relief) change with wear, others evidently do not. For example, cusp angularity showed no consistent change through the wear sequence, suggesting maintenance of some aspects of chewing efficiency. We conclude that this approach can be used to characterize and compare occlusal morphology in variably worn teeth. This will allow us to evaluate changes in chewing efficiency as teeth wear, a prerequisite to the inclusion of worn teeth in studies of mammalian dental functional anatomy.
Investigation of the mesoscale structure and volumetric features of biofilms using optical coherence tomography

Optical coherence tomography (OCT) was successfully applied to visualize the mesoscale structure of three different heterotrophic biofilms. For this purpose, biofilm volumes of 4 × 4 × 1.6 mm3 were scanned with spatial resolutions lower than 20 µm within an acquisition time of 2 min. A heterogeneous structure was detected for biofilms cultivated in laminar as well as transient flow conditions. The structure was found to be more homogeneous for the biofilm grown in turbulent flow. This biofilm structure was characterized by a volumetric porosity of 0.36, whereas the porosity calculated for biofilms grown in laminar and transient conditions was 0.65. These results were directly generated from the distribution of porosity calculated from the OCT images acquired and can be linked to structural properties. Up to now, the mesoscale biofilm structure was only observable with time‐consuming and expensive studies, for example, magnetic resonance microscopy. OCT will most certainly be helpful for improved understanding and prediction of biofilm physics with respect to macroscale processes, for example, mass transfer and detachment as the information about mesoscale is easily accessible using this method. In the context of this study, we show that CLSM images do not necessarily provide an accurate representation of the biofilm structure at the mesoscale. Additionally, the typical characteristic parameters obtained from CLSM image stacks differ largely from those calculated from OCT images. Nevertheless, to determine the local distribution of biofilm constituents, microscopic methods such as confocal laser scanning microscopy are required. Biotechnol. Bioeng. 2010;107: 844–853. © 2010 Wiley Periodicals, Inc.
Beta-Catenin Is Vital for the Integrity of Mouse Embryonic Stem Cells

β-catenin mediated Wnt-signaling is assumed to play a major function in embryonic stem cells in maintaining their stem cell character and the exit from this unique trait. The complexity of β-catenin action and conflicting results on the role of β-catenin in maintaining the pluripotent state have made it difficult to understand its precise cellular and molecular functions. To attempt this issue we have generated new genetically modified mouse embryonic stem cell lines allowing for the deletion of β-catenin in a controlled manner by taking advantage of the Cre-ER-T2 system and analyzed the effects in a narrow time window shortly after ablation. By using this approach, rather then taking long term cultured β-catenin null cell lines we demonstrate that β-catenin is dispensable for the maintenance of pluripotency associated genes. In addition we observed that the removal of β-catenin leads to a strong increase of cell death, the appearance of multiple clustered functional centrosomes most likely due to a mis-regulation of the polo-like-kinase 2 and furthermore, alterations in chromosome segregation. Our study demonstrates the importance of β-catenin in maintaining correct cellular functions and helps to understand its role in embryonic stem cells.
Early pharmacological inhibition of angiotensin-I converting enzyme activity induces obesity in adulthood

We have investigated early programming of body mass in order to understand the multifactorial etiology of obesity. Considering that the renin-angiotensin system (RAS) is expressed and functional in the white adipose tissue (WAT) and modulates its development, we reasoned whether early transitory inhibition of angiotensin-I converting enzyme activity after birth could modify late body mass development. Therefore, newborn Wistar rats were treated with enalapril (10 mg/kg of body mass) or saline, starting at the first day of life until the age of 16 days. Between days ninetieth and hundred and eightieth, a group of these animals received high fat diet (HFD). Molecular, biochemical, histological, and physiological data were collected. Enalapril treated animals presented hyperphagia, overweight, and increased serum level of triglycerides, total cholesterol and leptin, in adult life. Body composition analyses revealed higher fat mass with increased adipocyte size in these animals. Molecular analyses revealed that enalapril treatment increases neuropeptide Y (NPY) and cocaine- and amphetamine-regulated transcript (CART) gene expression in hypothalamus, fatty acid synthase (FAS), and hormone-sensitive lipase (HSL) gene expression in retroperitoneal WAT, and decreases peroxixome proliferators-activated receptor (PPAR)γ, PPARα, uncoupling protein (UCP)2, and UCP3 gene expression in WAT. The results of the current study indicate that enalapril administration during early postnatal development increases body mass, adiposity and serum lipids in adulthood associated with enhanced food intake and decreased metabolic activity in WAT, predisposing to obesity in adulthood.
Parallel and Distributed Methods for Constrained Nonconvex Optimization—Part I: Theory

In this two-part paper, we propose a general algorithmic framework for the minimization of a nonconvex smooth function subject to nonconvex smooth constraints, and also consider extensions to some structured, nonsmooth problems. The algorithm solves a sequence of (separable) strongly convex problems and maintains feasibility at each iteration. Convergence to a stationary solution of the original nonconvex optimization is established. Our framework is very general and flexible and unifies several existing successive convex approximation (SCA)-based algorithms. More importantly, and differently from current SCA approaches, it naturally leads to distributed and parallelizable implementations for a large class of nonconvex problems. This Part I is devoted to the description of the framework in its generality. In Part II, we customize our general methods to several (multiagent) optimization problems in communications, networking, and machine learning; the result is a new class of centralized and distributed algorithms that compare favorably to existing ad-hoc (centralized) schemes.
Locomotor Activity in D2 Dopamine Receptor-Deficient Mice Is Determined by Gene Dosage, Genetic Background, and Developmental Adaptations

Locomotor activity is a polygenic trait that varies widely among inbred strains of mice (Flint et al., 1995). To characterize the role of D2 dopamine receptors in locomotion, we generated F2hybrid (129/Sv × C57BL/6) D2 dopamine receptor (D2R)-deficient mice by gene targeting and investigated the contribution of genetic background to open-field activity and rotarod performance. Horizontal activity of D2R−/− mice was approximately half that of drug-naive, strain-matched controls but was significantly greater than haloperidol-treated controls, which were markedly hypokinetic. Wild-type 129/SvEv and C57BL/6 mice with functional D2 receptors had greater interstrain differences in spontaneous activity than those among the F2 hybrid mutants. Incipient congenic strains of D2R-deficient mice demonstrated an orderly gene dosage reduction in locomotion superimposed on both extremes of parental background locomotor activity. In contrast, F2 hybrid D2R−/− mice had impaired motor coordination on the rotarod that was corrected in the congenic C57BL/6 background. Wild-type 129/SvEv mice had the poorest rotarod ability of all groups tested, suggesting that linked substrain 129 alleles, not the absence of D2 receptors per se, were largely responsible for the reduced function of the F2hybrid D2R−/− and D2R+/− mice. Neurochemical and pharmacological studies revealed unexpectedly normal tissue striatal monoamine levels and no evidence for supersensitive D1, D3, or D4 dopamine receptors in the D2R−/− mice. However, after acute monoamine depletion, akinetic D2R+/− mice had a significantly greater synergistic restoration of locomotion in response to SKF38393 and quinpirole compared with any group of D2R+/+ controls. We conclude that D2R-deficient mice are not a model of Parkinson’s disease. Our studies highlight the interaction of multiple genetic factors in the analysis of complex behaviors in gene knock-out mice.
A Vision of the Pore

In his Research commentary “The vision of the pore” ( Science 's Compass, 3 Apr., [p. 56][1]), Clay Armstrong gives a lucid overview of the structural data in two reports in the same issue by Roderick MacKinnon and his co-workers in the context of the existing body of knowledge on potassium (K+) channels [“The structure of the potassium channel: Molecular basis of K+ conduction and selectivity” by D. A. Doyle et al. (p. [69][2]) and “Structural conservation in prokaryotic and eukaryotic potassium channels” by R. MacKinnon et al. (p. [106][3])]. I feel, however, that more credit should have been given to H. Schrempf and his collaborators, who cloned the KcsA K+ channel of Streptomyces lividans in 1995 ([1][4]). Their paper is a landmark in several respects. First, at the time of publication, a bacterial two-transmembrane K+ channel that exhibited homology to the COOH-terminal of a Shaker K+ channel was notable. Second, this study demonstrated functional reconstitution of a K+ channel in an artificial membrane system. And third, Schrempf and his co-authors pointed out that the S. lividans K+ channel would be an ideal candidate for structural studies—a prediction now borne out by the beautiful work of MacKinnon and his co-workers. 1. [↵][5]1. H. Schrempf 2. et al. , EMBO J. 14, 1570 (1995). [OpenUrl][6] [1]: /lookup/doi/10.1126/science.280. 5360.56 [2]: /lookup/doi/10.1126/science.280. 5360.69 [3]: /lookup/doi/10.1126/science.280. 5360.106 [4]: #ref-1 [5]: #xref-ref-1-1 "View reference 1 in text" [6]: {openurl}? query=rft.jtitle%253DEMBO%2BJ. %26rft.volume%253D14%26rft.spage%253D1570%26rft.atitle%253DEMBO%2BJ%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx
Statistical linear estimation with penalized estimators: an application to reinforcement learning

Motivated by value function estimation in reinforcement learning, we study statistical linear inverse problems, i.e., problems where the coefficients of a linear system to be solved are observed in noise. We consider penalized estimators, where performance is evaluated using a matrix-weighted two-norm of the defect of the estimator measured with respect to the true, unknown coefficients. Two objective functions are considered depending whether the error of the defect measured with respect to the noisy coefficients is squared or unsquared. We propose simple, yet novel and theoretically well-founded data-dependent choices for the regularization parameters for both cases that avoid data-splitting. A distinguishing feature of our analysis is that we derive deterministic error bounds in terms of the error of the coefficients, thus allowing the complete separation of the analysis of the stochastic properties of these errors. We show that our results lead to new insights and bounds for linear value function estimation in reinforcement learning.
On lower bounds for the Maximum Consecutive Subsums Problem and the (min,+)-convolution

Given a sequence of n numbers, the MAXIMUM CONSECUTIVE SUBSUMS PROBLEM (MCSP) asks for the maximum consecutive sum of lengths ℓ for each ℓ = 1, . , n. No algorithm is known for this problem which is significantly better than the naive quadratic solution. Nor a super linear lower bound is known. The best known bound for the MCSP is based on the the computation of the (min; +)-convolution, another problem for which neither an O(n2-ε) upper bound is known nor a super linear lower bound. We show that the two problems are in fact computationally equivalent by providing linear reductions between them. Then, we concentrate on the problem of finding super linear lower bounds and provide empirical evidence for our conjecture that the solution of both problems requires Ω(n log n) time in the decision tree model.