Miracle-dz/UniFAR-FTUs huggingface dataset:
Assortative Mixing in Close-Packed Spatial Networks

Background In recent years, there is aroused interest in expressing complex systems as networks of interacting nodes. Using descriptors from graph theory, it has been possible to classify many diverse systems derived from social and physical sciences alike. In particular, folded proteins as examples of self-assembled complex molecules have also been investigated intensely using these tools. However, we need to develop additional measures to classify different systems, in order to dissect the underlying hierarchy. Methodology and Principal Findings In this study, a general analytical relation for the dependence of nearest neighbor degree correlations on degree is derived. Dependence of local clustering on degree is shown to be the sole determining factor of assortative versus disassortative mixing in networks. The characteristics of networks constructed from spatial atomic/molecular systems exemplified by self-organized residue networks built from folded protein structures and block copolymers, atomic clusters and well-compressed polymeric melts are studied. Distributions of statistical properties of the networks are presented. For these densely-packed systems, assortative mixing in the network construction is found to apply, and conditions are derived for a simple linear dependence. Conclusions Our analyses (i) reveal patterns that are common to close-packed clusters of atoms/molecules, (ii) identify the type of surface effects prominent in different close-packed systems, and (iii) associate fingerprints that may be used to classify networks with varying types of correlations.
Thalamocingulate Interactions In Performance Monitoring

Performance monitoring is an essential prerequisite of successful goal-directed behavior. Research of the last two decades implicates the anterior midcingulate cortex (aMCC) in the human medial frontal cortex and frontostriatal basal ganglia circuits in this function. Here, we addressed the function of the thalamus in detecting errors and adjusting behavior accordingly. Using diffusion-based tractography, we found that, among the thalamic nuclei, the ventral anterior (VA) and ventral lateral anterior (VLa) nuclei have the relatively strongest connectivity with the aMCC. Patients with focal thalamic lesions showed diminished error-related negativity, behavioral error detection, and posterror adjustments. When the lesions specifically affected the thalamic VA/VLa nuclei, these effects were significantly pronounced, which was reflected by the complete absence of the error-related negativity. These results reveal that the thalamus, particularly its VA/VLa region, is a necessary constituent of the performance-monitoring network, anatomically well connected and functionally closely interacting with the aMCC.
The Cost of Convenience?

Individuals across the world use high-transaction-cost savings devices even when lower-cost technologies are available. High costs may help savers protect resources from the demands of others. I investigate this hypothesis by randomly assigning ATM cards to 1,100 newly opened bank accounts in rural Kenya. These cards reduced withdrawal fees by 50 percent. While the cards increased overall account use, the positive treatment effect is entirely driven by joint and male-owned accounts. I find evidence that these differences are driven by intrahousehold issues: Household bargaining power is a key mediator of the ATM treatment effect.
Error analysis of quadratic power spectrum estimates for cosmic microwave background polarization: sampling covariance

Quadratic methods with heuristic weighting (e.g. pseudo-C l or correlation function methods) represent an efficient way to estimate power spectra of the cosmic microwave background (CMB) anisotropies and their polarization. We construct the sample covariance properties of such estimators for CMB polarization, and develop semi-analytic techniques to approximate the pseudo-C l sample covariance matrices at high Legendre multipoles, taking account of the geometric effects of mode coupling and the mixing between the electric (E) and magnetic (B) polarization that arise for observations covering only part of the sky. The E-B mixing ultimately limits the applicability of heuristically weighted quadratic methods to searches for the gravitational-wave signal in the large-angle B-mode polarization, even for methods that can recover (exactly) unbiased estimates of the B-mode power. We show that for surveys covering 1 or 2 per cent of the sky, the contribution of E-mode power to the covariance of the recovered B-mode power spectrum typically limits the tensor-to-scalar ratio that can be probed with such methods to ∼0.05.
Analysis of Attacks on Common Watermarking Techniques

Watermarking is a technique that is used in copyright–protection for valuable medias. Watermarking is measured by four quantities: capacity, security, robustness, and imperceptibility. In this study, robustness of five watermarking algorithms will be assessed. The study will also lightly touch on imperceptibility characteristics of the algorithms. The five algorithms are CDMA Spatial Domain Spread Spectrum, Comparison-Based Correlation in DCT Midband, CDMA Wavelet Domain Spread Spectrum, Bruyndonckx, and Cox. The latter two algorithms are fingerprinting algorithms, which is a subset of watermarking algorithms with slightly different design goal. Our attacks, based on easy, unintentional image processing revealed that DCT domain algorithms – Comparison-Based Correlation in DCT Midband and Cox, have the best robustness property to JPEG compression, downscaling, median, and mean filters. However, spatial domain techniques such as Bruyndonckx can achieve better PSNR with less visual impact on the image.
Selective Chemokine Receptor Usage by Central Nervous System Myeloid Cells in CCR2-Red Fluorescent Protein Knock-In Mice

Background Monocyte subpopulations distinguished by differential expression of chemokine receptors CCR2 and CX3CR1 are difficult to track in vivo, partly due to lack of CCR2 reagents. Methodology/Principal Findings We created CCR2-red fluorescent protein (RFP) knock-in mice and crossed them with CX3CR1-GFP mice to investigate monocyte subset trafficking. In mice with experimental autoimmune encephalomyelitis, CCR2 was critical for efficient intrathecal accumulation and localization of Ly6Chi/CCR2hi monocytes. Surprisingly, neutrophils, not Ly6Clo monocytes, largely replaced Ly6Chi cells in the central nervous system of these mice. CCR2-RFP expression allowed the first unequivocal distinction between infiltrating monocytes/macrophages from resident microglia. Conclusion/Significance These results refine the concept of monocyte subsets, provide mechanistic insight about monocyte entry into the central nervous system, and present a novel model for imaging and quantifying inflammatory myeloid populations.
The LSD/sup h/-tree: an access structure for feature vectors

Efficient access structures for similarity queries on feature vectors are an important research topic for application areas such as multimedia databases, molecular biology or time series analysis. Different access structures for high dimensional feature vectors have been proposed, namely: the SS-tree, the VAMSplit R-tree, the TV-tree, the SR-tree and the X-tree. All these access structures are derived from the R-tree. As a consequence, the fanout of the directory of these access structures decreases drastically for higher dimensions. Therefore we argue that the R-tree is not the best possible starting point for the derivation of an access structure for high-dimensional data. We show that k-d-tree-based access structures are at least as well suited for this application area and we introduce the LSD/sup h/-tree as an example for such a k-d-tree-based access structure for high-dimensional feature vectors. We describe the algorithms for the LSD/sup h/-tree and present experimental results comparing the LSD/sup h/-tree and the X-tree.
ChurnVis: Visualizing mobile telecommunications churn on a social network with attributes

In this paper, we present ChurnVis, a system for visualizing components affected by mobile telecommunications churn and subscriber actions over time. We describe our experience of deploying this system in a network analytics company for use in data analysis and presentation tasks. As social influence seems to be a factor in mobile telecommunications churn (the decision of a subscriber to leave a particular service provider), the visualization is based on a social network inferred from calling data between subscribers. Using this network, churn components, or groups of churners who are connected in the social network, are segmented out and trends in their static and dynamic attributes are visualized. ChurnVis helps analysts understand trends in these components in a way that respects the data privacy constraints of the service provider. Through this two pipeline approach, we are able to visualize thousands of churn components filtered from a social network of hundreds of millions of edges.
A Generalisation of Lexical Functions for Composition in Distributional Semantics

Over the last two decades, numerous algorithms have been developed that successfully capture something of the semanticsof single words by looking at their distribution in text and comparing these distributions in a vector space model. However, it is not straightforward to construct meaning representations beyond the levelof individual words–i.e. the combination of words into larger units – using dis-tributional methods. Our contribution is twofold. First of all, we carry out a large-scale evaluation, comparing different composition methods within the distributional framework for the cases of both adjective-noun and noun-noun composition, makinguse of a newly developed dataset. Secondly, we propose a novel method focomposition, which generalises the approach by Baroni and Zamparelli (2010). The performance of our novel method is also evaluated on our new dataset andproves competitive with the best methods.
Jet schemes of rational double point singularities

We prove that for m ∈ N, m big enough, the number of irreducible components of the schemes of m−jets centered at a point which is a double point singularity is independent of m and is equal to the number of exceptional curves on the minimal resolution of the singularity. We also relate some irreducible components of the jet schemes of an E6 singularity to its ”minimal” embedded resolutions of singularities. 2010 Mathematics Subject Classification. Primary 14E18,14B05; Secondary 13D40.
Classification of Gene Expression Data by Majority Voting Genetic Programming Classifier

Recently, genetic programming (GP) has been applied to the classification of gene expression data. In its typical implementation, using training data, a single rule or a single set of rules is evolved with GP, and then it is applied to test data to get generalized test accuracy. However, in most cases, the generalized test accuracy is not higher. In this paper, we propose a majority voting technique for prediction of the labels of test samples. Instead of a single rule or a single set of rules, we evolve multiple rules with GP and then apply those rules to test samples to determine their labels by using the majority voting technique. We demonstrate the effectiveness of our proposed method by performing different types of experiments on two microarray data sets.
Mitochondrial Dihydrolipoyl Dehydrogenase Activity Shapes Photosynthesis and Photorespiration of Arabidopsis thaliana

The activity of the mitochondrial dihydrolipoyl dehydrogenase improves photorespiration and in turn stimulates photosynthetic carbon assimilation and plant growth. Mitochondrial dihydrolipoyl dehydrogenase (mtLPD; L-protein) is an integral component of several multienzyme systems involved in the tricarboxylic acid (TCA) cycle, photorespiration, and the degradation of branched-chain α-ketoacids. The majority of the mtLPD present in photosynthesizing tissue is used for glycine decarboxylase (GDC), necessary for the high-flux photorespiratory glycine-into-serine conversion. We previously suggested that GDC activity could be a signal in a regulatory network that adjusts carbon flux through the Calvin-Benson cycle in response to photorespiration. Here, we show that elevated GDC L-protein activity significantly alters several diagnostic parameters of cellular metabolism and leaf gas exchange in Arabidopsis thaliana. Overexpressor lines displayed markedly decreased steady state contents of TCA cycle and photorespiratory intermediates as well as elevated NAD(P)+-to-NAD(P)H ratios. Additionally, increased rates of CO2 assimilation, photorespiration, and plant growth were observed. Intriguingly, however, day respiration rates remained unaffected. By contrast, respiration was enhanced in the first half of the dark phase but depressed in the second. We also observed enhanced sucrose biosynthesis in the light in combination with a lower diel magnitude of starch accumulation and breakdown. These data thus substantiate our prior hypothesis that facilitating flux through the photorespiratory pathway stimulates photosynthetic CO2 assimilation in the Calvin-Benson cycle. They furthermore suggest that this regulation is, at least in part, dependent on increased light-capture/use efficiency.
Methods for semen and endocrinological evaluation of the stallion: a review

Juhasz J . , P . Nagy, M. Kulcsar , Gy. Huszenicza: Methods for Semen and Endocrinological Evaluation of The Stallion: A Review. Acta Vet. Brno 2000, 69: 247-259. Breeding soundness examination of stallions includes the examination of reproductive organs, behavior, quantity and quality of the ejaculate and function of the reproductive endocrine system. The paper reviews the current knowledge of this field. First, the morphology of the equine spermatozoa is described in details. Semen examination is divided into routine and advanced laboratory procedures and new techniques. During routine laboratory examination, the quantitative (volume, concentration, total sperm number) and the qualitative (appearance, motility, morphology) parameters of the ejaculate are determined. Owing to different evaluation systems and interpretation, data on morphology from different laboratories are difficult to compare. Following routine laboratory tests, morphological and functional membrane integrity and acrosome integrity can be determined. Several non fluorescent and fluorescent staining techniques have been developed to determine the viability and/or the acrosomal status of spermatozoa which can be used separately or in combination. Hypo-osmotic swelling (HOS) test is a relatively simple test to evaluate the functional integrity of the spermatozoal membrane. New automated techniques, such as computer assisted sperm analysis (CASA) and flow cytometry have been developed recently. These new methods allow us to evaluate different motility parameters, morphology, different compartments and functions of individual cells, including the nucleus, plasma membrane, mitochondria, capacitation, acrosomal status. The determination of baseline concentration of reproductive hormones helps to evaluate the breeding soundness of stallions. GnRH and hCG challenge-tests are also available to monitor the function of the hypothalamus-pituitary-testis axis. The accuracy of all these methods has to be confirmed on a large number of stallions and their correlation with fertility has to be determined. The content of the paper is the following:
Leukocyte telomere length and hippocampus volume: a meta-analysis

Leukocyte telomere length has been shown to correlate to hippocampus volume, but effect estimates differ in magnitude and are not uniformly positive. This study aimed primarily to investigate the relationship between leukocyte telomere length and hippocampus gray matter volume by meta-analysis and secondarily to investigate possible effect moderators. Five studies were included with a total of 2107 participants, of which 1960 were contributed by one single influential study. A random-effects meta-analysis estimated the effect to r = 0.12 [95% CI -0.13, 0.37] in the presence of heterogeneity and a subjectively estimated moderate to high risk of bias. There was no evidence that apolipoprotein E (APOE) genotype was an effect moderator, nor that the ratio of leukocyte telomerase activity to telomere length was a better predictor than leukocyte telomere length for hippocampus volume. This meta-analysis, while not proving a positive relationship, also is not able to disprove the earlier finding of a positive correlation in the one large study included in analyses. We propose that a relationship between leukocyte telomere length and hippocamus volume may be mediated by transmigrating monocytes which differentiate into microglia in the brain parenchyma.
GAB2 as an Alzheimer disease susceptibility gene: follow-up of genomewide association results.

BACKGROUND Genomewide association (GWA) studies have recently implicated 4 novel Alzheimer disease (AD) susceptibility loci (GAB2, GOLM1, and 2 uncharacterized loci to date on chromosomes 9p and 15q). To our knowledge, these findings have not been independently replicated. OBJECTIVE To assess these GWA findings in 4 large data sets of families affected by AD. DESIGN Follow-up of genetic association findings in previous studies. SETTING Academic research. PARTICIPANTS More than 4000 DNA samples from almost 1300 families affected with AD. MAIN OUTCOME MEASURES Genetic association analysis testing of 4 GWA signals (rs7101429 [GAB2], rs7019241 [GOLM1], rs10519262 [chromosome 15q], and rs9886784 [chromosome 9p]) using family-based methods. RESULTS In the combined analyses, only rs7101429 in GAB2 yielded significant evidence of association with the same allele as in the original GWA study (P =.002). The results are in agreement with recent meta-analyses of this and other GAB2 polymorphisms suggesting approximately a 30% decrease in risk for AD among carriers of the minor alleles. None of the other 3 tested loci showed consistent evidence for association with AD across the investigated data sets. CONCLUSIONS GAB2 contains genetic variants that may lead to a modest change in the risk for AD. Despite these promising results, more data from independent samples are needed to better evaluate the potential contribution of GAB2 to AD risk in the general population.
New Dynamic Enhancements to the Vertex-Based Rate-Distortion Optimal Shape Coding Framework

Existing vertex-based operational rate-distortion (ORD) optimal shape coding algorithms use a vertex band around the shape boundary as the source of candidate control points (CP) usually in combination with a tolerance band (TB) and sliding window (SW) arrangement, as their distortion measuring technique. These algorithms however, employ a fixed vertex-band width irrespective of the shape and admissible distortion (AD), so the full bit-rate reduction potential is not fulfilled. Moreover, despite the causal impact of the SW-length upon both the bit-rate and computational-speed, there is no formal mechanism for determining the most suitable SW-length. This paper introduces the concept of a variable width admissible CP band and new adaptive SW-length selection strategy to address these issues. The presented quantitative and qualitative results analysis endorses the superior performance achieved by integrating these enhancements into the existing vertex-based ORD optimal algorithms.
Genetic and Early-Life Environmental Influences on Dental Caries Risk: A Twin Study

In this longitudinal twin study, environmental rather than genetic factors predict dental caries risk, and modifiable risk factors are present from the prenatal period onward. OBJECTIVES: To explore the relative contributions of genetic and environmental influences on dental caries risk and to investigate fetal and developmental risk factors for dental caries. METHODS: We recruited children from 250 twin pregnancies midgestation and collected demographic, health, and phenotypic data at recruitment, 24 and 36 weeks’ gestational age, birth and 18 months, and 6 years of age. 25-hydroxyvitamin D was quantified in mothers at 28 weeks’ gestation and in infants at birth. Dental caries and enamel defects were measured at six years of age. We compared concordance for the presence of any caries and advanced caries in monozygotic and dizygotic twin pairs. To investigate environmental risk factors for caries, we fitted multiple logistic regression models using generalized estimating equations to adjust for twin correlation. RESULTS: A total of 345 twins underwent dental assessment, with 111 (32.2%) showing signs of any caries and 83 (24.1%) having advanced caries. There was no evidence of higher concordance in monozygotic twins compared with dizygotic twins, with a difference of 0.05 (95% confidence interval −0.14 to 0.25; P = .30) and 0.00 (95% confidence interval −0.26 to 0.26; P = .50) for any caries and advanced caries, respectively, suggesting that environmental factors, rather than genetics, are the predominant determinant of caries risk. After adjusting for potential confounders, lack of community water fluoridation, hypomineralized second primary molars, dichorionic placenta, and maternal obesity were associated with caries. CONCLUSIONS: Environmental rather than genetic factors drive dental caries risk and arise as early as prenatal life.
Microfluidic System Based High Throughput Drug Screening System for Curcumin/TRAIL Combinational Chemotherapy in Human Prostate Cancer PC3 Cells

We have developed a fully automated high throughput drug screening (HTDS) system based on the microfluidic cell culture array to perform combinational chemotherapy. This system has 64 individually addressable cell culture chambers where the sequential combinatorial concentrations of two different drugs can be generated by two microfluidic diffusive mixers. Each diffusive mixer has two integrated micropumps connected to the media and the drug reservoirs respectively for generating the desired combination without the need for any extra equipment to perfuse the solution such as syringe pumps. The cell array is periodically exposed to the drug combination with the programmed LabVIEW system during a couple of days without extra handling after seeding the cells into the microfluidic device and also, this device does not require the continuous generation of solutions compared to the previous systems. Therefore, the total amount of drug being consumed per experiment is less than a few hundred micro liters in each reservoir. The utility of this system is demonstrated through investigating the viability of the prostate cancer PC3 cell line with the combinational treatments of curcumin and tumor necrosis factor-alpha related apoptosis inducing ligand (TRAIL). Our results suggest that the system can be used for screening and optimizing drug combination with a small amount of reagent for combinatorial chemotherapy against cancer cells.
Physical Activity and Perceived Health Status in Persons with Multiple Sclerosis

&NA; Regular exercise and physical activity can minimize deconditioning and assist individuals with multiple sclerosis (MS) to maintain function at optimal levels. The purpose of this study was to explore the relationship of physical activity to social, mental and physical health and well‐being in persons with MS. A convenience sample of 37 persons with MS completed the Human Activity Profile and the Medical Outcomes Study Short‐Form Health Survey (SF36). Activity levels in persons with MS were much lower than norms reported for other groups of healthy adults and adults with a variety of chronic conditions. Higher activity scores were associated with higher scores on the measures of physical functioning and general health. The subgroup of persons who reported engaging in regular exercise had significantly higher scores on the measure of physical functioning than those who did not exercise. Additional research is needed to investigate barriers and facilitators of physical activity for persons with MS and whether increasing activity may have synergistic effects with other therapies.