Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced sampling schemes for MCMC based blind Bernoulli-Gaussian deconvolution

This paper proposes and compares two new sampling schemes for sparse deconvolution using a Bernoulli-Gaussian model. To tackle such a deconvolution problem in a blind and unsupervised context, the Markov Chain Monte Carlo (MCMC) framework is usually adopted, and the chosen sampling scheme is most often the Gibbs sampler. However, such a sampling scheme fails to explore the state space efficiently. Our first alternative, the $K$-tuple Gibbs sampler, is simply a grouped Gibbs sampler. The second one, called partially marginalized sampler, is obtained by integrating the Gaussian amplitudes out of the target distribution. While the mathematical validity of the first scheme is obvious as a particular instance of the Gibbs sampler, a more detailed analysis is provided to prove the validity of the second scheme. For both methods, optimized implementations are proposed in terms of computation and storage cost. Finally, simulation results validate both schemes as more efficient in terms of convergence time compared with the plain Gibbs sampler. Benchmark sequence simulations show that the partially marginalized sampler takes fewer iterations to converge than the $K$-tuple Gibbs sampler. However, its computation load per iteration grows almost quadratically with respect to the data length, while it only grows linearly for the $K$-tuple Gibbs sampler.
A Study on Performance Improvement Due to Linear Fusion in Biometric Authentication Tasks

In this paper, we initiate a theoretical study on N-expert fusion (N ≥ 2) in the context of biometric authentication (BA). Optimal fusion weights, which depend on performances and variances of, and correlations among individual base-experts have been found, and we also give and prove some new theorems that serve as the basis for analyzing the performance of the overall system. Our conclusion is that provided that optimal weights are used as fusion coefficients, linear fusion will definitely lead to a better performance than the best individual expert. This contradicts many existing conclusions, which assert that fusion is not always beneficial and that performance improvement due to fusion is guaranteed only when some conditions as to baseexperts' performances, variances, and correlations are satisfied. Besides, for the first time the definition of correlation in the context of BA is clearly and explicitly given to avoid the longstanding ambiguity and vagueness concerning this term, and we make an initial attempt to propose and investigate three types of correlation coefficients. Furthermore, the connection between our proposed optimal fusion method and Fisher's discriminant is discussed. Extensive experiments have been conducted to confirm our theoretical results and construct counter-examples for the existing conclusions.
Personality characteristics and affective status related to cognitive test performance and gender in patients with memory complaints

The aims are to study personality characteristics of patients with memory complaints and to assess the presence of objective (OMI) versus subjective (SMI) memory impairment, the affective status, as well as potential gender differences. The patients were assessed by means of a neuropsychiatric examination and a neuropsychological test-battery. The Swedish version of the revised NEO Personality Inventory (NEO PI-R) and the Hospital Anxiety and Depression Scale (HADS) were used. The 57 patients (38 women, 19 men, mean age 56.9) differed from the Swedish normative group in three of the five personality factors: neuroticism, extraversion and agreeableness. This was mainly because of the scores of the female patients. Approximately half of the patients had OMI. No differences regarding personality factors or affective status were found between OMI and SMI patients. The female patients scored significantly higher than the male patients on symptoms of anxiety and depression. Neuroticism and symptoms of depression interacted with memory performance and gender. Our findings demonstrate the importance of applying an objective assessment of memory functions and a gender perspective when studying patients with memory complaints. (JINS, 2007, 13, 911–919.)
A Fast Algorithm for Learning a Ranking Function from Large-Scale Data Sets

We consider the problem of learning a ranking function that maximizes a generalization of the Wilcoxon-Mann-Whitney statistic on the training data. Relying on an e-accurate approximation for the error function, we reduce the computational complexity of each iteration of a conjugate gradient algorithm for learning ranking functions from O(m2) to O(m), where m is the number of training samples. Experiments on public benchmarks for ordinal regression and collaborative filtering indicate that the proposed algorithm is as accurate as the best available methods in terms of ranking accuracy, when the algorithms are trained on the same data. However, since it is several orders of magnitude faster than the current state-of-the-art approaches, it is able to leverage much larger training data sets.
Properties of PC4 and an RNA Polymerase II Complex in Directing Activated and Basal Transcription in Vitro *

A human RNA polymerase II (pol II) complex was isolated from a HeLa-derived cell line that conditionally expresses an epitope-tagged RPB9 subunit of human pol II. The isolated FLAG-tagged pol II complex (f:pol II) contains a subset of general transcription factors but is devoid of TFIID and TFIIA. In conjunction with TATA-binding protein (TBP) or TFIID, f:pol II is able to mediate both basal and activated transcription by Gal4-VP16 when a transcriptional coactivator PC4 is also provided. Interestingly, PC4, in the absence of a transcriptional activator, actually functions as a repressor to inhibit basal transcription. Remarkably, TBP is able to mediate activator function in this transcription system. The presence of TBP-associated factors, however, helps overcome PC4 repression and further enhance the level of activation mediated by TBP. Alleviation of PC4 repression can also be achieved by preincubation of the transcriptional components with the DNA template. Sarkosyl disruption of preinitiation complex formation further illustrates that PC4 can only inhibit transcription prior to the assembly of a functional preinitiation complex. These results suggest that PC4 represses basal transcription by preventing the assembly of a functional preinitiation complex, but it has no effect on the later steps of the transcriptional process.
Idea Screening in Engineering Design Using Employee-Driven Wisdom of the Crowds

The paper investigates the question of screening ideas in the ‘fuzzy front end’ of engineering design, examining the validity of employee voting schemes and related biases. After an employee-driven innovation project at {Company Name removed for review}, 99 ideas were to be screened for further development. Based on the concept of ‘wisdom of the crowds’, all ideas were individually rated by a broad selection of employees, and their choices of ideas and idea categories compared to those of a small team of senior marketers. The study also tested for two biases: visual complexity and endowment effect/ownership of ideas. The study shows that the crowd wisdom of employees significantly correlates with the preferences of the marketing team: overall, in top 12 selected ideas and in choice of idea categories. This match increases when including only the ratings of the most experienced employees. The experienced employees also proved to be less affected by visual complexity in the ideas presented. The endowment effect was potent in that every employee proved to be more likely to select their own ideas over others, but this effect disappeared when aggregating across the crowd of employees.
Stress-Derived Corticotropin Releasing Factor Breaches Epithelial Endotoxin Tolerance

Background and aims Loss of the endotoxin tolerance of intestinal epithelium contributes to a number of intestinal diseases. The etiology is not clear. Psychological stress is proposed to compromise the intestinal barrier function. The present study aims to elucidate the role of the stress-derived corticotropin releasing factor (CRF) in breaching the established intestinal epithelial endotoxin tolerance. Methods Epithelial cells of HT-29, T84 and MDCK were exposed to lipopolysaccharide to induce the endotoxin tolerance; the cells were then stimulated with CRF. The epithelial barrier function was determined using as indicators of the endotoxin tolerant status. A water-avoid stress mouse model was employed to test the role of CRF in breaching the established endotoxin tolerance in the intestine. Results The established endotoxin tolerance in the epithelial cell monolayers was broken down by a sequent exposure to CRF and LPS manifesting a marked drop of the transepithelial resistance (TER) and an increase in the permeability to a macromolecular tracer, horseradish peroxidase (HRP). The exposure to CRF also increased the expression of Cldn2 in the epithelial cells, which could be mimicked by over expression of TLR4 in epithelial cells. Over expression of Cldn2 resulted in low TER in epithelial monolayers and high permeability to HRP. After treating mice with the 10-day chronic stress, the intestinal epithelial barrier function was markedly compromised, which could be prevented by blocking either CRF, or TLR4, or Cldn2. Conclusions Psychological stress-derived CRF can breach the established endotoxin tolerance in the intestinal mucosa.
The spatial distribution of galaxies within the cosmic microwave background cold spot in the Corona Borealis supercluster

We study the spatial distribution and colours of galaxies within the region covered by the cold spot in the cosmic microwave background recently detected by the Very Small Array interpherometer (VSA) towards the Corona Borealis supercluster (CrB-SC). The spot is in the northern part of a region with a radius ∼ 1° (∼5 Mpc at the redshift of CrB-SC) enclosing the clusters Abell 2056, 2065, 2059 and 2073, and where the density of galaxies, excluding the contribution from those clusters, is approximately two times higher than the mean value in typical intercluster regions of the CrB-SC. Two of such clusters (Abell 2056 and 2065) are members of the CrB-SC, while the other two are in the background. This high-density intercluster region is quite inhomogeneous, being the most remarkable feature a large concentration of galaxies in a narrow filament running from Abell 2065 with a length of ∼35 arcmin (∼3 Mpc at the redshift of CrB-SC) in the SW-NE direction. This intercluster population of galaxies probably results from the interaction of clusters Abell 2065 and 2056. The area subtended by the VSA cold spot shows an excess of faint (21 < r < 22) and red (1.1 < r - i < 1.3) galaxies as compared with typical values within the CrB-SC intercluster regions. This overdensity of galaxies shows a radial dependence and extends out to ∼ 15 arcmin. This could be the signature of a previously unnoted cluster in the background.
Harmonic Allocation of Authorship Credit: Source-Level Correction of Bibliometric Bias Assures Accurate Publication and Citation Analysis

Authorship credit for multi-authored scientific publications is routinely allocated either by issuing full publication credit repeatedly to all coauthors, or by dividing one credit equally among all coauthors. The ensuing inflationary and equalizing biases distort derived bibliometric measures of merit by systematically benefiting secondary authors at the expense of primary authors. Here I show how harmonic counting, which allocates credit according to authorship rank and the number of coauthors, provides simultaneous source-level correction for both biases as well as accommodating further decoding of byline information. I also demonstrate large and erratic effects of counting bias on the original h-index, and show how the harmonic version of the h-index provides unbiased bibliometric ranking of scientific merit while retaining the original's essential simplicity, transparency and intended fairness. Harmonic decoding of byline information resolves the conundrum of authorship credit allocation by providing a simple recipe for source-level correction of inflationary and equalizing bias. Harmonic counting could also offer unrivalled accuracy in automated assessments of scientific productivity, impact and achievement.
Adherence to a Mediterranean diet and survival in a Greek population.

BACKGROUND Adherence to a Mediterranean diet may improve longevity, but relevant data are limited. METHODS We conducted a population-based, prospective investigation involving 22,043 adults in Greece who completed an extensive, validated, food-frequency questionnaire at base line. Adherence to the traditional Mediterranean diet was assessed by a 10-point Mediterranean-diet scale that incorporated the salient characteristics of this diet (range of scores, 0 to 9, with higher scores indicating greater adherence). We used proportional-hazards regression to assess the relation between adherence to the Mediterranean diet and total mortality, as well as mortality due to coronary heart disease and mortality due to cancer, with adjustment for age, sex, body-mass index, physical-activity level, and other potential confounders. RESULTS During a median of 44 months of follow-up, there were 275 deaths. A higher degree of adherence to the Mediterranean diet was associated with a reduction in total mortality (adjusted hazard ratio for death associated with a two-point increment in the Mediterranean-diet score, 0.75 [95 percent confidence interval, 0.64 to 0.87]). An inverse association with greater adherence to this diet was evident for both death due to coronary heart disease (adjusted hazard ratio, 0.67 [95 percent confidence interval, 0.47 to 0.94]) and death due to cancer (adjusted hazard ratio, 0.76 [95 percent confidence interval, 0.59 to 0.98]). Associations between individual food groups contributing to the Mediterranean-diet score and total mortality were generally not significant. CONCLUSIONS Greater adherence to the traditional Mediterranean diet is associated with a significant reduction in total mortality.
The principal-agent relationship with an informed principal. II : Common values

A principal has private information that directly affects her agent's payoff (i.e., "common values" obtains). The authors analyze their relationship as a three-stage game: (1) the principal proposes a contract; (2) the agent accepts or rejects; and (3) the contract is executed. They show that the equilibrium outcomes are the allocations that weakly Pareto dominate the allocation maximizing the payoff of each "type" of the principal within the class of incentive-compatible allocations ensuring the agent his reservation utility irrespective of his beliefs about the principal's type. The authors also characterize the equilibria that are immune to renegotiation. Copyright 1992 by The Econometric Society.
Changes of glycogen content in liver, skeletal muscle, and heart from fasted rats

Glycogen content of white and red skeletal muscles, cardiac muscle, and liver was investigated in conditions where changes in plasma levels of non‐esterified fatty acids (NEFA) occur. The experiments were performed in fed and 12 and 48 h‐fasted rats. The animals were also submitted to swimming for 10 and 30 min. Glycogen content was also investigated in both pharmacologically induced low plasma NEFA levels fasted rats and pharmacologically induced high plasma NEFA levels fed rats. The participation of Akt and glycogen synthase kinase‐3 (GSK‐3) in the changes observed was investigated. Plasma levels of NEFA, glucose, and insulin were determined in all conditions. Fasting increased plasma NEFA levels and reduced glycogen content in the liver and skeletal muscles. However, an increase of glycogen content was observed in the heart under this condition. Akt and GSK‐3 phosphorylation was reduced during fasting in the liver and skeletal muscles but it remained unchanged in the heart. Our results suggest that in conditions of increased plasma NEFA levels, changes in insulin‐stimulated phosphorylation of Akt and GSK‐3 and glycogen content vary differently in liver, skeletal muscles, and heart. Akt and GSK‐3 phosphorylation and glycogen content are decreased in liver and skeletal muscles, but in the heart it remain unchanged (Akt and GSK‐3 phosphorylation) or increased (glycogen content) due to consistent increase of plasma NEFA levels. Copyright © 2009 John Wiley & Sons, Ltd.
Manure Refinement Affects Apple Rhizosphere Bacterial Community Structure: A Study in Sandy Soil

We used DNA-based pyrosequencing to characterize the bacterial community structure of the sandy soil of an apple orchard with different manure ratios. Five manure percentages (5%, 10%, 15%, 20% and 25%) were examined. More than 10,000 valid reads were obtained for each replicate. The communities were composed of five dominant groups (Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Bacteroidetes), of which Proteobacteria content gradually decreased from 41.38% to 37.29% as manure ratio increased from 0% to 25%, respectively. Redundancy analysis showed that 37 classes were highly correlated with manure ratio, 18 of which were positively correlated. Clustering revealed that the rhizosphere samples were grouped into three components: low manure (control, 5%) treatment, medium manure (10%, 15%) treatment and high manure (20%, 25%) treatment. Venn analysis of species types of these three groups revealed that the bacteria community difference was primarily reflected by quantity ratio rather than species variety. Although greater manure content led to higher soil organic matter content, the medium manure improved soil showed the highest urease activity and saccharase activity, while 5% to 20% manure ratio improvement also resulted in higher bacteria diversity than control and 25% manure ratio treatment. Our experimental results suggest that the use of a proper manure ratio results in significantly higher soil enzyme activity and different bacteria community patterns, whereas the use of excessive manure amounts has negative effect on soil quality.
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region

Terminal deoxynucleotidyltransferase (Tdt) and DNA polymerase μ (pol μ) are two eukaryotic highly similar proteins involved in DNA processing and repair. Despite their high sequence identity, they differ widely in their activity: pol μ has a templated polymerase activity, whereas Tdt has a non-templated one. Loop1, first described when the Tdt structure was solved, has been invoked as the major structural determinant of this difference. Here we describe attempts to transform Tdt into pol μ with the minimal number of mutations in and around Loop1. First we describe the effect of mutations on six different positions chosen to destabilize Tdt Loop1 structure, either by alanine substitution or by deletion; they result at most in a reduction of Tdt activity, but adding Co++ restores most of this Tdt activity. However, a deletion of the entire Loop1 as in pol λ does confer a limited template-dependent polymerase behavior to Tdt while a chimera bearing an extended pol μ Loop1 reproduces pol μ behavior. Finally, 16 additional substitutions are reported, targeted at the two so-called ‘sequence determinant’ regions located just after Loop1 or underneath. Among them, the single-point mutant F401A displays a sequence-specific replicative polymerase phenotype that is stable upon Co++ addition. These results are discussed in light of the available crystal structures.
The development of working memory: exploring the complementarity of two models.

The aim of the paper was to further explore the complementarity of the working memory models postulated by Pascual-Leone and Baddeley. Five-, six-, eight-, and nine-year-old children were assessed on two working memory tasks that have frequently been used within the respective streams of research: the Mr. Peanut task and the Corsi blocks task. Results indicated a developmental increase in spatial short-term memory for both tasks. Concurrent spatial suppression reduced performance on the two tasks in all four age groups. By contrast, articulatory suppression interfered with recall only on the Mr. Peanut task, and in only the older children. The two models were shown to make their own specific contribution to the interpretation of the data, attesting to their complementarity. Pascual-Leone's theory offered a clear explanation of the results concerning the central aspects of working memory, that is, the stepwise age-related increase in performance, whereas Baddeley's model provided a convincing account of the findings regarding the peripheral phonological and visuo-spatial components, that is, the effects of articulatory and spatial suppression.
THE INFLUENCE OF A COMPETITOR ON THE GEOGRAPHIC MOSAIC OF COEVOLUTION BETWEEN CROSSBILLS AND LODGEPOLE PINE

Abstract The geographic mosaic theory of coevolution posits that the form of selection between interacting species varies across a landscape with coevolution important and active in some locations (i.e., coevolutionary hotspots) but not in others (i.e., coevolutionary coldspots). We tested the hypothesis that the presence of red squirrels (Tamiasciurus hudsonicus) affects the occurrence of coevolution between red crossbills (Loxia curvirostra complex) and Rocky Mountain lodgepole pine (Pinus contorta ssp. latifolia) and thereby provides a mechanism giving rise to a geographic mosaic of selection. Red squirrels are the predominant predispersal seed predator and selective agent on lodgepole pine cones. However, in four isolated mountain ranges east and west of the Rocky Mountains, red squirrels are absent and red crossbills are the main predispersal seed predator. These isolated populations of pine have apparently evolved without Tamiasciurus for about 10,000 to 12,000 years. Based on published morphological, genetic, and paleobotanical studies, we infer that cone traits in these isolated populations that show parallel differences from cones in the Rocky Mountains have changed in parallel. We used data on crossbill and conifer cone morphology and feeding preferences and efficiency to detect whether red crossbills and lodgepole pine exhibit reciprocal adaptations, which would imply coevolution. Cone traits that act to deter Tamiasciurus and result in high ratios of cone mass to seed mass were less developed in the isolated populations. Cone traits that act to deter crossbills include larger and thicker scales and perhaps increased overlap between successive scales and were enhanced in the isolated populations. In the larger, isolated mountain ranges crossbills have evolved deeper, shorter, and therefore more decurved bills to exploit these cones. This provides crossbills with higher feeding rates, and the change in bill shape has improved efficiency by reducing the concomitant increases in body mass and daily energy expenditures that would have resulted if only bill size had increased. These parallel adaptations and counter adaptations in red crossbills and lodgepole pine are interpreted as reciprocal adaptations and imply that these crossbills and pine are in coevolutionary arms races where red squirrels are absent (i.e., coevolutionary hotspots) but not where red squirrels are present (i.e., coevolutionary coldspots).