Miracle-dz/UniFAR-FTUs huggingface dataset:
A simple procedure for estimating the false discovery rate

MOTIVATION The most used criterion in microarray data analysis is nowadays the false discovery rate (FDR). In the framework of estimating procedures based on the marginal distribution of the P-values without any assumption on gene expression changes, estimators of the FDR are necessarily conservatively biased. Indeed, only an upper bound estimate can be obtained for the key quantity pi0, which is the probability for a gene to be unmodified. In this paper, we propose a novel family of estimators for pi0 that allows the calculation of FDR. RESULTS The very simple method for estimating pi0 called LBE (Location Based Estimator) is presented together with results on its variability. Simulation results indicate that the proposed estimator performs well in finite sample and has the best mean square error in most of the cases as compared with the procedures QVALUE, BUM and SPLOSH. The different procedures are then applied to real datasets. AVAILABILITY The R function LBE is available at http://ifr69.vjf.inserm.fr/lbe CONTACT broet@vjf.inserm.fr.
Global effects estimation for multidimensional outcomes

Many health studies focus on multifaceted outcomes that are not easily measured with a single variable; examples include studies on quality of life (QOL) and general health. To fully explore such an outcome, researchers typically collect information on multiple endpoints. The resulting measurements constitute multidimensional outcome data. An object of great interest is the overall—or global—effect of a covariate, such as a treatment intervention, on the multidimensional outcome. Quantifying such an effect can be difficult because multiple clinical outcomes are usually measured on different scales; the problem is enhanced by the fact that multiple measurements on a given subject are typically correlated. We present a regression modeling scheme permitting estimation of global treatment effects when multiple continuous endpoints are examined in concert either once or for several times. The global effect is conceptualized as a change in the distribution functions of the outcome variables. It may thus be interpreted as a connection between outcome distribution quantiles for the treatment and control groups. This concept allows the presentation of a global effect as a scalar quantity applicable to all outcomes simultaneously, easing interpretation of results. Model estimation proceeds directly from existing methods for multivariate survival analysis. The assumption that the treatment effect is homogenous across different outcomes is testable. To illustrate the application, we present data analytic results from a motivating example, an analysis of patients' QOL during recovery from lower limb trauma. We also explore the performance properties of global effects estimation through simulation. Copyright © 2007 John Wiley & Sons, Ltd.
Loss of sulfur dioxide and changes in some chemical properties of Malatya apricots (Prunus armeniaca L.) during sulfuring and drying.

BACKGROUND This study was conducted to determine the differences in some analytical properties of four apricot cultivars and to determine the changes in these analytical properties during sulfuring and sun-drying. RESULTS There were significant differences in the contents of polyphenols, carotenoids and organic acids (OA) as well as antioxidant activities (AOAs) of the cultivars (P < 0.05). After sulfuring and drying, considerable reductions were detected in the contents of total polyphenols (TPCs, 11-26%), OAs (4-32%) and β-carotene (6-21%), and AOAs (2-21%) of the samples. Sun-drying resulted in 71-83% decreases in sulfur dioxide (SO2 ) contents of sulfured-dried apricots (SDAs) in comparison with apricots immediately after sulfuring. As the TPCs increased, the SO2 absorption by the samples also increased. In contrast, the OA contents had no effect on SO2 absorption, but an increase in OA content resulted in an increase in the browning values of the SDAs. As expected, increases in contents of ferulic acid (r = 0.932), chlorogenic acid (r = 0.850), epicatechin (r = 0.804) and quercetin (r = 0.750) led to an increase in browning values of the SDAs. CONCLUSION There were significant effects of cultivar and processing on the physico-chemical properties investigated in the study, and with the absorption of SO2 and the formation of a brown colour in the samples.
Is Inequality Harmful for Growth? Theory and Evidence

Is inequality harmful for growth? We suggest that it is. To summarize our main argument: in a society where distributional conflict is more important, political decisions are more likely to produce economic policies that allow private individuals to appropriate less of the returns to growth promoting activities, such as accumulation of capital and productive knowledge. In the paper we first formulate a theoretical model that formally captures this idea. The model has a politico-economic equilibrium, which determines a sequence of growth rates depending on structural parameters, political institutions, and initial conditions. We then confront the testable empirical implications with two sets of data. A first data set pools historical evidence-which goes back to the mid 19th century-from the US and eight European countries. A second data set contains post-war evidence from a broad cross-section of developed and less developed countries. In both samples we find a statistically significant and quantitatively important negative relation between inequality and growth. After a comprehensive sensitivity analysis, we conclude that our findings are not distorted by measurement error, reverse causation, hetroskedasticity, or other econometric problems.
Interaction of Size and Momentum Effects in Jordan Firms: 2005-2014

This study sought to disentangle the effects of size and whether there are size and momentum effects on Jordan firm returns. Initial findings showed that size effect has important role in explaining returns. For momentum effect, while in general there is no momentum effect in Jordan firm market, the study results founds that there is a strong evidence of momentum for the large-sized portfolios at Jordan firm returns. There is interaction between size and momentum. Two key findings emerge. First, there is a strong evidence for size effect. Second, the momentum premium is only evident for the large-sized portfolios.
Differences in Norovirus-Associated Hospital Visits Between Jewish and Bedouin Children in Southern Israel

Population-based surveillance during 2006–2013 showed that norovirus hospitalization rates among Bedouin (low-middle income settings) children <5 years old were 13.9/10,000 person-years compared with 7.1/10,000 among Jewish (high-income settings) children who were <5 years (rate ratio: 2.0, 95% confidence interval: 1.6–2.3). Differences were most prominent among infants (59.7 vs. 19.7/10,000, respectively; rate ratio: 3.0, 95% confidence interval: 2.5–3.8). GII.3 and GII.4 strains dominated (67%) in both populations.
The Bullwhip Effect—Impact of Stochastic Lead Time, Information Quality, and Information Sharing: A Simulation Study

We use a simulation model called ‘SISCO’ to examine the effects in supply chains of stochastic lead times and of information sharing and quality of that information in a periodic order‐up‐to level inventory system. We test the accuracy of the simulation by verifying the results in Chen et al. (2000a) and Dejonckheere et al. (2004). We find that lead‐time variability exacerbates variance amplification in a supply chain, and that information sharing and information quality are highly significant. For example, using the assumptions in Chen et al. (2000a) and Dejonckheere et al. (2004), we find in a numerical experiment of a customer‐retailer‐wholesaler‐distributor‐factory supply chain that variance amplification is attenuated by nearly 50 percent at the factory due to information sharing. Other assumptions we make are based on interviews or conversations with managers at large supply chains.
Insurance as maladaptation: Resilience and the ‘business as usual’ paradox

Insurance and compensation are cited as critical elements of resilience to natural and non-natural hazards alike. As a strategy of risk management, it emphasises peace of mind, financial recompense and the swift restoration of a ‘business as usual’ status for civil, social and commercial life. Yet despite the contribution of insurance to risk management, the synergies with progressive or adaptive articulations of resilience are not sufficiently explicated. This paper explores the fundamental contradictions of insurance as a form of resilience through a study of flood risk management. It demonstrates how insurance regimes serve to structurally embed risky behaviour and inhibit change after detrimental events. As such, transformative interpretations of resilience conflict with the long-standing principles and operational norms of insurance that privilege normality. The paper concludes that, despite its currency within resilience discourses, insurance is maladaptive and that insurance regimes reinforce exposure and vulnerability through underwriting a return to the ‘status-quo’ rather than enabling adaptive behaviour.
The Adipocyte Plasma Membrane Caveolin Functional/Structural Organization Is Necessary for the Efficient Endocytosis of GLUT4*

It is well established that insulin stimulation of glucose uptake requires the translocation of intracellular localized GLUT4 protein to the cell surface membrane. This plasma membrane-redistributed GLUT4 protein was partially co-localized with caveolin as determined by confocal fluorescent microscopy but was fully excluded from lipid rafts based upon Triton X-100 extractability. Cholesterol depletion with methyl-β-cyclodextrin, filipin, or cholesterol oxidase resulted in an insulin-independent increase in the amount of plasma membrane-localized GLUT4 that was fully reversible by cholesterol replenishment. This basal accumulation of cell surface GLUT4 occurred due to an inhibition of GLUT4 endocytosis. However, this effect was not specific since cholesterol extraction also resulted in a dramatic inhibition of clathrin-mediated endocytosis as assessed by transferrin receptor internalization. To functionally distinguish between caveolin- and clathrin-dependent endocytic processes, we took advantage of a dominant-interfering caveolin 1 mutant (Cav1/S80E) that specifically disrupts caveolae organization. Expression of Cav1/S80E, but not the wild type (Cav1/WT) or Cav1/S80A mutant, inhibited cholera toxin B internalization without any significant effect on transferrin receptor endocytosis. In parallel, Cav1/S80E expression increased the amount of plasma membrane-localized GLUT4 protein in an insulin-independent manner. Although Cav1/S80E also decreased GLUT4 endocytosis, the extent of GLUT4 internalization was only partially reduced (∼40%). In addition, expression of Cav1/WT and Cav1/S80A enhanced GLUT4 endocytosis by ∼20%. Together, these data indicate that the endocytosis of GLUT4 requires clathrin-mediated endocytosis but that the higher order structural organization of plasma membrane caveolin has a significant influence on this process.
Comparative Capitalisms, Ideational Political Economy and French Post-Dirigiste Responses to the Global Financial Crisis

This article advances the case for the more systematic incorporation of ideational factors into comparative capitalisms analysis as a corrective to the rational choice proclivities of the Varieties of Capitalism approach. It demonstrates the pay-off of such an ideationally attuned approach through analysis of French capitalist restructuring over the last 25 years, placing it in comparative context. A modus operandi for such ideational explanation is elaborated through delineating different national conceptions of the market, and setting out their impacts on practices of market-making. The claim made in this article is that understanding the evolution of French capitalism requires recognition of the ongoing market-making role of the French State, in combination with the French conception of the market and its embedding within a social context characterised by the inter-penetration of public and private elitist networks of France's ‘financial network economy’ which remains substantially intact. The ideational dimension is crucial because French understandings of the market and competition, the ideational building blocks of market-making, inform French state interventions and leave footprints on French institutions and market structures, and the evolutionary trajectory of French capitalism. In charting this trajectory, this article deploys the concept of post-dirigisme. We map out the parameters and causes of the post-dirigiste condition in France through examination of French bond market development, privatisation, the shift from a government- to a market- dominated financial system, and French capitalism's internationalisation. It then uses post-dirigisme to explain French state responses to the financial crisis and the banking bailout, noting how state actors, in concert with the banking elites, actively facilitated dominant market positions of French international champions.
The Genome Organization of Ralstonia eutropha Strain H16 and Related Species of the Burkholderiaceae

Ralstonia eutropha strain H16 is a facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium belonging to the family Burkholderiaceae of the Betaproteobacteria. The genome of R. eutropha H16 consists of two chromosomes (Chr1, Chr2) and one megaplasmid (pHG1), and thus shows a multi-replicon architecture, which is characteristic for all members of the Burkholderiaceae sequenced so far. The genes for housekeeping cell functions are located on Chr1. In contrast, many characteristic traits of R. eutropha H16 such as the ability to switch between alternative lifestyles and to utilize a broad variety of growth substrates are primarily encoded on the smaller replicons Chr2 and pHG1. The latter replicons also differ from Chr1 by carrying a repA-associated origin of replication typically found on plasmids. Relationships between the individual replicons from various Burkholderiaceae genomes were studied by multiple sequence alignments and whole-replicon protein comparisons. While strong conservation of gene content and order among the largest replicons indicate a common ancestor, the resemblance between the smaller replicons is considerably lower, suggesting a species-specific origin of Chr2. The megaplasmids, however, in most cases do not show any taxonomically related similarities. Based on the results of the comparative studies, a hypothesis for the evolution of the multi-replicon genomes of the Burkholderiaceae is proposed.
Effects of carvedilol on heart failure with preserved ejection fraction: the Japanese Diastolic Heart Failure Study (J‐DHF)

The therapeutic strategy for heart failure with preserved ejection fraction (HFPEF) has not been established. The Japanese Diastolic Heart Failure Study (J‐DHF) is a multicentre, prospective, randomized, open, blinded‐endpoint trial, designed to assess the effects of carvedilol in HFPEF patients.
Crime in a City in Transition: The Case of Tallinn, Estonia

The objective of this article is to characterise the criminogenic conditions of an eastern European city experiencing the transition from a planned to a market-oriented economy. Tallinn, the capital of Estonia, has been chosen as the case study. The article first describes the various levels of a set of expressive and acquisitive offences in Tallinn and then assesses whether patterns of crime in Tallinn are caused by underlying processes similar to the ones indicated in the Western literature of urban criminology. The study identifies variables that most significantly contribute to the variation of crime ratios using regression models, GIS and spatial statistical techniques. Findings suggest that, although there is no dramatic difference between the geography of crimes in Tallinn and those found in western European and North American cities, some of the explanatory variables function in ways which would not be predicted by Western literature.
Hemispheric organization in disorders of development

ABSTRACT A recent theoretical account posits that, during the acquisition of word recognition in childhood, the pressure to couple visual and language representations in the left hemisphere (LH) results in competition with the LH representation of faces, which consequently become largely, albeit not exclusively, lateralized to the right hemisphere (RH). We explore predictions from this hypothesis using a hemifield behavioural paradigm with words and faces as stimuli, with concurrent event-related potential (ERP) measurement, in a group of adults with developmental dyslexia (DD) or with congenital prosopagnosia (CP) and matched control participants. Behaviourally, the DD group exhibited clear deficits in both word and face processing relative to controls, while the CP group showed a specific deficit in face processing only. This pattern was mirrored in the ERP data too. The DD group evinced neither the normal ERP pattern of RH dominance for faces nor the LH dominance for words. In contrast, the CP group showed the typical ERP superiority for words in the LH but did not show the typical RH superiority for faces. These findings are consistent with the hypothesis that the typical hemispheric organization for words can develop in the absence of typical hemispheric organization for faces but not vice versa, supporting the account of interactive perceptual development.
The Effect of Population and Migration on Forest Cover in Indonesia

The massive loss of quantity and quality of natural forest cover in Indonesia threatens an important source of foreign exchange and employment. Several studies and government policies indicate that population growth, particularly among small landholders, is the principal cause of deforestation. Although there is an element of truth to these studies and policies, they greatly oversimplify and distort the issue of Indonesian deforestation. This article evaluates “population-centered” (neo-Malthusian) explanations of forest cover change in Indonesia in the light of non-population-centered (non-Malthusian) evidence. The conclusion is that although population growth is an important part of the explanation of Indonesian deforestation, it should be seen as an intermediate variable, and not as an independent variable. The policy implication is that nonpopulation factors should receive greater attention in policy measures directed at controlling inappropriate deforestation.
Glomerular haematuria: not so benign?

Isolated haematuria is a frequent finding in routine clinical practice. In most cases haematuria is caused by glomerular disorders, in particular IgA nephropathy (23 to 75%), thin basement membrane nephropathy (5 to 35%), and non-IgA mesangioproliferative glomerulonephritis (9 to 24%). Prognosis is considered to be good in these patients provided proteinuria, hypertension, and renal insufficiency are absent. Hence the term benign glomerular haematuria has been used to describe this condition. In many parts of Europe and the USA a renal biopsy is considered unnecessary in these patients, and they are referred to their general physician for life-long (bi)annual monitoring of serum creatinine concentration, proteinuria and blood pressure. In this issue of the Netherlands Journal of Medicine, Shen et al. present their analysis of patients with clinically early IgA nephropathy, defined as biopsy-proven IgA nephropathy with haematuria and no or minimal proteinuria, normal blood pressure, and normal renal function. The authors show that after a mean follow-up of ten years progressive renal failure occurred in up to 24% of patients. What lessons can be learned from these data and should we adopt a more vigorous renal biopsy policy?
Interpreting the Public Interest: A Survey of Professional Accountants

The accounting profession, like all professions, has a commitment to advance the interests of the general community, as well as those they are contractually bound to serve. Providing services altruistically, at times without compensation, is a salient feature of the public interest ideal. A review of the literature indicates that the profession has abandoned its public interest role so that serving self-interest now appears to have primacy ( Bedard 2001 ; Canning and O'Dwyer 2001 ; Parker 1994 ; Saravanamuthu 2004 ). The aim of this paper is to examine members' interpretation of the public interest ideal and to elicit their perceptions on issues arising from the literature. The results of a survey to members of CPA Australia indicate that members can iterate the formal definition of the public interest, but their application of the public interest in conflict of interest situations is inconsistent with this definition.
Time course of proteinuria after living-donor kidney transplantation1

Background. After cadaveric kidney transplantation, preservation-reperfusion damage results in glomerular and tubular proteinuria. There are no data on the time course of proteinuria after living-donor (LD) transplantation. Methods. In 10 patients receiving a kidney graft from an LD, the excretion of high molecular weight proteins (albumin, transferrin, and immunoglobulin G) and low molecular weight proteins (&bgr;2-microglobulin and &agr;1-microglobulin) was measured at various time points during the first 5 days after transplantation. Results. Immediately after restoration of the circulation, we observed a massive nonselective high molecular weight proteinuria, indicative of glomerular damage. This proteinuria rapidly decreased to slightly elevated values beyond 24 hr after transplantation. Low molecular weight proteinuria, reflecting tubular damage, was also prominent and remained grossly abnormal even at day 5. Conclusion. After LD transplantation, preservation-reperfusion injury causes massive proteinuria during the first 24 hr. Thereafter proteinuria rarely exceeds 1 g per day.
The Hedonic and Utilitarian Dimensions of Attendees' Attitudes Toward Festivals

This study examined the attendees'attitudes toward festivals by utilizing a two-dimensional consumer attitude scale, the Hedonic/Utilitarian (HED/UT) Scale, developed by Voss, Spangenberg, and Grohmann. The HED/UT Scale was originally developed to measure the hedonic and utilitarian dimensions of consumer attitudes toward product categories and different brands within categories. Findings suggested the scale has good reliability and validity and can be used successfully to measure attendees' attitudes toward festivals or other events and services. Results indicated that people attend festivals and other social events for both hedonic and utilitarian reasons. However, their hedonic attitudes have a stronger impact on attending the festival and other special events than their utilitarian attitude. Marketing and theoretical implications are discussed.