Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis1[OPEN]

Cis-regulatory elements and regulatory networks have diverged considerably in duplicated genes. Plant genomes contain large numbers of duplicated genes that contribute to the evolution of new functions. Following duplication, genes can exhibit divergence in their coding sequence and their expression patterns. Changes in the cis-regulatory element landscape can result in changes in gene expression patterns. High-throughput methods developed recently can identify potential cis-regulatory elements on a genome-wide scale. Here, we use a recent comprehensive data set of DNase I sequencing-identified cis-regulatory binding sites (footprints) at single-base-pair resolution to compare binding sites and network connectivity in duplicated gene pairs in Arabidopsis (Arabidopsis thaliana). We found that duplicated gene pairs vary greatly in their cis-regulatory element architecture, resulting in changes in regulatory network connectivity. Whole-genome duplicates (WGDs) have approximately twice as many footprints in their promoters left by potential regulatory proteins than do tandem duplicates (TDs). The WGDs have a greater average number of footprint differences between paralogs than TDs. The footprints, in turn, result in more regulatory network connections between WGDs and other genes, forming denser, more complex regulatory networks than shown by TDs. When comparing regulatory connections between duplicates, WGDs had more pairs in which the two genes are either partially or fully diverged in their network connections, but fewer genes with no network connections than the TDs. There is evidence of younger TDs and WGDs having fewer unique connections compared with older duplicates. This study provides insights into cis-regulatory element evolution and network divergence in duplicated genes.
Tax-Transfer Policy and Labor-Market Outcomes

The Earned Income Tax Credit provides nearly $40 billion to low-income families with children. A potential unintended consequence of the credit is lower pretax wages, in which case only part of the subsidy would accrue to workers. We examine the extent to which EITC expansions lower the pretax wages of working parents. Our findings are inconclusive. The gross hourly wages of less-skilled single women are found not to vary by the number of children, as does the EITC. In addition, the wages of black single mothers track the minimum wage for nearly the entire time period.
Subjective vs. objective evaluation of ontological statements with crowdsourcing

In this paper we propose and test a methodology for evaluation of statements of a multi‐viewpoint ontology by crowdsourcing. The task for the workers was to assess each of the given statement as true statements, controversial viewpoint statement or error. Typically, in crowdsourcing experiments the workers are asked for their personal opinions on the given subject. However, in our case their ability to objectively assess others’ opinions is examined as well. We conducted two large‐scale crowdsourcing experiments with about 750 ontological statements originating from diverse single‐viewpoint ontologies. Our results show substantially higher accuracy in evaluation for the objective assessment approach compared to the experiment based on personal opinions.
A systematic review of the relationships between craving and smoking cessation.

INTRODUCTION Craving is often portrayed as a defining feature of addiction, but the role of craving in the addictive process is controversial. Particularly contentious is the extent to which drug craving predicts subsequent relapse. METHODS This review synthesizes findings from 62 smoking cessation studies published through December 2011. Eligible studies measured craving for cigarettes in treatment-seeking smokers and related this to subsequent smoking status. The relationships of general craving and cue-specific craving with treatment outcome were examined separately. Further, analyses that related general craving to smoking status were divided into those that used craving data collected before the quit attempt, after the quit attempt, and those that used change in craving over time as a predictor. RESULTS Results across studies revealed a total of 198 indices of association with 94 (47%) of these being significant. In general, the findings indicated (a) there were only a few cases of significant associations between craving collected as part of cue-reactivity studies and treatment outcome, (b) postquit craving was a stronger predictor of treatment outcome than prequit craving, and (c) several moderators likely influence the relationship between craving and cessation outcome. CONCLUSIONS The overall results suggest that craving is not a necessary condition of relapse. In addition, inconsistent relationships between craving and treatment outcome call into question the value of craving as a target of treatment and underscore limitations in the prognostic utility of craving.
Almost sure stability and transient behavior of stochastic nonlinear jump systems motivated by networked control systems

The stability of networked control systems (NCS) can be analyzed using jump systems where the jumping characterizes packet loss or delay. This motivates our investigations on nonlinear jump systems (NLJS). In many cases, the transient behavior of such a system, i.e. the convergence rate to the equilibrium, is much more interesting than the mere stability. In this paper, we extend a recent result that describes this transient behavior for NCS with packet loss to NCS with random delays. In other words, the jump system exhibits an arbitrary but finite number of discrete states instead of only two states. In addition, we considerably reduce the conservatism of the former result, which is shown theoretically and through a simple numerical example.
The Distribution of Target Ownership and the Division of Gains in Successful Takeovers

This paper presents evidence that the distribution of target ownership is related to the division of the takeover gain between the target and the bidder for a sample of successful tender offers. In the whole sample, the target's gain is negatively related to bidder and institutional ownership. In the sample of multiple-bidder contests, the target's gain increases with managerial ownership and falls with institutional ownership. Copyright 1990 by American Finance Association.
Bridges in sequential CMOS circuits: current-voltage signature

The I/sub DDQ/-V/sub DD/ signature for sequential CMOS circuits with bridging defects is characterized. In combinational circuits with a bridging defect, an increase in V/sub DD/ results in a higher I/sub DDQ/ value flowing through the defect, however, the total current may decrease as it will be shown. In sequential circuits with bridging defects connecting control loop nodes, the V/sub DD/-I/sub DDQ/ signature may present intervals of constant non defective I/sub DDQ/ value. The signature may be used to diagnose certain types of bridging defects in sequential CMOS circuits.
Do the Best Hedge Funds Hedge?

We provide a simple argument that suggests that better-informed hedge funds choose to have less exposure to factor risk. Consistent with this argument, we find that hedge funds that exhibit lower R-squareds with respect to systematic factors have higher Sharpe ratios, higher information ratios, and higher alphas. They also exhibit higher manipulation-proof performance measures and charge higher fees. The Author 2010. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org. , Oxford University Press.
Measuring the degree of oligopsony power in the beef packing industry in the absence of marketing input quantity data

We develop a model to measure the degree of oligopsony power in the beef packing industry, while accommodating variable proportions technology, that can be estimated with fewer data requirements. In particular, nonspecialized input quantities, which are often not available, are not needed. Through application of the envelope theorem, we show that the relationship between value marginal product and marginal factor cost can be defined over the prices of the nonspecialized inputs rather than their corresponding quantities. When applied to the beef packing industry, we find no evidence of oligopsony power over our 1967-93 sample period.
Comparative Analysis of Ownership Transformation and Performance Relationship Among Major and Regional Banks in Australia

This article attempts to clarify existing doubts with respect to the performance of private and privatised banks versus public banks; that is, it is an attempt to clarify the ownership-performance relationship. The analysis takes explicit account of the privatisation transformation, including its intermediary stage, and the status of the economy. The ownership-performance model is estimated using cross-sectional time-series data and is used to test the influence of ownership changes on performance. Alternative performance measures are considered. The empirical findings show that ownership transformation in the case of regional banks has resulted in improved performance, whilst the benefits in the case of major banks were not significant, even though these banks have become more competitive.
Multipurpose vectors designed for the fast generation of N‐ or C‐terminal epitope‐tagged proteins

In this paper are described a set of new high‐copy‐number yeast vectors, which are specially designed for the conditional expression of epitope‐tagged proteins in vivo. One of the major advantages of these plasmids is that they allow polymerase chain reaction‐amplified open reading frames to be automatically fused in frame with the epitope‐coding sequence, avoiding longer procedures such as site‐directed mutagenesis. This heterologous construction can be realized either at the 5′‐end of the coding sequence, in the pYeF1 vector, or at its 3′‐end, in pYeF2, generating N‐ or C‐terminal tagged proteins, respectively. Moreover, to increase the usefulness of the method, derivatives of the two basic URA3‐borne pYeF1 and pYeF2 were constructed, carrying either the HIS3 or TRP1 gene as a marker of selection. These vectors could be of use for the purpose of functional analysis of the newly discovered genes resulting from the systematic sequencing of the yeast genome. Here, we present results showing the functional expression and the efficient immunoprecipitation of the epitope‐tagged Rna15 protein, which is involved in Saccharomyces cerevisiae mRNA stability.
A Golgi study of the class V cell in the visual thalamus of the cat

Golgi methods were used to study class V cells within the cat visual thalamus. Counterstaining was combined with Golgi staining to assess the distribution of dendrites relative to cytoarchitectural boundaries. Class V cells were encountered within all laminae of the lateral geniculate nucleus, the medial interlaminar nucleus, and the lateral posterior complex. The cells possess medium‐sized perikarya and smooth and varicose or moniliform dendrites. Dendritic appendages are sparse and occur as single or serial swellings on thin processes. Many class V cells exhibit large, sparse dendritic arbors which span laminar or nuclear borders; dendrites were seen to lie within and to cross the interlaminar zones of the lateral geniculate nucleus, and extend beyond this nucleus into the perigeniculate nucleus and medial interlaminar nucleus. Class V cells of the lateral posterior complex send dendrites into the external medullary lamina. Indirect evidence favors the interpretation that the class V cells are thalamo‐cortical relay cells.
The management of multiple sclerosis: current and future therapies.

Management of the patient with multiple sclerosis (MS) encompasses a number of distinct, if overlapping, areas. They include anticipation and prevention of problems, symptom control, drug therapies aimed at reducing disease activity and finally, rehabilitation and service delivery. The recent advent of new immunosuppressant treatments for MS is extremely exciting. Beta-interferons (1a and 1b) are now licensed worldwide and glatiramer acetate (Copaxane) is in use in the United States. Many more drugs, including intravenous immunoglobulin, mitoxantrone, methotrexate and cladribine, are undergoing trials and some are showing promising results. Future therapies with monoclonal antibodies and adhesion molecules are also undergoing extensive research. Realistically, however, these new treatments aimed at reducing disease activity will have little impact on existing problems or the degree of disability. Consequently, much of the management of a patient with MS relates to control of the vast array of symptoms. These range from the obvious problems of weakness and spasticity, ataxia and sphincter disturbance, to less common but still important problems such as visual, cognitive, swallowing and respiratory difficulties. Some of the most common, and to the patient most disabling, symptoms are fatigue, thermal sensitivity and pain, areas often neglected by the physician in the face of more obvious physical needs. Much can be done for the patient in all areas. A combination of education, physiotherapy and drug therapy is usually required but occasionally there is a place for more invasive treatments such as intrathecal baclofen administration for severe spasticity or thalamic surgery for cerebellar tremor. A multidisciplinary team approach is essential in the overall management of the patient with MS, particularly when assessing their needs as a basis for both inpatient rehabilitation programs and in the provision of a comprehensive community-based service.
A Prospect Dynamic Model of Decision-Making

In their 1979 article, Kahneman and Tversky introduced the world to the prospect theory of decision-making under risk as a critique of expected utility theory and its emphasis on final assets. Critics have noted that despite successful replications, its application outside the experimental arena is questionable. This article answers these critics by developing a formal model and theory of framing within prospect theory. Starting with an expected utility model, elements of risk, change and risk attitude are introduced in the context of the decision-maker’s belief sets and assumptions. The result is a finding that framing works because individual expectations shift when confidence in assumptions about the problem change. In conclusion, a number of analytic tools are applied to explore the dynamics of the model and the effect of changing a decision-maker’s view of the world and perception of a specific problem.
Conversion of Green Fluorescent Protein into a Toxic, Aggregation-prone Protein by C-terminal Addition of a Short Peptide*

A non-natural 16-residue “degron” peptide has been reported to convey proteasome-dependent degradation when fused to proteins expressed in yeast (Gilon, T., Chomsky, O., and Kulka, R. (2000) Mol. Cell. Biol. 20, 7214-7219) or when fused to green fluorescent protein (GFP) and expressed in mammalian cells (Bence, N. F., Sampat, R. M., and Kopito, R. R. (2001) Science 292, 1552-1555). We find that expression of the GFP::degron in Caenorhabditis elegans muscle or neurons results in the formation of stable perinuclear deposits. Similar perinuclear deposition of GFP::degron was also observed upon transfection of primary rat hippocampal neurons or mouse Neuro2A cells. The generality of this observation was supported by transfection of HEK 293 cells with both GFP::degron and DsRed(monomer)::degron constructs. GFP::degron expressed in C. elegans is less soluble than unmodified GFP and induces the small chaperone protein HSP-16, which co-localizes and co-immunoprecipitates with GFP::degron deposits. Induction of GFP::degron in C. elegans muscle leads to rapid paralysis, demonstrating the in vivo toxicity of this aggregating variant. This paralysis is suppressed by co-expression of HSP-16, which dramatically alters the subcellular distribution of GFP::degron. Our results suggest that in C. elegans, and perhaps in mammalian cells, the degron peptide is not a specific proteasome-targeting signal but acts instead by altering GFP secondary or tertiary structure, resulting in an aggregation-prone form recognized by the chaperone system. This altered form of GFP can form toxic aggregates if its expression level exceeds the capacity of chaperone-based degradation pathways. GFP::degron may serve as an instructive “generic” aggregating control protein for studies of disease-associated aggregating proteins, such as huntingtin, α-synuclein, and the β-amyloid peptide.
Use of cir-lac operon fusions to study transcriptional regulation of the colicin Ia receptor in Escherichia coli K-12

We describe cir-lac operon fusions constructed by using phage Mu d(Apr lac). Expression of beta-galactosidase in these fusion strains is analogous to known regulatory properties of cir gene expression. It is concluded that the observed regulation by iron of the cir gene is under transcriptional control.
Flexible estimation of transport demand functions: recommendations for public policy makers

In some situations, economic theory provides directions for constructing an econometric model, while in others (generalized) linear modeling is used only for convenience. The latter is especially true for modeling transport demand functions as economic theory is often limited to predicting whether a covariate is expected to have a positive or a negative impact. However, functional misspecification can have serious consequences for estimation, prediction, and further inferences. The authors introduce a semiparametric model and a corresponding estimation procedure that is easy to interpret and implement. Using an empirical study of university students’ transport choices in the Bilbao area, we illustrate how this procedure can help to significantly improve statistical analysis. More specifically, our procedure allows the utility that individuals get from the mode of transport to be modeled and estimated in a flexible way, thus essentially mitigating the danger of misspecification errors.
Fluorescence Polarization Immunoassay: Can It Result in an Overestimation of Vancomycin in Patients Not Suffering From Renal Failure?

It has been reported in scientific data that fluorescence polarization immunoassay (FPIA) results in overestimation of vancomycin in patients with renal failure. This overestimation is caused by interference of the degradation product, CDP-1, in this assay. Increases in vancomycin levels have also been reported in patients not suffering from renal failure (nonrenal failure patients) who are receiving vancomycin therapy for approximately 10 days or more. The authors tested whether this increase in vancomycin in nonrenal failure patients is a result of CDP-1 interfering with FPIA or a change in the pharmacokinetics of the drug. Serum vancomycin peak and trough samples were obtained from 10 adult (mean age ± SD: 55.9 years ± 17.5) nonrenal failure patients (mean ClCr ± SD: 76.2 mL/min ± 29.20) receiving vancomycin therapy for at least 10 days. These peaks and troughs were obtained at steady state and again at approximately 10 days of therapy. All serum samples were analyzed initially by fluorescence polarization immunoassay (FPIA, TDx®) (Abbot Diagnostics; Irving, TX) and again by enzyme multiplied immunoassay (EMIT Vancomycin Assay) (Dade Behring; San Jose, CA). Statistical analysis (Wilcoxon signed-rank test) determined that there was no difference between the values obtained from the two assays. This demonstrates that the increase in vancomycin levels is not caused by the accumulation of CDP-1 and may be the result of a change in the pharmacokinetics of the drug.
Examining Consumers' Attitudes toward Personal Injury Litigation

This study examines attitudes toward personal injury litigation and whether plaintiff’s attorney advertising, income, gender and desire for vengeance play a significant role in attitude formation. The study measured adults aged 18+, the same population targeted by this form of advertising. The results demonstrate a statistically significant relationship between this form of television advertising and positive attitudes about the act of filing a personal injury lawsuit. The results further detail the contribution of vengeance, advertising, and income on attitudes toward personal injury litigation. Previous studies have separately examined legal services advertising and vengeance; however, none has examined how a desire for vengeance factors into the manner in which consumers receive and/or react to plaintiff’s attorney advertising. These findings add to the literature related to legal services advertising and help expand the understanding of consumers’ desire for vengeance and how marketing communication strategies may or may not affect their resulting behavior.
Differential spreading of HinfI satellite DNA variants during radiation in Centaureinae.

BACKGROUND AND AIMS Subtribe Centaureinae appears to be an excellent model group in which to analyse satellite DNA and assess the influence that the biology and/or the evolution of different lineages have had on the evolution of this class of repetitive DNA. Phylogenetic analyses of Centaureinae support two main phases of radiation, leading to two major groups of genera of different ages. Furthermore, different modes of evolution are observed in different lineages, reflected by morphology and DNA sequences. METHODS The sequences of 502 repeat units of the HinfI satellite DNA family from 38 species belonging to ten genera of Centaureinae were isolated and compared. A phylogenetic reconstruction was carried out by maximum likelihood and Bayesian inference. KEY RESULTS Up to eight different HinfI subfamilies were found, based on the presence of a set of diagnostic positions given by a specific mutation shared by all the sequences of one group. Subfamilies V-VIII were mostly found in older genera (first phase of radiation in the subtribe, late Oligocene-Miocene), although some copies of these types of repeats were also found in some species of the derived genera. Subfamilies I-IV spread mostly in species of the derived clade (second phase of radiation, Pliocene to Pleistocene), although repeats of these subfamilies exist in older species. Phylogenetic trees did not group the repeats by taxonomic affinity, but sequences were grouped by subfamily provenance. Concerted evolution was observed in HinfI subfamilies spread in older genera, whereas no genetic differentiation was found between species, and several subfamilies even coexist within the same species, in recently radiated groups or in groups with a history of recurrent hybridization of lineages. CONCLUSIONS The results suggest that the eight HinfI subfamilies were present in the common ancestor of Centaureinae and that each spread differentially in different genera during the two main phases of radiation following the library model of satellite DNA evolution. Additionally, differential speciation pathways gave rise to differential patterns of sequence evolution in different lineages. Thus, the evolutionary history of each group of Centaureinae is reflected in HinfI satellite DNA evolution. The data reinforce the value of satellite DNA sequences as markers of evolutionary processes.
Public Opinion and Democratic Legitimacy

This paper examines on a global scale how important it is for young democracies to deliver economic welfare to win the hearts of their citizens. A decoupling of popular support for democratic form of government from economic performance is believed to be conducive to the consolidation of young democracies. We found an encouraging global pattern that clearly shows evaluations of economic condition are relatively unimportant in explaining level of popular support for democracy. However, high-income East Asian countries register a glaring exception to this global generalization, suggesting that their distinctive trajectory of regime transition has imposed on democratic regimes an additional burden of sustaining a record of miraculous economic growth of the past.