Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpreting lemma and palea homologies: a point of view from rice floral mutants

In contrast to eudicot flowers which typically exhibit sepals and petals at their periphery, the flowers of grasses are distinguished by the presence of characteristic outer organs. In place of sepals, grasses have evolved the lemma and the palea, two bract-like structures that partially or fully enclose the inner reproductive organs. With little morphological similarities to sepals, whether the lemma and palea are part of the perianth or non-floral organs has been a longstanding debate. In recent years, comparative studies of floral mutants as well as the availability of whole genome sequences in many plant species have provided strong arguments in favor of the hypothesis of lemma and palea being modified sepals. In rice, a feature of the palea is the bending of its lateral region into a hook-shaped marginal structure. This allows the palea to lock into the facing lemma region, forming a close-fitting lemma–palea enclosure. In this article, we focus on the rice lemma and palea and review some of the key transcription factors involved in their development and functional specialization. Alternative interpretations of these organs are also addressed.
The Effect of Female Quality on Male Ejaculatory Expenditure and Reproductive Success in a Praying Mantid

Strategic ejaculation is a behavioural strategy shown by many animals as a response to sperm competition and/or as a potential mechanism of cryptic male choice. Males invest more mating resources when the risk of sperm competition increases or they invest more in high quality females to maximize their reproductive output. We tested this hypothesis in the false garden mantid Pseudomantis albofimbriata, where females are capable of multiply mating and body condition is an indicator of potential reproductive fitness. We predicted male mantids would ejaculate strategically by allocating more sperm to high quality females. To determine if and how males alter their ejaculate in response to mate quality, we manipulated female food quantity so that females were either in good condition with many eggs (i.e. high quality) or poor condition with few eggs (i.e. low quality). Half of the females from each treatment were used in mating trials in which transferred sperm was counted before fertilisation occurred and the other half of females were used in mating trials where fertilisation occurred and ootheca mass and total eggs in the ootheca were recorded. Opposed to our predictions, the total number of sperm and the proportion of viable sperm transferred did not vary significantly between female treatments. Male reproductive success was entirely dependent on female quality/fecundity, rather than on the number of sperm transferred. These results suggest that female quality is not a major factor influencing postcopulatory male mating strategies in P. albofimbriata, and that sperm number has little effect on male reproductive success in a single mating scenario.
Approximate arithmetic coding for bus transition reduction in low power designs

We present a method for reducing the power consumption of compressed-code systems by selectively inverting bits that are transmitted on the bus. By incorporating bus inversion into code compression/decompression, we reduce power consumption with no cost in hardware or power relative to code compression without inversion. Inverting has to be done carefully to ensure that the codes can still be decoded. As an additional challenge, compression will generally increase bit-toggling as it removes redundancies from the code transmitted. Therefore, we need to find the right balance between compression ratio and bit-toggling reduction. This paper presents a suitable algorithm that will combine approximate compression techniques with bit-toggling reduction and will explore the various tradeoffs. We take advantage of the approximations introduced to modify codes and reduce bit-toggling, while maintaining compression performance and decoding speed. An interesting result that is derived from our work is that high compression ratios do not necessarily result in the lowest power consumption. By using our method, bus-related power consumption has been reduced by as much as 35% compared to a system with no compression, and as much as 14% compared to a compressed-code system. Bit-toggling reduction does not impose any additional hardware costs other than the decompression engine. We also present a detailed analysis on how bus widths affect bit-toggling when transmitting compressed code, and we show experimental results on ARM, MIPS, and SPARC code. We finally compare our work with Bus Invert and show results that are superior except for the random data case where Bus Invert performs better.
Controlled conversion of an immortalized mesodermal progenitor cell towards osteogenic, chondrogenic, or adipogenic pathways

The teratocarcinoma-derived C1 clone behaves as a mesodermal tripotential progenitor cell whose choice of fate, either osteoblast, chondroblast, or adipoblast, is strictly dependent on the spatial organization of the cells and the nature of the induction. In the absence of cell contact before the addition of inducers, the C1 cells maintain a stable undifferentiated phenotype while expressing potential regulators of embryonic mesodermal stem cell fate such a M-twist and Id1. Upon establishment of cell contacts before the induction of differentiation, the early genes characteristic of the three fates become expressed. In the presence of beta glycerophosphate and ascorbate, provided the cells have formed aggregates, 95% of the C1 cells mineralize with a kinetics of gene expression close to that of osteoblasts (Poliard, A., D. Lamblin, P. J. Marie, M. H. Buc, and O. Kellerman. 1993. J. Cell Sci. 106:503-512). With 10(-6)M dexamethasone, 80% of the same aggregates differentiate into foci of chondroblast-like cells. The kinetics of expression of the genes encoding type II, IX, X, and XI collagens, aggrecan and link protein during the conversion toward cartilage hypertrophy resembles that accompanying in vivo chondrogenesis. The synergistic action of dexamethasone and insulin convert most confluent C1 cells into functional adipocytes and induce a pattern of gene expression close to that reported for adipoblast cell lines. The C1 clone with its capacity to differentiate along three alternative pathways with high frequency, therefore appears as a valid in vitro model for deciphering the molecular basis of mesoblast ontogeny.
Polyomavirus enhancer contains multiple redundant sequence elements that activate both DNA replication and gene expression

Sequences that comprise the 244-base-pair polyomavirus enhancer region are also required in cis for viral DNA replication (Tyndall et al., Nucleic Acids Res. 9:6231-6250, 1981). We have studied the relationship between the sequences that activate replication and those that enhance transcription in two ways. One approach, recently described by de Villiers et al. (Nature [London], 312:242-246, 1984), in which the polyomavirus enhancer region was replaced with other viral or cellular transcriptional enhancers suggested that an enhancer function is required for polyomavirus DNA replication. The other approach, described in this paper, was to analyze a series of deletion mutants that functionally dissect the enhancer region and enabled us to localize four sequence elements in this region that are involved in the activation of replication. These elements, which have little sequence homology, are functionally redundant. Element A (nucleotides 5108 through 5130) was synthesized as a 26-mer with XhoI sticky ends, and one or more copies were introduced into a plasmid containing the origin of replication, but lacking the enhancer region. Whereas one copy of the 26-mer activated replication only to 2 to 5% of the wild-type level, two copies inserted in either orientation completely restored replication. We found that multiple copies of the 26-mer were also active as a transcriptional enhancer by measuring the beta-globin mRNA levels expressed from a plasmid that contained either the polyomavirus enhancer or one or more copies of the 26-mer inserted in a site 3' to the beta-globin gene. We observed a correlation between the number of inserted 26-mers and the level of beta-globin RNA expression.
Much more to it: The relation between facebook usage and self-esteem

The aim of this study was to examine closer the conflicting results from previous studies concerning the relationship between Facebook use and self-esteem using the Facebook Intensity Scale and Rosenberg's Self-Esteem Scale (N = 107). In line with some previous studies, our data confirmed that there is a relationship between Facebook usage and self-esteem, but the applied scales allowed a more refined assessment of it. The results showed, after controlling for demographic variables, that participants with low Facebook intensity reported on average higher self-esteem than those who did not use Facebook or those with high Facebook intensity, while those with medium Facebook intensity had significantly higher self-esteem compared to the participants with high Facebook intensity. Future studies should address the underlying causal relations using a time-bound observation method.
Formal and computational properties of the confidence boost of association rules

Some existing notions of redundancy among association rules allow for a logical-style characterization and lead to irredundant bases of absolutely minimum size. We push the intuition of redundancy further to find an intuitive notion of novelty of an association rule, with respect to other rules. Namely, an irredundant rule is so because its confidence is higher than what the rest of the rules would suggest; then, one can ask: how much higher? We propose to measure such a sort of novelty through the confidence boost of a rule. Acting as a complement to confidence and support, the confidence boost helps to obtain small and crisp sets of mined association rules and solves the well-known problem that, in certain cases, rules of negative correlation may pass the confidence bound. We analyze the properties of two versions of the notion of confidence boost, one of them a natural generalization of the other. We develop algorithms to filter rules according to their confidence boost, compare the concept to some similar notions in the literature, and describe the results of some experimentation employing the new notions on standard benchmark datasets. We describe an open source association mining tool that embodies one of our variants of confidence boost in such a way that the data mining process does not require the user to select any value for any parameter.
Aortic Root Dimension as an Independent Predictor for All‐Cause Death in Adults <65 Years of Age (from The Chin‐Shan Community Cardiovascular Cohort Study)

Background: Evidence on aortic root dimension for predicting cardiovascular morbidity and mortality is inconclusive. This cohort study sought to characterize the predictive power of aortic root dimension on cardiovascular morbidity and mortality in an ethnic Chinese population. Methods: We recruited 1,851 participants in the Chin–Shan Community Cardiovascular Cohort (CCCC) study who had received echocardiography without previous cardiovascular events. Aortic root dimension was measured by M‐mode echocardiography and indexed by body surface area to obtain aortic root dimension index (AOI). The end points were all‐cause death and incident cardiovascular events including coronary heart disease and stroke over a median follow‐up of 11.9 years. Results: Although tertiles of AOI was associated with an increased risk of cardiovascular events and all‐cause death in univariate analysis, the significance diminished after adjusting for age variable (P for trend = 0.11 for cardiovascular events; P for trend = 0.23 for all‐cause death). In subgroup analysis, we found a significant association between tertiles of AOI and risk of all‐cause death in the final multivariate Cox regression model in adults <65 years. The adjusted relative risk was 1.88 (95% CI, 1.04 to 3.40) in participants in the upper tertile of AOI compared with participants in the lower tertile (P for trend = 0.037). In adults ≥65 years, tertile of AOI was not associated with all‐cause death (P for trend = 0.14). Tertiles of AOI was not associated with cardiovascular events throughout this study. Conclusion: Our study showed a significant association between AOI and all‐cause death in adults <65 years in an ethnic Chinese population. (Echocardiography 2010;27:487‐495)
Focal palatine erosion associated with dental malocclusion in captive cheetahs

A severe palatine disorder caused by maloccluded molars was discovered in captive adult cheetahs at the San Diego Wild Animal Park. This defect has been labeled focal palatine erosion (FPE). Subsequently, a total of 59 cheetahs from several institutions have been examined to evaluate the occurrence and etiology of this disorder. Maloccluded lower molars contacting the palatal mucosa appear to be the primary source of irritation. Infection develops when decaying food and grass particles become lodged in the resulting defect. Eventually, complete palatine perforation results which can extend into the nasal passages and eventually lead to systemic disorders. Of 59 cheetahs studied, 15 displayed various stages of FPE. Examination of 26 museum skull specimens revealed four cases of palatine perforation. These four were from a group of eight animals that were zoo raised. Focal palatine erosion appears to be a result of dietary factors. All cheetahs with FPE received a commercially prepared soft diet while in captivity. The lack of normal biting, tearing, and pulling action associated with natural prey capture and consumption could result in malocclusion caused by atrophy from disuse of the masticatory apparatus. Improper occlusion could also stem from insufficient wear or unsynchronized development of the opposing dental arches. All but two cases of FPE were found in cheetahs imported from a limited area in southwest Africa in 1970, or their offspring. Since molar size and jaw structure can be inherited, there may be genetic factors involved but more data are needed to support this idea. Treatment includes changing diet, reducing the height of the offending molar, controlling infection, eliminating irritants, and in some cases, surgical reconstruction.
Association of Calcineurin with the COPI Protein Sec28 and the COPII Protein Sec13 Revealed by Quantitative Proteomics

Calcineurin is a calcium-calmodulin-dependent serine/threonine specific protein phosphatase operating in key cellular processes governing responses to extracellular cues. Calcineurin is essential for growth at high temperature and virulence of the human fungal pathogen Cryptococcus neoformans but the underlying mechanism is unknown. We performed a mass spectrometry analysis to identify proteins that associate with the calcineurin A catalytic subunit (Cna1) in C. neoformans cells grown under non-stress and high temperature stress conditions. A novel prioritization strategy for mass spectrometry data from immunoprecipitation experiments identified putative substrates and proteins potentially operating with calcineurin in common pathways. Cna1 co-purified with proteins involved in membrane trafficking including the COPI component Sec28 and the COPII component Sec13. The association of Cna1 with Sec28 and Sec13 was confirmed by co-immunoprecipitation. Cna1 exhibited a dramatic change in subcellular localization during high temperature stress from diffuse cytoplasmic to ER-associated puncta and the mother-bud neck and co-localized with Sec28 and Sec13.
Curiosity and pleasure

We discuss the hypothesis that acquisition of knowledge is a deeply rooted psychological need. But so is the desire for fast decisions and for minimizing cognitive efforts. There is a controversy between maximizing knowledge rationally for decision making or using Tversky and Kahneman heuristic mechanisms. Here we explore a basic aspect of learning, does it bring pleasure? We report experimental results showing that acquisition of knowledge is hedonically pleasing. Thus, the satisfaction of curiosity through acquiring knowledge brings pleasure and could improve decision making. Such a mechanism would confirm the hypothesis that curiosity is a fundamental and ancient motivation.
The phenotype of DFNA13/COL11A2.

Introduction. The objective was to analyse the phenotype of the disease trait in a large, American DFNA13 family with a missense mutation in COL11A21,2 and relate these findings to other disorders caused by (different) COL11A2 mutations. Methods. Audiograms of 20 mutation carriers were evaluated. We performed a cross-sectional analysis for pure-tone threshold at 0.25, 0.5, 1, 2, 4 and 8 kHz plotted against age. Audiometric configuration was evaluated according to an existing consensus protocol. Progression was evaluated with linear regression analyses of threshold. Results. The majority of cases showed mid-frequency (U-shaped) characteristics. The mean threshold in generations IV and V was 44 dB at 1–4 kHz (mid-frequencies); it was 29 dB at the other frequencies (0.25, 0.5 and 8 kHz). There was no significant progression beyond presbyacusis. Conclusion. The trait in this family can be characterized as an autosomal dominant, non-progressive, presumably prelingual, mid-frequency sensorineural hearing impairment.
Identification of 16S rRNA Methylase-Producing Acinetobacter baumannii Clinical Strains in North America

ABSTRACT Five highly amikacin-resistant Acinetobacter baumannii isolates were collected at a medical center in Pennsylvania. The aminoglycoside resistance was due to the production of the 16S rRNA methylase ArmA. Two of the isolates coproduced OXA-23 β-lactamase and were highly resistant to carbapenems as well. The isolates were genetically closely related by pulsed-field gel electrophoresis.
An Entropy Satisfying Conservative Method for the Fokker-Planck Equation of the Finitely Extensible Nonlinear Elastic Dumbbell Model

In this paper, we propose an entropy satisfying conservative method to solve the Fokker–Planck equation of the finitely extensible nonlinear elastic dumbbell model for polymers, subject to homogeneous fluids. Both semidiscrete and fully discrete schemes satisfy all three desired properties—(i) mass conservation, (ii) positivity preserving, and (iii) entropy satisfying—in the sense that these schemes satisfy discrete entropy inequalities for both the physical entropy and the quadratic entropy. These ensure that the computed solution is a probability density and the schemes are entropy stable and preserve the equilibrium solutions. We also prove convergence of the numerical solution to the equilibrium solution as time becomes large. Zero flux at boundary is naturally incorporated, and boundary behavior is resolved sharply. Both one- and two-dimensional numerical results are provided to demonstrate the good qualities of the scheme and the effects of some canonical homogeneous flows.
Implications of Edentulism on Quality of Life among Elderly

This study aimed was to test the association between quality of life and edentulism among elderly individuals in a city in southeastern Brazil. This cross-sectional study was carried out with 163 individuals aged 60 years or older, functionally independent and non-institutionalized. Data were collected with a questionnaire and oral examination. The edentulism was the dependent variable. The independent variables were sex, age, household income and quality of life (WHOQOL-Old) and their scores. To assess the association between the dependent variable and independent variables was used bivariate analysis (p < 0.10). Poisson regression model was performed, adjusting for age and sex. The average age of participants was 69 years (± 6.1), 68.7% were female and 52.8% were diagnosed as completely edentulous (90% CI: 0.33–1.24). When the independent variables were associated to the prevalence of edentulism, statistically significant associations were found for age (p = 0.03) and social participation dimension of the WHOQOL-Old (p = 0.08). In the Poisson regression, social participation remained statistically associated to edentulism {RP = 2.12 [90% CI (1.10–4.00)]}. The social participation proved to have a significant association to edentulism, thereby attesting to the negative effect of this condition on social aspects.
Quantum illumination versus coherent-state target detection

Entanglement is arguably the key quantum-mechanical resource for improving the performance of communication, precision measurement and computing systems beyond their classical-physics limits. Yet entanglement is fragile, being very susceptible to destruction by the decoherence arising from loss and noise. Surprisingly, Lloyd (2008 Science 321 1463) recently proved that a very large performance gain accrues from use of entanglement in single-photon target detection within an entanglement-destroying lossy, noisy environment when compared to what can be achieved with unentangled single-photon states. We extend Lloyd's analysis to the full multiphoton input Hilbert space. We show that the performance of Lloyd's single-photon‘quantum illumination’ system is, at best, equal to that of a coherent-state transmitter of the same average photon number, and may be substantially worse. We demonstrate that the coherent-state system derives its advantage from the coherence between a sequence of weak—single photon on average—transmissions, a possibility that was not allowed for in Lloyd's work. Nevertheless, as shown by Tan et al (2008 Phys. Rev. Lett. 101 253601), quantum illumination may offer a significant, although more modest, performance gain when operation is not limited to the single-photon regime.
A General Approach to Recovering Market Expectations from Futures Prices with an Application to Crude Oil

Futures markets are a potentially valuable source of information about market expectations. Exploiting this information has proved difficult in practice, because the presence of a timevarying risk premium often renders the futures price a poor measure of the market expectation of the price of the underlying asset. Even though the expectation in principle may be recovered by adjusting the futures price by the estimated risk premium, a common problem in applied work is that there are as many measures of market expectations as there are estimates of the risk premium. We propose a general solution to this problem that allows us to uniquely pin down the best possible estimate of the market expectation for any set of risk premium estimates. We illustrate this approach by solving the long-standing problem of how to recover the market expectation of the price of crude oil. We provide a new measure of oil price expectations that is considerably more accurate than the alternatives and more economically plausible. We discuss implications of our analysis for the estimation of economic models of energy-intensive durables, for the debate on speculation in oil markets, and for oil price forecasting.