Miracle-dz/UniFAR-FTUs huggingface dataset:
A High Variability of Mixed Infections and Recent Recombinations of Hepatitis B Virus in Laos

In Lao PDR, where more than 8% of the population are chronic carriers of HBsAg, multiple genotypes and subgenotypes co-circulate and are prone to generate recombinant viruses. Phylogenetic analyses of multiple clones per donor revealed mixed infections of subgenotypes B1, B2, B4, C1, C5, I1 and I2 in almost 6% of HBsAg positive rejected blood donors. Recombination analyses and distance calculations furthermore showed that about 65% (17/26) of the mixed infected donors showed recombinations in the S-gene alone, involving the predominant genotypes B and C. These results suggest that, at least in Laos, hepatitis B virus (HBV) mixed infections lead to frequent recombinations. In many donors with recombinant strains, the recombinant fragment and a non-recombinant strain of the same genotype co-existed (127/185 analysed recombinant fragments). For a large proportion of these (60/127), the most closely related known virus was found, although not always exclusively, in the same donor. Recombinant virus strains are largely distinct. This is reflected in an unexpected diversity in recombination breakpoints and the relatively rare recombinations with identical recombination patterns of the same genotypes in different donors. Recent recombination events would explain the limited spread of each of the recombinants. Using a published mutation rate of 4.2×10−5 mutations per site and year, the observed minimum genetic distances of 0–0.60% between parent strain and recombinant fragment would correspond to 0–71 years of evolution from a most recent common ancestor (MRCA). Thus several lines of evidence are suggestive of recent independent recombination events, a proportion of these even occurring within the same donors. In conclusion, our analyses revealed a high variability of mixed infections as a very probable breeding ground of multiple variable recombination events in Laos that so far have not led to new dominant strains.
Video-based intervention and assessing imitation 1 Video-based intervention for children with autism : Towards improved assessment of prerequisite imitation skills

Objective: To explore the relationship between responses to imitation assessment and video-based intervention (VBI) in children with autism. Methods: Interviewand observation-based imitation assessments were conducted for five boys with autism prior to VBI across three studies. In two of the three studies, the boys’ imitative responses to videos with an animated model and a human model were also compared. Results: Participants who were assessed to have strong imitation skills were also those who responded more positively to VBI. No clear differences were reported in the boys’ responses to the equivalent videos with the animated model and the human model. Conclusion: The level of imitation skills required for successful VBI is relative to the target behaviour. Revision of existing imitation assessment measures, as well as development and validation of more comprehensive measures is warranted for use in conjunction with VBI.
Image denoising via sparse representations over Sequential Generalization of K-means (SGK)

We have recently proposed a Sequential Generalization of K-means (SGK) to train dictionary for sparse representation. SGK's training performance is as effective as the standard dictionary training algorithm K-SVD, alongside it has a simpler implementation to its advantage. In this piece of work, through the problem of image denoising, we are making a fair comparison between the usability of SGK and K-SVD. The obtained results suggest that we can successfully replace K-SVD with SGK, due to its quicker execution and comparable outcomes. Similarly, it is possible to extend the use of SGK to other applications of sparse representation.
Power and Ownership Structures among German Companies. A Network Analysis of Financial Linkages

The literature on ownership structures has made continual use of notions such as cross-holdings and pyramids which are closely related to the vastly increasing network literature. We propose to transfer successfully applied network methods such as network graphs, the MAN-classification scheme, and centrality concepts to the corporate control and corporate governance branch as well. Given these concepts and a unique data set containing 2784 companies we can identify the most powerful German companies and their characteristics.
Aea and " People and Money " Conferences for Helpful Comments

Compensation, status, and press coverage of managers in the U.S. follow a highly skewed distribution: a small number of ‘superstars’ enjoy the bulk of the rewards. We evaluate the impact of CEOs achieving superstar status on the performance of their firms, using prestigious business awards to measure shocks to CEO status. We find that award-winning CEOs subsequently underperform, both relative to their prior performance and relative to a matched sample of non-winning CEOs. At the same time, they extract more compensation following the award, both in absolute amounts and relative to other top executives in their firms. They also spend more time on public and private activities outside their companies, such as assuming board seats or writing books. The incidence of earnings management increases after winning awards. The effects are strongest in firms with weak governance, even though the frequency of obtaining superstar status is independent of corporate governance. Our results suggest that the ex-post consequences of media-induced superstar status for shareholders are negative. ∗We would like to thank Stefano DellaVigna and Joshua Pollet for providing portions of the data. We would also like to thank Stefano DellaVigna, Mark Grinblatt, Dirk Hackbarth, Guido Imbens, Alan Krueger, David Laibson, Justin McCrary, Terry Odean, Jesse Rothstein, Andrei Shleifer, Betsey Stevenson, Justin Wolfers, David Yermack, Luigi Zingales, and participants in seminars at Berkeley, Drexel, Duke, LBS, LSE, Mannheim, Princeton, Stanford, UCLA, Wharton, Washington University, the 2004 Stanford Media, NBER Personnel Economics, and SITE Psychology & Economics and the 2005 NBER Summer Institute in Corporate Finance, AEA and “People and Money” conferences for helpful comments. Nicole Hammer, Jared Katseff, Camelia Kuhnen, and Catherine Leung provided excellent research assistance. We acknowledge financial support from the Russell Sage Foundation.
Options Pricing and Hedging in a Regime-Switching Volatility Model

Both deterministic and stochastic volatility models have been used to price and hedge options. Observation of real market data suggests that volatility, while stochastic, is well modelled as alternating between two states. Under this two-state regime-switching framework, we derive coupled pricing partial differential equations (PDEs) with the inclusion of a state-dependent market price of volatility risk (MPVR) term. Since there is no closed-form solution for this pricing problem, we apply and compare two approaches to solving the coupled PDEs, assuming constant Poisson intensities. First we solve the problem using numerical solution techniques, through the application of the CrankNicolson numerical scheme. We also obtain approximate solutions in terms of known BlackScholes formulae by reformulating our problem and applying the Cauchy-Kowalevski PDE theorem. Both our pricing equations and our approximate solutions give way to the analysis of the impact of our state-dependent MPVR on theoretical option prices. Using financially intuitive constraints on our option prices and Deltas, we prove the necessity of a negative MPVR. An exploration of the regime-switching option prices and their implied volatilities is given, as well as numerical results and intuition supporting our mathematical proofs. Given our regime-switching framework, there are several different hedging strategies to investigate. We consider using an option to hedge against a potential regime shift. Some practical problems arise with this approach, which lead us to set up portfolios containing a basket of two hedging options. To be more precise, we consider the effects of an option going too far inand out-of-the-money on our hedging strategy, and introduce limits on the magnitude of such hedging option positions. A complementary approach, where constant volatility is assumed and investor’s risk preferences are taken into account, is also analysed. Analysis of empirical data supports the hypothesis that volatility levels are affected by upcoming financial events. Finally, we present an extension of our regime-switching framework with deterministic Poisson intensities. In particular, we investigate the impact of time and stock varying Poisson intensities on option prices and their corresponding implied volatilities, using numerical solution techniques. A discussion of some event-driven hedging strategies is given.
Crystalline polymorphism induced by charge regulation in ionic membranes

Significance The crystallization of molecules with polar and hydrophobic groups, such as ionic amphiphiles and proteins, is of paramount importance in biology and biotechnology. This combined X-ray scattering and theoretical study demonstrates how crystalline order within membranes formed by coassembled cationic and anionic amphiphiles can be controlled by varying pH and molecular tail length. Our work suggests design of bilayer membranes with specific crystalline arrangements at ambient temperature and physiologically relevant pH environments with suitable choice of headgroup and tail. Changes in crystallinity are likely to affect molecular diffusion rates across membranes and may enable control over the encapsulation and release of molecules within the membrane. Moreover, pH-induced crystalline transformations are likely used by organisms to control metabolic flow in harsh environments. The crystallization of molecules with polar and hydrophobic groups, such as ionic amphiphiles and proteins, is of paramount importance in biology and biotechnology. By coassembling dilysine (+2) and carboxylate (–1) amphiphiles of various tail lengths into bilayer membranes at different pH values, we show that the 2D crystallization process in amphiphile membranes can be controlled by modifying the competition of long-range and short-range interactions among the polar and the hydrophobic groups. The pH and the hydrophobic tail length modify the intermolecular packing and the symmetry of their crystalline phase. For hydrophobic tail lengths of 14 carbons (C14), we observe the coassembly into crystalline bilayers with hexagonal molecular ordering via in situ small- and wide-angle X-ray scattering. As the tail length increases, the hexagonal lattice spacing decreases due to an increase in van der Waals interactions, as demonstrated by atomistic molecular dynamics simulations. For C16 and C18 we observe a reentrant crystalline phase transition sequence, hexagonal–rectangular-C–rectangular-P–rectangular-C–hexagonal, as the solution pH is increased from 3 to 10.5. The stability of the rectangular phases, which maximize tail packing, increases with increasing tail length. As a result, for very long tails (C22), the possibility of observing packing symmetries other than rectangular-C phases diminishes. Our work demonstrates that it is possible to systematically exchange chemical and mechanical energy by changing the solution pH value within a range of physiological conditions at room temperature in bilayers of molecules with ionizable groups.
Pattern-based automatic taxonomy learning from the Web

The construction of taxonomies is considered as the first step for structuring domain knowledge. Many methodologies have been developed in the past for building taxonomies from classical information repositories such as dictionaries, databases or domain text. However, in the last years, scientists have started to consider the Web as valuable repository of knowledge. In this paper we present a novel approach, especially adapted to the Web environment, for composing taxonomies in an automatic and unsupervised way. It uses a combination of different types of linguistic patterns for hyponymy extraction and carefully designed statistical measures to infer information relevance. The learning performance of the different linguistic patterns and statistical scores considered is carefully studied and evaluated in order to design a method that maximizes the quality of the results. Our proposal is also evaluated for several well distinguished domains, offering, in all cases, reliable taxonomies considering precision and recall.
Integrative and Comparative Biology Society for Integrative and Comparative Biology Integrative and Comparative Biology Advance Access Published

The study of behavior has an interesting history, born of conflict between continents and perspectives and generating separate lineages. Even today these lineages ignore one another, yet occasionally intellectually ''raid'' the other for ideas that, while popular, yield dubious hybrids. The well-known foray of psychologists into evolutionary biology for explanations of human behavior has yielded a curious product of doubtful legitimacy. Another offensive is at hand. Over the past decade there has emerged like a virus within behavioral ecology the cooption of the term ''personality'' as a new field of study in animal behavior. ''Personality'', a term traditionally reserved for humans to denote individuality and/or the experiences that lead to the development of a person has, until now not been applied to nonhuman animals. In the increasing anthropomorphic spirit evident among younger behavioral biologists (Kennedy 1992), ''animal personality'' has become defined as the phenotypic characteristics peculiar to individual animals. A prime example of selective scholarship to bolster a spurious scientific agenda is evident when the editors state that individual ''differences were rarely viewed as an extension of biological meaningful variation'' (p. 2). Surely the contributors to this volume know that the idea of individual variation as the basis of evolution existed before Charles Darwin! If the intent of this volume is to promote credibility in order to secure funds to pursue research, then the editors and most of the authors should be honest and straightforward. Nothing attracts curiosity of the uneducated, and disdain by scholars, as such pandering. Although most of the articles in this volume are by behavioral ecologists, Gosling and Mehta, both psychologists by training, briefly touch on the historical issue before summarily dismissing it. They argue that ''individual differences in adult animal behavior are a function of both biological tendencies and experience,'' with which I agree. To follow this reasoning by stating that since such elements also apply to humans, therefore human terminology can apply to animals, is illogical. Without going into too much historical detail, as it would be invidious and take from the authors' contributions , it is sufficient to forewarn the purveyors of this ''new'' field to heed the lessons of some of the early psychologists. First and foremost, from C. Lloyd Morgan (1903), the preeminent British psychologist , there is Morgan's Canon ''In no case is an animal activity to be interpreted in terms of higher psychological processes if it can be fairly …
The clinical characteristics and hospital and post‐hospital survival of patients with the obesity hypoventilation syndrome: analysis of a large cohort

The worldwide prevalence of obesity has reached epidemic proportions. Obesity hypoventilation syndrome (OHS) is a common yet largely undiagnosed and mistreated condition that likely carries a high mortality. The aim of this study was to determine the clinical characteristics, hospital outcome, outcome following hospital discharge and predictors of death in a large cohort of patients hospitalized with OHS. OHS is an important condition as many patients with this syndrome are misdiagnosed and receive inappropriate treatment.
Maximizing the spectral and energy efficiency of ARQ with a fixed outage probability

This paper studies the spectral and energy efficiency of automatic repeat request (ARQ) in Nakagami-m block-fading channels. The source encodes each packet into L similar sequences and transmits them to the destination in the L subsequent time slots. The destination combines the L sequences using maximal ratio combining and tries to decode the information. In case of decoding failure, the destination feeds back a negative acknowledgment and then the source sends the same L sequences to the destination. This process continues until successful decoding occurs at the destination with no limit on the number of retransmissions. We consider two optimization problems. In the first problem, we maximize the spectral efficiency of the system with respect to the rate for a fixed power. In the second problem, we maximize the energy efficiency with respect to the transmitted power for a fixed rate.
Automatic disambiguation of English puns

Traditional approaches to word sense disambiguation (WSD) rest on the assumption that there exists a single, unambiguous communicative intention underlying every word in a document. However, writers sometimes intend for a word to be interpreted as simultaneously carrying multiple distinct meanings. This deliberate use of lexical ambiguity---i.e., punning---is a particularly common source of humour. In this paper we describe how traditional, language-agnostic WSD approaches can be adapted to "disambiguate" puns, or rather to identify their double meanings. We evaluate several such approaches on a manually sense-annotated corpus of English puns and observe performance exceeding that of some knowledge-based and supervised baselines.
Double overexpression of DREB and PIF transcription factors improves drought stress tolerance and cell elongation in transgenic plants

Summary Although a variety of transgenic plants that are tolerant to drought stress have been generated, many of these plants show growth retardation. To improve drought tolerance and plant growth, we applied a gene‐stacking approach using two transcription factor genes: DEHYDRATION‐RESPONSIVE ELEMENT‐BINDING 1A (DREB1A) and rice PHYTOCHROME‐INTERACTING FACTOR‐LIKE 1 (OsPIL1). The overexpression of DREB1A has been reported to improve drought stress tolerance in various crops, although it also causes a severe dwarf phenotype. OsPIL1 is a rice homologue of Arabidopsis PHYTOCHROME‐INTERACTING FACTOR 4 (PIF4), and it enhances cell elongation by activating cell wall‐related gene expression. We found that the OsPIL1 protein was more stable than PIF4 under light conditions in Arabidopsis protoplasts. Transactivation analyses revealed that DREB1A and OsPIL1 did not negatively affect each other's transcriptional activities. The transgenic plants overexpressing both OsPIL1 and DREB1A showed the improved drought stress tolerance similar to that of DREB1A overexpressors. Furthermore, double overexpressors showed the enhanced hypocotyl elongation and floral induction compared with the DREB1A overexpressors. Metabolome analyses indicated that compatible solutes, such as sugars and amino acids, accumulated in the double overexpressors, which was similar to the observations of the DREB1A overexpressors. Transcriptome analyses showed an increased expression of abiotic stress‐inducible DREB1A downstream genes and cell elongation‐related OsPIL1 downstream genes in the double overexpressors, which suggests that these two transcription factors function independently in the transgenic plants despite the trade‐offs required to balance plant growth and stress tolerance. Our study provides a basis for plant genetic engineering designed to overcome growth retardation in drought‐tolerant transgenic plants.
Noise-source turbulence statistics and the noise from a Mach 0.9 jet

Turbulence statistics that are relevant to jet noise modeling but difficult to measure in experiments are computed using a previously validated simulation database of a Mach 0.9 cold jet. Initial focus is on fourth-order statistics that are at the core of acoustic analogy based models built on both the Lilley and Lighthill equations. Common simplifications of fourth-order correlations based on normal statistics are found to be accurate. We see that although two-point correlations are well fitted by exponential functions, as is typical of turbulence at all but the lowest Reynolds numbers, the spatially integrated fourth-order space/retarded-time covariances, which are used in the models, are instead very well fitted by Gaussian functions of different widths for different components, which is counter to conventional modeling practice. We also examine the components of Lighthill’s analogous noise source that are linear and quadratic in velocity fluctuations, as well as components that are deviations from p′=.
Statistics of Natural Binaural Sounds

Binaural sound localization is usually considered a discrimination task, where interaural phase (IPD) and level (ILD) disparities at narrowly tuned frequency channels are utilized to identify a position of a sound source. In natural conditions however, binaural circuits are exposed to a stimulation by sound waves originating from multiple, often moving and overlapping sources. Therefore statistics of binaural cues depend on acoustic properties and the spatial configuration of the environment. Distribution of cues encountered naturally and their dependence on physical properties of an auditory scene have not been studied before. In the present work we analyzed statistics of naturally encountered binaural sounds. We performed binaural recordings of three auditory scenes with varying spatial configuration and analyzed empirical cue distributions from each scene. We have found that certain properties such as the spread of IPD distributions as well as an overall shape of ILD distributions do not vary strongly between different auditory scenes. Moreover, we found that ILD distributions vary much weaker across frequency channels and IPDs often attain much higher values, than can be predicted from head filtering properties. In order to understand the complexity of the binaural hearing task in the natural environment, sound waveforms were analyzed by performing Independent Component Analysis (ICA). Properties of learned basis functions indicate that in natural conditions soundwaves in each ear are predominantly generated by independent sources. This implies that the real-world sound localization must rely on mechanisms more complex than a mere cue extraction.
Genetic Algorithm Approach in Prediction of Mass Transfer and Axial Dispersion Coefficients of Rotating Disc Liquid-Liquid Extraction Contactors

The liquid-liquid extraction process is well-known for its complexity and often entails intensive modeling and computational efforts to simulate its dynamic behavior. This paper presents a new application of Genetic Algorithm to predict the modeling parameters of a chemical pilot plant: a rotating disc liquid-liquid extraction contactor. In this process the droplet behavior of the dispersed phase has a strong influence on the mass transfer performance of the column. Mass transfer mechanism inside the drops of the dispersed phase was modeled by Handlos and Baron circulating drop model with considering the effect of forward mixing. Using the Genetic Algorithm method and the NAG software (Numerical Analysis Group) the mass transfer and axial dispersion coefficients in the continuous phase in these columns were optimized. In order to achieve RDC column parameters a least-square function of differences between the simulated and experimental concentration profiles (SSD) and %95 confidence limit in plug flow number of transfer unit prediction were considered. Minus %95 confidence limit and sum of square deviations for the GA method justified it as a successful method for optimization of mass transfer and axial dispersion coefficients of Liquid-liquid extraction columns.