Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetics of speciation: Insights from Fisher's geometric model

Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including “speciation genes” with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male–female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge.
Detection of human enteric viruses in oysters by in vivo and in vitro amplification of nucleic acids

This study describes the detection of enteroviruses and hepatitis A virus in 31 naturally contaminated oyster specimens by nucleic acid amplification and oligonucleotide probing. Viruses were extracted by adsorption-elution-precipitation from 50-g oyster samples harvested from an area receiving sewage effluent discharge. Ninety percent of each extract was inoculated into primate kidney cell cultures for virus isolation and infectivity assay. Viruses in the remaining 10% of oyster extract that was not inoculated into cell cultures were further purified and concentrated by a procedure involving Freon extraction, polyethylene glycol precipitation, and Pro-Cipitate precipitation. After 3 to 4 weeks of incubation, RNA was extracted from inoculated cultures that were negative for cytopathic effects (CPE). These RNA extracts and the RNA from virions purified and concentrated directly from oyster extracts were subjected to reverse transcriptase PCR (RT-PCR) with primer pairs for human enteroviruses and hepatitis A virus. The resulting amplicons were confirmed by internal oligonucleotide probe hybridization. For the portions of oyster sample extracts inoculated into cell cultures, 12 (39%) were positive for human enteroviruses by CPE and 6 (19%) were positive by RT-PCR and oligoprobing of RNA extracts from CPE-negative cell cultures. For the remaining sample portions tested by direct RT-PCR and oligoprobing after further concentration, five (about 16%) were confirmed to be positive for human enteroviruses. Hepatitis A virus was also detected in RNA extracts of two CPE-positive samples by RT-PCR and oligoprobing. Combining the data from all three methods, enteric viruses were detected in 18 of 31 (58%) samples. Detection by nucleic acid methods increased the number of positive samples by 50% over detection by CPE in cell culture. Hence, nucleic acid amplification methods increase the detection of noncytopathic human enteric viruses in oysters.
A novel decoding framework for extractive speech summarization with Rhetorical Structure modeling

We propose a novel decoding framework (Hybrid RSD-SE framework: Rhetorical Structure Decoding-Summary Extraction framework) for extracting summaries with rhetorical structure information from speech. Rhetorical structure hidden in speech data which helps us understand speech easier is always under-utilized. The hybrid RSDSE framework automatically decodes this underlying information in order to provide better-organized summaries by combining the process of rhetorical structure extraction with the process of summarization. We show that the hybrid RSD-SE framework gives a 82.24% ROUGE-L F-measure, a 3.33% absolute increase in lecture speech summarization performance compared to the baseline systems [1], [2].
Interaction of herpes simplex virus glycoprotein gC with mammalian cell surface molecules

The entry of herpes simplex virus (HSV) into mammalian cells is a multistep process beginning with an attachment step involving glycoproteins gC and gB. A second step requires the interaction of glycoprotein gD with a cell surface molecule. We explored the interaction between gC and the cell surface by using purified proteins in the absence of detergent. Truncated forms of gC and gD, gC1(457t), gC2(426t), and gD1(306t), lacking the transmembrane and carboxyl regions were expressed in the baculovirus system. We studied the ability of these proteins to bind to mammalian cells, to bind to immobilized heparin, to block HSV type 1 (HSV-1) attachment to cells, and to inhibit plaque formation by HSV-1. Each of these gC proteins bound to conformation-dependent monoclonal antibodies and to human complement component C3b, indicating that they maintained the same conformation of gC proteins expressed in mammalian cells. Biotinylated gC1(457t) and gC2(426t) each bind to several cell lines. Binding was inhibited by an excess of unlabeled gC but not by gD, indicating specificity. The attachment of gC to cells involves primarily heparan sulfate proteoglycans, since heparitinase treatment of cells reduced gC binding by 50% but had no effect on gD binding. Moreover, binding of gC to two heparan sulfate-deficient L-cell lines, gro2C and sog9, both of which are mostly resistant to HSV infection, was markedly reduced. Purified gD1 (306t), however, bound equally well to the two mutant cell lines. In contrast, saturating amounts of gC1(457t) interfered with HSV-1 attachment to cells but failed to block plaque formation, suggesting a role for gC in attachment but not penetration. A mutant form of gC lacking residues 33 to 123, gC1(delta 33-123t), expressed in the baculovirus system, bound significantly less well to cells than did gC1(457t) and competed poorly with biotinylated gC1(457t) for binding. These results suggest that residues 33 to 123 are important for gC attachment to cells. In contrast, both the mutant and wild-type forms of gC bound to immobilized heparin, indicating that binding of these proteins to the cell surface involves more than a simple interaction with heparin. To determine that the contribution of the N-terminal region of gC is important for HSV attachment, we compared several properties of a mutant HSV-1 which contains gC lacking amino acids 33 to 123 to those of its parental virus, which contains full-length gC. The mutant bound less well to cells than the parental virus but exhibited normal growth properties. (ABSTRACT TRUNCATED AT 400 WORDS)
Compensatory Eating Behaviors, Alcohol Consumption and Opioid Use in a Clinical Sample

Objectives, To estimate the prevalence of compensatory eating behaviors in relation to alcohol consumption in a clinical sample, to assess the moderating capabilities of opioid use in relation to alcohol use and compensatory behaviors, and to examine the predictive capabilities of gender-specific binge drinking in relation to compensatory behaviors. Methods, The Compensatory Eating Behaviors in Relation to Alcohol Consumption Scale (CEBRACS), an opioid use survey, and the Alcohol Use Disorders Identification Test (AUDIT) were administered to residents at an addiction treatment facility (n = 77) over a period of 6 months. Results, Morphine was the only opioid to have significant relationships with the CEBRACS alcohol effects (r = - .33), diet/exercise (r = - .38), and restrictive eating (r = - .31), subscales (all p
The Low- and Intermediate-Mass Stellar Population in the Small Magellanic Cloud: The Central Stars of Planetary Nebulae

We present a study on the central stars (CSs) of planetary nebulae (PNs) observed in the Small Magellanic Cloud (SMC) with the Space Telescope Imaging Spectrograph (STIS) instrument on board the Hubble Space Telescope (HST). The stellar magnitudes have been measured using broadband photometry, and Zanstra analysis of the nebulae provided the stellar temperatures. From the location of the CSs on the H-R diagram, and by comparing the observed CSs with current models of stellar evolution, we infer the CS masses. We examine closely the possibility of light contamination in the bandpass from an unrecognized stellar companion, and we establish strong constraints on the existence and nature of any binary companion. We find an average mass of 0.63 M☉, which is similar to the mass obtained for a sample of CSs in the LMC (0.65 M☉). However, the SMC and LMC CS mass distributions differ slightly, with the SMC sample lacking an intermediate-mass stellar population (0.65-0.75 M☉). We discuss the significance and possible reasons for the difference between the two mass distributions. In particular, we consider the differences in the star formation history between the clouds and the mass-loss rate dependence on metallicity.
Networked control of Wheeled Mobile Robots

This paper proposes a design approach to synthesis static state-feedback controller for Wheeled Mobile Robots (WMRs) controlled via a wireless communication networked. Variable delays considered in the Networked Control System (NCS) model to represent both of the data packet latency and dropout. Utilizing an appropriate Lyapunov-Krasovskii functional, an improved sufficient condition is derived to determine the controller gain in terms of Linear Matrix Inequalities (LMIs). Simulations demonstrate that the proposed method leads to remarkably less conservative results compared with the others' methods.
Caloric Restriction and Aging: Studies in Mice and Monkeys

It is widely accepted that caloric restriction (CR) without malnutrition delays the onset of aging and extends lifespan in diverse animal models including yeast, worms, flies, and laboratory rodents. The mechanism underlying this phenomenon is still unknown. We have hypothesized that a reprogramming of energy metabolism is a key event in the mechanism of CR (Anderson and Weindruch 2007). Data will be presented from studies of mice on CR, the results of which lend support to this hypothesis. Effects of long-term CR (but not short-term CR) on gene expression in white adipose tissue (WAT) are overt. In mice and monkeys, a chronic 30% reduction in energy intake yields a decrease in adiposity of approximately 70%. In mouse epididymal WAT, long-term CR causes overt shifts in the gene expression profile: CR increases the expression of genes involved in energy metabolism (Higami et al. 2004), and it down-regulates the expression of more than 50 pro-inflammatory genes (Higami et al. 2006). Whether aging retardation occurs in primates on CR is unknown. We have been investigating this issue in rhesus monkeys subjected to CR since 1989 and will discuss the current status of this project. A new finding from this project is that CR reduces the rate of age-associated muscle loss (sarcopenia) in monkeys (Colman et al. 2008).
A Multi-DOF Ultrasonic Motor Using In-plane Deformation of PZT Elements and Its Driving Circuit

Due to the increasing number of DOFs of systems and the reducing the volume and weight of the devices, multi-degrees-of-freedom (DOF) actuators have become more useful in the field of robotics. And the general features of ultrasonic motors are also suitable for constructing a direct-drive multi-DOF actuator. So, a new multi-DOF ultrasonic motor using in-plane deformation of PZT elements is introduced in this paper. Then its working principle and requirement for driving circuit are analyzed. At last, a driving circuit is proposed accordingly which generates sinusoidal actuating signals with a FPGA part (a Direct Digital Synthesizer (DDS) array is synthesized in it) and amplifies them with high voltage power operational amplifiers. It is characteristic of independent adjustment of amplitude and frequency for each output signal and independent adjustment phase between any two of output signals. The circuit meets the requirement of the motor.
MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles

Hepatitis C virus (HCV) has infected around 160 million individuals. Current therapies have limited efficacy and are fraught with side effects. To identify cellular HCV dependency factors, possible therapeutic targets, we manipulated signaling cascades with pathway-specific inhibitors. Using this approach we identified the MAPK/ERK regulated, cytosolic, calcium-dependent, group IVA phospholipase A2 (PLA2G4A) as a novel HCV dependency factor. Inhibition of PLA2G4A activity reduced core protein abundance at lipid droplets, core envelopment and secretion of particles. Moreover, released particles displayed aberrant protein composition and were 100-fold less infectious. Exogenous addition of arachidonic acid, the cleavage product of PLA2G4A-catalyzed lipolysis, but not other related poly-unsaturated fatty acids restored infectivity. Strikingly, production of infectious Dengue virus, a relative of HCV, was also dependent on PLA2G4A. These results highlight previously unrecognized parallels in the assembly pathways of these human pathogens, and define PLA2G4A-dependent lipolysis as crucial prerequisite for production of highly infectious viral progeny.
Age-Related Toxoplasma gondii Seroprevalence in Dutch Wild Boar Inconsistent with Lifelong Persistence of Antibodies

Toxoplasma gondii is an important zoonotic pathogen that is best known as a cause of abortion or abnormalities in the newborn after primary infection during pregnancy. Our aim was to determine the prevalence of T. gondii in wild boar to investigate the possible role of their meat in human infection and to get an indication of the environmental contamination with T. gondii. The presence of anti-T. gondii antibodies was determined by in-house ELISA in 509 wild boar shot in 2002/2003 and 464 wild boar shot in 2007. Most of the boar originated from the “Roerstreek” (n = 673) or the “Veluwe” (n = 241). A binormal mixture model was fitted to the log-transformed optical density values for wild boar up to 20 months old to estimate the optimal cut-off value (−0.685) and accompanying sensitivity (90.6%) and specificity (93.6%). The overall seroprevalence was estimated at 24.4% (95% CI: 21.1–27.7%). The prevalence did not show variation between sampling years or regions, indicating a stable and homogeneous infection pressure from the environment. The relation between age and seroprevalence was studied in two stages. Firstly, seroprevalence by age group was determined by fitting the binary mixture model to 200 animals per age category. The prevalence showed a steep increase until approximately 10 months of age but stabilized at approximately 35% thereafter. Secondly, we fitted the age-dependent seroprevalence data to several SIR-type models, with seropositives as infected (I) and seronegatives as either susceptible (S) or resistant (R). A model with a recovery rate (SIS) was superior to a model without a recovery rate (SI). This finding is not consistent with the traditional view of lifelong persistence of T. gondii infections. The high seroprevalence suggests that eating undercooked wild boar meat may pose a risk of infection with T. gondii.
Optical properties of humic-like substances (HULIS) in biomass-burning aerosols

We present here the optical properties of humic-like substances (HULIS) isolated from the fine fraction of biomass-burning aerosol collected in the Amazon basin during the LBA-SMOCC (Large scale Biosphere atmosphere experiment in Amazonia – SMOke aerosols, Clouds, rainfall and Climate) experiment in September 2002. From the isolated HULIS, aerosol particles were generated and their scattering and absorption coefficients measured. The size distribution and mass of the particles were also recorded. The value of the index of refraction was derived from "closure" calculations based on particle size, scattering and absorption measurements. On average, the complex index of refraction at 532 nm of HULIS collected during day and nighttime was 1.65–0.0019i and 1.69–0.0016i, respectively. In addition, the imaginary part of the complex index of refraction was calculated using the measured absorption coefficient of the bulk HULIS. The mass absorption coefficient of the HULIS at 532 nm was found to be quite low (0.031 and 0.029 m 2 g −1 for the day and night samples, respectively). However, due to the high absorption Angstrom exponent (6–7) of HULIS, the specific absorption increases substantially towards shorter wavelengths (~2–3 m 2 g −1 at 300 nm), causing a relatively high (up to 50%) contribution to the light absorption of our Amazonian aerosol at 300 nm. For the relative contribution of HULIS to light absorption in the entire solar spectrum, lower values (6.4–8.6%) are obtained, but those are still not negligible.
Live Migration of User Environments Across Wide Area Networks

A complex challenge in mobile computing is to allow the user to migrate her highly customised environment while moving to a different location and to continue work without interruption. I motivate why this is a highly desirable capability and conduct a survey of the current approaches towards this goal and explain their limitations. I then propose a new architecture to support user mobility by live migration of a user’s operating system instance over the network. Previous work includes the Collective and Internet Suspend/Resume projects that have addressed migration of a user’s environment by suspending the running state and resuming it at a later time. In contrast to previous work, this work addresses live migration of a user’s operating system instance across wide area links. Live migration is done by performing most of the migration while the operating system is still running, achieving very little downtime and preserving all network connectivity. I developed an initial proof of concept of this solution. It relies on migrating whole operating systems using the Xen virtual machine and provides a way to perform live migration of persistent storage as well as the network connections across subnets. These challenges have not been addressed previously in this scenario. In a virtual machine environment, persistent storage is provided by virtual block devices. The architecture supports decentralized virtual block device replication across wide area network links, as well as migrating network connection across subnetworks using the Host Identity Protocol. The proposed architecture is compared against existing solutions and an initial performance evaluation of the prototype implementation is presented, showing that such a solution is a promising step towards true seamless mobility of fully fledged computing environments.
Optimal distributed control for platooning via sparse coprime factorizations

We introduce a novel distributed control architecture for disturbances attenuation in heterogeneous platoons of linear and time-invariant autonomous agents that inherits the performance achievable by the leader-follower control policies. We provide a Youla-like parameterization for the class of all distributed controllers such that the sparsity constraints are imposed on the controllers' left coprime factors, outlining a new concept of structural constraints in distributed control. The proposed scheme lends itself to optimal controller design via norm based costs, it guarantees string stability and completely eliminates the accordion effect from the behavior of the platoon. The distributed controller is proven to attain global optimality for heterogeneous platoons and ℋ2 costs and can easily reconfigure such as to remain optimal during formation merging/exiting maneuvers. The scheme is amenable to a GPS time base synchronization mechanism, allowing for the exact compensation of the time delays induced by the wireless communications.
THE LINKAGE OF GENES FOR THE HUMAN INTERFERON-INDUCED ANTIVIRAL PROTEIN AND INDOPHENOL OXIDASE-B TRAITS TO CHROMOSOME G-21

13 independent mouse-human somatic cell hybrid clones derived from β-propiolactone-inactivated Sendai stimulated cell fusion of human cells with mouse cells were tested for their sensitivities to human and mouse interferon. All of them were protected by mouse interferon and only six of the clones were protected by both human and mouse interferon. Only the six that were protected by human interferon were shown to express the human dimeric form of indophenol oxidase. Complete chromosomal analysis of the clones indicated human chromosome G-21 to be the only human chromosome in common for the six clones which had both phenotypes present. Nine subclones were derived from one of the clones expressing both phenotypes. Eight of the nine subclones were shown to retain both phenotypes, whereas one subclone lost both. Chromosomal analysis of the subclones indicated the loss of chromosome G-21 from the subclone which lost both phenotypes. It is apparent from these findings that the gene(s) for indophenol oxidase (IPO-B) and the gene(s) for the antiviral protein are syntenic and that they are linked to human chromosome G-21.
A quality evaluation approach for OLAP metadata of multidimensional OLAP data

The quality of metadata in OnLine Analytical Processing(OLAP) process has remarkable influence on the stability and reliability of OLAP tools. Model-driven metadata integration approach introduces the metadata management concept based on the object oriented paradigm for modeling and querying OLAP metadata of multidimensional data. In this model, the basic concepts of the object oriented model including object, class, and relationship between objects are applied to describe objects of multidimensional data and the OLAP operations. Thus the metadata of multidimensional OLAP data is modeled as a fact and a set of elements that are organized into class hierarchy. However, the quality evaluation of OLAP metadata which describes multidimensional data is difficult because of the structural essential of the metadata. In this paper, we propose a quality evaluation approach for model-driven OLAP metadata. This approach depends on a static formalization mechanism, various reasoning procedures supported by the formalization can be used for the quality evaluation tasks.