Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Patterns Maintained in Early Caenorhabditis elegans Embryos Can Be Established by Gene Activity in the Parental Germ Cells

Epigenetic information, such as parental imprints, can be transmitted with genetic information from parent to offspring through the germ line. Recent reports show that histone modifications can be transmitted through sperm as a component of this information transfer. How the information that is transferred is established in the parent and maintained in the offspring is poorly understood. We previously described a form of imprinted X inactivation in Caenorhabditis elegans where dimethylation on histone 3 at lysine 4 (H3K4me2), a mark of active chromatin, is excluded from the paternal X chromosome (Xp) during spermatogenesis and persists through early cell divisions in the embryo. Based on the observation that the Xp (unlike the maternal X or any autosome) is largely transcriptionally inactive in the paternal germ line, we hypothesized that transcriptional activity in the parent germ line may influence epigenetic information inherited by and maintained in the embryo. We report that chromatin modifications and histone variant patterns assembled in the germ line can be retained in mature gametes. Furthermore, despite extensive chromatin remodeling events at fertilization, the modification patterns arriving with the gametes are largely retained in the early embryo. Using transgenes, we observe that expression in the parental germline correlates with differential chromatin assembly that is replicated and maintained in the early embryo. Expression in the adult germ cells also correlates with more robust expression in the somatic lineages of the offspring. These results suggest that differential expression in the parental germ lines may provide a potential mechanism for the establishment of parent-of-origin epigenomic content. This content can be maintained and may heritably affect gene expression in the offspring.
Writing with Collaborative Hypertext: Analysis and Modeling

This work explores a novel approach to the analysis and modeling of computer supported collaborative writing. The aim of this dynamic modeling approach is to capture the structure of user behavior as they interact with a computer system. Markov chains models are derived from the empirical data on the use of the system. These models are compared so as to highlight how the dynamic structure of collaborative writing is affected by factors such as the level of users' experience with the system and workspaces for different writing projects. A workspace is associated with a collaborative writing project in terms of both its structure and content. The study shows that the patterns of interactive behaviors of the users were clearly influenced by the system design. Users' experience and workspaces both significantly affected the structure of interactive behaviors in collaborative writing. Users intensively used the system for exploration, organization, and composition tasks in collaborative writing, whereas the use of collaboration facilities of the system was transient in nature. The descriptive‐prescriptive nature of the approach has the advantage of reducing the complexity of computer supported collaborative writing down to a more manageable level at which investigators can concentrate more directly on the essence of the dynamics. The experience from the study suggests that this approach is worth pursuing, and it may be fruitfully generalized by integrating with other process modeling techniques and the mainstream practice of software engineering. © 1997 John Wiley & Sons, Inc.
Dual sourcing problem with real option

This paper addresses a single-period dual sourcing problem with real option under uncertain supply and demand. A retailer, who faces the uncertain market demand, can source from a low-price but unreliable supplier and an expensive but reliable supplier. In order to manage the supply uncertainties and decrease the cost, the retailer orders product from the unreliable supplier and buys option from the reliable one at the beginning of the selling season. After the demand realizes and the order is delivered, the option is executed. We develop a model for this problem and characterize the optimal policy. Then we compare the new strategy with the traditional dual sourcing strategy and the instant replenishment strategy with capacity constraint. The conditions that the new strategy has an advantage over the other ones are identified. Numeric experiments are conducted to analyze the impact of the parameters on the optimal policy and the profit in the new strategy and to compare the performance of the traditional dual sourcing strategy and the instant replenishment strategy with capacity constraint.
Theory and finite element analysis of shallow ice shelves

This thesis concerns the dynamics of ice shelves, which are large, floating ice masses that are adjacent to and fed by the Antarctic ice sheet. Starting from the approaches found in the literature for the derivation of simplified, zeroth order equations describing the dynamics of ice sheets, these methods are applied to ice shelves taking the dominant stresses into account. Two different layers of ice are distinguished: Meteoric ice that is built from precipitation that accumulates either on the ice shelf itself or the adjacent inland ice sheet and marine ice. The latter is built from phase transition processes at the ice-ocean interface or from the aggregation of ice particles called frazil ice ascending through the water column to the ice-shelf base. Thermodynamical boundary conditions for all the transition surfaces as well as kinematic boundary conditions for the free moving boundaries are formulated. By the use of constitutive equations, more generally valid balance equations are specialized to describe the flow of ice masses on long time scales. The equations derived are subjected to a scaling analysis and the aspect ratio, which is the ratio between a typical length scale and the typical ice thickness is identified as a small parameter that is used to subject the equations to a zeroth order perturbation expansion. Some of the equations are subjected to a vertical integration. Finally, this leads to a system of partial integro-differential equations that is completed by the boundary conditions as well as equations for the temperature, the age of the ice and evolution equations for the position of the free surfaces. In the second chapter, a finite element formulation is proposed for the previously derived equations approximating the mechanical aspects of ice-shelf dynamics. The equations are solved using an object oriented C++ class library specially designed for this purpose only. At first, the numerical model is applied to several academic ice-shelf setups and it is compared to an analytical solution derived for a simplified case. Unfortunately, the data set of the Ross Ice Shelf used in the literature to compare different ice-shelf models is no longer available. Therefore, a new dataset had to be assembled from what is freely available in electronic form. This new dataset is used to apply the numerical model to the Ross Ice Shelf.
Effects of some macrobiota on the Weipa Bauxite, northern Australia

Bioturbation of the Weipa bauxite is effected primarily by termites and tree roots. Termite galleries extend into the Plasmic Zone to a depth of 20 m. Termite nests are constructed from the surrounding soil (averaging 30% kaolinite) and also from kaolinite derived from below the bauxite, with some parts of the nest containing 75% kaolinite. Measurement of termite nest volume from two 1 ha areas indicates nest materials amount to as much as 5 t/ha and that termites bring kaolinite to the surface to the extent of perhaps 10 kg/ha annually. Roots of Eucalyptus tetrodonta, the main forest tree of the region, penetrate the 3–6 m thickness of the bauxite at least as far as the top of the Mottled Zone and commonly some distance further. Penetrating roots displace the loose pisolithic bauxite, and eventually provide channels through the bauxite down which material may fall, thus tending to homogenise the deposit. Evidence of their effect on local redox conditions is revealed in mine faces by zones of variable ferruginous colouration. Tree-fall, mainly the result of cyclones, disturbs the soil and upper bauxite: about 0.5% of a 1 ha area is estimated to have been affected by tree-fall. Small nodules scattered throughout the bauxite, prolate ellipsoidal in shape, averaging 28 × 21 mm, are interpreted as the fossilised pupal cases of ground-dwelling beetle larvae, probably scarabs or weevils.
Molecular cloning, characterization, and expression of Cuc m 2, a major allergen in Cucumis melo.

BACKGROUND Several studies reported the clinical features of IgE-mediated hypersensitivity after ingestion of melon. Melon allergy is a common IgE-mediated fruit allergy in Iran. This prompted us to investigate immunochemical and molecular properties of the major allergen in melon fruit, to compare the IgE-binding capacity of the natural protein with the recombinant allergen, and to determine cross-reactivity of the major allergen with closely-related allergens from other plants displaying clinical cross-reactivity with melon. METHODS Identification and molecular characterization of the major melon allergen were performed using IgE immunoblotting, allergen-specific ELISA, affinity-based purifications, cross-inhibition assays, cloning, and expression of the allergen in Escherichia coli. RESULTS Melon profilin was identified and isolated as a major IgE-binding component and designated as Cuc m 2. Sequencing corresponding cDNA revealed an open reading frame of 363 bp coding for 131 amino acid residues and two fragments of 171 bp and 383 bps for the 5'and 3' UTRs, respectively. Significant cross-reactivity was found between melon profilin and Cynodon dactylon, tomato, peach, and grape profilins in cross-inhibition assays. Although the highest degree of amino acid identity was revealed with watermelon profilin, there was no significant cross-reactivity between melon and watermelon profilins. CONCLUSION Melon profilin is the major IgE-binding component in melon extract, and the recombinant and natural forms exhibited similar IgE-binding capacities. A part of the fruit-fruit and pollen-fruit cross-reactions could be explained by the presence of this conserved protein; however, sequence homology provides insufficient information to predict IgE cross-reactivity of profilins.
Probabilistic ω-automata

Probabilistic ω-automata are variants of nondeterministic automata over infinite words where all choices are resolved by probabilistic distributions. Acceptance of a run for an infinite input word can be defined using traditional acceptance criteria for ω-automata, such as Büchi, Rabin or Streett conditions. The accepted language of a probabilistic ω-automata is then defined by imposing a constraint on the probability measure of the accepting runs. In this paper, we study a series of fundamental properties of probabilistic ω-automata with three different language-semantics: (1) the probable semantics that requires positive acceptance probability, (2) the almost-sure semantics that requires acceptance with probability 1, and (3) the threshold semantics that relies on an additional parameter λ ∈ ]0,1[ that specifies a lower probability bound for the acceptance probability. We provide a comparison of probabilistic ω-automata under these three semantics and nondeterministic ω-automata concerning expressiveness and efficiency. Furthermore, we address closure properties under the Boolean operators union, intersection and complementation and algorithmic aspects, such as checking emptiness or language containment.
An instantaneous profile method for determining the hydraulic conductivity of unsaturated porous materials

The hydraulic conductivity-water content relationship, as used in the differential equation describing unsteady flow in unsaturated porous materials, is determined from measurements obtained during the drainage of an initially saturated sand column. The approach utilizes instantaneous profiles of the macroscopic flow velocity, the potential gradient, and the water content. The derived relationship exhibits a direct proportionality between the instantaneous velocity and the corresponding potential gradient, thus lending strong support to the contention that Darcy's Law is applicable to flow in unsaturated porous materials of the size range considered in this study.
Understanding eating interventions through an evolutionary lens

ABSTRACT Health psychologists aim to improve eating behaviour to achieve health. Yet the effectiveness of healthy eating interventions is often minimal. This ineffectiveness may be in part because many healthy eating interventions are in a battle against evolved mechanisms (e.g., hedonic and related systems) that promote the consumption of energy-dense foods. Such foods, once rare, are now abundant in our obesogenic society, and consequently the evolved desire for energy-dense foods can now easily lead to the overconsumption of sugary, processed, and unhealthy foods. However, humans have other evolved mechanisms that also impact eating behaviour. In this article, therefore, we review eating interventions through an evolutionary lens, and describe evolved mechanisms that are relevant to eating behaviour. We discuss how using this lens could help health psychologists design more effective eating interventions and policies. By learning to work with human nature, eating interventions can more effectively promote healthier eating and healthier lives.
Activation of Na+/H+ exchange in lymphocytes by osmotically induced volume changes and by cytoplasmic acidification

After swelling in hypotonic solutions, peripheral blood mononuclear cells (PBM) shrink toward their original volumes. Upon restoration of isotonicity, the cells initially shrink but then regain near-normal size again. This regulatory volume increase (RVI) is abolished by removal of Na+o or Cl-o or by addition of amiloride. RVI is unaffected by removal of K+o or by ouabain and is only partially inhibited by 1 mM furosemide. As a result of increased influx, the cells gain both Na+ and K+ during reswelling. In contrast, only Na+ content increases in the presence of ouabain. Amiloride largely eliminates the changes in the content of both cations. Using diS-C3-(5), no significant membrane potential changes were detected during RVI, which suggests that the fluxes are electroneutral. The cytoplasmic pH of volume-static cells was measured with 5,6-dicarboxyfluorescein. After acid loading, the addition of extracellular Na+ induced an amiloride-inhibitable alkalinization, which is consistent with Na+/H+ exchange. Cytoplasmic pH was not affected by cell shrinkage itself, but an internal alkalinization, which was also amiloride sensitive and Na+ dependent, developed during reswelling. In isotonic lightly buffered solutions without HCO-3, an amiloride-sensitive acidification of the medium was measurable when Na+ was added to shrunken PBM. K+ was unable to mimic this effect. The observations are compatible with the model proposed by Cala (J. Gen. Physiol. 1980. 76:683-708), whereby an electroneutral Na+o/H+i exchange is activated by osmotic shrinking. Cellular volume gain occurs as Cl-o simultaneously exchanges for either HCO-3i or OH-i. Na+i is secondarily replaced by K+ through the pump, but this step is not essential for RVI.
Integration of speaker and pitch adaptive training for HMM-based singing voice synthesis

A statistical parametric approach to singing voice synthesis based on hidden Markov models (HMMs) has been growing in popularity over the last few years. The spectrum, excitation, vibrato, and duration of the singing voice in this approach are simultaneously modeled with context-dependent HMMs and waveforms are generated from the HMMs themselves. Since HMM-based singing voice synthesis systems are “corpus-based,” the HMMs corresponding to contextual factors that rarely appear in the training data cannot be well-trained. However, it may be difficult to prepare a large enough quantity of singing voice data sung by one singer. Furthermore, the pitch included in each song is imbalanced, and there is the vocal range of the singer. In this paper, we propose “singer adaptive training” which can solve the data sparse-ness problem. Experimental results demonstrated that the proposed technique improved the quality of the synthesized singing voices.
Elastic P- and S-wave autofocus imaging with primaries and internal multiples

Conventional seismic imaging methods rely on the singlescattering Born approximation, requiring the removal of multiply scattered events from reflection data prior to imaging. Additionally, many methods use an acoustic approximation, representing the solid earth as an acoustic (fluid) medium. We have developed imaging methods for (solid) elastic media that use primaries and internal multiples, including their PS and SP conversions, thus obviating the need for internal multiple removal and improving handling of internal conversions. Our methods rely on the elastic autofocusing method, which estimates full multicomponent elastodynamic Green’s functions from virtual sources interior to the medium to receivers placed on the surface. They require only surface seismic reflection data and estimates of the direct waves from virtual sources interior to the medium, both of which are commonly available at the imaging step of seismic processing. We tested our methods on a synthetic model with constant P and S velocities and vertical and horizontal density variations, by producing, for the first time to our knowledge, PP and SS images from elastic autofocusing that are compared to reference seismic images based on conventional methods. The effects of multiples are greatly attenuated in the images, with fewer spurious reflectors than are observed when using Born imaging.
Bone mineral content and collagen metabolites in children receiving steroid treatment for nephrotic syndrome

Bone mineral density (BMD) and content (BMC) were measured in nine children treated with corticosteroids for nephrotic syndrome and in age‐matched controls, using dual‐energy X‐ray absorptiometry (DEXA). The urinary excretion of cross‐linked N‐telopeptide (NTx) released from collagen type I as a specific marker of bone resorption was also measured. There were no significant differences in body size, BMD results or NTx urinary concentrations between patients and controls, nor could any significant differences be found when the six patients given a cumulative corticosteroid dose of < 15 g were analysed separately. The lack of significant differences could be due to the small number of patients included in the study. But when the measured BMD and BMC were analysed according to methods that corrected for body size and puberty stage, values well within the normal range were found in patients as well as in controls. There was, however, a significant, negative correlation between the urinary excretion of NTx and the cumulative dose of corticosteroids.
An interaction between zyxin and alpha-actinin

Zyxin is an 82-kD protein first identified as a component of adhesion plaques and the termini of stress fibers near where they associate with the cytoplasmic face of the adhesive membrane. We report here that zyxin interacts with the actin cross-linking protein alpha-actinin. Zyxin cosediments with filamentous actin in an alpha-actinin-dependent manner and an association between zyxin and alpha-actinin is observed in solution by analytical gel filtration. The specificity of the interaction between zyxin and alpha-actinin was demonstrated by blot overlay experiments in which 125I-zyxin recognizes most prominently alpha-actinin among a complex mixture of proteins extracted from avian smooth muscle. By these blot overlay binding studies, we determined that zyxin interacts with the NH2-terminal 27-kD domain of alpha- actinin, a region that also contains the actin binding site. Solid phase binding assays were performed to evaluate further the specificity of the binding and to determine the affinity of the zyxin-alpha-actinin interaction. By these approaches we have demonstrated a specific, saturable, moderate-affinity interaction between zyxin and alpha- actinin. Furthermore, double-label immunofluorescence reveals that zyxin and alpha-actinin exhibit extensive overlap in their subcellular distributions in both chicken embryo fibroblasts and pigmented retinal epithelial cells. The significant colocalization of the two proteins is consistent with the possibility that the interaction between zyxin and alpha-actinin has a biologically relevant role in coordinating membrane- cytoskeletal interactions.
An MFS Transporter-Like ORF from MDR Acinetobacter baumannii AIIMS 7 Is Associated with Adherence and Biofilm Formation on Biotic/Abiotic Surface

A major facilitator superfamily (MFS) transporter-like open reading frame (ORF) of 453 bp was identified in a pathogenic strain Acinetobacter baumannii AIIMS 7, and its association with adherence and biofilm formation was investigated. Reverse transcription PCR (RT-PCR) showed differential expression in surface-attached biofilm cells than nonadherent cells. In vitro translation showed synthesis of a ~17 kDa protein, further confirmed by cloning and heterologous expression in E. coli DH5α. Up to 2.1-, 3.1-, and 4.1- fold biofilm augmentation was observed on abiotic (polystyrene) and biotic (S. cerevisiae/HeLa) surface, respectively. Scanning electron microscopy (SEM) and gfp-tagged fluorescence microscopy revealed increased adherence to abiotic (glass) and biotic (S. cerevisiae) surface. Extracellular DNA(eDNA) was found significantly during active growth; due to probable involvement of the protein in DNA export, strong sequence homology with MFS transporter proteins, and presence of transmembrane helices. In summary, our findings show that the putative MFS transporter-like ORF (pmt) is associated with adherence, biofilm formation, and probable eDNA release in A. baumannii AIIMS 7.
Insight into liquefaction by system identification

This paper introduces system-parameter modelling, commonly known as system identification, to the estimation of dynamic soil properties. These methods are optimized for short and non-stationary signals. The Wildlife Site in California, subject to two large earthquakes (Elmore Ranch and Superstition Hills) on 24 November 1987, was used in an example analysis as the associated data are the only publicly available record of buried and surface motions. During the second, larger, earthquake the site soils liquefied. For the first time, both stationary and recursive system-parameter modelling methods were applied to the unique input–output data from the two earthquakes. The results show weakening of the soils system as pore pressure increases. Estimates of natural frequency, damping ratio and participation factor are given. Cet article presente la modelisation par parametre-systeme, usuellement connue comme systeme d'identification, afin d'estimer les proprietes dynamiques des sols. Ces methodes sont optimisees.