Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical Reactions Between Fe and H2O up to Megabar Pressures and Implications for Water Storage in the Earth's Mantle and Core

We investigated the phase relations of the Fe‐H2O system at high pressures based on in situ X‐ray diffraction experiments and first‐principles calculations and demonstrate that FeHx and FeO are present at pressures less than ~78 GPa. A recently reported pyrite‐structured FeO2 was identified in the Fe‐H2O system at pressures greater than ~78 GPa after laser heating. The phase observed in this study has a unit cell volume 8%–11% larger than that of FeO2, produced in the Fe‐O binary system reported previously, suggesting that hydrogen might be retained in a FeO2Hx crystal structure. Our observations indicate that H2O is likely introduced into the deep Earth through reaction between iron and water during the accretion and separation of the metallic core. Additionally, reaction between Fe and H2O would occur at the core‐mantle boundary, given water released from hydrous subducting slabs that intersect with the metallic core. Accumulation of volatile‐bearing iron compounds may provide new insights into the enigmatic seismic structures observed at the base of the lower mantle.
Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or owing to introductions. The ability to detect hybridization and introgression between the two species would be greatly improved by the development of more diagnostic markers validated across the two species’ many phylogenetic lineages. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.
Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Molecular dynamics is a widely used simulation technique to investigate material properties and structural changes under external forces. The availability of more powerful clusters and algorithms continues to increase the spatial and temporal extents of the simulation domain. This poses a particular challenge for the visualization of the underlying processes which might consist of millions of particles and thousands of time steps. Some application domains have developed special visual metaphors to only represent the relevant information of such data sets but these approaches typically require detailed domain knowledge that might not always be available or applicable. We propose a general technique that replaces the huge amount of simulated particles by a smaller set of representatives that are used for the visualization instead. The representatives capture the characteristics of the underlying particle density and exhibit coherency over time. We introduce loose capacity-constrained Voronoi diagrams for the generation of these representatives by means of a GPU-friendly, parallel algorithm. This way we achieve visualizations that reflect the particle distribution and geometric structure of the original data very faithfully. We evaluate our approach using real-world data sets from the application domains of material science, thermodynamics and dynamical systems theory.
Unintended consequences : how human intervention affects the ecology of urban birds

Urbanisation is an ever-growing threat to global wildlife. Nevertheless, urban areas around the world hold significant wild bird populations and urban birds provide a key connection between people and wildlife. Many people provide supplementary resources, such as food and nesting sites. However, even apparently beneficial actions may have unintended negative consequences. This work explores some of these direct and indirect effects. Grey Squirrels Sciurus carolinensis are a widespread, introduced species in the UK, acting both as a competitor for resources with birds and predator of their nests. When present, Grey Squirrels effectively excluded birds from supplementary feeding stations. Allowing them unrestricted access both supports their energy requirements and reduces its availability to target taxa, through both behavioural exclusion and food consumption. In addition, nest predation was higher in artificial nests adjacent to filled bird feeders which were frequented by potential nest predators and the exclusion of these predators did not significantly reduce nest predation. Providing point attractants during the breeding season may therefore depress local urban bird breeding success in addition to directly supporting predator/competitor populations. Garden supplementary feeding stations may also represent a threat to wild bird and human health through pathogen transmission. Bacterial communities were found to differ between two bird feeder types but there was little association between feeder usage by animals and bacterial load or pathogen presence in a typical UK suburban garden bird-feeding setting. Nest boxes are commonly provided for cavity nesting urban birds as an additional supplementary resource. Nest box using Blue Tits Cyanistes caeruleus and Great Tits Parus major differed in their use of anthropogenic material. Anthropogenic nest material was associated with lower arthropod diversity and ectoparasite predator abundance but higher ectoparasite loads. Higher arthropod diversity was linked to lower flea numbers, implying more complex arthropod communities depressed ectoparasite abundance though no direct link was found between these factors with breeding success. Domestic cats Felis catus are the most abundant predator in many urban ecosystems. Cat home ranges varied with level of urbanisation and they ranged significantly further during the night. To reduce the probability of Domestic Cats entering local protected areas a management zone of 300-400m from the nearest housing was estimated to be of management value and must be adjusted to the local landscape to ensure effectiveness. Despite the various negative effects highlighted in this thesis, the findings suggest that many of them can be mitigated, to ensure that our best intentions do effectively benefit urban birds.
Receding Horizon Control

In this article we have shown that receding horizon control offers a straightforward method for designing feedback controllers that deliver good performance while respecting complex constraints. A designer specifies the RHC controller by specifying the objective, constraints, prediction method, and horizon, each of which has a natural choice suggested directly by the application. In more traditional approaches, such as PID control, a designer tunes the controller coefficients, often using trial and error, to handle the objectives and constraints indirectly. In contrast, RHC con trollers can often obtain good performance with little tuning. In addition to the straightforward design process, we have seen that RHC controllers can be implemented in real time at kilohertz sampling rates. These speeds are useful for both real-time implementation of the controller as well as rapid Monte Carlo simulation for design and testing purposes. Thus, receding horizon control can no longer be considered a slow, computationally intensive policy. Indeed, RHC can be applied to a wide range of control problems, including applications involving fast dynamics.
Gamification of Behavior Change: Mathematical Principle and Proof-of-Concept Study

Background: Many people want to build good habits to become healthier, live longer, or become happier but struggle to change their behavior. Gamification can make behavior change easier by awarding points for the desired behavior and deducting points for its omission. Objective: In this study, we introduced a principled mathematical method for determining how many points should be awarded or deducted for the enactment or omission of the desired behavior, depending on when and how often the person has succeeded versus failed to enact it in the past. We called this approach optimized gamification of behavior change . Methods: As a proof of concept, we designed a chatbot that applies our optimized gamification method to help people build healthy water-drinking habits. We evaluated the effectiveness of this gamified intervention in a 40-day field experiment with 1 experimental group (n=43) that used the chatbot with optimized gamification and 2 active control groups for which the chatbot’s optimized gamification feature was disabled. For the first control group (n=48), all other features were available, including verbal feedback. The second control group (n=51) received no feedback or reminders. We measured the strength of all participants’ water-drinking habits before, during, and after the intervention using the Self-Report Habit Index and by asking participants on how many days of the previous week they enacted the desired habit. In addition, all participants provided daily reports on whether they enacted their water-drinking intention that day. Results: A Poisson regression analysis revealed that, during the intervention, users who received feedback based on optimized gamification enacted the desired behavior more often (mean 14.71, SD 6.57 times) than the active (mean 11.64, SD 6.38 times; P <.001; incidence rate ratio=0.80, 95% CI 0.71-0.91) or passive (mean 11.64, SD 5.43 times; P =.001; incidence rate ratio=0.78, 95% CI 0.69-0.89) control groups. The Self-Report Habit Index score significantly increased in all conditions ( P <.001 in all cases) but did not differ between the experimental and control conditions ( P >.11 in all cases). After the intervention, the experimental group performed the desired behavior as often as the 2 control groups ( P ≥ .17 in all cases). Conclusions: Our findings suggest that optimized gamification can be used to make digital behavior change interventions more effective.
Extracting related named entities from blogosphere for event mining

We propose a method of extracting named entities that are related to a single input word. Focusing on the syntactic dependency relation in sentences, it is reasonable to extract a case element that syntactically depends on the predicate that the input word depends on. In Japanese, though, a word which has appeared in a previous sentence is often omitted or replaced. Our proposed method, first, extracts "predicate patterns" consisting of case elements with case particles and a predicate. Then it combines predicate patterns that have the same predicate to form possible unabridged dependence relations.
A general mathematical model of probabilistic ripple-carry adders

Probabilistic CMOS is considered a promising technology for future generations of computing devices. By embracing possibly incorrect calculations, the technology makes it possible to trade correctness of circuit operations for potentially significant energy saving. For systematic design of probabilistic circuits, accurate mathematical models are indispensable. To this end, we propose a model of probabilistic ripplecarry adders. Compared to existing models, ours is applicable under a wide range of noise assumptions, including the popular additive-noise assumption. Our model provides recursive equations that can accurately capture propagation of carry errors. The proposed model is validated by HSPICE simulation, and we find that the model is able to predict multi-bit error-rates of a simulated probabilistic ripple-carry adder with reasonable accuracy.
Standardized T2* map of normal human heart in vivo to correct T2* segmental artefacts

A segmental, multislice, multi‐echo T2* MRI approach could be useful in heart iron‐overloaded patients to account for heterogeneous iron distribution, demonstrated by histological studies. However, segmental T2* assessment in heart can be affected by the presence of geometrical and susceptibility artefacts, which can act on different segments in different ways. The aim of this study was to assess T2* value distribution in the left ventricle and to develop a correction procedure to compensate for artefactual variations in segmental analysis. MRI was performed in four groups of 22 subjects each: healthy subjects (I), controls (II) (thalassemia intermedia patients without iron overload), thalassemia major patients with mild (III) and heavy (IV) iron overload. Three short‐axis views (basal, median, and apical) of the left ventricle were obtained and analyzed using custom‐written, previously validated software. The myocardium was automatically segmented into a 16‐segment standardized heart model, and the mean T2* value for each segment was calculated. Punctual distribution of T2* over the myocardium was assessed, and T2* inhomogeneity maps for the three slices were obtained. In group I, no significant variation in the mean T2* among slices was found. T2* showed a characteristic circumferential variation in all three slices. The effect of susceptibility differences induced by cardiac veins was evident, together with low‐scale variations induced by geometrical artefacts. Using the mean segmental deviations as correction factors, an artefact correction map was developed and used to normalize segmental data. The correction procedure was validated on group II. Group IV showed no significant presence of segmental artefacts, confirming the hypothesis that susceptibility artefacts are additive in nature and become negligible for high levels of iron overload. Group III showed a greater variability with respect to normal subjects. The correction map failed to compensate for these variations if both additive and percentage‐based corrections were applied. This may reinforce the hypothesis that true inhomogeneity in iron deposition exists. Copyright © 2007 John Wiley & Sons, Ltd.
Projection-Based Ensemble Learning for Ordinal Regression

The classification of patterns into naturally ordered labels is referred to as ordinal regression. This paper proposes an ensemble methodology specifically adapted to this type of problem, which is based on computing different classification tasks through the formulation of different order hypotheses. Every single model is trained in order to distinguish between one given class (k) and all the remaining ones, while grouping them in those classes with a rank lower than k, and those with a rank higher than k. Therefore, it can be considered as a reformulation of the well-known one-versus-all scheme. The base algorithm for the ensemble could be any threshold (or even probabilistic) method, such as the ones selected in this paper: kernel discriminant analysis, support vector machines and logistic regression (LR) (all reformulated to deal with ordinal regression problems). The method is seen to be competitive when compared with other state-of-the-art methodologies (both ordinal and nominal), by using six measures and a total of 15 ordinal datasets. Furthermore, an additional set of experiments is used to study the potential scalability and interpretability of the proposed method when using LR as base methodology for the ensemble.
Multimedia in Biochemistry and Molecular Biology Education Different Energy Sources in Sports

This work describes software designed to promote the association between the content of a basic undergraduate biochemistry course and the professional activities of physical education students. The software contains three main content sections: (A) Structure of skeletal muscle, (B) Contraction mechanism, and (C) Adaptations to physical exercise. A fourth section asks questions of the students. The software offers students a brief introduction on muscle structure and function, focusing on the energy sources required by different kinds of physical activities. The software was field tested at Universidade Estadual de Campinas (Unicamp), Brazil and has been adopted by several Brazilian universities. The students are required to examine the software, to discuss its contents, and to produce a list of questions arising from their work with the software. These questions are answered during the development of the curriculum, thereby connecting biochemical knowledge with the energetic needs for the practice of sports.
Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action -- Extended Version

In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of the element being regulated. It has been postulated that this paradoxical behavior can be explained by activating and repressing transcription factors competing for binding to other possible targets. It is very difficult to prove this hypothesis in mammalian cells, due to the large number of potential players and the complexity of endogenous intracellular regulatory networks. Instead, this paper analyzes this issue through an analogous synthetic biology construct which aims to reproduce the paradoxical behavior using standard bacterial gene expression networks. The paper first reviews the motivating cancer biology work, and then describes a proposed synthetic construct. A mathematical model is formulated, and basic properties of uniqueness of steady states and convergence to equilibria are established, as well as an identification of parameter regimes which should lead to observing such paradoxical phenomena (more activator leads to less activity at steady state). A proof is also given to show that this is a steady-state property, and for initial transients the phenomenon will not be observed. This work adds to the general line of work of resource competition in synthetic circuits.
Current and emerging drugs for the treatment of inflammatory bowel disease

: During the last decade a large number of biological agents against tumor necrosis factor- α (TNF- α ), as well as many biochemical substances and molecules specifically for the medical treatment of patients with inflammatory bowel disease (IBD), have been developed. This enormous progress was a consequence of the significant advances in biotechnology along with the increased knowledge of the underlying pathophysiological mechanisms involved in the pathogenesis of IBD. However, conventional therapies remain the cornerstone of treatment for most patients. During recent years conventional and biologic IBD therapies have been optimized. Newer mesalazine formulations with a reduced pill size and only one dose per day demonstrate similar efficacy to older formulations. New corticosteroids retain the efficacy of older corticosteroids while exhibiting a higher safety profile. The role of antibiotics and probiotics has been further clarified. Significant progress in understanding thiopurine metabolism has improved the effective dose along with adjunctive therapies. Quite a large number of substances and therapies, including biologic agents other than TNF- α inhibitors, unfractionated or low-molecular-weight heparin, omega-3 polyunsaturated fatty acids, microbes and microbial products, leukocytapheresis, and other substances under investigation, could offer important benefits to our patients. In this paper we review the established and emerging therapeutic strategies in patients with Crohn’s disease and ulcerative colitis.
BI-RADIAL TRANSFER FUNCTIONS

The most common transfer functions in neural networks are of the sigmoidal type. In this article other transfer functions are considered. Advantages of simple gaussians, giving hyperelliptical densities, and gaussian bar functions (sums of one-dimensional gaussians) are discussed. Bi-radial functions are formed from products of two sigmoids. Product of M bi-radial functions in N -dimensional parameter space give arbitrarily shaped densities offering great flexibility. Extensions of bi-radial functions are proposed. Bi-radial functions can be used as transfer functions in many neural networks, such as RBF, RAN or FSM systems.
Single-breath pulmonary diffusing capacity. Reference values and application in connective tissue diseases and in various lung diseases.

1.1. Diffusing capacity of the lungs was measured by using a Mark 4 Resparameter. The single-breath diffusing capacity (D) for carbon monoxide was found to be dependent on the lung volume (VA) during the breath-hold. The same applied to D/VA and to the time constant (tau) for carbon monoxide uptake. This confirms the theoretical considerations and the results of other investigators. This effect should be taken into account especially when making serial determinations of D on the same subject. 1.2. The repeatability of the method was found to be reasonably good; the coefficient of variation was about 4% in normal subjects, as well as in a series of patients with rheumatoid arthritis. 1.3. The effect of the correction for haemoglobin concentration was calculated and tabulated for a set of possible values of DM/Vc and haemoglobin. This correction did not reduce the scatter of D values in normal subjects, but it was adopted for clinical use for theoretical reasons. Caution in its use and interpretation of the correction is emphasized. 2.1. Healthy males and females, 20-69 years of age, were examined to establish reference values for the D measurement. Multiple linear regression equations were calculated stepwise, and equations based on age and height were then used in the clinical prediction equations. Similarly, prediction equations were calculated for clinical spirometry. 2.2. The prediction equations were compared with some published reference values. The equations provide a basis for the evaluation of the effect of various factors, such as age and smoking, in different populations. 3.1. Respiratory function, clinical symptoms and chest x-ray findings were examined in patients with connective tissue diseases. Three different investigations were thus formed: a) consecutive patients (free of lung disease other than that possibly due to a connective tissue disease) with definite rheumatoid arthritis (RA, 21 cases), systemic lupus erythematosus (SLE, 18 cases) or scleroderma (SCL, 6 cases) were subjected to detailed tests. b) 129 patients from the Rheumatism Foundation Hospital, Heinola, Finland, were subjected to measurement of diffusing capacity and vital capacity in addition to chest radiography and routine clinical assessment c) the histological findings on 12 patients subjected to a needle biopsy of the lung in order to exclude other conditions were compared with the results of diffusing capacity and x-ray examinations. 3.2. Restrictive impairment of the respiratory function was the general finding in all of these groups. The reduction in diffusing capacity was out of proportion to the reduction in lung volume, however, in most cases with abnormally low values. Low D values were encountered in about half of the RA and SLE and in all of the SCL patients in group a, and in 13% of the "average" RA patients studied in Heinola. The typical histological finding in patients with reduced D was a thickening of the alveolar wall.