Miracle-dz/UniFAR-FTUs huggingface dataset:
Will Coral Islands Maintain Their Growth over the Next Century? A Deterministic Model of Sediment Availability at Lady Elliot Island, Great Barrier Reef

A geomorphic assessment of reef system calcification is conducted for past (3200 Ka to present), present and future (2010–2100) time periods. Reef platform sediment production is estimated at 569 m3 yr−1 using rate laws that express gross community carbonate production as a function of seawater aragonite saturation, community composition and rugosity and incorporating estimates of carbonate removal from the reef system. Key carbonate producers including hard coral, crustose coralline algae and Halimeda are mapped accurately (mean R2 = 0.81). Community net production estimates correspond closely to independent census-based estimates made in-situ (R2 = 0.86). Reef-scale outputs are compared with historic rates of production generated from (i) radiocarbon evidence of island deposition initiation around 3200 years ago, and (ii) island volume calculated from a high resolution island digital elevation model. Contemporary carbonate production rates appear to be remarkably similar to historical values of 573 m3 yr−1. Anticipated future seawater chemistry parameters associated with an RCP8.5 emissions scenario are employed to model rates of net community calcification for the period 2000–2100 on the basis of an inorganic aragonite precipitation law, under the assumption of constant benthic community character. Simulations indicate that carbonate production will decrease linearly to a level of 118 m3 yr−1 by 2100 and that by 2150 aragonite saturation levels may no longer support the positive budgetary status necessary to sustain island accretion. Novel aspects of this assessment include the development of rate law parameters to realistically represent the variable composition of coral reef benthic carbonate producers, incorporation of three dimensional rugosity of the entire reef platform and the coupling of model outputs with both historical radiocarbon dating evidence and forward hydrochemical projections to conduct an assessment of island evolution through time. By combining several lines of evidence in a deterministic manner, an assessment of changes in carbonate production is carried out that has tangible geomorphic implications for sediment availability and associated island evolution.
Optimizing spectral CT parameters for material classification tasks

In this work, we propose a framework for optimizing spectral CT imaging parameters and hardware design with regard to material classification tasks. Compared with conventional CT, many more parameters must be considered when designing spectral CT systems and protocols. These choices will impact material classification performance in a non-obvious, task-dependent way with direct implications for radiation dose reduction. In light of this, we adapt Hotelling Observer formalisms typically applied to signal detection tasks to the spectral CT, material-classification problem. The result is a rapidly computable metric that makes it possible to sweep out many system configurations, generating parameter optimization curves (POC’s) that can be used to select optimal settings. The proposed model avoids restrictive assumptions about the basis-material decomposition (e.g. linearity) and incorporates signal uncertainty with a stochastic object model. This technique is demonstrated on dual-kVp and photon-counting systems for two different, clinically motivated material classification tasks (kidney stone classification and plaque removal). We show that the POC’s predicted with the proposed analytic model agree well with those derived from computationally intensive numerical simulation studies.
Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24

Old English Sheepdogs and Gordon Setters suffer from a juvenile onset, autosomal recessive form of canine hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex. The clinical and histological characteristics are analogous to hereditary ataxias in humans. Linkage and genome-wide association studies on a cohort of related Old English Sheepdogs identified a region on CFA4 strongly associated with the disease phenotype. Targeted sequence capture and next generation sequencing of the region identified an A to C single nucleotide polymorphism (SNP) located at position 113 in exon 1 of an autophagy gene, RAB24, that segregated with the phenotype. Genotyping of six additional breeds of dogs affected with hereditary ataxia identified the same polymorphism in affected Gordon Setters that segregated perfectly with phenotype. The other breeds tested did not have the polymorphism. Genome-wide SNP genotyping of Gordon Setters identified a 1.9 MB region with an identical haplotype to affected Old English Sheepdogs. Histopathology, immunohistochemistry and ultrastructural evaluation of the brains of affected dogs from both breeds identified dramatic Purkinje neuron loss with axonal spheroids, accumulation of autophagosomes, ubiquitin positive inclusions and a diffuse increase in cytoplasmic neuronal ubiquitin staining. These findings recapitulate the changes reported in mice with induced neuron-specific autophagy defects. Taken together, our results suggest that a defect in RAB24, a gene associated with autophagy, is highly associated with and may contribute to canine hereditary ataxia in Old English Sheepdogs and Gordon Setters. This finding suggests that detailed investigation of autophagy pathways should be undertaken in human hereditary ataxia.
Association between vitamin D and urinary tract infection in children

Purpose The present study aimed to determine the relationship between serum 25-hydroxyvitamin D (25(OH)D) level and Urinary tract infections (UTIs) in children. Methods In this case-control study, 70 children with UTI (case group) were compared with 70 healthy children (control group) in terms of serum 25(OH)D levels. The children were between 1 month and 12 years of age. Serum 25(OH)D levels were measured using enzyme-linked immunosorbent assay (ELISA). The results were analyzed and compared between both groups. Results Among 70 children with UTI (case group), 5 children (7.2%) were male and 65 (92.8%) were female. Among the healthy children (control group), 9 (12.8%) and 61 children (87.2%) were male and female, respectively (P=0.39). The mean±standard deviation of age in the case and control groups were 53.2±35.6 and 36.1±60.2 months, respectively (P=0.24). The mean level of serum 25(OH)D in the case group was significantly higher than that of the control group (20.4±8.6 ng/mL vs. 16.9±7.4 ng/mL, P=0.01). Conclusion This study showed that there was a relationship between serum 25(OH)D levels and UTI in children. It seems that 25(OH)D plays a role in the pathogenesis of UTI.
Effect of pasta in the context of low-glycaemic index dietary patterns on body weight and markers of adiposity: a systematic review and meta-analysis of randomised controlled trials in adults

Objective Carbohydrate staples such as pasta have been implicated in the obesity epidemic. It is unclear whether pasta contributes to weight gain or like other low-glycaemic index (GI) foods contributes to weight loss. We synthesised the evidence of the effect of pasta on measures of adiposity. Design Systematic review and meta-analysis using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Data sources MEDLINE, Embase, CINAHL and the Cochrane Library were searched through 7 February 2017. Eligibility criteria for selecting studies We included randomised controlled trials ≥3 weeks assessing the effect of pasta alone or in the context of low-GI dietary patterns on measures of global (body weight, body mass index (BMI), body fat) and regional (waist circumference (WC), waist-to-hip ratio (WHR), sagittal abdominal diameter (SAD)) adiposity in adults. Data extraction and synthesis Two independent reviewers extracted data and assessed risk of bias. Data were pooled using the generic inverse-variance method and expressed as mean differences (MDs) with 95% CIs. Heterogeneity was assessed (Cochran Q statistic) and quantified (I2 statistic). GRADE assessed the certainty of the evidence. Results We identified no trial comparisons of the effect of pasta alone and 32 trial comparisons (n=2448 participants) of the effect of pasta in the context of low-GI dietary patterns. Pasta in the context of low-GI dietary patterns significantly reduced body weight (MD=−0.63 kg; 95% CI −0.84 to –0.42 kg) and BMI (MD=−0.26 kg/m2; 95% CI −0.36 to –0.16 kg/m2) compared with higher-GI dietary patterns. There was no effect on other measures of adiposity. The certainty of the evidence was graded as moderate for body weight, BMI, WHR and SAD and low for WC and body fat. Conclusions Pasta in the context of low-GI dietary patterns does not adversely affect adiposity and even reduces body weight and BMI compared with higher-GI dietary patterns. Future trials should assess the effect of pasta in the context of other ‘healthy’ dietary patterns. Trial registration number NCT02961088; Results.
Epitaxial niobium dioxide thin films by reactive-biased target ion beam deposition

Epitaxial NbO2 thin films were synthesized on Al2O3 (0001) substrates via reactive bias target ion beam deposition. X-ray diffraction and Raman spectra were used to confirm the tetragonal phase of pure NbO2. Through XPS, it was found that there was a ∼1.3 nm thick Nb2O5 layer on the surface and the bulk of the thin film was NbO2. The epitaxial relationship between the NbO2 film and the substrate was determined. Electrical transport measurement was measured up to 400 K, and the conduction mechanism was discussed.
Image Classification by Codebook Updating via Joint i-Pat Topic Model Feedback Wai

Image classification is an important task in computer vision as it plays a major role in content-based image retrieval. For an image classification system that uses the Bagof-Words model representation, visual codebook is an essential part. Randomized forest (RF) as a tree-structure discriminative codebook has been proven highly time-efficient for real-world applications, by utilizing the image class labels which the detected features are associated with (i.e. weakly supervised learning). However, the RF codebook can be degraded if the image class labels are poorly labeled. In this paper, we tackle this image class label problem by proposing a feedback mechanism from the topic model. This statistical model can hypothesize the ‘correct’ labels for images, to enhance the effectiveness of the RF codebook. Besides, the feedback mechanism employs a joint image-patch (i-Pat) level information in predicting the ‘correct’ labels, which is in contrast to the state-of-the-art RF learning. Experiments on both the 15-Scene and C-Pascal datasets had shown that the proposed method outperforms existing methods by a margin. Besides, even with limited labeled training images, the proposed solution still able to achieve comparable accuracy compared to the fully labeled training data algorithm.
Identification and Phytotoxicity Assessment of Phenolic Compounds in Chrysanthemoides monilifera subsp. monilifera (Boneseed)

Chrysanthemoides monilifera subsp. monilifera (boneseed), a weed of national significance in Australia, threatens indigenous species and crop production through allelopathy. We aimed to identify phenolic compounds produced by boneseed and to assess their phytotoxicity on native species. Phenolic compounds in water and methanol extracts, and in decomposed litter-mediated soil leachate were identified using HPLC, and phytotoxicity of identified phenolics was assessed (repeatedly) through a standard germination bioassay on native Isotoma axillaris. The impact of boneseed litter on native Xerochrysum bracteatum was evaluated using field soil in a greenhouse. Collectively, we found the highest quantity of phenolic compounds in boneseed litter followed by leaf, root and stem. Quantity varied with extraction media. The rank of phenolics concentration in boneseed was in the order of ferulic acid > phloridzin > catechin > p-coumaric acid and they inhibited germination of I. axillaris with the rank of ferulic acid > catechin > phloridzin > p-coumaric acid. Synergistic effects were more severe compared to individual phenolics. The litter-mediated soil leachate (collected after15 days) exhibited strong phytotoxicity to I. axillaris despite the level of phenolic compounds in the decomposed leachate being decreased significantly compared with their initial level. This suggests the presence of other unidentified allelochemicals that individually or synergistically contributed to the phytotoxicity. Further, the dose response phytotoxic impacts exhibited by the boneseed litter-mediated soil to native X. bracteatum in a more naturalistic greenhouse experiment might ensure the potential allelopathy of other chemical compounds in the boneseed invasion. The reduction of leaf relative water content and chlorophyll level in X. bracteatum suggest possible mechanisms underpinning plant growth inhibition caused by boneseed litter allelopathy. The presence of a substantial quantity of free proline in the target species also suggests that the plant was in a stressed condition due to litter allelopathy. These findings are important for better understanding the invasive potential of boneseed and in devising control strategies.
Testing Sleep Consolidation in Skill Learning: A Field Study Using an Online Game

Using an observational sample of players of a simple online game (n > 1.2 million), we are able to trace the development of skill in that game. Information on playing time, and player location, allows us to estimate time of day during which practice took place. We compare those whose breaks in practice probably contained a night's sleep and those whose breaks in practice probably did not contain a night's sleep. Our analysis confirms experimental evidence showing a benefit of spacing for skill learning, but it fails to find any additional benefit of sleeping during a break from practice. We discuss reasons why the well-established phenomenon of sleep consolidation might not manifest in an observational study of skill development. We put the spacing effect into the context of the other known influences on skill learning: improvement with practice, and individual differences in initial performance. Analysis of performance data from games allows experimental results to be demonstrated outside of the lab and for experimental phenomenon to be put in the context of the performance of the whole task.
mantle Poisson ’ s ratio , subduction , and crustal structure in central

[1] Subduction zones alter the upper plate in a variety of ways, including metasomatism via slab-derived fluids and accretion of exotic terranes. These processes should produce distinctive seismic signatures, as seismic velocities are sensitive to compositional variations. A new method is developed to estimates depths to interfaces and Poisson’s ratio (Vp/Vs ratio) for dipping layered structures, by stacking teleseismic receiver functions. It also estimates crustal Vp/Vs and thickness. Using this method, we analyze a broadband data set from the central Alaska subduction zone, to seek evidence for mantle wedge composition. Crustal thickness varies from 27 to 45 km, and crustal Vp/Vs indicates an intermediate to mafic composition, expected for these accreted island arc terranes. Inversions for mantle structure confirm the presence of a 15–20 km thick low-velocity zone atop of the downgoing plate to 130 km depth, perhaps subducted crust of an exotic terrane. Vp/Vs in the mantle wedge allows for 15 ± 15% serpentinization where the slab is <80 km deep and the wedge is cold. Where the slab is deeper, Vp/Vs for the mantle wedge is unusually low, <1.7. This value is lower than predicted for any common mantle mineral and may indicate significant quantities of quartz, provided that past physical properties measurements are not grossly in error. These results suggest that the mantle wedge in subduction zones can occasionally differ substantially in bulk composition from normal subcrustal mantle, perhaps because collisions of exotic terranes cause tectonic mixing of crustal material into the mantle.
Review: Synovial Cell Metabolism and Chronic Inflammation in Rheumatoid Arthritis

Metabolomic studies of body fluids show that immune‐mediated inflammatory diseases such as rheumatoid arthritis (RA) are associated with metabolic disruption. This is likely to reflect the increased bioenergetic and biosynthetic demands of sustained inflammation and changes in nutrient and oxygen availability in damaged tissue. The synovial membrane lining layer is the principal site of inflammation in RA. Here, the resident cells are fibroblast‐like synoviocytes (FLS) and synovial tissue macrophages, which are transformed toward overproduction of enzymes that degrade cartilage and bone and cytokines that promote immune cell infiltration. Recent studies have shown metabolic changes in both FLS and macrophages from RA patients, and these may be therapeutically targetable. However, because the origins and subset‐specific functions of synoviocytes are poorly understood, and the signaling modules that control metabolic deviation in RA synovial cells are yet to be explored, significant additional research is needed to translate these findings to clinical application. Furthermore, in many inflamed tissues, different cell types can forge metabolic collaborations through solute carriers in their membranes to meet a high demand for energy or biomolecules. Such relationships are likely to exist in the synovium and have not been studied. Finally, it is not yet known whether metabolic change is a consequence of disease or whether primary changes to cellular metabolism might underlie or contribute to the pathogenesis of early‐stage disease. In this review article, we collate what is known about metabolism in synovial tissue cells and highlight future directions of research in this area.
Measuring medical students' motivation to learning anatomy by cadaveric dissection

Motivation and learning are inter‐related. It is well known that motivating learners is clearly a complex endeavor, which can be influenced by the educational program and the learning environment. Limited research has been conducted to examine students' motivation as a method to assess the effectiveness of dissection in medical education. This study aimed to assess and analyze students' motivation following their dissection experience. A 29‐item survey was developed based on the Attention, Relevance, Confidence, and Satisfaction model of motivation. Descriptive statistics were undertaken to describe students' motivation to the dissection experience. T‐test and ANOVA were used to compare differences in motivational scores between gender and educational characteristics of students. Dissection activities appear to promote students' motivation. Gender difference was statistically significant as males were more motivated by the dissection experience than females. Comparison between students with different knowledge of anatomy was also significantly different. The study is an important step in the motivational design to improve students' motivation to learn. The outcome of this study provides guidance to the selection of specific strategies to increase motivation by generating motivational strategies/tactics to facilitate learning. Anat Sci Educ 10: 363–371. © 2016 American Association of Anatomists.
Corrosion Behavior of Alloy 600 Coupled with Electrodeposited Magnetite in Simulated Secondary Water of PWRs

The corrosion behavior of Alloy 600 coupled with magnetite was investigated in simulated secondary water of pressurized water reactors using a potentiodynamic polarization test and zero-resistance ammeter. Passive film formed on the surface of Alloy 600 was also analyzed using X-ray photoelectron spectroscopy. Alloy 600 was the anodic element of the galvanic pair since its corrosion potential was less noble than that of the magnetite. Galvanic coupling increased the corrosion current density of Alloy 600 due to the shifting of the potential of Alloy 600 to the positive value. The passive film of coupled Alloy 600 was more slowly stabilized and was thinner and less protective than that of non-coupled Alloy 600. [doi:10.2320/matertrans.M2015322]
A Mechanistic Study of Plant and Microbial Controls over R* for Nitrogen in an Annual Grassland

Differences in species' abilities to capture resources can drive competitive hierarchies, successional dynamics, community diversity, and invasions. To investigate mechanisms of resource competition within a nitrogen (N) limited California grassland community, we established a manipulative experiment using an R* framework. R* theory holds that better competitors within a N limited community should better depress available N in monoculture plots and obtain higher abundance in mixture plots. We asked whether (1) plant uptake or (2) plant species influences on microbial dynamics were the primary drivers of available soil N levels in this system where N structures plant communities. To disentangle the relative roles of plant uptake and microbially-mediated processes in resource competition, we quantified soil N dynamics as well as N pools in plant and microbial biomass in monoculture plots of 11 native or exotic annual grassland plants over one growing season. We found a negative correlation between plant N content and soil dissolved inorganic nitrogen (DIN, our measure of R*), suggesting that plant uptake drives R*. In contrast, we found no relationship between microbial biomass N or potential net N mineralization and DIN. We conclude that while plant-microbial interactions may have altered the overall quantity of N that plants take up, the relationship between species' abundance and available N in monoculture was largely driven by plant N uptake in this first year of growth.
Feature Selection for Nonstationary Data: Application to Human Recognition Using Medical Biometrics

Electrocardiogram (ECG) and transient evoked otoacoustic emission (TEOAE) are among the physiological signals that have attracted significant interest in biometric community due to their inherent robustness to replay and falsification attacks. However, they are time-dependent signals and this makes them hard to deal with in across-session human recognition scenario where only one session is available for enrollment. This paper presents a novel feature selection method to address this issue. It is based on an auxiliary dataset with multiple sessions where it selects a subset of features that are more persistent across different sessions. It uses local information in terms of sample margins while enforcing an across-session measure. This makes it a perfect fit for aforementioned biometric recognition problem. Comprehensive experiments on ECG and TEOAE variability due to time lapse and body posture are done. Performance of the proposed method is compared against seven state-of-the-art feature selection algorithms as well as another six approaches in the area of ECG and TEOAE biometric recognition. Experimental results demonstrate that the proposed method performs noticeably better than other algorithms.