Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial dysbiosis predicts the diagnosis of Crohn's disease in Saudi children

Background: Studies have reached different conclusions regarding the accuracy of dysbiosis in predicting the diagnosis of Crohn's disease (CD). The aim of this report is to assess the utility of mucosal and fecal microbial dysbiosis as predictors in the diagnosis of this condition in Saudi children. Methods: Tissue and fecal samples were collected prospectively from children with final diagnosis of CD and from controls. Bacterial DNA was extracted and sequenced using Illumina MiSeq chemistry. The abundance and diversity of bacteria in tissue and fecal samples were determined in relation to controls. Sparse logistic regression was calculated to predict the diagnosis of CD based on subject's microbiota profile. Results: There were 17 children with CD and 18 controls. All children were Saudis. The median age was 13.9 and 16.3 years for children with CD and controls respectively. Sex distribution showed that 11/17 (65%) of the CD and 12/18 (67%) of the control subjects were boys. The mean area under the curve (AUC) was significantly higher in stool (AUC = 0.97 ± 0.029) than in tissue samples (AUC = 0.83 ±0.055) (P < 0.001). Conclusions: We found high AUC in mucosal and fecal samples. The higher AUC for fecal samples suggests higher accuracy in predicting the diagnosis of CD.
Gaming Helps! Learning from Strategic Interactions in Natural Dynamics

We consider an online regression setting in which individuals adapt to the regression model: arriving individuals are aware of the current model, and invest strategically in modifying their own features so as to improve the predicted score that the current model assigns to them. Such feature manipulation has been observed in various scenarios—from credit assessment to school admissions— posing a challenge for the learner. Surprisingly, we find that such strategic manipulations may in fact help the learner recover the meaningful variables—that is, the features that, when changed, affect the true label (as opposed to non-meaningful features that have no effect). We show that even simple behavior on the learner’s part allows her to simultaneously i) accurately recover the meaningful features, and ii) incentivize agents to invest in these meaningful features, providing incentives for improvement.
The Role of Ru and RuO2 in the Catalytic Transfer Hydrogenation of 5‐Hydroxymethylfurfural for the Production of 2,5‐Dimethylfuran

We have previously shown that 2,5‐dimethylfuran (DMF) can be produced selectively from 5‐hydroxymethylfurfural in up to 80 % yield via catalytic transfer hydrogenation with 2‐propanol as a hydrogen donor and Ru/C as a catalyst. Herein, we investigate the active phase of the Ru/C catalyst by using extended X‐ray absorption fine structure, X‐ray photoelectron spectroscopy, and high‐resolution TEM analyses. The results reveal that RuO2 is the dominant phase in the fresh (active) catalyst and is reduced to metallic Ru during the reaction with the hydrogen produced in situ from 2‐propanol. The deactivation of the catalyst is correlated with the reduction of the surface of RuO2. Reactivity studies of individual phases (bulk RuO2 and reduced Ru/C catalysts) indicate that RuO2 mainly catalyzes the Meerwein–Ponndorf–Verley reaction of 5‐hydroxymethylfurfural that produces 2,5‐bis(hydroxymethyl)furan and the etherification of 2,5‐bis(hydroxymethyl)furan or other intermediates with 2‐propanol and that the reduced Ru/C catalyst has moderate hydrogenolysis activity for the production of DMF (30 % selectivity) and other intermediates (20 %). In contrast, a physical mixture of the two phases increases the DMF selectivity up to 70 %, which suggests that both metallic Ru and RuO2 are active phases for the selective production of DMF. The oxidation of the reduced Ru/C catalyst at different temperatures and the in situ hydrogen titration of the oxidized Ru/C catalysts were performed to quantify the bifunctional role of Ru and RuO2 phases. The mild oxidation treatment of the Ru/C catalyst at 403 K could activate the catalyst for the selective production of DMF in up to 72 % yield by generating a partially oxidized Ru catalyst.
Short-term Traffic Flow Prediction Based on Multi-Auxiliary Information

Aiming at the problem of short-term traffic flow prediction, on the basis of considering the dynamic change of traffic flow diffusion, this paper proposes a spatio-temporal prediction model that integrates multiple-auxiliary information, and carries out spatio-temporal modeling for the traffic flow state of a single detector, and then realizes the forecast goal of traffic flow. In this paper, firstly, based on the PageRank algorithm, the RoadRank algorithm is proposed to obtain the real-time traffic flow diffusion characteristics of the road network. Secondly, feature construction of multiple auxiliary information such as time, period, weather, etc., and on the basis of the above multiple auxiliary features, combined with the Encoder-Decoder framework that considers the attention mechanism, a spatio-temporal prediction model framework for multi-auxiliary information fusion is given. Based on METR-LA traffic dataset and NOAA weather dataset, a case study is carried out to verify effectiveness of multi-auxiliary features and superiority of the hybrid model.
Veiled agency? Children, innovation and the archaeological record

Abstract Abstract Children and subadults were obviously part of ancient human communities, and almost certainly, in important ways their activities were distinctive; they did not routinely act like scaled down adults. Yet their presence was quite cryptic, but not entirely hidden. Their lives and acts did leave traces, although these tend to be be fragile, ambiguous and fast-fading. In addition to pursuing the methodological issues posed by the detection of subadult lives, this special issue raises important questions about the role of children, and their willingness to experiment and play, on innovation. It is true that ethnographically known forager children are almost certainly more autonomous, experimental and adventurous than WEIRD children, and this was probably true of the young foragers of the early Holocene and late Pleistocene too. Their greater willingness to experiment probably fuelled a supply of variation, and perhaps occasionally adaptation as well, especially finding new uses for existing materials. Much more certainly, innovations tend to be noted, taken up and spread by adolescents. They were vectors of change, even if perhaps only rarely initiators of change.
Keypoint detection by wave propagation

Abstract. We propose to rely on the wave equation for the detection of repeatable keypoints invariant up to image scale and rotation and robust to viewpoint variations, blur, and lighting changes. The algorithm exploits the properties of local spatial–temporal extrema of the evolution of image intensities under the wave propagation to highlight salient symmetries at different scales. Although the image structures found by most state-of-the-art detectors, such as blobs and corners, occur typically on highly textured surfaces, salient symmetries are widespread in diverse kinds of images, including those related to poorly textured objects, which are hardly dealt with by current pipelines based on local invariant features. The impact on the overall algorithm of different numerical wave simulation schemes and their parameters is discussed, and a pyramidal approximation to speed-up the simulation is proposed and validated. Experiments on publicly available datasets show that the proposed algorithm offers state-of-the-art repeatability on a broad set of different images while detecting regions that can be distinctively described and robustly matched.
Formation of an orifice-generated vortex ring

Abstract The formation of orifice-generated vortex rings, at a Reynolds number of $5300$ and for a tube-to-orifice diameter ratio of $2.0$, is experimentally investigated for stroke-to-diameter ratios of $0.5(0.5)5.0$. A significant increase is observed in the production of the total invariants of the motion, namely the circulation $\varGamma$, the hydrodynamic impulse $I$ and the kinetic energy $E$, compared with the equivalent nozzle-generated vortex rings. The formation number, as defined by Gharib et al. (J. Fluid Mech., vol. 360, 1998, pp. 121–140), is found to be approximately $2.0$. By measuring the kinematics and the invariants of the ring for increasing stroke ratios, a limiting process in the ring formation is observed, which allows us to define the critical parameters and time scales in the vortex formation process. In particular, it was shown that the ring circulation, impulse, and energy do not reach their asymptotic state at the same non-dimensional time and stroke ratio, hence these two terms cannot be used interchangeably. The stroke ratio required to produce a ring with maximum energy is defined as the ‘optimal stroke ratio’, which is found to be around $4$. The non-dimensional time at which the ring reaches this state, termed the ‘optimal formation time’, is found to be approximately 6–7. The non-dimensional vortex ring numbers $\alpha =E/\rho ^{1/2}\varGamma ^{3/2}I^{1/2}$, $\beta =\varGamma /\rho ^{-1/3}I^{1/3}U^{2/3}$ and , are measured to be $0.33$, $1.8$ and $1.9$, respectively, consistent with previous experimental, numerical and analytical work, suggesting these numbers to be universal for all isolated vortex rings.
Fabrication of polydopamine functionalized halloysite nanotube/polyetherimide membranes for heavy metal removal

Polydopamine modified halloysite nanotubes (HNTs) were synthesised through a one step facile procedure and employed as a well dispersed hydrophilic additive to enhance the filtration properties of polyetherimide (PEI) membranes. The nanocomposite membranes were prepared by an immersion precipitation method with different amounts of modified HNTs (MHNTs) in the casting solution. The good dispersion of MHNTs throughout the membrane matrix was confirmed by elemental mapping analysis. The prepared nanocomposite membranes were extensively studied in terms of their porosity, morphology, membrane hydraulic resistance and hydrophilicity. The permeation experiments showed that the modified membranes exhibited higher water flux than a pristine PEI membrane. The antifouling and anti-biofouling behaviour of the modified membranes was investigated in detail. The results revealed that a membrane with a 3 wt% MHNT dosage showed a higher Fouling Resistance Ratio (FRR) of 74.5% with reversible membrane fouling of 64.3%. Moreover, the membrane showed excellent resistance to microbial growth on the membrane surface. The well performing membrane was subjected to heavy metal ion rejection. Results indicated that membranes had the capacity to adsorb Pb2+ and Cd2+. Overall, PEI–MHNTs nanocomposite membranes could have great potential to improve antifouling, anti-biofouling and filtration properties.
Theoretical analysis and experimental research on multi-layer elastic damping track structure

The increase of axle load and train speed would cause intense wheelrail interactions, and lead to potential vibration related problems in train operation. For the low-frequency vibration reduction of a track system, a multi-layer track structure was proposed and analyzed theoretically and experimentally. Firstly, the analytical solution was derived theoretically, and followed by a parametric analysis to verify the vibration reduction performance. Then, a finite element simulation is carried out to highlight the influence of the tuned slab damper. Finally, the vibration and noise tests are performed to verify the results of the analytical solution and finite element simulation. As the finite element simulation indicates, after installation of the tuned slab damper, the peak reaction force of the foundation can be reduced by 60%, and the peak value of the vertical vibration acceleration would decrease by 50%. The vibration test results show that the insertion losses for the total vibration levels are 13.3 dB in the vertical direction and 21.7 dB in the transverse direction. The noise test results show that the data of each measurement point is smoother and smaller, and the noise in the generating position and propagation path can be reduced by 1.9 dB–5.5 dB.
Performance of Strong Ionic Hydrogels Based on 2-Acrylamido-2-Methylpropane Sulfonate as Draw Agents for Forward Osmosis

AbstractWhile forward osmosis (FO) has great potential to be the next generation water treatment technology, it is constrained by the development of ideal draw agents and membranes. Herein, a series of copolymerized hydrogels based on strong ionic monomer sodium 2-acrylamido-2-methylpropane sulfonate (AMPS-Na) and thermosensitive monomer N-isopropylacrylamide (NIPAM) have been synthesized and used for the first time as draw agents in the FO process. The effects of the composition of poly(NIPAM-co-AMPS-Na) [P(NIPAM-co-AMPS)] hydrogels and operational conditions including draw agent concentrations, temperature, membrane orientation, salinity of feed solution, velocity of feed solution, and running times on the FO performance have been evaluated systematically. The results demonstrate that the water flux increases with increases of the content of AMPS-Na incorporated into the hydrogel and hydrogel concentration in the draw solution, e.g., from 0.40 LMH rising up to 2.85 LMH. Besides, the water flux increases.
Antioxidant and Cytotoxic Activities of Myrtaceae Essential Oils Rich in Terpenoids From Brazil

This work analyzed the chemical compositions and evaluated the antioxidant and cytotoxic activities of essential oils (EO) of Eugenia patrisii (Epat), Eugenia stipitata (Esti), Myrcia splendens (Mspl), Myrcia sylvatica (Msyl), Psidium guajava (Pgua), and Psidium guineense (Pgui-1 and Pgui-2) from the Brazilian Amazon. Sesquiterpenoids were found in high concentrations in the oils of E. patrisii and M. splendens, which were rich in E-caryophyllene (32.0% and 45.8%); E. stipitata and M. sylvatica, which displayed germacrene D (11.8%) and germacrene B (24.5%); and P. guajava that showed epi-β-bisabolol (16.1%) as the main compound. However, P. guineense samples (Pgui-1 and Pgui-2) were rich in monoterpenoids such as limonene (Pgui-1: 30.2%; Pgui-2 30.4%) and α-pinene (Pgui-1: 22.5%; Pgui-2: 17.7%). The samples showed a weak and moderate antioxidant activities in the DPPH assay, displaying inhibition rates from 11.5% to 38.6% (at 10 mg/mL). All samples were cytotoxic against human cancer cells by the MTT method. Epat oil showed higher activity against melanoma (SKMEL-19, IC505.8 µg/mL), gastric (AGP01, IC503.2 µg/mL), and colon (HCT116, IC506.7 µg/mL). Meanwhile, the samples Pgua and Pgui were more active against breast cancer cells (MCF7, IC5012.4 µg/mL and 11.6 µg/mL, respectively).
Chemical Constituents of the Marine Sponge Aaptos aaptos (Schmidt, 1864) and Their Cytotoxic Activity

Seven compounds (1-7) were isolated from the marine sponge Aaptos aaptos living in the Vietnamese sea. Their structures were determined as 2 hours, 5H,7H,9H-9S-hydroxy-imidazo[1,5-α]pyridine-1,3-dione (1), 3-([9-methylhexadecyl]oxy)propane-1,2-diol 2, 2,3-dihydro-2,3-dioxoaaptamine (3), indol-3-aldehyde (4), methyl indole-3-carboxylate (5) 4-hydroxy-5-(indole-3-yl)−5-oxo-pentan-2-one (6), and thymidine (7) by extensive analysis of HR-ESI-MS, 1D, and 2D NMR spectral data, as well as by comparison of the spectral data with those reported in the literature. In addition, the absolute configuration of 1 was determined from the experimental ECD spectrum and comparison of this with the theoretical ECD calculations using the TDDFT method. Compounds 1 and 2 were isolated from nature for the first time. Compound 3 induced cytotoxic activity against SK-LU-1, MCF-7, HepG2, and SK-Mel-2 cell lines with IC50 values of 41.27 ± 2.63, 40.70 ± 2.65, 34.31 ± 3.43, and 36.63 ± 1.40 µM, respectively.
Recent applications of plant cell culture technology in cosmetics and foods

Plants have been used as the main source of phytochemicals with nutritional, medicinal, cultural and cosmetic applications since times immemorial. Nowadays, achieving sustainable development, global climate change, restricted access to fresh water, limited food supply and growing energy demands are among the critical global challenges faced by humanity. Plant cell culture technology has the potential to address some of these challenges by providing effective tools for sustainable supply of phyto‐ingredients with reduced energy, carbon and water footprints. The main aim of this review is to discuss the recent trends in the development of plant cell culture technologies for production of plant‐derived substances with application in food products and cosmetic formulations. The specific technological steps and requirements for the final products are discussed in the light of the advances in cultivation technologies used for growing differentiated and undifferentiated plant in vitro systems. Future prospects and existing challenges of the commercialization of plant cell culture‐derived products have been outlined through the prism of the authors’ point of view. We expect this review will encourage scientists, policymakers and business enterprises to join efforts for speeding‐up the mass commercialization and popularization of plant cell culture technology as an eco‐friendly alternative method for sustainable production of plant‐derived additives with application in food and cosmetic products.
Photocatalytic Activities of Heterojunction Semiconductors Bi2O3/BaTiO3: A Strategy for the Design of Efficient Combined Photocatalysts

The heterojunction semiconductors Bi2O3/BaTiO3 were prepared by a milling-annealing method. The powders were characterized by X-ray diffraction (XRD), the Brunauer−Emmett−Teller (BET) method, transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), and UV−vis diffuse reflection spectroscopy (DRS). Their UV-induced photocatalytic activities were evaluated by the degradations of methyl orange and methylene blue. The results generally show that the heterojunction semiconductors Bi2O3/BaTiO3 exhibit better photocatalytic properties than the single-phase BaTiO3 or Bi2O3. The obviously increased performance of Bi2O3/BaTiO3 is ascribed mainly to the electric-field-driven electron−hole separations both at the interface and in the semiconductors. A strategy for the design of efficient heterojunction photocatalysts was proposed. That is, an electron-accepting semiconductor and a hole-accepting semiconductor with matching band potentials, which respectively possess high electron and hole c.
Global Genetic Heterogeneity in Adaptive Traits

Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS for a variety of phenotypes in the model plant species Arabididopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, while others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis-regulated, whereas the latter are predominately affected by trans-acting variants. Our result illustrate that conclusions about genetic architecture can be incredibly sensitive to sampling and population structure.
Towns and Trails Drive Carnivore Connectivity using a Step Selection Approach

Global increases in human activity threaten connectivity of animal populations. Protection and restoration of animal movement corridors requires robust models to forecast the effects of human activity on connectivity. Recent advances in the field of animal movement ecology and step selection functions offer new approaches for estimating connectivity. We show how a combination of hidden Markov movement models and step selection functions can be used to simulate realistic movement paths with multiple behavioral states. Simulated paths can be used to generate utilization distributions and estimate changes in connectivity for multiple land use scenarios. We applied movement models to 20 years of grizzly bear (Ursus arctos) and gray wolf (Canis lupus) data collected in and around Banff National Park, Canada. These carnivores avoided areas near towns in all seasons, avoided areas of high trail density in most seasons, and campgrounds during summer and fall. We simulated movement paths for three landscape scenarios: reference conditions with no anthropogenic development, current conditions, and future conditions with expanded town footprints and trail networks. We counted the number of paths that crossed valley-wide, digital transects through mountain tourist towns of Banff and Canmore, Alberta. We divided current and future crossing rates by the reference crossing rates to estimate connectivity. Current connectivity rates ranged between 7 and 45% of reference values with an average of 21% for grizzly bears and 25% for wolves. Potential town expansion and increased development of trails further decreased connectivity an average of 6% in future scenarios. Anthropogenic developments reduced the amount of available high quality large carnivore habitat in the Bow Valley by an average of 14% under current conditions and 16% under future conditions. Our approach for estimating connectivity provides a robust and flexible method for combining movement models with step selection analyses to estimate connectivity for a variety of species.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.