Miracle-dz/UniFAR-FTUs huggingface dataset:
Dispersion in Fractures With Ramified Dissolution Patterns

The injection of a reactive fluid into an open fracture may modify the fracture surface locally and create a ramified structure around the injection point. This structure will have a significant impact on the dispersion of the injected fluid due to increased permeability, which will introduce large velocity fluctuations into the fluid. Here, we have injected a fluorescent tracer fluid into a transparent artificial fracture with such a ramified structure. The transparency of the model makes it possible to follow the detailed dispersion of the tracer concentration. The experiments have been compared to two dimensional (2D) computer simulations which include both convective motion and molecular diffusion. A comparison was also performed between the dispersion from an initially ramified dissolution structure and the dispersion from an initially circular region. A significant difference was seen both at small and large length scales. At large length scales, the persistence of the anisotropy of the concentration distribution far from the ramified structure is discussed with reference to some theoretical considerations and comparison with simulations.
Digital image analysis of Ki67 in hot spots is superior to both manual Ki67 and mitotic counts in breast cancer

During pathological examination of breast tumours, proliferative activity is routinely evaluated by a count of mitoses. Adding immunohistochemical stains of Ki67 provides extra prognostic and predictive information. However, the currently used methods for these evaluations suffer from imperfect reproducibility. It is still unclear whether analysis of Ki67 should be performed in hot spots, in the tumour periphery, or as an average of the whole tumour section. The aim of this study was to compare the clinical relevance of mitoses, Ki67 and phosphohistone H3 in two cohorts of primary breast cancer specimens (total n = 294).
Relationship of low doses of alcohol voluntarily consumed during adolescence and early adulthood with subsequent behavioral flexibility

Previous alcohol use is associated with impaired decision-making and impulsivity in humans, but the relationship between alcohol use and decision-making/impulsivity is unclear. In two experiments, we determined whether chronic intermittent access to alcohol during adolescence and early adulthood would alter or be correlated with performance in a go/no-go reversal task, a devaluation task, or operant extinction. Rats received 6 weeks of chronic intermittent access to 20% alcohol or water from postnatal day 26 to 66 and then behavioral testing was initiated 1.5–2.5 weeks later. We found no evidence that voluntary alcohol consumption altered behavior in either task. However, we found that rats that consumed more alcohol made fewer commission errors in reversal learning compared with rats that drank less. There was no relationship between alcohol consumption and reversal learning omission errors. Alcohol consumption was not correlated with the magnitude of the devaluation effect, but rats that consumed more alcohol showed faster extinction during the devaluation test. Our results suggest that the relationships between behavioral flexibility and alcohol consumption may represent individual differences. Future work will determine the neurobiological and genetic bases of these behavioral differences.
An Exercise and Sports Equipment Recognition System

Most mobile health management applications today require manual input or use sensors like the accelerometer or GPS to record user data. The onboard camera remains underused. We propose an Exercise and Sports Equipment Recognition System (ESRS) that can recognize physical activity equipment from raw image data. This system can be integrated with mobile phones to allow the camera to become a primary input device for recording physical activity. We employ a deep convolutional neural network to train models capable of recognizing 14 different equipment categories. Furthermore, we propose a preprocessing scheme that uses color normalization and denoising techniques to improve recognition accuracy. Our best model is able to achieve a a top-3 accuracy of 83.3% on the test dataset. We demonstrate that our model improves upon GoogLeNet for this dataset, the state-of-the-art network which won the ILSVRC 2014 challenge. Our work is extendable as improving the quality and size of the training dataset can further boost predictive accuracy.
A Novel Perspective on the ApoM-S1P Axis, Highlighting the Metabolism of ApoM and Its Role in Liver Fibrosis and Neuroinflammation

Hepatocytes, renal proximal tubule cells as well as the highly specialized endothelium of the blood brain barrier (BBB) express and secrete apolipoprotein M (apoM). ApoM is a typical lipocalin containing a hydrophobic binding pocket predominantly carrying Sphingosine-1-Phosphate (S1P). The small signaling molecule S1P is associated with several physiological as well as pathological pathways whereas the role of apoM is less explored. Hepatic apoM acts as a chaperone to transport S1P through the circulation and kidney derived apoM seems to play a role in S1P recovery to prevent urinal loss. Finally, polarized endothelial cells constituting the lining of the BBB express apoM and secrete the protein to the brain as well as to the blood compartment. The review will provide novel insights on apoM and S1P, and its role in hepatic fibrosis, neuroinflammation and BBB integrity.
DeepFM: An End-to-End Wide & Deep Learning Framework for CTR Prediction

Learning sophisticated feature interactions behind user behaviors is critical in maximizing CTR for recommender systems. Despite great progress, existing methods have a strong bias towards low- or high-order interactions, or rely on expertise feature engineering. In this paper, we show that it is possible to derive an end-to-end learning model that emphasizes both low- and high-order feature interactions. The proposed framework, DeepFM, combines the power of factorization machines for recommendation and deep learning for feature learning in a new neural network architecture. Compared to the latest Wide & Deep model from Google, DeepFM has a shared raw feature input to both its "wide" and "deep" components, with no need of feature engineering besides raw features. DeepFM, as a general learning framework, can incorporate various network architectures in its deep component. In this paper, we study two instances of DeepFM where its "deep" component is DNN and PNN respectively, for which we denote as DeepFM-D and DeepFM-P. Comprehensive experiments are conducted to demonstrate the effectiveness of DeepFM-D and DeepFM-P over the existing models for CTR prediction, on both benchmark data and commercial data. We conduct online A/B test in Huawei App Market, which reveals that DeepFM-D leads to more than 10% improvement of click-through rate in the production environment, compared to a well-engineered LR model. We also covered related practice in deploying our framework in Huawei App Market.
PortoLivingLab: An IoT-Based Sensing Platform for Smart Cities

Smart cities aim to improve the citizens’ quality of life by leveraging information about urban scale processes extracted from heterogeneous data sources collected on city-wide deployments. The Internet-of-Things (IoT) is, thus, the enabler of smart city technologies at urban scale. In this paper, we present PortoLivingLab, a multisource sensing infrastructure that leverages IoT technology to achieve city-scale sensing of four phenomena: weather, environment, public transport, and people flows. To sense these processes on a city scale, we deployed a vehicular network with over 600 vehicles and 19 static environmental sensors. We also developed an easily reconfigurable crowdsensing platform and carried out several crowdsensing campaigns with more than 600 participants. The data is collected in a common backend and stored using similar spatio-temporal data models to simplify sharing and joint analysis for the characterization of urban dynamics. We describe the architecture and composing elements of PortoLivingLab, highlighting the IoT technologies, and challenges faced. We present several proof-of-concept use cases (e.g., passenger flows from WiFi connections) that provide new insights into different components of an evolving and moving city. Finally, we lay out the future lines of work that will strive for finding hidden phenomena by leveraging data from the three complementary platforms.
PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

Significance Hybrids are of high value in agriculture. Hybrid vigor applies only to the F1 generation. Pure breeding lines, which maintain the hybrid phenotype, hybrid mimics, together with the small phenotype line have proven to be powerful in identifying genes and pathways critical for hybrid vigor. PHYTOCHROME-INTERACTING FACTOR (PIF4), regulating auxin biosynthesis and action, features in the development of the hybrid vigor phenotype. The homozygous hybrid mimic lines all have the same particular 12 chromosomal segments, 4 from the C24 parent and 8 from Ler. The small phenotype line has each of these segments derived from the genome of the alternative parent, so one or more loci needed for the large hybrid mimic phenotype are likely to be on each segment. F1 hybrids in Arabidopsis and crop species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding hybrid mimic lines by recurrent selection and also selected a pure breeding small phenotype line. The hybrid mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and 8 from Ler were present in all of the hybrid mimic lines, whereas in the F6 small phenotype line, the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in hybrid mimics and F1 plants but not in the small phenotype line. These genes may be critical for the generation of hybrid vigor. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signaling gene IAA29. A number of auxin responsive genes promoting leaf growth were up-regulated in the F1 hybrids and hybrid mimics, suggesting that increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The hybrid mimic seeds had earlier germination as did the seeds of the F1 hybrids, indicating cosegregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids.
Conference on ‘ Multidisciplinary approaches to nutritional problems ’ Nutrition Society Silver Medal Lecture Nutrigenetics and personalised nutrition : how far have we progressed and are we likely to get there ?

Nutrigenetics and personalised nutrition are components of the concept that in the future genotyping will be used as a means of defining dietary recommendations to suit the individual. Over the last two decades there has been an explosion of research in this area, with often conflicting findings reported in the literature. Reviews of the literature in the area of apoE genotype and cardiovascular health, apoA5 genotype and postprandial lipaemia and perilipin and adiposity are used to demonstrate the complexities of genotype–phenotype associations and the aetiology of apparent between-study inconsistencies in the significance and size of effects. Furthermore, genetic research currently often takes a very reductionist approach, examining the interactions between individual genotypes and individual disease biomarkers and how they are modified by isolated dietary components or foods. Each individual possesses potentially hundreds of ‘atrisk’ gene variants and consumes a highly-complex diet. In order for nutrigenetics to become a useful public health tool, there is a great need to use mathematical and bioinformatic tools to develop strategies to examine the combined impact of multiple gene variants on a range of health outcomes and establish how these associations can be modified using combined dietary strategies.
Effect of incremental amounts of fish oil in the diet on ruminal lipid metabolism in growing steers

Based on the potential benefits to human health, there is interest in developing sustainable nutritional strategies to enhance the concentration of long-chain n-3 fatty acids in ruminant-derived foods. Four Aberdeen Angus steers fitted with rumen and duodenal cannulae were used in a 4 × 4 Latin square experiment with 21 d experimental periods to examine the potential of fish oil (FO) in the diet to enhance the supply of 20 : 5n-3 and 22 : 6n-3 available for absorption in growing cattle. Treatments consisted of total mixed rations based on maize silage fed at a rate of 85 g DM/kg live weight0·75/d containing 0, 8, 16 and 24 g FO/kg diet DM. Supplements of FO reduced linearly (P < 0·01) DM intake and shifted (P < 0·01) rumen fermentation towards propionate at the expense of acetate and butyrate. FO in the diet enhanced linearly (P < 0·05) the flow of trans-16 : 1, trans-18 : 1, trans-18 : 2, 20 : 5n-3 and 22 : 6n-3, and decreased linearly (P < 0·05) 18 : 0 and 18 : 3n-3 at the duodenum. Increases in the flow of trans-18 : 1 were isomer dependent and were determined primarily by higher amounts of trans-11 reaching the duodenum. In conclusion, FO alters ruminal lipid metabolism of growing cattle in a dose-dependent manner consistent with an inhibition of ruminal biohydrogenation, and enhances the amount of long-chain n-3 fatty acids at the duodenum, but the increases are marginal due to extensive biohydrogenation in the rumen.
A Reduced-Order Model of a Lithium-Ion Cell Using the Absolute Nodal Coordinate Formulation Approach

The widespread use of lithium-ion batteries motivates the need for robust battery management systems (BMSs) that can both observe the internal states of a cell and update degraded physical parameters over time. Many models that are capable of accurately replicating the internal dynamics of cells during high discharge and charging cycles contain too many states to perform real-time estimation, and many models that contain a reasonable number of states for estimation do not adequately replicate the performance of cells at higher rates. In this paper, a model is proposed based on the absolute nodal coordinate formulation approach, which includes as its states concentration levels at different spatial locations within the solid electrode and electrolyte. Its behavior is demonstrated through simulation results reproducing high performance solutions and tractable state representation for use with advanced BMSs.
Modulation of the inwardly rectifying potassium channel Kir4.1 by the pro-invasive miR-5096 in glioblastoma cells

Inwardly rectifying potassium channels (Kir), and especially the barium-sensitive Kir4.1 encoded by KCNJ10, are key regulators of glial functions. A lower expression or mislocation of Kir4.1 is detected in human brain tumors. MicroRNAs participate in the regulation of ionic channels and associated neurologic disorders. Here, we analyze effects of miR-5096 on the Kir4.1 expression and function in two glioblastoma cell lines, U87 and U251. Using whole-cell patch-clamp and western-blot analysis, we show that cell loading with miR-5096 decreases the Kir4.1 protein level and associated K+ current. Cell treatment with barium, a Kir4.1 blocker, or cell loading of miR-5096 both increase the outgrowth of filopodia in glioma cells, as observed by time-lapse microscopy. Knocking-down Kir4.1 expression by siRNA transfection similarly increased both filopodia formation and invasiveness of glioma cells as observed in Boyden chamber assay. MiR-5096 also promotes the release of extracellular vesicles by which it increases its own transfer to surrounding cells, in a Kir4.1-dependent manner in U251 but not in U87. Altogether, our results validate Kir4.1 as a miR-5096 target to promote invasion of glioblastoma cells. Our data highlight the complexity of microRNA effects and the role of K+ channels in cancer.
Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells

The term “nonsense-mediated mRNA decay” (NMD) originally described the degradation of mRNAs with premature translation–termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%–10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5–SMG7 or SMG5–PNRC2 binding to UPF1. However, the existence, dominance, and mechanistic details of these exonucleolytic pathways are divisive. Therefore, we have investigated the possible exonucleolytic modes of mRNA decay in NMD by examining the roles of UPF1, SMG5, SMG7, and PNRC2 using a combination of functional assays and interaction mapping. Confirming previous work, we detected an interaction between SMG5 and SMG7 and also a functional need for this complex in NMD. In contrast, we found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2. Instead, we show that UPF1 interacts with PNRC2 and that it triggers 5′–3′ exonucleolytic decay of reporter transcripts in tethering assays. PNRC2 interacts mainly with decapping factors and its knockdown does not affect the RNA levels of NMD reporters. We conclude that PNRC2 is probably an important mRNA decapping factor but that it does not appear to be required for NMD.
VLSI friendly fast CU/PU mode decision for HEVC intra encoding: Leveraging convolution neural network

To alleviate the computational intensity of Intra encoding for High Efficiency Video Coding (HEVC), we introduce the convolution neural network to reduce the number of the promising CU/PU candidate modes to carry out the exhaustive RDO processing. The practical merits include: Firstly, the proposed algorithm reduces the maximum computational complexity at the grain of 64 × 64 coding tree unit(CTU), which makes it efficient to ameliorate the complexity of the real-time hardwired encoder implementation. Secondly, because the CU/PU mode decision is made based on the analysis of source block textures, our algorithm does not depend on intermediate results of encoding. That is, the proposed algorithm will not deteriorate the processing schedule of CTU encoding. Experimental results show that, when our algorithm is integrated with HM12.0, the 61.1% Intra encoding time was saved, whereas the averaging BDBR augment is merely 3.39%.
Low Plasma ApoE Levels Are Associated with Smaller Hippocampal Size in the Alzheimer's Disease Neuroimaging Initiative Cohort

Apolipoprotein E (APOE) genotype is the strongest known genetic risk factor for sporadic Alzheimer's disease (AD), but the utility of plasma ApoE levels for assessing the severity of underlying neurodegenerative changes remains uncertain. Here, we examined cross-sectional associations between plasma ApoE levels and volumetric magnetic resonance imaging indices of the hippocampus from 541 participants [57 with normal cognition (NC), 375 with mild cognitive impairment (MCI), and 109 with mild AD] who were enrolled in the Alzheimer's Disease Neuroimaging Initiative. Across the NC and MCI groups, lower plasma ApoE levels were significantly correlated with smaller hippocampal size, as measured by either hippocampal volume or hippocampal radial distance. These associations were driven primarily by findings from carriers of an APOE ε4 allele and are consistent with prior reports that lower plasma ApoE levels correlate with greater global cortical Pittsburgh Compound B retention. In this high-risk group, plasma ApoE levels may represent a peripheral marker of underlying AD neuropathology in nondemented elderly individuals.
Effects of Polarized Debye Sheath and Trapped Ions on Solitary Structures in a Strongly Coupled Inhomogeneous Dusty Plasma

The effects of polarized Debye sheath (i.e., polarization force) and trapped ions on the nonlinear propagation of dust-acoustic (DA) waves are investigated, including the dust inhomogeneity in the strongly coupled dusty plasma. Dispersion relation and propagation of possible modes are calculated from the underlying usual hydrodynamic model. Then, a variable coefficient’s modified Korteweg-de Vries equation describing the dynamics of DA solitary waves is derived from a weakly nonlinear analysis, and is solved to get the stationary solutions using a sine–cosine method. It is found that for experimental conditions under which the interaction of resonant ions and highly negatively charged dust grains is important, only soliton with negative potential can propagate in such a strongly coupled inhomogeneous dusty plasma. In the presence of trapped ions, the amplitude of solitary waves is found to be smaller compared with that for the Boltzmann distribution. Moreover, it is argued that the soliton profile is highly sensitive to the effects of modified strength of the polarization force, dust temperature, and dust density inhomogeneity.
Electron Microscopic Analysis of Hippocampal Axo‐Somatic Synapses in a Chronic Stress Model for Depression

Stress can alter the number and morphology of excitatory synapses in the hippocampus, but nothing is known about the effect of stress on inhibitory synapses. Here, we used an animal model for depression, the chronic mild stress model, and quantified the number of perisomatic inhibitory neurons and their synapses. We found reduced density of parvalbumin‐positive (PV+) neurons in response to stress, while the density of cholecystokinin‐immunoreactive (CCK+) neurons was unaffected. We did a detailed electron microscopic analysis to quantify the frequency and morphology of perisomatic inhibitory synapses in the hippocampal CA1 area. We analyzed 1100 CA1 pyramidal neurons and 4800 perisomatic terminals in five control and four chronically stressed rats. In the control animals we observed the following parameters: Number of terminals/soma = 57; Number of terminals/100 µm cell perimeter = 10; Synapse/terminal ratio = 32%; Synapse number/100 terminal = 120; Average terminal length = 920nm. None of these parameters were affected by the stress exposure. Overall, these data indicate that despite the depressive‐like behavior and the decrease in the number of perisomatic PV+ neurons in the light microscopic preparations, the number of perisomatic inhibitory synapses on CA1 pyramidal cells was not affected by stress. In the electron microscope, PV+ neurons and the axon terminals appeared to be normal and we did not find any apoptotic or necrotic cells. This data is in sharp contrast to the remarkable remodeling of the excitatory synapses on spines that has been reported in response to stress and depressive‐like behavior. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc.