Miracle-dz/UniFAR-FTUs huggingface dataset:
Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

DNA methylation in plants plays a role in transposon silencing, genome stability and gene expression regulation. Environmental factors alter the methylation pattern of DNA and recently nutrient stresses, such as phosphate starvation, were shown to alter DNA methylation. Furthermore, DNA methylation had been frequently addressed in plants with notably small genomes that are poor in transposons. Here, we compare part of the DNA methylome of nitrogen- and phosphorus-deficient maize roots by reduced representation sequencing and analyze their relationship with gene expression under prolonged stresses. Tremendous DNA methylation loss was encountered in maize under nitrogen-deficiency, but much less with phosphorus-deficiency. This occurred only in the symmetrical cytosine context, predominantly in CG context, but also in the CHG context. In contrast to other plants, differential methylation in the more flexible CHH context was essentially absent. In both deficiency conditions a similar number of differentially expressed genes were found and differentially methylated regions (DMRs) were predominantly identified in transposable elements (TEs). A minor fraction of such DMRs was associated with altered gene expression of nearby genes. Interestingly, although these TEs were mostly hypomethylated, they were associated with both up- or down regulated gene expression. Our results suggest a different methylome regulation in maize compared to rice and Arabidopsis upon nutrient deficiencies and point to highly nutrient- and species-specific dynamics of genomic DNA methylation. Description of Significance: DNA methylation suppresses transposons in plant genomes, but was also associated with other genome protective functions and gene expression regulation. Recently it was shown that DNA methylation dynamically responds to several abiotic and biotic environmental factors, but to a large instance, DNA methylation is also heritable. DNA methylation changes have also been reported under phosphorus starvation in rice and Arabidopsis, but its relation with other nutrients and its importance for individual gene expression remains unclear. Here, DNA methylation changes upon the deficiency of two major essential nutrients, nitrogen and phosphorus, were studied in parallel with gene expression responses in maize roots. We show context, nutrient- and species-specific patterns in the methylome, as well as its relation with the nutrient-deficiency transcriptome. While cases of differentially methylated regions in the vicinity of differentially expressed genes were apparent, both positive and negative roles on the gene expression were identified, irrespective of the context.
A Healthy Asian A Posteriori Dietary Pattern Correlates with A Priori Dietary Patterns and Is Associated with Cardiovascular Disease Risk Factors in a Multiethnic Asian Population.

Background Healthful dietary patterns are associated with cardiovascular disease risk factors in Western populations. However, a consistent healthful dietary pattern across major Asian ethnic groups has yet to be identified. Objective We aimed to identify a posteriori dietary patterns for Chinese, Malay, and Indian ethnic groups in an urban Asian setting, compare these with a priori dietary patterns, and ascertain associations with cardiovascular disease risk factors including hypertension, obesity, and abnormal blood lipid concentrations. Methods We used cross-sectional data from 8433 Singapore residents (aged 21-94 y) from the Multi-Ethnic Cohort study of Chinese, Malay, and Indian ethnicity. Food consumption was assessed using a validated 169-item food-frequency questionnaire. With the use of 28 food groups, dietary patterns were derived by principal component analysis, and their association with cardiovascular disease risk factors was assessed using multiple linear regression. Associations between derived patterns and a priori patterns (aHEI-2010-Alternative Healthy Eating Index-2010, aMED-alternate Mediterranean Diet, and DASH-Dietary Approaches to Stop Hypertension) were assessed, and the magnitude of associations with risk factors compared. Results We identified a "healthy" dietary pattern, similar across ethnic groups, and characterized by high intakes of whole grains, fruit, dairy, vegetables, and unsaturated cooking oil and low intakes of Western fast foods, sugar-sweetened beverages, poultry, processed meat, and flavored rice. This "healthy" pattern was inversely associated with body mass index (BMI; in kg/m2) (-0.26 per 1 SD of the pattern score; 95% CI: -0.36, -0.16), waist circumference (-0.57 cm; 95% CI: -0.82, -0.32), total cholesterol (-0.070 mmol/L; 95% CI: -0.091, -0.048), LDL cholesterol (-0.054 mmol/L; 95% CI: -0.074, -0.035), and fasting triglycerides (-0.22 mmol/L; 95% CI: -0.04, -0.004) and directly associated with HDL cholesterol (0.013 mmol/L; 95% CI: 0.006, 0.021). Generally, "healthy" pattern associations were at least as strong as a priori pattern associations with cardiovascular disease risk factors. Conclusion A healthful dietary pattern that correlated well with a priori patterns and was associated with lower BMI, serum LDL cholesterol, total cholesterol, and fasting triglyceride concentrations was identified across 3 major Asian ethnic groups.
Detecting Seronegative-Early HIV Infections Among Adult Versus Student Kenyan Blood Donors, by Using Stimmunology

Background: Undetectable HIV infection in blood banks poses a serious threat to public health. Thus, donations from high school students are preferred over adult samples in Kenyan blood banks, due to lower HIV infection prevalence within this population, as detected by conventional serology testing. However, the number of recently infected individuals remains difficult to identify, as HIV-induced immunological window periods can span months. This study focuses on the potential contribution of a novel mode of diagnostic testing in revealing early, seronegative HIV carriers. Methods and Findings: Stimmunology, an in vitro lymphocyte stimulation technique, was used to detect early HIV infection among random samples of adult and adolescent blood donors. The Stimmunology protocol unveiled a significant number of early, pre-seroconversion HIV carriers both among adult and teenage Kenyan populations, undetected by typical serological diagnostic kits. Both populations demonstrated a significant increase in HIV-specific antibody formation following activation using the Stimmunology assay. The younger population exhibited a higher proportion of early HIV infection (0.45) than the adult (0.27) population. Conclusions: While blood samples of young donors are preferred over adult donations, these data demonstrate a worrisome ratio of early, seronegative HIV carriers within this population. This simple, cost-effective, and reliable HIV-boosting antibody assay can be used in a resource-poor setting to increase blood supply safety and quality. Incorporation of Stimmunology into basic blood bank testing and into diagnostic protocols can also decrease undesirable disease transmission.
Reaction to fire of glass/ hemp/ furan composites

investigating the reaction to fire for two composites using a resin of furfuryl and glass fibers as well as hemp fibers. The composites are made at DTU wind energy using vacuum compression moulding and are tested for their mechanical strength. The samples used for the fire tests been stored for some years under ambient conditions inside a laboratory environment. Different methods are used to investigate the reaction to fire: Vertical upward flame spread; Bomb calorimeter, Mass loss cone calorimeter, STA tests under inert atmosphere.
Effect of feeding broccoli floret residues on leghorn layer performance and egg quality and nutrient digestibility

ABSTRACT 1. A study was conducted to determine the effects of dried broccoli floret (DBF) on egg production parameters, egg quality and apparent nutrient digestibility of laying hens. It was hypothesised that feeding DBF can improve egg quality without adversely affecting layer performance.2. Seventy-two White Leghorn layers aged 62 weeks were randomly allotted to 4 dietary treatments (6 cage replicates with 3 hens each) and fed diets containing 0, 40, 80 and 120 g/kg DBF in feed for 56 d.3. Inclusion of DBF had no effect on feed intake, egg production, feed conversion ratio or egg components. However, egg weight increased (linear effect, P < 0.05) as the level of DBF in the diet increased. Egg breakage strength, eggshell strength and Haugh unit were not influenced by dietary treatments. Egg yolk colour (quadratic effect, P = 0.002) and α-tocopherol concentration (quadratic effect, P < 0.0001) improved as a result of DBF inclusion. Egg yolk cholesterol concentration was not altered by DBF inclusion. Apparent total tract nutrient (dry matter, organic matter and crude protein) digestibility coefficients decreased (linear effect, P < 0.05) as the level of DBF increased.4. Feeding DBF to layers up to 120 g/kg of the diet had no negative effects on feed intake, egg production and feed efficiency and improved egg yolk colour and α-tocopherol concentration. However, total tract nutrient digestibility coefficients were negatively decreased as a result of DBF inclusion.
Improving Anonymization Clustering

Microaggregation is a technique to preserve privacy when confidential information about individuals shall be used by third parties. A basic property to be established is called k-anonymity. It requires that identifying information about individuals should not be unique, instead there has to be a group of size at least k that looks identical. This is achieved by clustering individuals into appropriate groups and then averaging the identifying information. The question arises how to select these groups such that the information loss by averaging is minimal. This problem has been shown to be NP-hard. Thus, several heuristics called MDAV ,V-MDAV , . have been proposed for finding at least a suboptimal clustering. This paper proposes a more sophisticated, but still efficient strategy called MDAV∗ to construct a good clustering. The question whether to extend a group locally by individuals close by or to start a new group with such individuals is investigated in more depth. This way, a noticeable lower information loss can be achieved which is shown by applying MDAV∗ to several established benchmarks of real data and also to specifically designed random data.
Densely Connected High Order Residual Network for Single Frame Image Super Resolution

Deep convolutional neural networks (DCNN) have been widely adopted for research on super resolution recently, however previous work focused mainly on stacking as many layers as possible in their model, in this paper, we present a new perspective regarding to image restoration problems that we can construct the neural network model reflecting the physical significance of the image restoration process, that is, embedding the a priori knowledge of image restoration directly into the structure of our neural network model, we employed a symmetric non-linear colorspace, the sigmoidal transfer, to replace traditional transfers such as, sRGB, Rec.709, which are asymmetric non-linear colorspaces, we also propose a "reuse plus patch" method to deal with super resolution of different scaling factors, our proposed methods and model show generally superior performance over previous work even though our model was only roughly trained and could still be underfitting the training set.
Correlation of Nasal Eosinophilia and Response after Nasal Provocation Test in Patients with Nonallergic Rhinitis

Objectives We aimed to evaluate the relationship between nasal eosinophilia and nasal hyperresponsiveness to allergen extract. Study Design Retrospective chart review. Setting Academic tertiary rhinologic practice. Subjects and Methods We performed allergy tests (skin prick test and multiple allergosorbent test) and nasal cytology for 194 patients with rhinitis symptoms (76 males and 118 females; age, 11-69 years). According to the results, they were classified into 4 groups: group A (allergic rhinitis with eosinophilia, n = 26), group B (allergic rhinitis without eosinophilia, n = 77), group C (nonallergic rhinitis with eosinophilia syndrome, n = 20), and group D (nonallergic rhinitis without eosinophilia, n = 71). We performed a nasal provocation test (NPT) using house dust mite extract and assessed the changes in symptoms and the decrease in acoustic parameters (total nasal volume and minimal cross-sectional area [MCA]). Results Patients in group C were more likely to have severe rhinorrhea and sneezing than those in group D (P < .001). After NPT, group C had greater aggravation of nasal obstruction than group D (P < .001). Group C also showed markedly greater MCA changes as compared with group D 15 minutes after the antigen challenge (P = .002). There was significant correlation between the number of eosinophils and an increase in nasal obstruction (r = 0.319, P = .0009), rhinorrhea (r = 0.302, P = .0017), sneezing (r = 0.219, P = .0241), change in the total nasal volume 15 minutes after NPT (r = 0.287, P = .0028), and change in the MCA 15 minutes (r = 0.322, P = .0008) and 30 minutes (r = 0.250, P = .0098) after NPT. Conclusion In patients with NAR, nasal eosinophilia is associated with provocative response after NPT. Further research should be performed to elucidate the mechanisms that underlie this phenomenon.
Cortical networks for rotational uncertainty effect in mental rotation task by partial directed coherence analysis of EEG

Partial directed coherence (PDC) as a frequency-domain representation of Granger casuality (GC) could detect both strength and direction of cortical interactions by multivari-ate autoregressive (MVAR) model of electroencephalography (EEG). In the present study, we investigate the underlying neural networks mechanisms of “rotational uncertainty effect” during mental rotation (MR) task by PDC analysis of multichannel EEG signals before and after the visual stimuli presented, we found that (i) temporally the “rotational uncertainty effect” involved an activated network before the visual stimuli presented, which could also affect the cognitive process of MR later; (ii) the causality functional connectivity network indicated that the bi-directional frontal ⇀↽ parietal networks played critical roles in maintaining the readiness during the MR task. These findings suggest that functional networks of un-cued preparation before visual stimuli presented are worth to be paid more attention. And these networks provide crucial casuality information to understand the neural mechanism for “rotational uncertainty effect” in MR task.
Body size–dependent bioaccumulation, tissue distribution, and trophic and maternal transfer of phenolic endocrine‐disrupting contaminants in a freshwater ecosystem

Parabens, bisphenol A (BPA), triclosan, and triclocarban are recognized endocrine‐disrupting contaminants (EDCs); and their occurrence in the environment has attracted increasing concern. Body size–dependent bioaccumulation, tissue distribution, trophic magnification, and maternal transfer of methyl‐, ethyl‐, propyl‐, and butylparabens; 2‐phenylphenol (PHP); BPA; triclosan; and triclocarban were investigated in freshwater fish of the Pearl River catchment, China. Most of the EDCs were detected in more than half of the biota samples, ranging from not detected to 6750 ng g−1 lipid weight, with median concentrations of 5 to 72 ng g−1 lipid weight. Livers generally contained the highest EDC levels (1609 ± 1860 ng g−1 lipid wt, mean ± standard deviation), followed in decreasing order by eggs (842 ± 1317 ng g−1 lipid wt), belly fats (488 ± 465 ng g−1 lipid wt), and dorsal muscles (240 ± 239 ng g−1 lipid wt) of the wildlife. Body size–dependent bioaccumulation of the EDCs was observed in the freshwater fish, which varied according to species, tissue, and compound. The concentrations of triclosan, PHP, and BPA usually showed decreasing trends, whereas parabens mostly demonstrated increasing tendency with increasing fish weights, indicating effects of growth dilution and bioaccumulation, respectively. Potential biomagnification was shown by triclosan with trophic magnification factors of 3.0, 4.3, and 4.0 in liver, belly fat, and dorsal muscle, respectively. In addition, the potential of maternal transfer in the fish was primarily revealed for methyl‐ and propylparabens, PHP, triclosan, and BPA. Presence of the EDCs in the freshwater organisms of the Pearl River catchment warrants more attention considering the potential of trophic magnification and maternal transfer. Environ Toxicol Chem 2018;37:1811–1823. © 2018 SETAC
Learning to Color from Language

Automatic colorization is the process of adding color to greyscale images. We condition this process on language, allowing end users to manipulate a colorized image by feeding in different captions. We present two different architectures for language-conditioned colorization, both of which produce more accurate and plausible colorizations than a language-agnostic version. Furthermore, we demonstrate through crowdsourced experiments that we can dramatically alter colorizations simply by manipulating descriptive color words in captions.
The limits and potentials of deep learning for robotics

The application of deep learning in robotics leads to very specific problems and research questions that are typically not addressed by the computer vision and machine learning communities. In this paper we discuss a number of robotics-specific learning, reasoning, and embodiment challenges for deep learning. We explain the need for better evaluation metrics, highlight the importance and unique challenges for deep robotic learning in simulation, and explore the spectrum between purely data-driven and model-driven approaches. We hope this paper provides a motivating overview of important research directions to overcome the current limitations, and helps to fulfill the promising potentials of deep learning in robotics.
Low uptake of palliative care for COPD patients within primary care in the UK

Mortality and symptom burden from chronic obstructive pulmonary disease (COPD) and lung cancer are similar but there is thought to be an inequality in palliative care support (PCS) between diseases. This nationally representative study assessed PCS for COPD patients within primary care in the UK. This was a cohort study using electronic healthcare records (2004–2015). Factors associated with receiving PCS were assessed using logistic regression for the whole cohort and deceased patients. There were 92 365 eligible COPD patients, of which 26 135 died. Only 7.8% of the whole cohort and 21.4% of deceased patients received PCS. Lung cancer had a strong association with PCS compared with other patient characteristics, including Global Initiative for Chronic Obstructive Lung Disease stage and Medical Research Council Dyspnoea score (whole cohort, lung cancer: OR 14.1, 95% CI 13.1–15; deceased patients, lung cancer: OR 6.5, 95% CI 6–7). Only 16.7% of deceased COPD patients without lung cancer received PCS compared with 56.5% of deceased patients with lung cancer. In patients that received PCS, lung cancer co-diagnosis significantly increased the chances of receiving PCS before the last month of life (1–6 versus ≤1 month pre-death: risk ratio 1.4, 95% CI 1.3–1.7). Provision of PCS for COPD patients in the UK is inadequate. Lung cancer, not COPD, was the dominant driver for COPD patients to receive PCS. Palliative care provision for COPD patients without lung cancer is poor in the UK http://ow.ly/IIC230gWOOV
All-optical attoclock: accessing exahertz dynamics of optical tunnelling through terahertz emission

The hot debate regarding attosecond dynamics of optical tunneling has, so far, been focused on the presence, or absence, of time delays associated to the electron tunnelling through the classically forbidden region during atomic ionization in intense infrared laser fields. Strong theoretical and experimental arguments have been put forward to advocate the polar opposite points of view. The underlying dynamics are richer. Here we propose to use the nonlinear optical responses of the tunnelling electrons to tailored light fields to track these dynamics in full complexity. Using the combination of single-color and two-color fields, we resolve not only ionization delays, but also temporal re-shaping and spatial re-focusing of the tunnelling wavepacket as it emerges from the classically forbidden region. Access to these details of the dynamics is facilitated by the near-instantaneous nature of the nonlinear optical response driven by ionization, and by using tailored laser pulses to induce this response. Our work introduces a new type of attoclock for optical tunnelling, one that is based on measuring light rather than photo-electrons. Our conclusions suggest a possible middle ground between the two conflicting points of view.
Understanding the Rise in Corporate Cash: Precautionary Savings or Foreign Taxes

What has driven the dramatic rise in U.S. corporate cash? Using non-public data, we show that the run-up is not uniform across firms but is concentrated in the foreign subsidiaries of multinational firms. Standard precautionary motives explain only domestic cash holdings, not these burgeoning foreign cash balances. Falling foreign tax rates, coupled with relaxed restrictions on income shifting, are the root of the changing foreign cash patterns. Firms with intellectual property have the greatest ability to shift income to low tax jurisdictions, and their foreign subsidiaries are where we observe the largest accumulations of cash. Received September 6, 2017; editorial decision August 22, 2018 by Editor David Denis. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Degrees of Freedom and Achievable Rate of Wide-Band Multi-Cell Multiple Access Channels With No CSIT

This paper considers a $K$ -cell multiple access channel with inter-symbol interference. The primary finding of this paper is that, without instantaneous channel state information at the transmitters, interference-free degrees-of-freedom (DoF) per cell is achievable, provided that the delay spread of the desired links is significantly longer than that of the interfering links when the number of user per cell is sufficiently large. This achievability is shown by a blind interference management method that exploits the relativity in delay spreads between desired and interfering links. In this method, all inter-cell-interference signals are aligned-and-cancelled by using discrete-Fourier-transform-based precoding and combining, both depend only on the lengths of channel-impulse-response. In addition to the DoF analysis, the achievable rate of the proposed method is characterized in a closed-form expression. Some illustrative examples are presented to show an additional sum-DoF gain obtained by exploiting propagation delay in the interfering links or the heterogeneity of the channel coherence time between the desired and interfering links.