Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of ORMDL3 with rhinovirus‐induced endoplasmic reticulum stress and type I Interferon responses in human leucocytes

Children with risk alleles at the 17q21 genetic locus who wheeze during rhinovirus illnesses have a greatly increased likelihood of developing childhood asthma. In mice, overexpression of the 17q21 gene ORMDL3 leads to airway remodelling and hyperresponsiveness. However, the mechanisms by which ORMDL3 predisposes to asthma are unclear. Previous studies have suggested that ORMDL3 induces endoplasmic reticulum (ER) stress and production of the type I interferon (IFN)‐regulated chemokine CXCL10.
On the Performance of Network NOMA in Uplink CoMP Systems: A Stochastic Geometry Approach

To improve the system throughput, this paper proposes a network non-orthogonal multiple access (N-NOMA) technique for the uplink coordinated multi-point transmission (CoMP). In the considered scenario, multiple base stations collaborate with each other to serve a single user, referred to as the CoMP user, which is the same as for conventional CoMP. However, unlike conventional CoMP, each base station in N-NOMA opportunistically serves an extra user, referred to as the NOMA user, while serving the CoMP user at the same bandwidth. The CoMP user is typically located far from the base stations, whereas users close to the base stations are scheduled as NOMA users. Hence, the channel conditions of the two kinds of users are very distinctive, which facilitates the implementation of NOMA. Compared to the conventional orthogonal multiple access-based CoMP scheme, where multiple base stations serve a single CoMP user only, the proposed N-NOMA scheme can support larger connectivity by serving the extra NOMA users, and improve the spectral efficiency by avoiding the CoMP user solely occupying the spectrum. A stochastic geometry approach is applied to model the considered N-NOMA scenario as a Poisson cluster process, based on which insightful closed-form or quasi closed-form analytical expressions for outage probabilities and ergodic rates are obtained. Numerical results are presented to show the accuracy of the analytical results and also demonstrate the superior performance of the proposed N-NOMA scheme.
A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation

Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and temporal distribution of cAMP at the subcellular level could be important for developing new strategies for the prevention or treatment of unfavorable responses associated with different disease states.
Teaching by Listening: The Importance of Adult-Child Conversations to Language Development

OBJECTIVE: To test the independent association of adult language input, television viewing, and adult-child conversations on language acquisition among infants and toddlers. METHODS: Two hundred seventy-five families of children aged 2 to 48 months who were representative of the US census were enrolled in a cross-sectional study of the home language environment and child language development (phase 1). Of these, a representative sample of 71 families continued for a longitudinal assessment over 18 months (phase 2). In the cross-sectional sample, language development scores were regressed on adult word count, television viewing, and adult-child conversations, controlling for socioeconomic attributes. In the longitudinal sample, phase 2 language development scores were regressed on phase 1 language development, as well as phase 1 adult word count, television viewing, and adult-child conversations, controlling for socioeconomic attributes. RESULTS: In fully adjusted regressions, the effects of adult word count were significant when included alone but were partially mediated by adult-child conversations. Television viewing when included alone was significant and negative but was fully mediated by the inclusion of adult-child conversations. Adult-child conversations were significant when included alone and retained both significance and magnitude when adult word count and television exposure were included. CONCLUSIONS: Television exposure is not independently associated with child language development when adult-child conversations are controlled. Adult-child conversations are robustly associated with healthy language development. Parents should be encouraged not merely to provide language input to their children through reading or storytelling, but also to engage their children in two-sided conversations.
Active immunization of Japanese quail hens with a recombinant chicken inhibin fusion protein enhances production performance.

The effects of active immunization against inhibin on production performance in female Japanese quail (Coturnix coturnix japonica) were assessed in two separate trials using an MBP-cINA521 fusion protein as an immunogen. The fusion protein, MBP-cINA521, consisted of the bacterial maltose binding protein (MBP) and a truncated form of the mature alpha-subunit of chicken inhibin (cINA521). MBP-cINA1521 was constructed by: 1) excising a 521-bp PstI fragment from a chicken inhibin alpha-subunit cDNA (cINA6; gift of P. A. Johnson), 2) cloning this fragment, which encodes all but the first 11 amino acid residues of the mature alpha-subunit, into the pMal-c2 vector of the MBP fusion expression system, and 3) expressing the fusion protein (MBP-cINA521) from the Escherichia coli and purifying it using affinity chromatography. In each trial, quail were randomly and equally assigned to one of two injection treatments as follows: 1) MBP-cINA521 in Freund's adjuvant, or 2) Freund's adjuvant (vehicular controls; CON). All immunizations were given subcutaneously and Freund's complete and incomplete adjuvant were used for primary and booster injections, respectively. In Trial 1, birds were given a primary challenge of 0.2 mg MBP-cINA521 per bird at 25 d of age, followed by booster immunizations (0.1 mg MBP-cINA521 per bird) at 33, 40, 47, 54 and 61 d of age and every 35 d thereafter. The CON birds received vehicular immunizations at the same time intervals. In Trial 2, birds treated with MBP-cINA521 received a primary challenge of 0.2 mg MBP-cINA521 per bird at 26 d of age, followed by booster immunizations (0.1 mg MBP-cINA521 per bird) using the same schedule as that used in Trial 1, with the exception that no boosters were given after 61 d of age. The CON birds received vehicular immunizations at the same time intervals. Collection of production performance data was initiated coincident with the laying of the first egg in each trial (i.e., beginning at 41 and 44 d of age for Trials 1 and 2, respectively) and continued for 30 1-wk periods of lay. Combined data from Trials 1 and 2 indicated that the mean +/- SE age at first egg lay was markedly decreased (P < 0.005) in MBP-cINA521-treated quail (53.4 +/- 0.9 d of age) when compared to the CON (57.6 +/- 1.3 d of age). Likewise, the mean +/- SE age at 50% egg production was reduced (P < 0.03) in quail immunized against inhibin (65.4 +/- 2.1 d of age) when compared to the CON (77.6 +/- 4.7 d of age). Total hen-day egg production was also higher (P < 0.05, Trial 1; P < 0.01, Trial 2) in MBP-cINA521-treated quail (88.7 +/- 1.4%, Trial 1; 90.1 +/- 1.2%, Trial 2) than in the CON birds (81.9 +/- 2.9%, Trial 1; 73.6 +/- 6.5%, Trial 2). Collectively, these findings provide evidence that inhibin immunoneutralization accelerated puberty and enhanced hen-day egg production during a 30-wk period of egg lay in Japanese quail.
Comparing the sensitivity of chlorophytes, cyanobacteria, and diatoms to major‐use antibiotics

The occurrence of antibiotic residues in the aquatic environment is an emerging concern. In contrast to daphnia and fish, algae are known to be particularly sensitive to antibiotic exposure. However, to date, a systematic evaluation of the sensitivity of different algal species to antibiotics has not been performed. The aim of the present study was therefore to explore the sensitivity of a battery of algal species toward antibiotic exposures. The present study investigated the growth inhibition effects of 3 major‐use antibiotics, tylosin, lincomycin, and trimethoprim, on 7 algal species from the chlorophyte, cyanobacteria, and diatom groups. Based on median effective concentration (EC50) values, cyanobacteria (EC50 = 0.095–0.13 μmol/L) were found to be the most sensitive group to lincomycin followed by chlorophytes (EC50 = 7.36–225.73 μmol/L) and diatoms (EC50 > 225.73 μmol/L). Cyanobacteria were also the most sensitive group to tylosin (EC50 = 0.09–0.092 μmol/L), but, for this compound, diatoms (EC50 = 1.33–5.7 μmol/L) were more sensitive than chlorophytes (EC50 = 4.14–81.2 μmol/L). Diatoms were most sensitive to trimethoprim (EC50 = 7.36–74.61 μmol/L), followed by cyanobacteria (EC50 = 315.78–344.45 μmol/L), and chlorophytes (EC50 > 344.45 μmol/L) for trimethoprim. Although these results partly support the current approach to regulatory environmental risk assessment (whereby cyanobacterial species are recommended for use with antibiotic compounds), they indicate that for some antibiotics this group might not be the most appropriate test organism. It is therefore suggested that environmental risk assessments consider data on 3 algal groups (chlorophytes, cyanobacteria, and diatoms) and use test species from these groups, which are consistently found to be the most sensitive (Pseudokirchneriella subcapitata, Anabaena flos‐aquae, and Navicula pelliculosa). Environ Toxicol Chem 2016;35:2587–2596. © 2016 SETAC
Broiler pigmentation potency of neoxanthin and violaxanthin relative to lutein.

Abstract THE xanthophylls from dehydrated alfalfa meal as measured by the new Western Regional Research Laboratory (W.R.R.L.) analytical procedure include lutein, zeazanthin, cryptoxanthin, neoxanthin, violaxanthin, carotenoid oxidation products, and various cis isomers of these (Kohler et al., 1967). Lutein, zeaxanthin, and cryptoxanthin have been reported to be good skin pigmenters while indications are the polyoxycarotenoids are relatively poor skin pigmenters (Quackenbush et al., 1965; Kuzmicky et al., 1968). Violaxanthin has been reported to be ineffective as a yolk pigmenter (Marusich et al., 1960). However, the effectiveness of violaxanthin and neoxanthin as skin pigmenters has not been established. This study was undertaken to determine the relative skin pigmentation potency (R.S.P.P.) of pure all-trans neoxanthin and all-trans violaxanthin relative to pure all-trans lutein. GENERAL PROCEDURE 1 For the two experiments conducted in this study, day-old Cornish-White Rock type cross-bred cockerels (Kimber) were depleted of pigment on a 22% protein soy-starch ration (Table 1) for…
Performance evaluation of 2D and 3D deep learning approaches for automatic segmentation of multiple organs on CT images

The purpose of this study is to evaluate and compare the performance of modern deep learning techniques for automatically recognizing and segmenting multiple organ regions on 3D CT images. CT image segmentation is one of the important task in medical image analysis and is still very challenging. Deep learning approaches have demonstrated the capability of scene recognition and semantic segmentation on nature images and have been used to address segmentation problems of medical images. Although several works showed promising results of CT image segmentation by using deep learning approaches, there is no comprehensive evaluation of segmentation performance of the deep learning on segmenting multiple organs on different portions of CT scans. In this paper, we evaluated and compared the segmentation performance of two different deep learning approaches that used 2D- and 3D deep convolutional neural networks (CNN) without- and with a pre-processing step. A conventional approach that presents the state-of-the-art performance of CT image segmentation without deep learning was also used for comparison. A dataset that includes 240 CT images scanned on different portions of human bodies was used for performance evaluation. The maximum number of 17 types of organ regions in each CT scan were segmented automatically and compared to the human annotations by using ratio of intersection over union (IU) as the criterion. The experimental results demonstrated the IUs of the segmentation results had a mean value of 79% and 67% by averaging 17 types of organs that segmented by a 3D- and 2D deep CNN, respectively. All the results of the deep learning approaches showed a better accuracy and robustness than the conventional segmentation method that used probabilistic atlas and graph-cut methods. The effectiveness and the usefulness of deep learning approaches were demonstrated for solving multiple organs segmentation problem on 3D CT images.
Learning to select relevant perspective in a dynamic environment

When an agent observes its environment, there are two important characteristics of the perceived information. One is the relevance of information and the other is redundancy. The irrelevant and redundant features which commonly exists within an environment, commonly leads to agent state explosion and associated high computational cost within the learning process. This paper presents an efficient method concerning both the relevance of information and the correlation in order to improve the learning of reinforcement learning agent. We introduce a new concurrent online learning method to calculate the match count C(s) and relevance degree I(s) to quantify the redundancy and correlation of features with respect to a desired learning task. Our analysis shows that the correlation relationship of the features can be extracted and projected to concurrent biased learning threads. By comparing the commonalities of these learning threads, we can evaluate the relevance degree of a feature that contributes to a particular learning task. We explain the method using random walk examples and then demonstrate the method on the chase object domain. Our validation results show that, using the concurrent learning method, we can efficiently detect redundancy and irrelevant features from the environment on sequential tasks, and significantly improve the efficiency of learning. After relevant features are extracted, the agent can remarkably accelerate its succeeding learning speed.
Energy-Efficient CMOS Memristive Synapses for Mixed-Signal Neuromorphic System-on-a-Chip

Emerging non-volatile memory (NVM), or memristive, devices promise energy-efficient realization of deep learning, when efficiently integrated with mixed-signal integrated circuits on a CMOS substrate. Even though several algorithmic challenges need to be addressed to turn the vision of memristive Neuromorphic Systems-on-a-Chip (NeuSoCs) into reality, issues at the device and circuit interface need immediate attention from the community. In this work, we perform energy-estimation of a NeuSoC system and predict the desirable circuit and device parameters for energy-efficiency optimization. Also, CMOS synapse circuits based on the concept of CMOS memristor emulator are presented as a system prototyping methodology, while practical memristor devices are being developed and integrated with general-purpose CMOS. The proposed mixed-signal memristive synapse can be designed and fabricated using standard CMOS technologies and open doors to interesting applications in cognitive computing circuits.
Estimating the Proportion of Equivalently Expressed Genes in Microarray Data Based on Transformed Test Statistics

In microarray data analysis, false discovery rate (FDR) is now widely accepted as the control criterion to account for multiple hypothesis testing. The proportion of equivalently expressed genes (pi(0)) is a key component to be estimated in the estimation of FDR. Some commonly used pi(0) estimators (BUM, SPLOSH, QVALUE, and LBE ) are all based on p-values, and they are essentially upper bounds of pi(0). The simulations we carried out show that these four methods significantly overestimate the true pi(0) when differentially expressed genes and equivalently expressed genes are not well separated. To solve this problem, we first introduce a novel way of transforming the test statistics to make them symmetric about 0. Then we propose a pi(0) estimator based on the transformed test statistics using the symmetry assumption. Real data application and simulation both show that the pi(0) estimate from our method is less conservative than BUM, SPLOSH, QVALUE, and LBE in most of the cases. Simulation results also show that our estimator always has the least mean squared error among these five methods.
Effects of feeding white Leghorn hens diets that contain deoxynivalenol (vomitoxin)-contaminated wheat.

A short-term (10 weeks, Experiment 1) and a long-term experiment (24 weeks, Experiment 2) were done to determine effects of incorporating either white winter wheat, naturally contaminated with 1 mg deoxynivalenol (DON)/kg, or spring wheats, containing up to 6.5 mg DON/kg, into the diets of White Leghorn hens. Based on chemical analysis, the diets in Experiment 1 contained less than . 05 to . 7 mg DON/kg, while those in Experiment 2 contained from . 2 to 4.9 mg/kg. Incorporation of winter or spring wheat in the experimental diets had no effect (P greater than .05) on feed intake and efficiency, egg production and yield, the number of soft shell and cracked eggs observed in the laying house, body weight at the completion of the experimental period, fertility, hatchability of fertile eggs, and the proportion of malformed embryos and pips. In addition, presence of DON-contaminated wheat did not influence (P greater than .05) the organ weight to body weight ratio for a randomly selected sample of hens necropsied at the completion of each experiment. There was little evidence of lesions in the oral cavity, esophagus, proventriculus and gizzard, hemorrhaging in the viscera or skeletal muscles, or of changes in the appearance of spleen, heart, and kidney. However, the livers from DON hens were fatty in appearance. Furthermore, vomiting (emesis), diarrhea, or changes in behaviour were not apparent and mortality, normally very low, was not increased during either experiment. Inverse linear relationships were obtained in Experiment 1 between dietary DON concentrations and egg weight (P less than .05), shell weight and thickness (P less than .01), and percent shell (P less than .05). Although egg and shell variables measured in Experiment 2 were not significantly influenced (P greater than .05) by DON treatment, trends towards lower values with higher dietary DON levels were evident. Egg specific gravity, nondestructive deformation, and quasistatic compression fracture strength of the egg's shell were not influenced (P greater than .05) by dietary DON levels. The results from these experiments indicate that laying hens can tolerate diets containing up to 5 mg DON/kg from white winter or spring wheat for extended periods of time without serious adverse effects on health and productivity.
On the Self-Similarity of the 1999 DARPA/Lincoln Laboratory Evaluation Data

While intrusion detection systems (IDSs) are becoming ubiquitous defence, no comprehensive and scientifically rigorous benchmark is available to evaluate their performances. In 1998 and again in 1999, the Lincoln Laboratory of MIT conducted a comprehensive evaluation of IDSs and produced the DARPA off-line evaluation data to train and test IDSs. However, there is the lack of detailed characteristics of the DARPA/Lincoln Laboratory evaluation data. This paper examines the self-similarity of the 1999 DARPA/Lincoln Laboratory evaluation data sets for training and indicates that the evaluation data clearly exhibits self-similarity during preceding tens of hours period, while not during other time periods. Also the likely causes failing self-similarity are explored. These finding results can help evaluators to understand and use the 1999 DARPA/Lincoln Laboratory evaluation data well to evaluate IDSs.
alpha-lipoic acid corrects late-phase supernormal retinal oxygenation response in experimental diabetic retinopathy.

PURPOSE To test the hypothesis that preventative alpha-lipoic acid (LPA) treatment corrects an abnormal retinal oxygenation response in experimental diabetic retinopathy. METHODS Retinal oxygenation (DeltaPO2) was measured by MRI before (room air [ra]) and during a 4-minute carbogen inhalation challenge in five groups: control Sprague-Dawley (SD) and Lewis (LEW) rats, 3- to 4-month diabetic SD and LEW rats, and 4-month diabetic LEW rats preventatively treated with a chow LPA admix (400 mg/kg per chow). Comparisons were made between the initial 2 minutes of oxygenation change (measured using ra and first carbogen periods [t1 - ra]) and the next 2-minute change (assessed with first and second carbogen periods [t2-t1]) for superior and inferior hemiretinal DeltaPO2. RESULTS In control SD rats, DeltaPO2(t1-ra) > DeltaPO2(t2-t1) (P <0.05) was found panretinally. In diabetic SD rats, the superior, but not the inferior, hemiretina had subnormal DeltaPO2(t1- ra) (P < 0.05) and supernormal DeltaPO2(t2-t1) (P < 0.05). In control LEW rats, DeltaPO2(t1-ra) and DeltaPO2(t2-t1) were not significantly different (P > 0.05). Also, control and diabetic LEW rat panretinal DeltaPO2(t1-ra) were lower (P < 0.05) than in the respective SD groups. In diabetic LEW rats, a supernormal (P < 0.05) panretinal DeltaPO2(t2-t1) was found that could be corrected with preventative LPA treatment. CONCLUSIONS These data support the hypothesis and suggest that the influence of strain differences on the interpretation of retinovascular DeltaPO2 as a surrogate of drug treatment efficacy for diabetic retinopathy may be minimized by measuring a late-phase supernormal response. The LPA data raise the possibility that oxidative stress contributes to diabetes-induced supernormal DeltaPO2.