Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between proteome changes of Longissimus muscle and intramuscular fat content in finishing pigs fed conjugated linoleic acid

The present experiment was conducted to determine proteome changes in Longissimus muscle of finishing pigs fed conjugated linoleic acid (CLA), in association with alteration of intramuscular fat content. Previously, seventy-two Duroc × Landrace × Large White gilts (approximately 60 kg) had been fed maize–soyabean meal-based diets with 0, 12·5 and 25 g CLA/kg diet. The CLA contained 369·1 mg/g cis-9, trans-11 CLA, 374·6 mg/g trans-10, cis-12 CLA and 53·7 mg/g other isomers. Six pigs per treatment were slaughtered when they reached a body weight of approximately 100 kg. Data published from a previous experiment demonstrated that supplementation with 12·5 or 25 g CLA/kg diet increased intramuscular fat content (P < 0·05). The present study investigated the proteome changes in Longissimus muscle of control and pigs supplemented with 25 g CLA/kg diet. CLA significantly influenced the abundance of proteins related to energy metabolism, fatty acid oxidation and synthesis, amino acid metabolism, defence, transport and other miscellaneous processes (P < 0·05). The increase in intramuscular fat content was positively correlated with the increased abundance of carbonic anhydrase 3 and aspartate aminotransferase (P < 0·05). We suggest that the proteome changes in Longissimus muscle contributed to greater intramuscular lipid content in CLA-supplemented pigs.
Effects of pitavastatin and pravastatin on markers of immune activation and arterial inflammation in HIV

Objective: Persistent immune activation is thought to contribute to increased cardiovascular disease risk in HIV and statins may help modulate systemic immune activation. We aimed to compare the effects of two key statins on markers of systemic immune activation and arterial inflammation in the HIV population. Design: Double-blind, active-controlled, parallel-group comparative trial performed in 45 sites. Methods: Two hundred and fifty-two antiretroviral therapy-treated HIV-infected participants with dyslipidemia were randomized (1 : 1) to pitavastatin 4 mg daily vs. pravastatin 40 mg daily in the HIV-infected patieNts and TREatment with PItavastatin vs. pravastatin for Dyslipidemia (INTREPID) trial. In this analysis of the INTREPID trial, we assessed markers of immune activation and arterial inflammation using a modified intent-to-treat population. This trial is registered with ClinicalTrials.gov (NCT01301066). Results: One hundred and twenty-six participants were randomized to receive pitavastatin and 126 to pravastatin. Ninety-nine participants in the pitavastatin group and 91 participants in the pravastatin group completed the study. Median age was 50 (45, 56) years [median (interquartile range)]. Baseline, low-density lipoprotein-cholestrol (LDL-C) was 153 (135, 171) mg/dl, log HIV-1 viral load was 1.1 ± 0.2 copies/ml, and CD4+ cell count was 580 (439, 794) cells/&mgr;l. At week 52, the pitavastatin group had a significantly greater reduction (% change) compared with pravastatin in soluble CD14 (sCD14), (−10.0 vs. 0.6%, P = 0.02), oxidized LDL (oxLDL) (−26.9 vs. −17.5%, P = 0.02), and lipoprotein-associated phospholipase 2 (Lp-PLA2) (−26.6 vs. −15.5%, P = 0.005) (pitavastatin vs. pravastatin). Conclusion: Fifty-two weeks of pitavastatin 4 mg daily (vs. pravastatin 40 mg daily) led to a greater reduction in select markers of immune activation and arterial inflammation (sCD14, oxLDL, and LpPLA2) among HIV-infected participants. Further work is needed to assess whether immune-modulatory effects of pitavastatin reduce cardiovascular disease risk in HIV.
Menadione is a metabolite of oral vitamin K

Phylloquinone is converted into menaquinone-4 and accumulates in extrahepatic tissues. Neither the route nor the function of the conversion is known. One possible metabolic route might be the release of menadione from phylloquinone by catabolic activity. In the present study we explored the presence of menadione in urine and the effect of vitamin K intake on its excretion. Menadione in urine was analysed by HPLC assay with fluorescence detection. Urine from healthy male volunteers was collected before and after administration of a single dose of K vitamins. Basal menadione excretion in non-supplemented subjects (n 6) was 5·4 (sd 3·2) μg/d. Urinary menadione excretion increased greatly after oral intake of the K vitamins, phylloquinone and menaquinone-4 and -7. This effect was apparent within 1–2h and peaked at about 3h after intake. Amounts of menadione excreted in 24h after vitamin K intake ranged, on a molar basis, from 1 to 5% of the administered dose, indicating that about 5–25% of the ingested K vitamins had been catabolized to menadione. Menadione excretion was not enhanced by phylloquinone administered subcutaneously or by 2′,3′-dihydrophylloquinone administered orally. In archived samples from a depletion/repletion study (Booth et al. (2001)Am J Clin Nutr74, 783–790), urinary menadione excretion mirrored dietary phylloquinone intake. The present study shows that menadione is a catabolic product of K vitamins formed after oral intake. The rapid appearance in urine after oral but not subcutaneous administration suggests that catabolism occurs during intestinal absorption. The observations make it likely that part of the menaquinone-4 in tissues results from uptake and prenylation of circulating menadione
Space-Time Derivative-Based Prediction: A Novel Trickling Mechanism for WSN

Time series prediction techniques reduce the number of messages generated at the application level, saving energy spent in the communication and, consequently, extending the network lifetime. Trickle is a well-known time series prediction mechanism commonly used to decrease the number of transmitted messages in Wireless Sensor Networks (WSN) and thus save energy. This paper presents the Space-Time Derivative-Based Prediction (ST-DBP), a novel Trickling mechanism to suppress data transmission in space-time regions in WSNs. We integrate ST-DBP with the Trustful Space-Time Protocol (TSTP), an application-oriented, cross-layer communication protocol, and compare two variations of the ST-DBP with the original DBP using real data from a Solar Farm in terms of suppression data ratio. Our results show that the two variations of the ST-DBP outperform the original DBP.
The alignment of LC side-chain polymers in directing electric fields: theory and practice

The factors that control the alignment of LC side-chain polymers in directing a.c. and d.c. electric fields are critically reviewed. The principles involved when alignment is attempted by cooling from the melt in the presence of an electric field or by direct application of the field to a material in its liquid-crystalline (LC) state are outlined, and the difficulties which may be encountered in practice are described and evaluated. An “electrical cleaning” method whereby the low-frequency conductance losses in a sample may be reduced is described and is applied to LC polymer materials. Experimental dielectric data are presented and analysed for two LC polymers which contain azo-groups in the side chains.
Mining heterogeneous causal effects for personalized cancer treatment

Motivation : Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses. Results : In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients. Availability and Implementation : Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree. Contact : weijia.zhang@mymail.uinsa. edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Air pollution and DNA methylation alterations in lung cancer: A systematic and comparative study

The lung cancer incidence in the Xuanwei and neighboring region, Yunnan, China, is among the highest in China and is attributed to severe air pollution with high benzo(a)pyrene levels. We systematically and comparatively analyzed DNA methylation alterations at genome and gene levels in Xuanwei lung cancer tissues and cell lines, as well as benzo(a)pyrene-treated cells and mouse samples. We obtained a comprehensive dataset of genome-wide cytosine-phosphate-guanine island methylation in air pollution-related lung cancer samples. Benzo(a)pyrene exposure induced multiple alterations in DNA methylation and in mRNA expressions of DNA methyltransferases and ten-11 translocation proteins; these alterations partially occurred in Xuanwei lung cancer. Furthermore, benzo(a)pyrene-induced DKK2 and EN1 promoter hypermethylation and LPAR2 promoter hypomethylation led to down-regulation and up-regulation of the genes, respectively; the down-regulation of DKK2 and EN1 promoted the cellular proliferation. Thus, DNA methylation alterations induced by benzo(a)pyrene contribute partially to abnormal DNA methylation in air pollution-related lung cancer, and these DNA methylation alterations may affect the development and progression of lung cancer. Additionally, vitamin C and B6 can reduce benzo(a)pyrene-induced DNA methylation alterations and may be used as chemopreventive agents for air pollution-related lung cancer.
Improving tag matrix completion for image annotation and retrieval

Image annotation is a fundamental and challenging task in the field of semantic image retrieval. In this paper, we deal with image annotation via matrix completion. Concretely, we formulate the problem of annotating the tags of an image into a constrained optimization problem, in which the constraint is to keep the consistency with the given initial labels and the objective is to minimize the discrepancy between the correlation in visual content and the correlation in semantic tags. We solve the optimization problem with the linearized alternating direction method. Experimental results on benchmark data demonstrate the effectiveness of our proposals.
Effects of an Inhibitor of Monocyte Recruitment on Recovery from Traumatic Brain Injury in Mice Treated with Granulocyte Colony-Stimulating Factor

Administration of the hematopoietic growth factor granulocyte-colony stimulating Factor (G-CSF) has been reported to enhance recovery from controlled cortical impact (CCI) in rodent models. G-CSF exerts actions in both the periphery (stimulation of hematopoiesis) and in the brain, where it serves as a neurotrophic factor, promoting neuronal survival and stimulating neural stem/progenitor cell proliferation in the hippocampus. In order to distinguish the direct CNS actions of G-CSF from its peripheral actions, experiments were designed to block the recruitment of peripheral monocytes to the site of the lesion produced by CCI. The selective C-C motif receptor 2 (CCR2) antagonist (RS504303) was co-administered with G-CSF for three days after CCI in a chimeric mouse previously transplanted with GFP-expressing (GFP+) blood stem-progenitor cells. Results: The drug significantly impaired infiltration of GFP+ bone marrow-derived cells to the frontal cortex and striatum without impeding recovery performance and hippocampal neurogenesis in the behavioral test, the Radial Arm Water Maze (RAWM). Administration of the CCR2 antagonist alone, without G-CSF, was effective in promoting recovery in RAWM. These results support the hypothesis that the direct action of G-CSF on neural cells, independent of its hematopoietic effects, is primarily responsible for enhanced recovery from CCI. In addition, this study confirms the importance of CCR2 and its ligand, monocyte chemotactic protein-1 (MCP-1), in mediating the inflammatory response following CCI.
Encoding the Consistency of Relational Bayesian Networks

Given an input structure, a relational Bayesian network returns a Bayesian network over ground atoms. In this paper, we analyze the problem of checking the consistency of a relational Bayesian network for a given class of input structures. This consistency is defined as the acyclicity of the output Bayesian network. We employ first-order logic to encode both the input structure and the structure of the corresponding output Bayesian network. Then we use a transitive closure operator to express the acyclicity of the resulting Bayesian network, translating the consistency of a relational Bayesian network for a given input class into the validity of a logical formula.
Extended Kalman Filter in 2S1 Tracked Vehicle System with Hybrid Control

The essence of the undertaken topic is the problem of estimation of state vector in the model of 2S1 tracked vehicle suspension system through the use of Extended Kalman Filter. The use of non-linear filter has become necessary due to the magnetorheological damper located at suspension system, which has been described by hyperbolic model. Application of the damper caused the tested suspension system has become a semi-active structure in which the hybrid control was applied. The choice of this type of control stems from the fact that in the case of tracked combat vehicles in addition to the advantageous conditions of work of vehicle crew also cornering stability and the possibility of sudden acceleration or braking is important. The hybrid control allows to determine a compromise between ride comfort and stability of 2S1 platform.
MRI artifact correction using sparse + low‐rank decomposition of annihilating filter‐based hankel matrix

Magnetic resonance imaging (MRI) artifacts are originated from various sources including instability of an magnetic resonance (MR) system, patient motion, inhomogeneities of gradient fields, and so on. Such MRI artifacts are usually considered as irreversible, so additional artifact‐free scan or navigator scan is necessary. To overcome these limitations, this article proposes a novel compressed sensing‐based approach for removal of various MRI artifacts.
Unsupervised Classification of Opinions

Opinion mining is gaining more interest thanks to the ever growing data available on the internet. This work proposes an unsupervised approach that clusters opinions in fine grain ranges. The approach is able to generate its own seed words for better applicability to the context and eliminating user input. Furthermore, we devise a computation strategy for the influence of valence shifters and negations on opinion words. The method is general enough to perform well while reducing subjectivity to a minimum.
Not all that glitters is gold: A guide to the critical interpretation of drug trials in epilepsy

Clinical trials represent the best source of evidence on which to base treatment decisions. For such evidence to be utilized meaningfully, however, it is essential that results are interpreted correctly. This requires a good understanding of strengths and weaknesses of the adopted design, the clinical relevance of the outcome measures, and the many factors that could affect such outcomes. As a general rule, uncontrolled studies tend to provide misleading evidence as a result of the impact of confounders such as regression to the mean, patient‐related bias, and observer bias. On the other hand, although randomized controlled trials (RCTs) are qualitatively superior, aspects of their execution may still decrease their validity. Bias and decreased validity in RCTs may occur by chance alone (for example, treatment groups may not necessarily be balanced for important variables despite randomization) or because of specific features of the trial design. In the case of industry‐driven studies, bias often influences the outcome in favor of the sponsor's product. Factors that need to be carefully scrutinized include (1) the purpose for which the trial is conducted; (2) potential bias due to unblinding or lack of blinding; (3) the appropriateness of the control group; (4) the power of the study in detecting clinically relevant differences; (5) the extent to which eligibility criteria could affect outcomes and be representative of routine clinical practice; (6) whether the treatments being compared are used optimally in terms of dosing, duration of treatment, and other variables; (7) the appropriateness of the statistical comparisons; (8) the clinical relevance of the outcome measures and whether all key outcome information is reported (for example, responder rates in completers); and (9) potential bias in the way results are presented and discussed. This article discusses each of these aspects and illustrates the discussion with examples taken from published antiepileptic drug trials.
Empirical Evaluation of Speaker Adaptation on DNN based Acoustic Model

Speaker adaptation aims to estimate a speaker specific acoustic model from a speaker independent one to minimize the mismatch between the training and testing conditions arisen from speaker variabilities. A variety of neural network adaptation methods have been proposed since deep learning models have become the main stream. But there still lacks an experimental comparison between different methods, especially when DNN-based acoustic models have been advanced greatly. In this paper, we aim to close this gap by providing an empirical evaluation of three typical speaker adaptation methods: LIN, LHUC and KLD. Adaptation experiments, with different size of adaptation data, are conducted on a strong TDNN-LSTM acoustic model. More challengingly, here, the source and target we are concerned with are standard Mandarin speaker model and accented Mandarin speaker model. We compare the performances of different methods and their combinations. Speaker adaptation performance is also examined by speaker's accent degree.
Physical Activity Levels and Well-Being in Older Adults

The objective of this study was to identify the interconnectedness of different intensity levels of physical activity and psychological (life satisfaction and positive affect) and physical (physical health) well-being. Participants were from the National Study of Midlife in the United States with assessments in 2004 and aged 25 to 74 living in the United States were included in the analyses. We conducted bivariate correlations to examine significant relationships among the study variables. In addition, after multicollinearity among the independent variable was checked, a series of hierarchical regression analyses with physical health, positive affect, and life satisfaction as criterion variables were conducted. The results showed that light physical activities were positively associated with physical health and life satisfaction in summer, whereas light physical activities and all dependent variables were positively correlated in winter. Furthermore, engaging in moderate physical activities was positively related only with physical health. Meanwhile, vigorous physical activities were not associated with life satisfaction, physical health, and positive affect in summer and winter.
Pedestrian Detection and Tracking in Thermal Images from Aerial MPEG Videos

Video surveillance for security and intelligence purposes has been a precious tool as long as the technology has been available but is computationally heavy. In this paper, we present a fast and efficient framework for pedestrian detection and tracking using thermal images. It is designed for automatic surveillance applications in an outdoor environment like preventing border intrusions or attacks on sensitive facilities using image and video processing techniques implemented on-board Unmanned Aerial Vehicles (UAV)s. The proposed framework exploits raw H.264 compressed video streams with limited computational overhead. Our work is driven by the fact that Motion Vectors (MV) are an integral part of any video compression technique, by day and night capabilities of thermal sensors and the distinguished thermal signature of humans. Six different scenarios were carried out and filmed using a thermal camera in order to simulate suspicious events. The obtained results show the effectiveness of the proposed framework and its low computational requirements which make it adequate for on-board processing and real-time applications.
Processing Technologies for 3D Nanostructured Tissue Engineering Scaffolds

Engineered scaffolds made from synthetic or natural biomaterials are crucial elements in tissue engineering strategies. Numerous biomaterials are being used to fabricate scaffolds, including glasses, ceramics, metals, polymers, and their composites. Although materials chemistry and scaffold architecture (pore size, pore volume) are important factors affecting cell–surface interactions, the roughness and topography of the scaffold surface plays an essential part too, especially nanoscale features are relevant. Extensive research has been carried out on introducing nanoscale features on 2D, flat surfaces, but much limited efforts have been focused on nanostructuring the surface of 3D scaffolds. This paper specifically reviews the current techniques that are available to introduce or engineer nanoscale topography on the surfaces of 3D scaffolds or on 2D surfaces that can be successfully assembled into 3D scaffolds via post‐processing. The literature reviewed provides evidence about the influence of nanoscale topography on cell attachment, migration, and proliferation. While the paper is focused on bone tissue scaffolds, several technologies reviewed are equally applicable to scaffolds suitable for engineering and regeneration of other tissues.
DARGS: Dynamic AR Guiding System for Indoor Environments

Complex public buildings, such as airports, use various systems to guide people to a certain destination. Such approaches are usually implemented by showing a floor plan that has guiding signs or color coded lines on the floor. With a technology that supports six degrees of freedom (6DoF) tracking in indoor environments, it is possible to guide people individually, thereby considering obstacles, path lengths, or pathways for handicapped people. With an augmented reality (AR) device, such as a smart phone or AR glasses, the path can be presented on top of the real environment. In this paper, we present DARGS, an algorithm, which calculates a path through a complex building in real time. Usual path planning algorithms use either shortest paths or dynamic paths for robot interaction. The human factor in a real environment is not considered. The main advantage of DARGS is the incorporation of the current field of view (FOV) of the used device to visualize a more dynamic presentation. Rather than searching for the AR content with a small FOV, with the presented approach the user always gets a meaningful three-dimensional overlay of the path independent of the viewing direction. A detailed user study is performed to prove the applicability of the system. The results indicate that the presented system is especially helpful in the first few important seconds of the guiding process, when the user is still disoriented.