Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of plaque composition by intravascular ultrasound "virtual histology": the impact of dense calcium on the measurement of necrotic tissue.

AIMS We aimed to evaluate if the co-localisation of calcium and necrosis in intravascular ultrasound virtual histology (IVUS-VH) is due to artefact, and whether this effect can be mathematically estimated. METHODS AND RESULTS We hypothesised that, in case calcium induces an artefactual coding of necrosis, any addition in calcium content would generate an artificial increment in the necrotic tissue. Stent struts were used to simulate the "added calcium". The change in the amount and in the spatial localisation of necrotic tissue was evaluated before and after stenting (n=17 coronary lesions) by means of a especially developed imaging software. The area of "calcium" increased from a median of 0.04 mm2 at baseline to 0.76 mm2 after stenting (p<0.01). In parallel the median necrotic content increased from 0.19 mm2 to 0.59 mm2 (p<0.01). The "added" calcium strongly predicted a proportional increase in necrosis-coded tissue in the areas surrounding the calcium-like spots (model R2=0.70; p<0.001). CONCLUSIONS Artificial addition of calcium-like elements to the atherosclerotic plaque led to an increase in necrotic tissue in virtual histology that is probably artefactual. The overestimation of necrotic tissue by calcium strictly followed a linear pattern, indicating that it may be amenable to mathematical correction.
FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

Due to the large numbers of transcription factors (TFs) and cell types, querying binding profiles of all TF/cell type pairs is not experimentally feasible, owing to constraints in time and resources. To address this issue, we developed a convolutional-recurrent neural network model, called FactorNet, to computationally impute the missing binding data. FactorNet trains on binding data from reference cell types to make accurate predictions on testing cell types by leveraging a variety of features, including genomic sequences, genome annotations, gene expression, and single-nucleotide resolution sequential signals, such as DNase I cleavage. To the best of our knowledge, this is the first deep learning method to study the rules governing TF binding at such a fine resolution. With FactorNet, a researcher can perform a single sequencing assay, such as DNase-seq, on a cell type and computationally impute dozens of TF binding profiles. This is an integral step for reconstructing the complex networks underlying gene regulation. While neural networks can be computationally expensive to train, we introduce several novel strategies to significantly reduce the overhead. By visualizing the neural network models, we can interpret how the model predicts binding which in turn reveals additional insights into regulatory grammar. We also investigate the variables that affect cross-cell type predictive performance to explain why the model performs better on some TF/cell types than others, and offer insights to improve upon this field. Our method ranked among the top four teams in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge.
Fatores explicativos da evidenciação de informações ambientais das empresas potencialmente poluidoras listadas na BM&FBOVESPA

A presente pesquisa tem como objetivo identificar os fatores explicativos da evidenciacao de informacoes ambientais das empresas potencialmente poluidoras listadas na BM&FBOVESPA. Para tanto, foram utilizadas as Demonstracoes Financeiras Padronizadas (DFPs), Formularios de Referencia, Relatorios Anuais e de Sustentabilidade dessas empresas, no periodo de 2005 a 2015. A amostra da pesquisa e formada por todas as companhias de capital aberto com acoes negociadas na BM&FBOVESPA, e pertencentes aos setores de alto, medio e baixo potencial poluidor, segundo a Lei no 10.165/2000, que dispoe sobre a Politica Nacional do Meio Ambiente. Com base nas teorias da Legitimidade e dos Stakeholders, e nos estudos anteriores, foram formuladas doze hipoteses sobre os possiveis fatores explicativos da evidenciacao ambiental, sendo que a variavel setores reguamentados foi excluida do modelo devido problemas de multicolinearidade, e a variavel empresas regulamentadas foi omitida por se manter fixa durante todo o periodo estudado. A partir da utilizacao da analise de conteudo, para examinar a evidenciacao de informacoes ambientais, e aplicacao do modelo de regressao com dados em painel desbalanceado, de efeitos fixos com robustez, foi possivel rejeitar ou nao rejeitar as hipoteses de pesquisa. Os resultados mostram, a um nivel de significância de 1% e 5%, que o tamanho da empresa, a rentabilidade, a internacionalizacao e o relatorio de sustentabilidade sao fatores explicativos da evidenciacao de informacoes ambientais. Apesar do endividamento ter apresentado uma relacao inversa com a variavel dependente, verificou-se que tal variavel tambem explica a evidenciacao ambiental. Por outro lado, a auditoria, o tamanho do conselho de administracao, a independencia do conselho de administracao, a dispersao acionaria e a sustentabilidade nao sao fatores relevantes para explicar a evidenciacao ambiental. Dessa forma, das doze hipoteses, quatro nao foram rejeitadas e seis foram rejeitadas. Tais resultados sao condizentes com os de algumas pesquisas realizadas em âmbito nacional e internacional, e estao de acordo com as teorias da Legitimidade e dos Stakeholders. Este estudo visa contribuir com o conhecimento da ciencia contabil, no que se refere a evidenciacao ambiental, preenchendo algumas lacunas nesta area e somando resultados a literatura existente.
Unified Backpropagation for Multi-Objective Deep Learning

A common practice in most of deep convolutional neural architectures is to employ fully-connected layers followed by Softmax activation to minimize cross-entropy loss for the sake of classification. Recent studies show that substitution or addition of the Softmax objective to the cost functions of support vector machines or linear discriminant analysis is highly beneficial to improve the classification performance in hybrid neural networks. We propose a novel paradigm to link the optimization of several hybrid objectives through unified backpropagation. This highly alleviates the burden of extensive boosting for independent objective functions or complex formulation of multiobjective gradients. Hybrid loss functions are linked by basic probability assignment from evidence theory. We conduct our experiments for a variety of scenarios and standard datasets to evaluate the advantage of our proposed unification approach to deliver consistent improvements into the classification performance of deep convolutional neural networks.
Diabetic Complication Models SOD 2 Protects Neurons from Injury in Cell Culture and Animal Models of Diabetic Neuropathy

Hyperglycemia-induced oxidative stress is an inciting event in the development of diabetic complications including diabetic neuropathy. Our observations of significant oxidative stress and morphological abnormalities in mitochondria led us to examine manganese superoxide dismutase (SOD2), the enzyme responsible for mitochondrial detoxification of oxygen radicals. We demonstrate that over expression of SOD2 decreases superoxide (O2) in cultured primary dorsal root ganglion (DRG) neurons and subsequently blocks caspase-3 activation and cellular injury. Under expression of SOD2 in dissociated DRG cultures from adult SOD2 mice results in increased levels of O2, activation of caspase-3 cleavage and decreased neurite outgrowth under basal conditions that are exacerbated by hyperglycemia. These profound changes in sensory neurons led us to explore the effects of decreased SOD2 on the development of diabetic neuropathy (DN) in mice. DN was assessed in SOD2 C57BL/6J mice and their SOD2 litter mates following streptozotocin (STZ) treatment. These animals, while hyperglycemic, do not display any signs of DN. DN was observed in the C57BL/6Jdb/db mouse, and decreased expression of SOD2 in these animals increased DN. Our data suggest that SOD2 activity is an important cellular modifier of neuronal oxidative defense against hyperglycemic injury.
Demonstration of circularly-polarized leaky-wave antenna based on pseudo-traveling wave resonance

A circularly-polarized leaky-wave radiation from metamaterial-inspired antenna based on pseudo-traveling wave resonance was demonstrated for the first time. The resonant structure was composed of a phase-nonreciprocal composite right/left handed microstrip line fabricated on the circumference of a normally magnetized polycrystalline yttrium iron garnet disc. Rotation direction of the circular polarization was successfully switched by changing the direction of the applied dc magnetic field.
Effect of Pregnancy on Psychosis: Life Circumstances and Psychiatric Symptoms

As part of an ongoing prospective study to correlate mother and infant outcome with social isolation during pregnancy, the Schedule for Affective Disorders, SADS-C, was administered to twenty-seven psychotic patients late in pregnancy. Extensive standardized evaluation of life stresses and social supports included a Prenatal Interview with sixty items relating to demographics, drug use, health and obstetrical history, family involvement and development expectations of the infant, and a thirty-item Difficult Life Circumstances questionnaire. In this sample the patients' previous life adjustments were stabilized by their pregnancy unless the pregnancy itself created personal stress for the patient. Higher scores on Difficult Life Circumstances were found to be associated with more psychiatric symptomatology. Symptoms of pregnancy confounded SADS-C items measuring vegetative signs of depression. One group of items on the SADS-C appeared to selectively identify a subset of women whose underlying affective symptomatology was potentiated by pregnancy. A second group of items identified women whose symptoms appeared to be reactive to current situational strains.
Magnetic resonance volumetric measurement of endolymphatic space in patients without vertiginous or cochlear symptoms

Abstract Conclusion: Magnetic resonance volumetric measurement of inner ear endolymphatic space (ELS) was performed in patients without vertiginous or cochlear symptoms. The existence of the ELS in patients with chronic rhinosinusitis (CRS) was shown. The ELS in the cochlea and vestibule was classified into four categories. These findings could be useful as a standard reference for further research. Objectives: To identify normal values of the ELS in the cochlea and vestibule. Methods: Twenty-four patients with CRS were enrolled. Inner ear fluid space images and positive perilymph/positive endolymph images were acquired using a 3.0-tesla unit. Three-dimensional (3-D) images were constructed semi-automatically using both anatomical and tissue information by fusing the 3-D images of the inner ear fluid space and the ELS. Results: Among all patients, the mean ELS/the total fluid space (TFS) ratio in the cochlea was 8.8% and that in the vestibule was 16.2%. The ELS in the cochlea and vestibule was classified into four categories. Age-related differences were found in the TFS, ELS, and ELS/TFS ratio in the inner ear and the ELS and ELS/TFS ratio in the vestibule.
Rheumatoid arthritis bone erosion volumes on CT and MRI: reliability and correlations with erosion scores on CT, MRI and radiography

Objectives: To investigate intramodality and intermodality agreements of CT and MRI erosion volumes in metacarpophalangeal (MCP) joints in rheumatoid arthritis (RA), and to compare the volumes with erosion scores for CT, MRI and radiography. Methods: In total, 17 patients with RA and four healthy controls underwent unilateral CT, MRI and radiography of second to fifth MCP joints in one hand. Erosion volumes (using OSIRIS software) and scores were determined from CT, MRI and radiography (scores only). Results: CT, MRI and radiography detected 77, 62 and 12 erosions, respectively. On CT, the mean erosion volume was 26 mm3 (median 10; range 0 to 248) and 30 mm3 (18; 1 to 163) on MRI. Total erosion volumes (per patient/control) were 97 mm3 (29; 0 to 485) on CT and 90 mm3 (46; 0 to 389) on MRI. For volumes, Spearman correlation coefficients were 0.96 to 0.99 (CT vs CT), 0.95 to 0.98 (MRI vs MRI) and 0.64 to 0.89 (CT vs MRI), all p<0.01. MRI erosion volumes correlated with the Outcome Measures in Rheumatology Clinical Trials/Rheumatoid Arthritis Magnetic Resonance Imaging Score (OMERACT RAMRIS) erosion scores (0.91 to 0.99; p<0.01) and the Sharp/van der Heijde erosion score (0.49 to 0.63; p<0.01). Conclusion: Very high intramodality and high intermodality agreements of CT and MRI erosion volumes were found, encouraging further testing in longitudinal studies. A close correlation with CT and MRI erosion volumes supports the OMERACT RAMRIS erosion score as a valid measure of joint destruction in RA.
Vesicular Stomatitis Viruses with Rearranged Genomes Have Altered Invasiveness and Neuropathogenesis in Mice

ABSTRACT Transcription of vesicular stomatitis virus is controlled by the position of a gene relative to the single 3′ genomic promoter: promoter-proximal genes are transcribed at higher levels than those in more 5′ distal positions. In previous work, we generated viruses having rearranged gene orders. These viruses had the promoter-proximal gene that encodes the nucleocapsid protein, N, moved to the second or fourth position in the genome in combination with the glycoprotein gene, G, moved from its usual promoter-distal fourth position to the first or third position. This resulted in three new viruses identified by the positions of the N and G genes in the gene order: G3N4, G1N4, and G1N2. The viruses G3N4 and G1N4 were attenuated for lethality in mice. In the present study, we addressed the basis of this attenuation by measuring the ability of each of the rearranged viruses to travel to and replicate in the olfactory bulb and brain following intranasal inoculation. In addition, the neuropathogenicity, serum cytokine levels, and immunoglobulin G isotype profiles in infected mice were determined. All the viruses reached the olfactory bulb and brain, but the outcomes of these infections were dramatically different. Viruses N1G4(wt) and G1N2 caused lethal encephalitis in 100% of animals within 7 days postinoculation; however, viruses G3N4 and G1N4 were cleared from the brain by 7 days postinoculation and all animals survived without apparent distress. The viruses differed in the distribution and intensity of lesions produced and the type and levels of cytokines induced. Animals inoculated with N1G4(wt) or G1N2 displayed extensive encephalitis and meningitis and had elevated levels of serum gamma interferon compared to what was seen with G3N4- or G1N4-infected mice. In contrast to what occurred with intranasal inoculation, all four viruses caused lethal encephalitis when administered by direct inoculation to the brain, a route that circumvents the majority of the host immune response, demonstrating that G3N4 and G1N4 were not deficient in their abilities to cause disease in the brain. These findings indicate that gene rearrangement and its consequent alteration of gene expression can, without any other changes, alter the viral spread and cytokine response following intranasal infection.
In Vivo Inactivation of Lysozyme by Ozone

Bronchial mucus contains large quantities of the antibacterial enzyme lysozyme. Acutely exposing mice or rabbits to ozone reduced the amount of active lysozyme obtainable by bronchopulmonary lavage. The effect was proportional to ozone concentration, as well as to duration of exposure. Enzyme activity returned to normal levels during the 12 hr following exposure. Ozone (5 μliters/liter; 5 parts per million) for 3 hr reduced lysozyme levels approximately 30%. Studies of the release of lysozyme by alveolar cells support the theory that loss of activity is due to in vivo oxidation of lysozyme.
The effect of nanoparticles on the liquid–gas surface tension of Bi2Te3 nanofluids

This work investigates the effect of size and concentration of nanoparticles on the effective gas–liquid surface tension of aqueous solutions of bismuth telluride nanoparticles functionalized with thioglycolic acid. The gas–liquid surface tension is obtained by solving the Laplace–Young equation under experimentally measured boundary conditions and droplet parameters. The results demonstrate that the gas–liquid surface tension depends on concentration as well as nanoparticle size. Solutions containing 2.5 and 10.4 nm nanoparticle diameters have been tested. For both, a minimum surface tension exists within the range of tested mass concentrations. The largest reduction in the surface tension (>50% versus bulk liquid) occurred for the 2.5 nm nanoparticle nanofluid. Accumulation and assembly of the charged nanoparticles at the liquid–gas interface was assumed to be responsible for the surface tension of the nanofluids investigated in this work.
Timeliness of Abnormal Screening and Diagnostic Mammography Follow-up at Facilities Serving Vulnerable Women

Background:Whether timeliness of follow-up after abnormal mammography differs at facilities serving vulnerable populations, such as women with limited education or income, in rural areas, and racial/ethnic minorities is unknown. Methods:We examined receipt of diagnostic evaluation after abnormal mammography using 1998–2006 Breast Cancer Surveillance Consortium-linked Medicare claims. We compared whether time to recommended breast imaging or biopsy depended on whether women attended facilities serving vulnerable populations. We characterized a facility by the proportion of mammograms performed on women with limited education or income, in rural areas, or racial/ethnic minorities. Results:We analyzed 30,874 abnormal screening examinations recommended for follow-up imaging across 142 facilities and 10,049 abnormal diagnostic examinations recommended for biopsy across 114 facilities. Women at facilities serving populations with less education or more racial/ethnic minorities had lower rates of follow-up imaging (4%–5% difference, P<0.05), and women at facilities serving more rural and low-income populations had lower rates of biopsy (4%–5% difference, P<0.05). Women undergoing biopsy at facilities serving vulnerable populations had longer times until biopsy than those at facilities serving nonvulnerable populations (21.6 vs. 15.6 d; 95% confidence interval for mean difference 4.1–7.7). The proportion of women receiving recommended imaging within 11 months and biopsy within 3 months varied across facilities (interquartile range, 85.5%–96.5% for imaging and 79.4%–87.3% for biopsy). Conclusions:Among Medicare recipients, follow-up rates were slightly lower at facilities serving vulnerable populations, and among those women who returned for diagnostic evaluation, time to follow-up was slightly longer at facilities that served vulnerable population. Interventions should target variability in follow-up rates across facilities, and evaluate effectiveness particularly at facilities serving vulnerable populations.
A robust kernel PCA algorithm

This paper presents a novel algorithm - robust kernel principal component analysis (robust KPCA), on the basis of the research of kernel principal component analysis (KPCA) and robust principal component analysis (RPCA). First, this algorithm sets the radius of the images of the training samples in the feature space using kernel tricks, then determines whether the samples are outliers or not, and finally analyzes the training samples which have eliminated the outliers using KPCA algorithm. The improved KPCA algorithm not only retains the non-linearity property of KPCA algorithm but also gets better robustness. Because the effects of outliers are eliminated, robust KPCA algorithm gets higher accuracy than KPCA algorithm for data analysis. The simulation experiments show that the robust KPCA algorithm developed is better than the KPCA algorithm.
Caffeine delays autonomic recovery following acute exercise

Background Impaired autonomic recovery of heart rate (HR) following exercise is associated with an increased risk of sudden death. Caffeine, a potent stimulator of catecholamine release, has been shown to augment blood pressure (BP) and sympathetic nerve activity; however, whether caffeine alters autonomic function after a bout of exercise bout remains unclear. Methods In a randomized, crossover study, 18 healthy individuals (26 ± 1 years; 23.9 ± 0.8 kg·m−2) ingested caffeine (400 mg) or placebo pills, followed by a maximal treadmill test to exhaustion. Autonomic function and ventricular depolarization/repolarization were determined using heart rate variability (HRV) and corrected QT interval (QTc), respectively, at baseline, 5, 15, and 30 minutes post-exercise. Results Maximal HR (HRmax) was greater with caffeine (192 ± 2 vs. 190 ± 2 beat·min−1, p < 0.05). During recovery, HR, mean arterial pressure (MAP), and diastolic blood pressure (DBP) remained elevated with caffeine (p < 0.05). Natural log transformation of low-to-high frequency ratio (LnLF/LnHF) of HRV was increased compared with baseline at all time points in both trials (p < 0.05), with less of an increase during 5 and 15 minutes post-exercise in the caffeine trial (p < 0.05). QTc increased from baseline at all time points in both trials, with greater increases in the caffeine trial (p < 0.05). Conclusions Caffeine ingestion disrupts post-exercise autonomic recovery because of increased sympathetic nerve activity. The prolonged sympathetic recovery time could subsequently hinder baroreflex function during recovery and disrupt the stability of autonomic function, potentiating a pro-arrhythmogenic state in young adults.
Training ‘clerks of the [global] empire’ for 21st-century Asia? English for Research Purposes (ERP) in Vietnam

© 2017 The Contributors. This work is licenced under the Creative Commons AttributionNonCommercialNoDerivatives 4.0 International (CC BY-NC-ND 4.0) License. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0 or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. This licence allows for the copying, distribution, display and performance of this work for noncommercial purposes providing the work is clearly attributed to the copyright holders.
Fathers’ Emotional Awareness and Children’s Empathy and Externalizing Problems

Emerging evidence suggests that fathers, more so than mothers, socialize emotions in a gender-stereotyped manner. Gender-stereotyped emotion socialization may be particularly pronounced in men perpetrating intimate partner violence (IPV), and may be detrimental to child adjustment, particularly for boys. This study explored the relation between fathers’ socialization of children’s emotions and child adjustment in families where IPV is present. We hypothesized that in families where there is IPV, fathers’ awareness of their children’s sadness and fear will be associated with negative child outcomes. Participants were 74 families recruited for a longitudinal study. Interview and questionnaire measures were used to assess IPV and fathers’ emotional awareness when children were 5 years old. Child adjustment was measured when children were 16 years old. Results suggested that in families where there is IPV, fathers who were more aware of their children’s fear had children who showed lower levels of empathy and higher levels of externalizing problems than children whose fathers were less aware of their fear, specifically for boys. Results are discussed in terms of gender socialization in families where there is IPV.