Miracle-dz/UniFAR-FTUs huggingface dataset:
Echocardiographic arterial measurements in complex congenital diseases before bidirectional Glenn: comparison with cardiovascular magnetic resonance imaging

Aims This study sought to investigate diagnostic accuracy of echocardiographic measures of great vessels in patients before bidirectional cavopulmonary connection (BCPC) compared with cardiovascular magnetic resonance (CMR). Methods and results Seventy‐two patients (61% after Norwood operation) undergoing BCPC between 2007 and 2012 were assessed pre‐operatively using echocardiography and CMR. Bland–Altman analysis and correlation coefficients were used for comparison of echocardiography and CMR measurements. Sensitivity, specificity, and positive and negative predictive values were calculated to assess the ability of echocardiography to detect vessel stenosis. Twenty‐four percent of all vessel measurements could not be made by echocardiography due to poor image quality. Acquisition of unsatisfactory images was higher in non‐sedated patients. Although there was a reasonable correlation (0.68–0.90) and low bias (−0.8 to 0.5), there were wide limits of agreement between echocardiography and CMR demonstrating poor agreement. Sensitivity and specificity for pulmonary branches were moderate [sensitivity for right pulmonary artery (RPA) 67%, left pulmonary artery (LPA) 54%, specificity for RPA 65%, LPA 72%] with low levels of accuracy (RPA and LPA 42%). Sensitivity, specificity, and accuracy were better for aorta (82, 86, and 63%, respectively). Conclusion This study demonstrates modest agreement between echocardiographic and CMR measures of vessel diameter and stenosis detection. Approximately a quarter of all vessel segments could not be measured using echocardiography due to poor image quality, which was significantly lower in non‐sedated patients. These findings show that echocardiography cannot substitute CMR for reliable identification of great vessel stenoses in complex patients prior to the BCPC, particularly those with Blalock–Taussig shunts.
Contribution of Plasmodium knowlesi to Multispecies Human Malaria Infections in North Sumatera, Indonesia

Summary Indonesia is aiming for malaria elimination by 2030. A parasitological survey of 3731 individuals in North Sumatera province used polymerase chain reaction to identify 1169 with parasitemia and highly specific amplification of sicavar genes to identify Plasmodium knowlesi infection in 377.
Generalized Group Profiling for Content Customization

There is an ongoing debate on personalization, adapting results to the unique user exploiting a user's personal history, versus customization, adapting results to a group profile sharing one or more characteristics with the user at hand. Personal profiles are often sparse, due to cold start problems and the fact that users typically search for new items or information, necessitating to back-off to customization, but group profiles often suffer from accidental features brought in by the unique individual contributing to the group. In this paper we propose a generalized group profiling approach that teases apart the exact contribution of the individual user level and the `abstract' group level by extracting a latent model that captures all, and only, the essential features of the whole group. Our main findings are the followings. First, we propose an efficient way of group profiling which implicitly eliminates the general and specific features from users' models in a group and takes out the abstract model representing the whole group. Second, we employ the resulting models in the task of contextual suggestion. We analyse different grouping criteria and we find that group-based suggestions improves the customization. Third, we see that the granularity of groups affects the quality of group profiling. We observe that grouping approach should compromise between the level of customization and groups' size.
A Japanese diet with low glycaemic index and glycaemic load is associated with both favourable and unfavourable aspects of dietary intake patterns in three generations of women

Abstract Objective Western studies have suggested cultural differences in food and nutrient intake patterns associated with dietary glycaemic index (GI) and glycaemic load (GL). Here, we conducted a cross-sectional study to examine the GI and GL of Japanese diets in relation to food and nutrient intakes. Design Dietary intake was assessed using a validated, self-administered, diet history questionnaire. Setting A total of thirty-five of forty-seven prefectures in Japan. Subjects Young (age 18 years), middle-aged (mean age 48 years) and older (mean age 74 years) Japanese women (n 3961, 3800 and 2202, respectively). Results Irrespective of age, a positive association with dietary GI was seen for white rice only, which contributed most (37–42 %) to the variation in dietary GI. Conversely, all other food groups (such as fruit and vegetable juice, dairy products, noodles and fruit) were negative predictors of dietary GI. For dietary GL, 95–96 % of variation was explained by carbohydrate-rich food groups, all of which were positive predictors of GL. After adjustment for potential confounding factors, only carbohydrate intake was positively associated with dietary GI and GL, irrespective of age. Conversely, dietary GI and GL were inversely associated with intakes of all other nutrients examined (including SFA and Na). Conclusions A low-GI and -GL diet, which was characterized principally by a low intake of white rice, was associated with both favourable (higher intakes of dietary fibre and key vitamins and minerals) and unfavourable (higher intakes of SFA and Na) aspects of dietary intake patterns in three generations of Japanese women.
CAPS : Cache Allocation with Partial Sharing

In a multicore system, effective management of shared last level cache (LLC) has attracted significant research attention. However, almost none of the existing solutions had been implemented on a real system until Intel introduced Cache Allocation Technology (CAT) to its commodity processors recently. CAT itself implements way partitioning and thus can only allocate at a coarse granularity, which does not scale well for a large thread or program count to serve their various performance goals effectively. We overcome these limitations by deliberately and precisely sharing part of the allocations among programs and cores.
Facial Anthropometric Evaluation of Unilateral Cleft Lip and Palate Patients: Infancy Through Adolescence

Introduction: Craniofacial anthropometric studies measure the differences in humans’ craniofacial dimensions. The aim of this study was to determine facial anthropometric dimensions of newborn to 12-year-old girls with nonsyndromic unilateral cleft lip and palate (UCLP). Methods: In this cross-sectional analytical study, data was collected from 65 infant to 12-year old girls with UCLP. Digital frontal and profile facial photographs were transferred to a computer and desired anthropometric landmarks were traced on each image. Fifteen anthropometric parameters were measured which were the angles of facial, nasofacial, nasomental, Z, nasolabial, inclination of nasal base and labial fissure, nasal deviation, mentocervical, facial convexity and also ratios of nasal prominence relative to nasal height, middle to lower facial third, upper lip to lower lip height, columellar length relative to upper lip, and incisal show relative to incisal width. Pearson coefficient and linear regression were used for statistical analysis. Results: Upper lip to lower lip height ratio and angles of nasofacial, nasolabial, and facial convexity decreased with the age of the patients. In contrast, nasomental angle and the ratios of columellar length to upper lip length, middle facial height to lower facial height, and incisal show relative to incisal width increased. Other parameters studied did not appear to have any significant correlation with age. Conclusion: In the girls with UCLP, various craniofacial dimensions have different growth rates with some parts growing slower than others. Some of the parameters studied were significantly correlated with age, thus growth-related curves and equations were obtained and presented.
The influence of progression of atrial fibrillation on quality of life: a report from the Euro Heart Survey

Aims Progression of atrial fibrillation (AF) from paroxysmal to persistent forms is an active field of research. The influence of AF progression on health related quality of life (HRQoL) is currently unknown. We aimed to assess the influence of AF progression on HRQoL, and whether this association is mediated through symptoms, treatment, and major adverse events. Methods and results In the Euro Heart Survey, 967 patients were included with paroxysmal AF who filled out EuroQoL-5D at baseline and at 1 year follow-up. Those who progressed (n = 132, 13.6%) developed more problems during follow-up than those who did not, on all EuroQoL-5D domains (increase in problems on mobility 20.5% vs. 11.4%; self-care 12.9% vs. 6.2%; usual activities 23.5% vs. 14.0%; pain/discomfort 20.5% vs. 13.7%; and anxiety/depression 22.7% vs. 15.7%; all P < 0.05), leading to a decrease in utility [baseline 0.744 ± 0.26, follow-up 0.674 ± 0.36; difference -0.07 (95% CI [-0.126,-0.013], P = 0.02)]. Multivariate analysis showed that the effect of progression on utility is mediated by a large effect of adverse events [stroke (-0.27 (95% CI [-0.43,-0.11]); P = 0.001], heart failure [-0.12 (95% CI [-0.20,-0.05]); P = 0.001], malignancy (-0.31 (95% CI [-0.56,-0.05]); P = 0.02] or implantation of an implantable cardiac defibrillator [-0.12 (95% CI [-0.23,-0.02]); P = 0.03)], as well as symptomatic AF [-0.04 (95% CI [-0.08,-0.01]); P = 0.008]. Conclusion AF progression is associated with a decrease in HRQoL. However, multivariate analysis revealed that AF progression itself does not have a negative effect on HRQoL, but that this effect can be attributed to a minor effect of the associated symptoms and a major effect of associated adverse events.
Role of neuroinflammation in ischemic stroke

Ischemic stroke causes the depletion of energy and induce excitotoxicity and neuroinflammation in the brain that results from thrombotic blockage. Neuroinflammation occurs initially depending on activated resident microglia that has the same function as the macrophage. Activated microglia participates in the neuroinflammatory process by phagocytosing the injured brain cells and producing the proand anti-inflammatory mediators. In this review, the authors present an overview of the role of microglia in mediating neuroinflammation in ischemic stroke.
Chromatin accessibility prediction via a hybrid deep convolutional neural network

Motivation A majority of known genetic variants associated with human‐inherited diseases lie in non‐coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and precisely decipher their implications in a comprehensive manner. Although computational approaches have been complementing high‐throughput biological experiments towards the annotation of the human genome, it still remains a big challenge to accurately annotate regulatory elements in the context of a specific cell type via automatic learning of the DNA sequence code from large‐scale sequencing data. Indeed, the development of an accurate and interpretable model to learn the DNA sequence signature and further enable the identification of causative genetic variants has become essential in both genomic and genetic studies. Results We proposed Deopen, a hybrid framework mainly based on a deep convolutional neural network, to automatically learn the regulatory code of DNA sequences and predict chromatin accessibility. In a series of comparison with existing methods, we show the superior performance of our model in not only the classification of accessible regions against background sequences sampled at random, but also the regression of DNase‐seq signals. Besides, we further visualize the convolutional kernels and show the match of identified sequence signatures and known motifs. We finally demonstrate the sensitivity of our model in finding causative noncoding variants in the analysis of a breast cancer dataset. We expect to see wide applications of Deopen with either public or in‐house chromatin accessibility data in the annotation of the human genome and the identification of non‐coding variants associated with diseases. Availability and implementation Deopen is freely available at https://github.com/kimmo1019/Deopen. Contact ruijiang@tsinghua.edu. cn Supplementary information Supplementary data are available at Bioinformatics online.
Predictors of the effectiveness of accreditation on hospital performance: A nationwide stepped-wedge study

Objective To identify predictors of the effectiveness of hospital accreditation on process performance measures. Design A multi-level, longitudinal, stepped-wedge, nationwide study. Participants All patients admitted for acute stroke, heart failure, ulcers, diabetes, breast cancer and lung cancer at Danish hospitals. Intervention The Danish Healthcare Quality Programme that was designed to create a framework for continuous quality improvement. Main outcome Measure(s) Changes in week-by-week trends of hospitals' process performance measures during the study period of 269 weeks prior to, during and post-accreditations. Process performance measures were based on 43 different processes of care obtained from national clinical quality registries. Analyses were stratified according to condition, type of care (i.e. treatment, diagnostics, secondary prevention and patient monitoring) and hospital characteristics (i.e. university affiliation, location, size, experience with accreditation and accreditation compliance). Results A total of 1 624 518 processes of care were included. The impact of accreditation differed across the conditions. During accreditation, heart failure and breast cancer showed less improvement than other disease areas. Across all conditions, diagnostic processes improved less rapidly than other types of processes. However, after stratifying the data by hospital characteristics, process performance measures improved more uniformly. In respect of the measures that had an unsatisfactory level of quality, the processes related to diabetes, diagnostics and patient monitoring all responded to accreditation and showed an increased improvement during the preparatory work. Conclusion Hospital characteristics were not found to be predictors for the effects of accreditation, whereas conditions and types of care to some extent predicted the effectiveness.
A β-galactosidase-expressing E. coli culture as an alternative test to identify skin sensitizers and non-sensitizers

ABSTRACT Although the Organization for Economic Cooperation and Development (OECD) has adopted several in vitro methods with reasonable predictive capacity, alternative methods for identifying skin sensitizers and non-sensitizers with reliability and simplicity are still required for more efficient and economic prediction. The present study was to design an in vitro system with the use of a β-galactosidase-expressing E. coli culture for simpler but sufficiently accurate classification of skin sensitizers and non-sensitizers. A LacZ gene-containing E. coli strain that is capable of producing β-galactosidase enzyme was induced by isopropyl β-D-1-thiogalactopyranoside with concomitant treatment with test chemicals. After 6-hr incubation, cells were lysed and β-galactosidase enzyme activity was monitored colorimetrically by using O-nitrophenyl-D-galactopyranoside as a substrate. Following optimization of several experimental conditions, 22 skin sensitizers and 11 non-sensitizers were examined to assess predictive capacity of this method. The results indicated that predictivity was as follows: 90.9% sensitivity, 81.8% specificity, and 87.9% accuracy, when 17.3% of control activity was used as the cut-off value to separate sensitizers from non-sensitizers. Data suggested that the current bacterial system expressing β-galactosidase may serve as a useful alternative test for classifying skin sensitizers and non-sensitizers, without the utilization of animals or mammalian cell cultures.
Duration of device-detected subclinical atrial fibrillation and occurrence of stroke in ASSERT

Background ASSERT demonstrated that subclinical atrial fibrillation (SCAF) is common in pacemaker patients without prior AF and is associated with increased risk of ischemic stroke or systemic embolism. SCAF episodes vary in duration and little is known about the incidence of different durations of SCAF, or their prognosis. Methods and results ASSERT followed 2580 patients receiving a pacemaker or ICD, aged >65 years with hypertension, without prior AF. The effect of SCAF duration on subsequent risk of ischemic stroke or embolism was evaluated with time-dependent covariate Cox models. Patients in whom the longest SCAF was ⩽6 min were excluded from the analysis (n=125). Among 2455 patients during mean follow-up of 2.5 years, the longest single episode of SCAF lasted >6 min to 6 h in 462 patients (18.8%), >6–24 h in 169 (6.9%), and >24 h in 262 (10.7%). SCAF duration >24 h was associated with a significant increased risk of subsequent stroke or systemic embolism (adjusted hazard ratio [HR] 3.24, 95% confidence interval [CI] 1.51–6.95, P=0.003). The risk of ischemic stroke or systemic embolism in patients with SCAF between 6 min and 24 h was not significantly different from patients without SCAF. Conclusions SCAF >24 h is associated with an increased risk of ischemic stroke or systemic embolism.
An Integrated Framework for Software Defined Networking, Caching, and Computing

Although some excellent works have been done on networking, caching and computing, these three important areas have traditionally been addressed separately in the literature. In this article, we propose a novel framework that jointly considers networking, caching and computing techniques in order to improve end-to-end system performance. This integrated framework can enable dynamic orchestration of networking, caching and computing resources to meet the requirements of different applications. We define and develop the key components of this framework: the data plane, the control plane, and the management plane. The data plane consists of the devices that are responsible for networking, caching and computing operations. The control plane has a logically centralized controller to guide these operations. The management plane enables not only traditional applications, such as traffic engineering, but also new applications, such as content distribution and big data analytics. Simulation results are presented to show the effectiveness of the proposed framework. In addition, we discuss a number of challenges of implementing the proposed framework of software defined networking, caching and computing.
Activation of the same mGluR5 receptors in the amygdala causes divergent effects on specific versus indiscriminate fear

Although mGluR5-antagonists prevent fear and anxiety, little is known about how the same receptor in the amygdala gives rise to both. Combining in vitro and in vivo activation of mGluR5 in rats, we identify specific changes in intrinsic excitability and synaptic plasticity in basolateral amygdala neurons that give rise to temporally distinct and mutually exclusive effects on fear-related behaviors. The immediate impact of mGluR5 activation is to produce anxiety manifested as indiscriminate fear of both tone and context. Surprisingly, this state does not interfere with the proper encoding of tone-shock associations that eventually lead to enhanced cue-specific fear. These results provide a new framework for dissecting the functional impact of amygdalar mGluR-plasticity on fear versus anxiety in health and disease. DOI: http://dx.doi. org/10.7554/eLife.25665. 001
AQUA‐DUCT: a ligands tracking tool

Motivation: The identification and tracking of molecules which enter active site cavity requires screening the positions of thousands of single molecules along several thousand molecular dynamic steps. To fill the existing gap between tools searching for tunnels and pathways and advanced tools employed for accelerated water flux investigations, we have developed AQUA‐DUCT. Results: AQUA‐DUCT is an easy‐to‐use tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein. It can be used for any type of molecules, e.g. water, oxygen, carbon dioxide, organic solvents, ions. Availability and Implementation: Linux, Windows, macOS, OpenBSD, http://www.aquaduct.pl. Contact: a.gora@tunnelinggroup.pl or info@aquaduct.pl Supplementary information: Supplementary data are available at Bioinformatics online.
GGE Biplot vs. AMMI Analysis of Genotype-by-Environment Data

The use of genotype main effect (G) plus genotype-by-environment (GE) interaction (G+GE) biplot analysis by plant breeders and other agricultural researchers has increased dramatically during the past 5 yr for analyzing multi-environment trial (MET) data. Recently, however, its legitimacy was questioned by a proponent of Additive Main Effect and Multiplicative Interaction (AMMI) analysis. The objectives of this review are: (i) to compare GGE biplot analysis and AMMI analysis on three aspects of genotype-by-environment data (GED) analysis, namely mega-environment analysis, genotype evaluation, and test-environment evaluation; (ii) to discuss whether G and GE should be combined or separated in these three aspects of GED analysis; and (iii) to discuss the role and importance of model diagnosis in biplot analysis of GED. Our main conclusions are: (i) both GGE biplot analysis and AMMI analysis combine rather than separate G and GE in mega-environment analysis and genotype evaluation, (ii) the GGE biplot is superior to the AMMI1 graph in mega-environment analysis and genotype evaluation because it explains more G+GE and has the inner-product property of the biplot, (iii) the discriminating power vs. representativeness view of the GGE biplot is effective in evaluating test environments, which is not possible in AMMI analysis, and (iv) model diagnosis for each dataset is useful, but accuracy gain from model diagnosis should not be overstated.
A Survey : On Content Based Image Retrieval

Content based Image Retrieval is the task of retrieve the images from the large collection of database on the basis of their own visual content. CBIR is used for automatic indexing and retrieval of images depending upon contents of images known as features. This paper provides the survey of technical achievements in the research area of image retrieval. In this paper, a survey is done on the different methods of content based image retrieval for the classification of texture and color. For the classification of the extracted features we have used SVM. Classification using cascaded SVM is also used here for solving large-scale pattern classification problems. Cascaded SVM has advantages over conventional SVM. Keywords-CBIR, Feature Extraction, Texture and Pattern Classification.