Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of blinding on the results of a randomized, placebo‐controlled multiple sclerosis clinical trial

In the randomized, placebo-controlled, physician-blinded Canadian cooperative trial of cyclophosphamide and plasma exchange, neither active treatment regimens (group I: IV cyclophosphamide and prednisone; group II: weekly plasma exchange, oral cyclophosphamide, and prednisone) were superior to placebo (group III: sham plasma exchange and placebo medications) using the blinded, evaluating neurologists' assessments of disease course (primary analysis). All patients were examined by both a blinded and an unblinded neurologist at each assessment in this trial. We compared the blinded and unblinded neurologists' judgment of treatment response and analyzed the clinical behavior of patients who correctly guessed their treatment. The unblinded (but not the blinded) neurologists' scores demonstrated an apparent treatment benefit at 6, 12, and 24 months for the group II patients (not group I or placebo; p <0.05, two-tailed). There were no significant differences in the time to treatment failure or in the proportions of patients improved, stable, or worse between the group II and group III patients who correctly guessed their treatment assignments and those who did not. Physician blinding prevented an erroneous conclusion about treatment efficacy (false positive, type 1 error).
Recognizing activities with cluster-trees of tracklets

We address the problem of recognizing complex activities, such as pole vaulting, which are characterized by the composition of a large and variable number of different spatio-temporal parts. We represent a video as a hierarchy of mid-level motion components. This hierarchy is a data-driven decomposition specific to each video. We introduce a divisive clustering algorithm that can efficiently extract a hierarchy over a large number of local trajectories. We use this structure to represent a video as an unordered binary tree. This tree is modeled by nested histograms of local motion features. We provide an efficient positive definite kernel that computes the structural and visual similarity of two tree decompositions by relying on models of their edges. Contrary to most approaches based on action decompositions, we propose to use the full hierarchical action structure instead of selecting a small fixed number of parts. We present experimental results on two recent challenging benchmarks that focus on complex activities and show that our kernel on per-video hierarchies allows to efficiently discriminate between complex activities sharing common action parts. Our approach improves over the state of the art, including unstructured activity models, baselines using other motion decomposition algorithms, graph matching, and latent models explicitly selecting a fixed number of parts.
Computer-Aided Nodule Detection and Volumetry to Reduce Variability Between Radiologists in the Interpretation of Lung Nodules at Low-Dose Screening Computed Tomography

ObjectiveThe aim of this study was to evaluate whether a computer-aided diagnosis (CAD) system improves interobserver agreement in the interpretation of lung nodules at low-dose computed tomography (CT) screening for lung cancer. Materials and MethodsBaseline low-dose screening CT examinations from 134 participants enrolled in the National Lung Screening Trial were reviewed by 7 chest radiologists. All participants consented to the use of their deidentified images for research purposes. Screening results were classified as positive when noncalcified nodules larger than 4 mm in diameter were present. Follow-up evaluation was recommended according to the nodule diameter: 4 mm or smaller, more than 4 to 8 mm, and larger than 8 mm. When multiple nodules were present, recommendations were based on the largest nodule. Readers initially assessed the nodule presence visually and measured the average nodule diameter manually. Revision of their decisions after reviewing the CAD marks and size measurement was allowed. Interobserver agreement evaluated using multirater &kgr; statistics was compared between initial assessment and that with CAD. ResultsMultirater &kgr; values for the positivity of the screening results and follow-up recommendations were improved from moderate (&kgr; = 0.53–0.54) at initial assessment to good (&kgr; = 0.66–0.67) after reviewing CAD results. The average percentage of agreement between reader pairs on the positivity of screening results and follow-up recommendations per case was also increased from 77% and 72% at initial assessment to 84% and 80% with CAD, respectively. ConclusionComputer-aided diagnosis may improve the reader agreement on the positivity of screening results and follow-up recommendations in the assessment of low-dose screening CT.
Simulating the Growth of Viruses

To explore how the genome of an organism defines its growth, we have developed a computer simulation for the intracellular growth of phage T7 on its E. coli host. Our simulation, which incorporates 30 years of genetic, biochemical, physiological, and biophysical data, is used here to study how the intracellular resources of the host, determined by the specific growth rate of the host, contribute toward phage development. It is also used to probe how changes in the linear organization of genetic elements on the T7 genome can affect T7 development. Further, we show how time-series trajectories of T7 mRNA and protein levels generated by the simulation may be used as raw data to test data-mining strategies, specifically, to identify partners in protein-protein interactions. Finally, we suggest how generalization of this work can lead to a knowledge-driven simulation for the growth of any virus.
Surgical management of a failed internal root resorption treatment: a histological and clinical report

This article presents the successful surgical management of a failed mineral trioxide aggregate (MTA) orthograde obturation of a tooth with a history of impact trauma and perforated internal root resorption. A symptomatic maxillary lateral incisor with a history of perforation due to internal root resorption and nonsurgical repair using MTA was referred. Unintentional overfill of the defect with MTA had occurred 4 yr before the initial visit. The excess MTA had since disappeared, and a radiolucent lesion adjacent to the perforation site was evident radiographically. Surgical endodontic retreatment was performed using calcium enriched mixture (CEM) cement as a repair material. Histological examination of the lesion revealed granulation tissue with chronic inflammation, and small fragments of MTA encapsulated within fibroconnective tissue. At the one and two year follow up exams, all signs and symptoms of disease had resolved and the tooth was functional. Complete radiographic healing of the lesion was observed two years after the initial visit. This case report illustrates how the selection of an appropriate approach to treatment of a perforation can affect the long term prognosis of a tooth. In addition, extrusion of MTA into a periradicular lesion should be avoided.
LOX-1, mtDNA damage, and NLRP3 inflammasome activation in macrophages: implications in atherogenesis.

AIMS Lectin-like ox-LDL scavenger receptor-1 (LOX-1) and mitochondrial DNA (mtDNA) damage play a key role in a variety of cardiovascular diseases, including atherosclerosis, hypertension, and inflammation. We posited that damaged mtDNA could trigger autophagy and NLRP3 inflammasome activation, and LOX-1 may play a critical role in this process. METHODS AND RESULTS In order to examine this hypothesis, cultured human THP-1 macrophages exposed to lipopolysaccharide (LPS) were applied to study the link between LOX-1, mtDNA damage, autophagy, and NLRP3 inflammasome expression. Our data showed that LPS markedly induced LOX-1 expression, reactive oxygen species (ROS) generation, autophagy, mtDNA damage, and NLRP3 inflammasome. LOX-1 inhibition with a binding antibody or siRNA inhibited ROS generation, autophagy and mtDNA damage, and a decreased expression of NLRP3 inflammasome. To study the LOX-1-NLRP3 inflammasome signalling, we performed studies using ROS inhibitors and an autophagy inducer, and found that both decreased the expression of NLRP3. On the other hand, autophagy inhibitor enhanced the expression of NLRP3 inflammasome. Knockdown of DNase II inhibited autophagy and NLRP3 inflammasome, providing further support for our hypothesis. Finally, we confirmed the relationship between LOX-1, ROS, mtDNA damage, autophagy, and NLRP3 inflammasome activation in primary macrophages. CONCLUSIONS This study based on THP-1 macrophages and primary macrophages indicates that LOX-1-mediated autophagy and mtDNA damage play an essential role in NLRP3 inflammasome activation in inflammatory disease states.
Morphology and barrier mechanism of biaxially oriented poly(ethylene terephthalate)/poly(ethylene 2,6-naphthalate) blends

To improve the barrier properties of poly(ethylene terephthalate) (PET), PET/poly(ethylene 2,6-naphthalate) (PEN) blends with different concentrations of PEN were prepared and were then processed into biaxially oriented PET/PEN films. The air permeability of bioriented films of pure PET, pure PEN, and PET/PEN blends were tested by the differential pressure method. The morphology of the blends was studied by scanning electron microscopy (SEM) observation of the impact fracture surfaces of extruded PET/PEN samples, and the morphology of the films was also investigated by SEM. The results of the study indicated that PEN could effectively improve the barrier properties of PET, and the barrier properties of the PET/PEN blends improved with increasing PEN concentration. When the PEN concentration was equal to or less than 30%, as in this study, the PET/PEN blends were phase-separated; that is, PET formed the continuous phase, whereas PEN formed a dispersed phase of particles, and the interface was firmly integrated because of transesterification. After the PET/PEN blends were bioriented, the PET matrix contained a PEN microstructure consisting of parallel and extended, separate layers. This multilayer microstructure was characterized by microcontinuity, which resulted in improved barrier properties because air permeation was delayed as the air had to detour around the PEN layer structure. At a constant PEN concentration, the more extended the PEN layers were, the better the barrier properties were of the PET/PEN blends. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 1309–1316, 2006
Prevalence of early childhood caries and associated risk factors in preschool children of urban Bangalore, India: A cross-sectional study

ABSTRACT Objectives: Early childhood caries (ECC) is a devastating form of dental decay with multi-factorial origin. The aim of this cross-sectional study is to investigate the prevalence and related risk factors of ECC in preschool children of urban Bangalore (India) Methods: A random sample of 1,500 children aged between 8 and 48 months were selected from various parts of urban Bangalore. The status of dental caries was recorded according to the World Health Organization (WHO) criteria. Information regarding oral hygiene practices, feeding habits, socio-economic status, birth weight, and educational status of the mother was obtained through a structured questionnaire given to mothers of preschool children. The data was subjected to statistical analysis using the Statistical package for social sciences (SPSS) version 12 Results: The prevalence of ECC in preschool children was 27.5%, while the mean deft was 0.854. ECC increased significantly with age. Children whose mothers had no schooling and those who belonged to low socioeconomic group showed higher caries prevalence. A significant increase in caries prevalence was found in children accustomed to the practice of on-demand breast feeding and bottle feeding at night. Caries also increased significantly when snacks were consumed between meals. However, increased frequency of tooth-brushing, parental supervision, use of a baby toothbrush, and fluoridated dentifrice significantly decreased caries prevalence Conclusion: ECC is a serious public health problem in this population and measures to increase awareness should be undertaken. The target candidates for oral health promotion programs should include mothers, general dentists, pediatricians, nurses, primary care health workers, care-takers at day-care centers and gynecologists. (Eur J Dent 2012;6:141-152)
The Potential of Automatic Word Comparison for Historical Linguistics

The amount of data from languages spoken all over the world is rapidly increasing. Traditional manual methods in historical linguistics need to face the challenges brought by this influx of data. Automatic approaches to word comparison could provide invaluable help to pre-analyze data which can be later enhanced by experts. In this way, computational approaches can take care of the repetitive and schematic tasks leaving experts to concentrate on answering interesting questions. Here we test the potential of automatic methods to detect etymologically related words (cognates) in cross-linguistic data. Using a newly compiled database of expert cognate judgments across five different language families, we compare how well different automatic approaches distinguish related from unrelated words. Our results show that automatic methods can identify cognates with a very high degree of accuracy, reaching 89% for the best-performing method Infomap. We identify the specific strengths and weaknesses of these different methods and point to major challenges for future approaches. Current automatic approaches for cognate detection—although not perfect—could become an important component of future research in historical linguistics.
Pathwise accuracy and ergodicity of metropolized integrators for SDEs

Metropolized integrators for ergodic stochastic differential equations (SDEs) are proposed that (1) are ergodic with respect to the (known) equilibrium distribution of the SDEs and (2) approximate pathwise the solutions of the SDEs on finite‐time intervals. Both these properties are demonstrated in the paper, and precise strong error estimates are obtained. It is also shown that the Metropolized integrator retains these properties even in situations where the drift in the SDE is nonglobally Lipschitz, and vanilla explicit integrators for SDEs typically become unstable and fail to be ergodic. © 2009 Wiley Periodicals, Inc.
Robust nonlinear canonical correlation analysis: application to seasonal climate forecasting

Abstract. Robust variants of nonlinear canonical correlation analysis (NLCCA) are introduced to improve performance on datasets with low signal-to-noise ratios, for example those encountered when making seasonal climate forecasts. The neural network model architecture of standard NLCCA is kept intact, but the cost functions used to set the model parameters are replaced with more robust variants. The Pearson product-moment correlation in the double-barreled network is replaced by the biweight midcorrelation, and the mean squared error (mse) in the inverse mapping networks can be replaced by the mean absolute error (mae). Robust variants of NLCCA are demonstrated on a synthetic dataset and are used to forecast sea surface temperatures in the tropical Pacific Ocean based on the sea level pressure field. Results suggest that adoption of the biweight midcorrelation can lead to improved performance, especially when a strong, common event exists in both predictor/predictand datasets. Replacing the mse by the mae leads to improved performance on the synthetic dataset, but not on the climate dataset except at the longest lead time, which suggests that the appropriate cost function for the inverse mapping networks is more problem dependent.
Diffusion Distance for Histogram Comparison

In this paper we propose diffusion distance, a new dissimilarity measure between histogram-based descriptors. We define the difference between two histograms to be a temperature field. We then study the relationship between histogram similarity and a diffusion process, showing how diffusion handles deformation as well as quantization effects. As a result, the diffusion distance is derived as the sum of dissimilarities over scales. Being a cross-bin histogram distance, the diffusion distance is robust to deformation, lighting change and noise in histogram-based local descriptors. In addition, it enjoys linear computational complexity which significantly improves previously proposed cross-bin distances with quadratic complexity or higher. We tested the proposed approach on both shape recognition and interest point matching tasks using several multi-dimensional histogram-based descriptors including shape context, SIFT, and spin images. In all experiments, the diffusion distance performs excellently in both accuracy and efficiency in comparison with other state-of-the-art distance measures. In particular, it performs as accurately as the Earth Mover’s Distance with much greater efficiency.
The use of pre-conceptional folic acid as an indicator of uptake of a health message amongst white and Bangladeshi women in Tower Hamlets, east London.

BACKGROUND The benefit of folic acid is a simple health promotion message of proven effectiveness that is particularly pertinent to a young population with a high birth rate. OBJECTIVE The aim of the present study was to compare the uptake of a folic acid health message in two different ethnic groups. METHODS Community antenatal teams in Tower Hamlets were asked to recruit women attending for a booking between October 1997 and July 1998 to the study. Tower Hamlets, in east London, is one of the poorest areas in England and Wales, with an ethnically diverse population. A questionnaire enquiring about age, employment, level of education, use of folic acid in their current pregnancy, understanding of the benefits of folic acid and self-described ethnic group was administered verbally immediately before the booking appointment to those women who agreed to participate. RESULTS Completed questionnaires were received on 249 women. Univariate analysis showed that white women were 5.7 [95% confidence interval (CI) 2.5, 13.2] times more likely to have taken folic acid supplements before conception than Bangladeshi women. Having controlled for the variables, age, school leaving age, social class, parity, planned pregnancy and 'heard of folic acid', ethnic status remained a significant predictor of taking folic acid, with the odds ratio dropping to 5.2 with a 95% CI (1.1, 25.2). CONCLUSION The Bangladeshi community in the UK have been shown to have poor access to health information sources, which is consistent with the results of this survey, which shows that a simple and important message has not been acted upon equally by white and Bangladeshi women in east London. This survey lends support to the view that resources and innovative forms of health promotion are needed to ensure that ethnic minority groups have adequate access to health promotion messages.
Fracture behaviour of precracked specimens of a TiAl alloy

Abstract Fracture behaviour of a two phase TiAl alloy was investigated based on observations of fracture surfaces of three point bending (3PB) precracked specimens and detailed observations of configuration changes at precrack tips, based on which new findings are presented. The higher toughness of coarse, near fully lamellar microstructure as compared to that of finer duplex microstructure is attributed to the path of crack propagation. In coarser NFL microstructure, the crack should cross more large grains with unfavourable orientation or bypass them by much more tortuous path, which causes a much rougher fracture surface than that observed in the finer duplex microstructure. The inverse relationships, showing a low tensile ductility but a higher fracture toughness of the coarser NFL microstructure, are explained by the difference in sampling volume between tensile testing and toughness testing. In the precracked 3PB specimens, the sampling volume is restricted to the vicinity along the precrack direction. The coarser NFL microstructure shows the higher toughness. However, in tensile tests, where a much higher sampling volume includes the entire region within the gauge, the cleavage fracture of the coarser NFL microstructure is able to take the weakest route via the high number of interlamellar cracks. The toughening mechanisms, which make the main crack difficult to propagate or cause it to be stopped, are attributed to reducing the tensile stress perpendicular to the interface between lamellae.
Multicast Routing and Distance-Adaptive Spectrum Allocation in Elastic Optical Networks With Shared Protection

We consider an elastic all-optical network, where each node is multicast-capable and does not support spectrum conversion. In such a network, for a given set of static multicast demands, we consider distance-adaptive spectrum resource allocation, and aim to optimize multicast routing, modulation, and spectrum assignment with shared protection in a way that minimizes the required spectrum resources for accommodating all multicast sessions. In our design, we provision each multicast demand by a light-tree where spectrum resources are allocated in all links included in the tree. We protect each light-tree from any single link failure in both directions by having a backup path that is link-disjoint to the path from the source to each destination on the primary tree. We reserve spectrum resources in the links that are not in the primary tree but in the backup paths between all source-destination pairs. The reserved spectrum resources can be shared to protect multiple light-trees as long as they do not fail simultaneously. For such a problem, we provide a mixed integer linear programming formulation. We also develop a scalable heuristic algorithm with an attribute that enables it to improve the quality of the results at the cost of longer running times. Numerical results for small problems show that the heuristic algorithm performs close to the optimum. In addition, we use a Markov chain simulation of the network to evaluate the performance of our proposed algorithm in terms of blocking probability in a dynamic environment, which demonstrates a significant improvement over straightforward approaches.
Tunable Ultra-Broadband Microwave Frequency Combs Generation Based on a Current Modulated Semiconductor Laser Under Optical Injection

We have demonstrated and characterized the generation of ultra-broadband microwave frequency combs (MFCs) based on a current modulated distributed feedback semiconductor laser (DFB-SL) subject to optical injection, and the comb spacing of MFCs can be tuned easily through adjusting the modulation frequency <inline-formula> <tex-math notation="LaTeX">$\text{f}_{m}$ </tex-math></inline-formula>. For the DFB-SL under only current modulation with modulation frequency <inline-formula> <tex-math notation="LaTeX">$\text{f}_{m }= 1.2$ </tex-math></inline-formula> GHz and modulation power <inline-formula> <tex-math notation="LaTeX">$\text{P}_{m }= 22$ </tex-math></inline-formula> dBm, the generated MFC has a bandwidth of about 15.6 GHz within ±5.0 dB amplitude variation. Further, introducing continuous-wave optical injection into the current modulated DFB-SL with injection power <inline-formula> <tex-math notation="LaTeX">$\text{P}_{i }= 1170~\mu \text{W}$ </tex-math></inline-formula> and no frequency detuning between the injection light frequency and the oscillation frequency of the free-running DFB-SL, the bandwidth of MFC can be increased to 57.6 GHz. Through measuring the single sideband (SSB) phase noises of some representative comb lines, the performances of the MFCs generated before and after introducing optical injection are compared, and the SSB phase noises at 10 kHz offset frequency can be increased by 10 dB for the harmonics with frequencies of more than <inline-formula> <tex-math notation="LaTeX">$40\text {f}_{m}$ </tex-math></inline-formula> after adopting optical injection. Moreover, the influences of operation parameters on the bandwidths of MFCs are analyzed, and the optimized parameter range for generating ultra-broadband MFCs has been determined.