Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated identification of implausible values in growth data from pediatric electronic health records

Objective Large electronic health record (EHR) datasets are increasingly used to facilitate research on growth, but measurement and recording errors can lead to biased results. We developed and tested an automated method for identifying implausible values in pediatric EHR growth data. Materials and Methods Using deidentified data from 46 primary care sites, we developed an algorithm to identify weight and height values that should be excluded from analysis, including implausible values and values that were recorded repeatedly without remeasurement. The foundation of the algorithm is a comparison of each measurement, expressed as a standard deviation score, with a weighted moving average of a child's other measurements. We evaluated the performance of the algorithm by (1) comparing its results with the judgment of physician reviewers for a stratified random selection of 400 measurements and (2) evaluating its accuracy in a dataset with simulated errors. Results Of 2 000 595 growth measurements from 280 610 patients 1 to 21 years old, 3.8% of weight and 4.5% of height values were identified as implausible or excluded for other reasons. The proportion excluded varied widely by primary care site. The automated method had a sensitivity of 97% (95% confidence interval [CI], 94-99%) and a specificity of 90% (95% CI, 85-94%) for identifying implausible values compared to physician judgment, and identified 95% (weight) and 98% (height) of simulated errors. Discussion and Conclusion This automated, flexible, and validated method for preparing large datasets will facilitate the use of pediatric EHR growth datasets for research.
TritanDB: Time-series Rapid Internet of Things Analytics

The efficient management of data is an important prerequisite for realising the potential of the Internet of Things (IoT). Two issues given the large volume of structured time-series IoT data are, addressing the difficulties of data integration between heterogeneous Things and improving ingestion and query performance across databases on both resource-constrained Things and in the cloud. In this paper, we examine the structure of public IoT data and discover that the majority exhibit unique flat, wide and numerical characteristics with a mix of evenly and unevenly-spaced time-series. We investigate the advances in time-series databases for telemetry data and combine these findings with microbenchmarks to determine the best compression techniques and storage data structures to inform the design of a novel solution optimised for IoT data. A query translation method with low overhead even on resource-constrained Things allows us to utilise rich data models like the Resource Description Framework (RDF) for interoperability and data integration on top of the optimised storage. Our solution, TritanDB, shows an order of magnitude performance improvement across both Things and cloud hardware on many state-of-the-art databases within IoT scenarios. Finally, we describe how TritanDB supports various analyses of IoT time-series data like forecasting.
Dementia, post-traumatic stress disorder and major depressive disorder: a review of the mental health risk factors for dementia in the military veteran population

Abstract Background Dementia is currently incurable, irreversible and a major cause of disability for the world's older population. The association between mental health difficulties, such as post-traumatic stress disorder (PTSD) and major depressive disorder (MDD), and dementia has a long history within the civilian population. Despite the increased importance of this link within the military veteran population, who suffer a greater propensity of mental health difficulties and consist largely of over 65s, attention is only recently being paid to the salience of such an association for this group. This paper aims to explore the relationship between PTSD and MDD with dementia within the military veteran population. Method A systematic review was conducted on articles from 1990 to July 2016 on MEDLINE, EMBASE, EBSCO and Web of Science electronic databases with an update conducted in February 2017. Results Six empirical studies were identified from the review, the majority of which originated from the USA. Five of the studies asserted that veterans with a diagnosis of either PTSD or MDD are at a significantly greater risk of developing dementia than ‘healthy’ controls. The final study, conducted in Australia, found only a small, but non-significant, correlation between earlier MDD and future dementia, but no concurrent correlation. Conclusions While causality cannot be determined, it is likely that PTSD and depressive disorders are related to an increased risk of dementia in military veterans. Potential pathological explanations and risk factors are reviewed and the clinical and neuroscience implications of these findings are explored.
Hybrid eye center localization using cascaded regression and robust circle fitting

We propose a new cascaded regressor for eye center detection. Previous methods start from a face or an eye detector and use either advanced features or powerful regressors for eye center localization, but not both. Instead, we detect the eyes more accurately using an existing facial feature alignment method. We improve the robustness of localization by using both advanced features and powerful regression machinery. Finally, unlike most other methods that do not refine the regression results, we make the localization more accurate by adding a robust circle fitting post-processing step. We evaluate our new approach and show that it achieves state-of-the-art performance on the BioID, GI4E, and the TalkingFace datasets. At an average normalized error of less than 5%, the regressor trained on manually annotated data yields an accuracy of 95.07% (BioID), 99.27% (GI4E), and 95.68% (TalkingFace).
Delay Bounds under Arbitrary Multiplexing: When Network Calculus Leaves You in the Lurch...

Network calculus has proven as a valuable and versatile methodology for worst-case analysis of communication networks. One issue in which it is still lacking is the treatment of aggregate multiplexing, in particular if the FIFO property cannot be assumed when flows are merged. In this paper, we address the problem of bounding the delay of individual traffic flows in feed-forward networks under arbitrary multiplexing. Somewhat surprisingly, we find that direct application of network calculus results in loose bounds even in seemingly simple scenarios. The reasons for this "failure" of network calculus are discussed in detail and a method to arrive at tight delay bounds for arbitrary (aggregate) multiplexing is presented. This method is based on the solution of an optimization problem. For the special case of sink-tree networks this optimization problem is solved explicitly, thus arriving at a closed-form expression for the delay bound. Numerical experiments illustrate that in sink-tree networks the improvement over bounds based on direct application of network calculus can be considerable.
Implementing an Evidence-based Tobacco Control Program at Five 2-1-1 Call Centers: An Evaluation Using the Consolidated Framework for Implementation Research

Introduction The Smoke-Free Homes (SFH) Program is an evidence-based intervention offered within 2-1-1 information and referral call centers to promote smoke-free homes in low-income populations. We used the Consolidated Framework for Implementation Research to conduct a mixed-methods analysis of facilitators and barriers to scaling up SFH to five 2-1-1 sites in the United States. Methods Data were collected from staff in 2015-2016 via online surveys administered before (N = 120) and after SFH training (N = 101) and after SFH implementation (N = 79). Semi-structured telephone interviews were conducted in 2016 with 25 staff to examine attitudes towards SFH, ways local context affected implementation, and unintended benefits and consequences of implementing SFH. Results Post-implementation, 79% of respondents reported that SFH was consistent with their 2-1-1's mission, 70% thought it led to more smoke-free homes in their population, 62% thought it was easy to adapt, and 56% thought participants were satisfied. Composite measures of perceived appropriateness of SFH for 2-1-1 callers and staff positivity toward SFH were significantly lower post-implementation than pre-implementation. In interviews, staff said SFH fit with their 2-1-1's mission but expressed concerns about intervention sustainability, time and resources needed for delivery, and how SFH fit into their workflow. Conclusions Sites' SFH implementation experiences were affected both by demands of intervention delivery and by SFH's perceived effectiveness and fit with organizational mission. Future implementation of SFH and other tobacco control programs should address identified barriers by securing ongoing funding, providing dedicated staff time, and ensuring programs fit with staff workflow. Implications Smoke-free home policies reduce exposure to secondhand smoke. Partnering with social service agencies offers a promising way to scale up evidence-based smoke-free home interventions among low-income populations. We found that the SFH intervention was acceptable and feasible among multiple 2-1-1 delivery sites. There were also significant challenges to implementation, including site workflow, desire to adapt the intervention, time needed for intervention delivery, and financial sustainability. Addressing such challenges will aid future efforts to scale up evidence-based tobacco control interventions to social service agencies such as 2-1-1.
Aether: leveraging linear programming for optimal cloud computing in genomics

Across biology we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Here, we present Aether (http://aether.kosticlab.org), an intuitive, easy-to-use, cost-effective, and scalable framework that uses linear programming (LP) to optimally bid on and deploy combinations of underutilized cloud computing resources. Our approach simultaneously minimizes the cost of data analysis while maximizing its efficiency and speed. As a test, we used Aether to de novo assemble 1572 metagenomic samples, a task it completed in merely 13 hours with cost savings of approximately 80% relative to comparable methods.
Transforming growth factor &bgr; receptor inhibition prevents ventricular fibrosis in a mouse model of progressive cardiac conduction disease

Aims Loss-of-function mutations in SCN5A, the gene encoding NaV1.5 channel, have been associated with inherited progressive cardiac conduction disease (PCCD). We have proposed that Scn5a heterozygous knock-out (Scn5a+/-) mice, which are characterized by ventricular fibrotic remodelling with ageing, represent a model for PCCD. Our objectives were to identify the molecular pathway involved in fibrosis development and prevent its activation. Methods and results Our study shows that myocardial interstitial fibrosis occurred in Scn5a+/- mice only after 45 weeks of age. Fibrosis was triggered by transforming growth factor β (TGF-β) pathway activation. Younger Scn5a+/- mice were characterized by a higher connexin 43 expression than wild-type (WT) mice. After the age of 45 weeks, connexin 43 expression decreased in both WT and Scn5a+/- mice, although the decrease was larger in Scn5a+/- mice. Chronic inhibition of cardiac sodium current with flecainide (50 mg/kg/day p.o) in WT mice from the age of 6 weeks to the age of 60 weeks did not lead to TGF-β pathway activation and fibrosis. Chronic inhibition of TGF-β receptors with GW788388 (5 mg/kg/day p.o.) in Scn5a+/- mice from the age of 45 weeks to the age of 60 weeks prevented the occurrence of fibrosis. However, current data could not detect reduction in QRS duration with GW788388. Conclusion Myocardial fibrosis secondary to a loss of NaV1.5 is triggered by TGF-β signalling pathway. Those events are more likely secondary to the decreased NaV1.5 sarcolemmal expression rather than the decreased Na+ current per se. TGF-β receptor inhibition prevents age-dependent development of ventricular fibrosis in Scn5a+/- mouse.
A comprehensive study of universal time-domain windowed OFDM-based LTE downlink system

For the 5G system and beyond, several new-waveforms with low out-of-band emission (OOBE) have been proposed to improve spectral efficiency. The universal timedomain windowed OFDM (UTW-OFDM) have been proposed as a waveform that has the low OOBE characteristics and high compatibility with the conventional cyclic prefix OFDM (CP-OFDM)-based systems. To indicate the feasibility of the UTW-OFDM-based system in the 5G and beyond, the comprehensive evaluation of the UTW-OFDM-based LTE system is important, however, the evaluation of the UTW-OFDM-based LTE system complexity has been not reported. Furthermore, the communication quality of the UTW-OFDM-based LTE system was evaluated by using BER characteristics on the short delay multipath propagation channel in the previous studies. In this paper, to show the feasibility of the UTW-OFDM for the 5G and beyond, the complexity of the UTW-OFDM-based LTE downlink (DL) system is evaluated and compared with one of the LTE-DL system with the conventional CP-OFDM and the filtering-based waveform (UF-OFDM). The complexity of the conventional CP-OFDM-based system and the UTW-OFDM-based system is about 0.45 % of the complexity of the UF-OFDM-based system. Furthermore, the communication quality of the UTW-OFDM-based LTE-DL system is evaluated by using BLER on the 3GPP Extended Typical Urban (ETU) channel model with the 70 Hz Doppler shift. The UTW-OFDM-based LTE-DL system can improve the OOBE of the conventional CP-OFDM-based LTE-DL system by 45 dB with only 2.0 dB deterioration of EN0 to achieve BLER = 10−1 even if the 64QAM is applied with a half coding rate.
Multimodal noncontact photoacoustic and optical coherence tomography imaging using wavelength-division multiplexing

Abstract. We present multimodal noncontact photoacoustic (PA) and optical coherence tomography (OCT) imaging. PA signals are acquired remotely on the surface of a specimen with a Mach-Zehnder interferometer. The interferometer is realized in a fiber-optic network using a fiber laser at 1550 nm as the source. In the same fiber-optic network, a spectral-domain OCT system is implemented. The OCT system utilizes a supercontinuum light source at 1310 nm and a spectrometer with an InGaAs line array detector. Light from the fiber laser and the OCT source is multiplexed into one fiber using a wavelength-division multiplexer; the same objective is used for both imaging modalities. Reflected light is spectrally demultiplexed and guided to the respective imaging systems. We demonstrate two-dimensional and three-dimensional imaging on a tissue-mimicking sample and a chicken skin phantom. The same fiber network and same optical components are used for PA and OCT imaging, and the obtained images are intrinsically coregistered.
Uniform Recovery Bounds for Structured Random Matrices in Corrupted Compressed Sensing

We study the problem of recovering an <inline-formula><tex-math notation="LaTeX">$s$</tex-math></inline-formula> -sparse signal <inline-formula><tex-math notation="LaTeX">$\mathbf{x}^{\star }\in \mathbb {C}^n$</tex-math> </inline-formula> from corrupted measurements <inline-formula><tex-math notation="LaTeX"> $\mathbf{y}=\mathbf{A}\mathbf{x}^{\star }+\mathbf{z}^{\star }+\mathbf{w}$</tex-math></inline-formula>, where <inline-formula><tex-math notation="LaTeX">$\mathbf{z}^{\star }\in \mathbb {C}^m$</tex-math></inline-formula> is a <inline-formula><tex-math notation="LaTeX">$k$</tex-math></inline-formula>-sparse corruption vector whose nonzero entries may be arbitrarily large and <inline-formula><tex-math notation="LaTeX">$\mathbf{w}\in \mathbb {C}^m$ </tex-math></inline-formula> is a dense noise with bounded energy. The aim is to exactly and stably recover the sparse signal with tractable optimization programs. In this paper, we prove the <italic>uniform recovery guarantee</italic> of this problem for two classes of structured sensing matrices. The first class can be expressed as the product of a unit-norm tight frame (UTF), a random diagonal matrix, and a bounded columnwise orthonormal matrix (e.g., partial random circulant matrix). When the UTF is bounded (i.e. <inline-formula><tex-math notation="LaTeX">$\mu (\mathbf{U})\sim 1/\sqrt{m}$</tex-math></inline-formula>), we prove that with high probability, one can recover an <inline-formula><tex-math notation="LaTeX">$s$</tex-math></inline-formula>-sparse signal exactly and stably by <inline-formula><tex-math notation="LaTeX">$l_1$</tex-math></inline-formula> minimization programs even if the measurements are corrupted by a sparse vector, provided <inline-formula><tex-math notation="LaTeX"> $m=\mathcal{O}(s\log ^2s\log ^2n)$</tex-math></inline-formula> and the sparsity level <inline-formula> <tex-math notation="LaTeX">$k$</tex-math></inline-formula> of the corruption is a constant fraction of the total number of measurements. The second class considers a randomly subsampled orthonormal matrix (e.g., random Fourier matrix). We prove the uniform recovery guarantee provided that the corruption is sparse on certain sparsifying domain. Numerous simulation results are also presented to verify and complement the theoretical results.
Band structure and unconventional electronic topology of CoSi

Semimetals with certain crystal symmetries may possess unusual electronic structure topology, distinct from that of the conventional Weyl and Dirac semimetals. Characteristic property of these materials is the existence of band-touching points with multiple (higher than two-fold) degeneracy and nonzero Chern number. CoSi is a representative of this group of materials exhibiting the so-called ‘new fermions’. We report on an ab initio calculation of the electronic structure of CoSi using density functional methods, taking into account the spin–orbit interactions. The linearized k⋅p Hamiltonian, describing the anisotropic electronic structure of CoSi near the Γ point is derived. The topological features of band-touching nodes with four- and six-fold degeneracy located at the Γ and R points in the first Brillouin zone are analysed using the linearized Hamiltonians and first principle calculations. In particular, we show, using the non-Abelian Berry curvature, that these band-touching points carry topological charges of ±4, which change signs at certain values of parameters of the Hamiltonians. We describe the resulting Fermi arc surface states and their spin texture. We also discuss the influence of many body G0W0 corrections on the electronic band structure and the topological properties of CoSi.
Footfall for finer food forecasts

Short shelf-lives and low-to-moderate profit margins are common characteristics among fresh-food products, leading to short replenishment cycles and frequent stock-outs. Forecasting of such products is challenged particularly by stock-outs; customers walk past empty shelves, their demand failing to register as sales. We develop an analytical approach for estimating total demand from data on sales and footfall, i.e. the daily customer count. Our investigation reveals that consideration of footfall does not significantly improve forecasts in steady state, but it enables the automatic re-introduction of discontinued products when footfall rises. Additionally, it enables forecasting of the customer conversion rate across stores.
Barriers to Hepatitis C Virus (HCV) Treatment Initiation in Patients With Human Immunodeficiency Virus/HCV Coinfection: Lessons From the Interferon Era

Abstract Background. Hepatitis C is a major cause of mortality among human immunodeficiency virus (HIV)-infected patients, yet hepatitis C virus (HCV) treatment uptake has historically been low. Although the removal of interferon removes a major barrier to HCV treatment uptake, oral therapies alone may not fully eliminate barriers in this population. Methods. Within the Johns Hopkins Hospital HIV cohort, a nested case-control study was conducted to identify cases, defined as patients initiating HCV treatment between January 1996 and 2013, and controls, which were selected using incidence density sampling (3:1 ratio). Controls were matched to cases on date of enrollment. Conditional logistic regression was used to evaluate factors associated with HCV treatment initiation. Results. Among 208 treated cases and 624 untreated controls, the presence of advanced fibrosis (odds ratio [OR], 2.23; 95% confidence interval [CI], 1.26–3.95), recent active drug use (OR, 0.36; 95% CI, 0.19–0.69), and non-black race (OR, 2.01; 95% CI, 1.26–3.20) were independently associated with initiation of HCV therapy. An increasing proportion of missed visits was also independently associated with lower odds of HCV treatment (25%–49% missed visits [OR, 0.49; 95% CI, 0.27–0.91] and ≥50% missed visits [OR, 0.24; 95% CI, 0.12–0.48]). Conclusions. Interferon-free treatments may not be sufficient to fully overcome barriers to HCV care in HIV-infected patients. Interventions to increase engagement in care for HIV and substance use are needed to expand HCV treatment uptake.
Experimental Analysis of Decohesive Phenomenon in Expanded Polystyrene under Bending and Tensile Loading Conditions

In this paper, the decohesive phenomenon of expanded polystyrene (EPS) is analysed using bending and tensile tests. Globally, the typical stress-strain curve is characterised by a wide linear or nonlinear elastic part, the plastic phase being almost neglected. The mechanical properties, such as the elastic modulus E* and the stress threshold σth*, increase with the EPS apparent density ρ*. The empirical equations have been proposed from experimental data fitting curve. The failure strain called εf, corresponding to the point where the final breakage occurs, decreases when the density value increases. Globally, these observations indicate a brittle behaviour of the EPS material under bending and tensile loading. On the other the hand, scanning electron microscopy (SEM) has been used in order to analyse the EPS fracture surfaces. The trans-beads (TB) fracture mode, where the crack grows through the beads, has sometimes been observed for the high diameters beads. But, according to all observations, the inter-beads (IB) mode generally seems to be the major mode of fracture. Therefore, this indicates that the EPS mechanical strength under bending and tensile loading essentially depends on the beads fusion quality.
Myeloablative busulfan/cytoxan conditioning versus reduced-intensity fludarabine/melphalan conditioning for allogeneic hematopoietic stem cell transplant in patients with acute myelogenous leukemia

Abstract Fludarabine and melphalan (Flu/Mel) has emerged as a more tolerable chemotherapy-based conditioning regimen compared with busulfan and cyclophosphamide (Bu/Cy) for allogeneic stem cell transplant (allo-hematopoietic stem cell transplantation (HSCT)) patients with acute myelogenous leukemia (AML). We conducted a retrospective review of a single-institution database including patients with AML who received allo-HSCT following conditioning with Mel/Flu or Bu/Cy-based regimens. We performed descriptive statistical analysis to examine patient demographics and clinical outcomes. We identified 156 patients meeting criteria between 2005 and 2014. Overall, patients conditioned with Bu/Cy were significantly younger, but more likely to be treated in an earlier era than those receiving Flu/Mel. Regimen choice was not associated with relapse rates (RR), relapse-free survival (RFS), or overall survival (OS) on both univariate and multivariable analyses. Bu/Cy was associated with increased non-relapse mortality (NRM) on multivariable analysis. These findings demonstrate that Flu/Mel provides non-inferior disease control and could be an appropriate regimen for selected patients.