Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Logical Clinical Context Clusters in Nursing Orders for the Purpose of Information Retrieval

Nurses information needs relate to nursing orders and nursing orders have many contexts including body systems, safety practices and other clinical categories. When searching for information related to orders one search term might retrieve documents related to multiple orders. We clustered nursing orders into sets that are related by the same logical clinical context. We then generated clusters and their search terms from a data set of 636 orders obtained from a CIS/CPOE system at an academic medical center. We refined those cluster search terms by searching an electronic nursing procedure manual to retrieve resources that could answer one of six generic nursing questions. Sixty-three cluster search terms were identified. The search terms for 100 (16%) of the orders were validated in a second hospitals electronic nursing procedure manual; precision was 32.5%. Our process of identifying cluster search terms may be a useful method to obtain clinically relevant information resources.
Internet service classes under competition

This paper analyzes competition between two Internet service providers (ISPs), either or both of which may choose to offer multiple service classes. In the model analyzed, a social planner who maximizes the total benefit from network usage and a profit maximizing monopolist will both form multiple service classes; but two networks competing to maximize profits will not. The reason is that a competition effect always outweighs a segmentation effect. Networks wish to offer multiple service classes in order to increase user benefits and hence charge higher prices. In doing so, however, they effectively increase the number of points in the service quality range at which they compete. Consequently, in any equilibrium competitive outcome, both ISPs offer a single service class. The analysis has particular implications for the Paris Metro pricing (PMP) proposal, which is considered in depth in this paper, since it suggests that PMP may not be viable under competition.
Exposure of Mycobacteria to Cell Wall-inhibitory Drugs Decreases Production of Arabinoglycerolipid Related to Mycolyl-arabinogalactan-peptidoglycan Metabolism*

Background: Mycolyl-arabinogalactan-peptidoglycan (mAGP) represents the hallmark of the mycobacterial cell envelope and the target of several antitubercular drugs. Results: Loss of a glycolipid structurally analogous to the terminal portion of mAGP correlates with drug treatment in mycobacteria. Conclusion: This work establishes the versatility of arabinoglycerolipids in M. tuberculosis. Significance: Further work will define the importance of the metabolic relationship between the two components in cell wall remodeling and/or pathogenesis. The “cell wall core” consisting of a mycolyl-arabinogalactan-peptidoglycan (mAGP) complex represents the hallmark of the mycobacterial cell envelope. It has been the focus of intense research at both structural and biosynthetic levels during the past few decades. Because it is essential, mAGP is also regarded as a target for several antitubercular drugs. Herein, we demonstrate that exposure of Mycobacterium bovis Bacille Calmette-Guérin or Mycobacterium marinum to thiacetazone, a second line antitubercular drug, is associated with a severe decrease in the level of a major apolar glycolipid. This inhibition requires MmaA4, a methyltransferase reported to participate in the activation process of thiacetazone. Following purification, this glycolipid was subjected to detailed structural analyses, combining gas-liquid chromatography, mass spectrometry, and nuclear magnetic resonance. This allowed to identify it as a 5-O-mycolyl-β-Araf-(1→2)-5-O-mycolyl-α-Araf-(1→1)-Gro, designated dimycolyl diarabinoglycerol (DMAG). The presence of DMAG was subsequently confirmed in other slow growing pathogenic species, including Mycobacterium tuberculosis. DMAG production was stimulated in the presence of exogenous glycerol. Interestingly, DMAG appears structurally identical to the terminal portion of the mycolylated arabinosyl motif of mAGP, and the metabolic relationship between these two components was provided using antitubercular drugs such as ethambutol or isoniazid known to inhibit the biosynthesis of arabinogalactan or mycolic acid, respectively. Finally, DMAG was identified in the cell wall of M. tuberculosis. This opens the possibility of a potent biological function for DMAG that may be important to mycobacterial pathogenesis.
SAT-based complete don't-care computation for network optimization

The paper describes an improved approach to Boolean network optimization using internal don't-cares. The improvements concern the type of don't-cares computed, their scope, and the computation method. Instead of the traditionally used compatible observability don't-cares (CODCs), we introduce and justify the use of complete don't-cares (CDC). To ensure the robustness of the don't-care computation for very large industrial networks, an optional windowing scheme is implemented that computes substantial subsets of the CDCs in reasonable time. Finally, we give a SAT-based don't-care computation algorithm that is more efficient than BDD-based algorithms. Experimental results confirm that these improvements work well in practice. Complete don't-cares allow for a reduction in the number of literals compared to the CODCs. Windowing guarantees robustness, even for very large benchmarks on which previous methods could not be applied. SAT reduces the runtime and enhances robustness, making don't-cares affordable for a variety of other Boolean methods applied to the network.
Exploring biomedical ontology mappings with graph theory methods

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. Methods We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. Results With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.
'Hyper Parameters' Approach to Joint Estimation: Applications to Cepheid-Calibrated Distances and X-Ray Clusters

We use a generalized procedure for the combined likelihood analysis of different cosmological probes, the 'hyper-parameters' method, that allows freedom in the relative weights of the raw measurements. We perform a joint analysis of the Cepheid-calibrated data from the Hubble Space Telescope Key Project and the baryon mass fraction in clusters to constrain the total matter density of the Universe, Ωm, and the Hubble parameter, h. We compare the results obtained using the hyper-parameters method with the estimates from standard x 2 analysis. We assume that the Universe is spatially flat, with a cosmological constant. We adopt the big bang nucleosynthesis constraint for the baryon density, assuming the uncertainty is Gaussian distributed. Using this and the cluster baryon fraction data, we find that the matter density and the Hubble constant are correlated, Ωm h 0 . 5 0.25, with preference for a very high h. To break the degeneracy, we add in the Cepheid-calibrated data and find the best-fitting values (Ωm, h) = (0.26 + 0 . 0 6 0.72 + 0 . 0 4 ) (68 per cent confidence limits) using the hyper-parameters approach. We use the derived hyper-parameters to 'grade' the six different data sets we analyse. Although our analysis is free of assumptions about the power spectrum of fluctuations, our results are in agreement with the A cold dark matter 'concordance' parameters derived from the cosmic microwave background anisotropies combined with Type la supernovae, redshift surveys and other probes.
Calcium Signaling through Protein Kinases. The Arabidopsis Calcium-Dependent Protein Kinase Gene Family1

In plants, numerous Ca2+-stimulated protein kinase activities occur through calcium-dependent protein kinases (CDPKs). These novel calcium sensors are likely to be crucial mediators of responses to diverse endogenous and environmental cues. However, the precise biological function(s) of most CDPKs remains elusive. The Arabidopsis genome is predicted to encode 34 different CDPKs. In this Update, we analyze the Arabidopsis CDPK gene family and review the expression, regulation, and possible functions of plant CDPKs. By combining emerging cellular and genomic technologies with genetic and biochemical approaches, the characterization of Arabidopsis CDPKs provides a valuable opportunity to understand the plant calcium-signaling network.
Characterization Of Field-dependent ElasticModulus And Damping In Pure Nickel And IronSpecimens Using A New Experimental System

The main objective of this work is to characterize the dependence on the applied magnetic field of both the Young’s modulus (∆E-effect) and the specific damping capacity (∆Ψ-effect) in pure nickel and iron specimens. The high quantity of direct and indirect information they provide requires very precise and accurate results, which can be achieved by means of a recently developed experimental set-up. The experimentally measured ∆Eand ∆Ψ-effects in pure nickel and iron are in good agreement with magnetic domain theory and they show better magnetoelastic behaviour of nickel in comparison to iron.
Low-Fluence Photodynamic Therapy in Longstanding Chronic Central Serous Chorioretinopathy with Foveal and Gravitational Atrophy

Purpose To describe anatomic and functional outcomes in two patients with long-standing severe chronic central serous chorioretinopathy (CSC) with foveal and gravitational atrophy treated with low-fluence photodynamic therapy (PDT). Methods Two patients with a history of over 10 years of chronic CSC and development of gravitational tracts, with best-corrected visual acuity <20/200, were treated with PDT guided by indocyanine green angiography (ICGA) with a fluence of 25 J/cm2 at an irradiance of 300 mW. Follow-up examinations 1 and 9 months after therapy included measurement of near and far best-corrected visual acuity, fundus biomicroscopy, fluorescein angiography and ICGA, optical coherence tomography, and microperimetry. Results At 1 and 9 months after low-fluence PDT, complete resolution of subretinal, intraretinal, and under retinal pigment epithelium fluid was observed in both patients. Far and near visual acuity improved in both eyes. Improvement of sensitivity and fixation stability were demonstrated by microperimetry. No treatment-related side effects were seen. Conclusions ICGA-guided low-fluence PDT seems effective and safe for treating long-standing chronic CSC.
Wavelength Locking and Thermally Stabilizing Microring Resonators Using Dithering Signals

The bandwidth bottleneck looming for traditional electronic interconnects has driven the consideration of optical communications technologies as realized through the complementary metal-oxide-semiconductor-compatible silicon nanophotonic platform. Within the silicon photonics platform, silicon microring resonators have received a great deal of attention for their ability to implement the critical functionalities of an on-chip optical network while offering superior energy-efficiency and small footprint characteristics. However, silicon microring-based structures have a large susceptibility to fabrication errors and changes in temperature. Integrated heaters that provide local heating of individual microrings offer a method to correct for these effects, but no large-scale solution has been achieved to automate their tuning process. In this context, we present the use of dithering signals as a broad method for automatic wavelength tuning and thermal stabilization of microring resonators. We show that this technique can be manifested in low-speed analog and digital circuitry, lending credence to its ability to be scaled to a complete photonic interconnection network.
Prosodic structure and syntactic acquisition: the case of the head-direction parameter

We propose that infants may learn about the relative order of heads and complements in their language before they know many words, on the basis of prosodic information (relative prominence within phonological phrases). We present experimental evidence that 6‐12-week-old infants can discriminate two languages that differ in their head direction and its prosodic correlate, but have otherwise similar phonological properties (i.e. French and Turkish). This result supports the hypothesis that infants may use this kind of prosodic information to bootstrap their acquisition of word order.
Reunderstanding slice sampling as parallel MCMC

A robust slice sampler, which guarantees no repeated samples, is found as a special case of Metropolis sampling that can interact with parallel chains to efficiently sample from multi-modal densities even with possibly isolated support sets. The algorithm is completely automated with no tuning required. Implications to particle filtering design for on-line state and parameter joint estimation is also discussed.
Aether

The shift to multi-core hardware brings new challenges to database systems, as the software parallelism determines performance. Even though database systems traditionally accommodate simultaneous requests, a multitude of synchronization barriers serialize execution. Write-ahead logging is a fundamental, omnipresent component in ARIES-style concurrency and recovery, and one of the most important yet-to-be addressed potential bottlenecks, especially in OLTP workloads making frequent small changes to data. In this paper, we identify four logging-related impediments to database system scalability. Each issue challenges different level in the software architecture: (a) the high volume of small-sized I/O requests may saturate the disk, (b) transactions hold locks while waiting for the log flush, (c) extensive context switching overwhelms the OS scheduler with threads executing log I/Os, and (d) contention appears as transactions serialize accesses to in-memory log data structures. We demonstrate these problems and address them with techniques that, when combined, comprise a holistic, scalable approach to logging. Our solution achieves a 20%-69% speedup over a modern database system when running log-intensive workloads, such as the TPC-B and TATP benchmarks. Moreover, it achieves log insert throughput over 1.8GB/s for small log records on a single socket server, an order of magnitude higher than the traditional way of accessing the log using a single mutex.
On the Scalability of Loop Tiling Techniques

The Polyhedral model has proven to be a valuable tool for improving memory locality and exploiting parallelism for optimizing dense array codes. This model is expressive enough to describe transformations of imperfectly nested loops, and to capture a variety of program transformations, including many approaches to loop tiling. Tools such as the highly successful PLuTo automatic parallelizer have provided empirical confirmation of the success of polyhedral-based optimization, through experiments in which a number of benchmarks have been executed on machines with smallto medium-scale parallelism. In anticipation of ever higher degrees of parallelism, we have explored the impact of various loop tiling strategies on the asymptotic degree of available parallelism. In our analysis, we consider “weak scaling” as described by Gustavson, i.e., in which the data set size grows linearly with the number of processors available. Some, but not all, of the approaches to tiling provide weak scaling. In particular, the tiling currently performed by PLuTo does not scale in this sense. In this article, we review approaches to loop tiling in the published literature, focusing on both scalability and implementation status. We find that fully scalable tilings are not available in general-purpose tools, and call upon the polyhedral compilation community to focus on questions of asymptotic scalability. Finally, we identify ongoing work that may resolve this issue.
Physical activity and injuries during pregnancy.

BACKGROUND Although physical activity can provide health benefits to pregnant women, population-based research on the circumstances surrounding injuries from physical activity during pregnancy is lacking. METHODS Physical activity and subsequent injuries among a cohort of 1469 pregnant women in North Carolina were examined prospectively from the third phase of the Pregnancy, Infection, and Nutrition Study between 2001 and 2005. Chi-square analyses were used to compare distributions of maternal characteristics among women who sustained injuries from physical activity and women who reported no injuries during pregnancy. Injury incidence rates were calculated. RESULTS Few pregnant women (N = 34) reported a physical activity-related injury during pregnancy. The rates of physical activity-related and exercise-related injuries during pregnancy were 3.2 per 1000 physical activity hours and 4.1 per 1000 exercise hours, respectively. The most common types of injuries were bruises or scrapes (55%). Among all injuries, 33% resulted from exercise and 67% resulted from nonexercise physical activities. Sixty-four percent of all injuries were due to falls. CONCLUSIONS The incidence of injury from physical activity was low during pregnancy. Women should continue to be encouraged to maintain involvement in physical activity during pregnancy, while being aware of the potential for injury, particularly falls, from these activities.
Barrier Lyapunov Based Control of dual-arm exoskeleton robots performing asymmetric bimanual tasks

This paper presents Barrier Lyapunov Based Control of a dual-arm exoskeleton system by using the relative Jacobian technique. Two upper exoskeletons operates in a constrained region of the operational space, whose end-effector motions are defined by the relative motion between the two end effectors. Barrier composite energy function (BCEF) scheme with a novel Barrier Lyapunov Function is developed to help exoskeleton tracking desired trajectories within the constrained range and provides a convenient way of dynamics cancellation with minimal knowledge of the dynamics parameters of the dual arm. Finally, the performance of the proposed adaptive control is illustrated through extensive experiments using the developed exoskeleton.
Cancer Antigen 72-4 for the Monitoring of Advanced Tumors of the Gastrointestinal Tract, Lung, Breast and Ovaries.

BACKGROUND Cancer antigen CA72-4 is a tumor marker found to be elevated in a variety of human adenocarcinomas. Using the DRG TM-CA72-4, we quantified the elevation of CA72-4 compared to current United States Food And Drug Administration-approved tumor markers in various cancer types. MATERIALS AND METHODS We conducted a prospective, single-center study enrolling 96 patients between March 2013 and August 2016 with different locally advanced, unresectable or metastatic cancer known to express CA72-4. Quantification of CA72-4 was performed according to the manufacturer's instructions using the DRG TM-CA72-4 enzyme-linked immunosorbent assay kit and the positivity rates were calculated. RESULTS CA72-4 expression varied with tumoral site of origin, with the highest positivity rates found in pancreatic and ovarian malignancies. Correlation with clinical activity was also noted in some patients. CONCLUSION CA72-4 may have a potential role as an adjunct to conventional biomarkers in disease monitoring of pancreatic, ovarian and colorectal carcinomas.
Effects of sleep apnea on nocturnal free fatty acids in subjects with heart failure.

STUDY OBJECTIVES Sleep apnea is common in patients with congestive heart failure, and may contribute to the progression of underlying heart disease. Cardiovascular and metabolic complications of sleep apnea have been attributed to intermittent hypoxia. Elevated free fatty acids (FFA) are also associated with the progression of metabolic, vascular, and cardiac dysfunction. The objective of this study was to determine the effect of intermittent hypoxia on FFA levels during sleep in patients with heart failure. DESIGN AND INTERVENTIONS During sleep, frequent blood samples were examined for FFA in patients with stable heart failure (ejection fraction < 40%). In patients with severe sleep apnea (apnea-hypopnea index = 65.5 ± 9.1 events/h; average low SpO₂ = 88.9%), FFA levels were compared to controls with milder sleep apnea (apnea-hypopnea index = 15.4 ± 3.7 events/h; average low SpO₂ = 93.6%). In patients with severe sleep apnea, supplemental oxygen at 2-4 liters/min was administered on a subsequent night to eliminate hypoxemia. MEASUREMENTS AND RESULTS Prior to sleep onset, controls and patients with severe apnea exhibited a similar FFA level. After sleep onset, patients with severe sleep apnea exhibited a marked and rapid increase in FFA relative to control subjects. This increase persisted throughout NREM and REM sleep exceeding serum FFA levels in control subjects by 0.134 mmol/L (P = 0.0038). Supplemental oxygen normalized the FFA profile without affecting sleep architecture or respiratory arousal frequency. CONCLUSION In patients with heart failure, severe sleep apnea causes surges in nocturnal FFA that may contribute to the accelerated progression of underlying heart disease. Supplemental oxygen prevents the FFA elevation.
Temporal-Difference Networks for Dynamical Systems with Continuous Observations and Actions

Temporal-difference (TD) networks are a class of predictive state representations that use well-established TD methods to learn models of partially observable dynamical systems. Previous research with TD networks has dealt only with dynamical systems with finite sets of observations and actions. We present an algorithm for learning TD network representations of dynamical systems with continuous observations and actions. Our results show that the algorithm is capable of learning accurate and robust models of several noisy continuous dynamical systems. The algorithm presented here is the first fully incremental method for learning a predictive representation of a continuous dynamical system.