Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypertension identification using inpatient clinical notes from electronic medical records: an explainable, data-driven algorithm study

Background: Case identification is important for health services research, measuring health system performance and risk adjustment, but existing methods based on manual chart review or diagnosis codes can be expensive, time consuming or of limited validity. We aimed to develop a hypertension case definition in electronic medical records (EMRs) for inpatient clinical notes using machine learning. Methods: A cohort of patients 18 years of age or older who were discharged from 1 of 3 Calgary acute care facilities (1 academic hospital and 2 community hospitals) between Jan. 1 and June 30, 2015, were randomly selected, and we compared the performance of EMR phenotype algorithms developed using machine learning with an algorithm based on the Canadian version of the International Statistical Classification of Diseases and Related Health Problems, 10th Revision (ICD), in identifying patients with hypertension. Hypertension status was determined by chart review, the machine-learning algorithms used EMR notes and the ICD algorithm used the Discharge Abstract Database (Canadian Institute for Health Information). Results: Of our study sample (n = 3040), 1475 (48.5%) patients had hypertension. The group with hypertension was older (median age of 71.0 yr v. 52.5 yr for those patients without hypertension) and had fewer females (710 [48.2%] v. 764 [52.3%]). Our final EMR-based models had higher sensitivity than the ICD algorithm (> 90% v. 47%), while maintaining high positive predictive values (> 90% v. 97%). Interpretation: We found that hypertension tends to have clear documentation in EMRs and is well classified by concept search on free text. Machine learning can provide insights into how and where conditions are documented in EMRs and suggest nonmachine-learning phenotypes to implement.
Can the Public–Private Business Model Provide a Sustainable Quality Pediatric Cardiac Surgery Program in Low- and Middle-Income Countries?

Over 90% of the world's children with congenital heart disease do not have access to cardiac care. Although many models provide pediatric cardiac surgery in low- and middle-income countries, sustainability poses a barrier. We explore one model providing care for the underserved in Chennai, India, that came into existence through trial and error over 30 years across three phases. Phase 1 was a Tamilnadu state government–sponsored program that soon became unsustainable with unmet demands. Phase 2 utilized a grassroots foundation of a public–private partnership (PPP) with few donors and a hospital with suboptimal infrastructure. Phase 3 is the ongoing fine-tuning of the PPP model, with upgraded infrastructure and a well-trained team. Through indigenization, an average cardiac surgery costs Rupees (Rs.) 1,80,000 ($2400). The government funds Rs. 60,000 to 80,000 ($800-$1066.67), and the rest is funded through the fund pool. The goal is to perform 100 free surgeries annually by maintaining a fund pool of Rs. 50 lakhs ($66,666.67), which supplements government funds. This ensures equitable distribution of funds with no compromise on resources (disposables, single-use cannulas, etc). Our model ensures the dignity of the patient, fair compensation for workers, and is practical, affordable, and easily adaptable. Thus far, this model provided free cardiac surgery for 357 children from Risk Adjusted Congenital Heart Surgery Score of 1 to 4, with an overall mortality of 2.73%. The prerequisites for this model are having a “spark plug,” a dedicated surgical team, a partnership with state-of-the-art infrastructure, and a steady flow of funds.
Analysis on the cryogenic stability and mechanical properties of the LHD helical coils

Transient normal-transitions have been observed in the superconducting helical coils of LHD. Propagation of a normal-zone is analyzed with a numerical simulation code that deals with the magnetic diffusion process in a pure aluminum stabilizer. During excitation tests, a number of spike signals are observed in the balance voltage of the helical coils, which seem to be caused by mechanical disturbances. The spike signals are analyzed by applying pulse height analysis and the mechanical properties of the coil windings are investigated.
Intergenerational Transmission of Child Abuse Among Married Women in South Korea: A Multigroup Analysis of Empathetic Communication (TSL: Thanks, Sorry, and Love)

Intergenerational transmission of child abuse (hereinafter referred to as ITCA) has been continuously reported. Supportive relations with others have also been discussed as a protective factor to prevent this cycle. However, research has mainly investigated supportive adult and peer relationships formed in childhood, with little discussion of the impact of supportive partner relationships formed after becoming an adult. This study examined whether empathetic communication (hereinafter referred to as TSL: “Thanks, Sorry, and Love”) attenuates the transmission of married women’s child abuse experiences to subsequent generations mediated by intimate partner violence (hereinafter referred to as IPV). TSL is a communication strategy that promotes positive communication between intimate partners. We expected TSL to promote positive communication between couples through a process of self-transformation. Data from 1,122 married women were obtained from a nation-wide survey conducted in South Korea. All the survey respondents lived with partners and their own children simultaneously. For this study, structural equation model multigroup analysis was conducted to determine whether the pathways would be attenuated by TSL levels, showing that a high level of TSL communication attenuated the ITCA mediated by IPV. However, this process was maintained in the low-level TSL group. TSL is thus a protective factor against the ITCA. The findings suggest that healing processes can occur not only through childhood relationships but also through those formed after adulthood. Ultimately, to help victims recover, it is necessary to expand communication programs such as TSL that help victims learn how to express their feelings through healthy relationships with their partners.
Counterfactuals, Hypotheticals and Potential Responses: A Philosophical Examination of Statistical Causality

Statisticians have developed a variety of conceptions, frameworks and tools for causal inference. We study some of these from a philosophical angle, focusing in particular on two formal frameworks, “Potential responses” (PR) and “Decision Theory” (DT), and their use in problems of inferring the “eects of causes”. Although PR is currently the predominant methodology, it is argued that DT is preferable both philosophically and pragmatically.
The structure of the sculptor dwarf elliptical galaxy. I - The radial profile

Automated star counts of the UK Schmidt telescope unit have been used to obtain the radial profile of the Sculptor dwarf elliptical galaxy. Adopting a core radius of 8.9 arcmin and a tidal radius of 95 arcmin, a Galaxy mass of about 1.5 + or - 1.1 x 10 to the 11th solar masses has been derived. However, an overdensity above that expected from the King (1966) model is found beyond R(maj) = 50 arcmin. This overdensity is roughly a 2sigma effect above the determined background level, and it accounts for about 13 percent of the stars counted. A physical scale length r sub e of about 0.43 kpc is indicated. The present data do not conflict with the theory that halo dwarfs are the results of ram-pressure stripping of dI systems by the Galactic halo. 44 references.
Markov Chain Applications to Non Parametric Option Pricing Theory

Summary In this paper we propose to use a Markov chain in order to price contingent claims. In particular, we describe a non parametric markovian approach to price American and European options. First, we discuss the risk neutral valuation of the non parametric approach. Secondly, we examine the problems of the computational complexity and of the stability with respect to the number of the states of the Markov chain. Finally, we propose an ex post comparison between the Markovian model and the Black and Scholes one.
Minimal model for the secondary structures and conformational conversions in proteins

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced offlattice model that can express α-helix and β-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a β-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling — physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both α-helix and β-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of β-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method — an efficient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between α-helix and β-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined.
NFATc1 marks articular cartilage progenitors and negatively determines articular chondrocyte differentiation

The origin and differentiation mechanism of articular chondrocytes remain poorly understood. Broadly, the difference in developmental mechanisms of articular and growth-plate cartilage is still less elucidated. Here, we identified that the nuclear factor of activated T-cells cytoplasmic 1 (NFATc1) is a crucial regulator of articular, but not growth-plate, chondrocyte differentiation during development. At the early stage of mouse knee development (embryonic day 13.5), NFATc1-expressing cells were mainly located in the flanking region of the joint interzone. With development, NFATc1-expressing cells generated almost all articular chondrocytes but not chondrocytes in limb growth-plate primordium. NFATc1-expressing cells displayed prominent capacities for colony formation and multipotent differentiation. Transcriptome analyses revealed a set of characteristic genes in NFATc1-enriched articular cartilage progenitors. Strikingly, the expression of NFATc1 was diminished with articular chondrocyte differentiation, and suppressing NFATc1 expression in articular cartilage progenitors was sufficient to induce spontaneous chondrogenesis while overexpressing NFATc1 suppresses chondrogenesis. Mechanistically, NFATc1 negatively regulated the transcriptional activity of the Col2a1 gene. Thus, our results reveal that NFATc1 characterizes articular, but not growth-plate, cartilage progenitors during development and negatively determines articular chondrocyte differentiation at least partly through regulating COL2A1 gene transcription.
A Regression Based Non-Intrusive Method Using Separated Representation for Uncertainty Quantification

This paper aims at handling high dimensional uncertainty propagation problems by proposing a tensor product approximation method based on regression techniques. The underlying assumption is that the model output functional can be well represented in a separated form, as a sum of elementary tensors in the stochastic tensor product space. The proposed method consists in constructing a tensor basis with a greedy algorithm and then in computing an approximation in the generated approximation space using regression with sparse regularization. Using appropriate regularization techniques, the regression problems are well posed for only few sample evaluations and they provide accurate approximations of model outputs.Copyright © 2012 by ASME
Higher-order alternative direction implicit FDTD method

A second-order in time and fourth-order in space alternative direction implicit (ADI) finite difference time domain (FD-TD) method has been developed. The dispersion relation is derived and compared with the ADI-FDTD method. Numerical results demonstrated that the higher-order ADI-FDTD has a better accuracy compared to the ADI-FDTD method.
Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions

Various forms of PVs have been used as tools to evaluate vaccine efficacy and study virus entry steps. When PV infectivity is inherently low, such as that of SARS-CoV-2, a CT-truncated version of the viral entry glycoprotein is widely used to enhance PV infectivity, but the mechanism underlying this enhanced PV infectivity has been unclear. ABSTRACT Truncations of the cytoplasmic tail (CT) of entry proteins of enveloped viruses dramatically increase the infectivity of pseudoviruses (PVs) bearing these proteins. Several mechanisms have been proposed to explain this enhanced entry, including an increase in cell surface expression. However, alternative explanations have also been forwarded, and the underlying mechanisms for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein remain undetermined. Here, we show that the partial or complete deletion of the CT (residues 19 to 35) does not modify SARS-CoV-2 S protein expression on the cell surface when the S2 subunit is measured, whereas it is significantly increased when the S1 subunit is measured. We also show that the higher level of S1 in these CT-truncated S proteins reflects the decreased dissociation of the S1 subunit from the S2 subunit. In addition, we demonstrate that CT truncation further promotes S protein incorporation into PV particles, as indicated by biochemical analyses and cryo-electron microscopy. Thus, our data show that two distinct mechanisms contribute to the markedly increased infectivity of PVs carrying CT-truncated SARS-CoV-2 S proteins and help clarify the interpretation of the results of studies employing such PVs. IMPORTANCE Various forms of PVs have been used as tools to evaluate vaccine efficacy and study virus entry steps. When PV infectivity is inherently low, such as that of SARS-CoV-2, a CT-truncated version of the viral entry glycoprotein is widely used to enhance PV infectivity, but the mechanism underlying this enhanced PV infectivity has been unclear. Here, our study identified two mechanisms by which the CT truncation of the SARS-CoV-2 S protein dramatically increases PV infectivity: a reduction of S1 shedding and an increase in S protein incorporation into PV particles. An understanding of these mechanisms can clarify the mechanistic bases for the differences observed among various assays employing such PVs.
Factors Associated With Delirium in Children: A Systematic Review and Meta-Analysis*

OBJECTIVES: Pediatric delirium (PD) is a neuropsychiatric syndrome caused by a complex interplay between predisposing factors (e.g., age, cognitive impairment), acute illness, and environmental triggers. PD is associated with substantial morbidity and mortality. The objective of this study is to systematically review and evaluate factors associated with PD in hospitalized pediatric patients. DATA SOURCES: A systematic search of PubMed, Embase, Ovid Medline, Web- of-Science, Cochrane, CIHNAL, and Google Scholar databases was conducted for relevant studies (1990–2022). STUDY SELECTION: We included studies that compared pediatric patients with and without delirium. Reviews, editorials, congress abstracts, or studies that did not report factors for PD were excluded. No restrictions were imposed on language. Data Extraction: Title and abstract were independently screened by two reviewers. Individual characteristics, study design, and outcomes were independently extracted. DATA SYNTHESIS: Categorical dichotomous data were summarized across groups using Mantel-Haenszel odds ratios (ORs) with 95% 95% CIs. Either fixed-effect or random effects models were used as indicated by the results of a heterogeneity test. Of 1,846 abstracts, 24 studies were included. We identified 54 factors studied in univariate analyses, and 27 of these were associated with PD in multivariable analyses. In pooled analyses, greater odds of PD were associated with developmental delay (OR 3.98; 95% CI 1.54–10.26), need for mechanical ventilation (OR 6.02; 95% CI 4.43–8.19), use of physical restraints (OR 4.67; 95% CI 1.82–11.96), and receipt of either benzodiazepines (OR 4.10; 95% CI 2.48–6.80), opiates (OR 2.88; 95% CI 1.89–4.37), steroids (OR 2.02; 95% CI 1.47–2.77), or vasoactive medication (OR 3.68; 95% CI 1.17–11.60). CONCLUSIONS: In this meta-analysis, we identified seven factors associated with greater odds of developing delirium during pediatric critical illness.
Existence of Dressed One Electron States in a Class of Persistent Models

In this paper the dynamics of a class of simple models (so called persistent models) including Nelson's model is studied. These models describe conserved, non relativistic, scalar electrons interacting with neutral, scalar bosons. Special attention is paid to the so called one particle problem: the existence of dressed one electron states – corresponding to an isolated one particle shell in the spectrum of the energy-momentum operator (H, P) – is established for the models with massive bosons and the ones with bosons of rest mass zero and an infrared cutoff in the interaction. In dieser Arbeit studieren wir die Dynamik einer Klasse einfacher (sog. persistenter) Modelle, unter anderen diejenige des Modelles von Nelson [15]. Solche Modelle beschreiben Systeme von erhaltenen, nicht relativistischen, spinlosen Elektronen, die mit neutralen, skalaren Bosonen wechselwirken. Besonders sorgfaltig wird das Einteilchenproblem studiert: Fur die Modelle mit Bosonen positiver Ruhemasse und diejenigen mit Bosonen der Ruhemasse 0 und Infrarot-Cutoff im Wechselwirkungsoperator beweisen wir die Existenz physikalischer Einelektronen Zustande, oder, in anderen Worten, wir zeigen, das das gemeinsame Spektrum von Energie- und Impulsoperator eine isolierte Einteilchenschale hat.
When others control risks: Others‐focused coping with risks from energy projects

Energy projects can cause various risks over which people have little control, because they are usually developed, implemented, and managed by external parties, such as governments and industry. This study aims to examine how people cope with such externally controlled risks from energy projects, in particular earthquakes induced by gas extraction in their region. Specifically, we studied which factors influence people's intentions to engage in emotion‐focused coping aimed at reducing negative emotions, and problem‐focused coping aimed at reducing the risks and/or their negative consequences. Extending previous studies, we distinguish two types of problem‐focused coping that may be relevant when facing externally controlled risks, namely self‐focused coping, in which individual themselves take action to reduce the negative consequences of the risks, and others‐focused coping, in which case individuals urge responsible parties to take actions to reduce the risks. Our results show that the three types of coping can be distinguished empirically, and people are likely to engage in others‐focused coping. Further, people are most likely to engage in others‐focused coping when they experience strong morality‐based emotions toward the risks from energy projects, whereas they are most likely to engage in self‐focused coping and emotion‐focused coping when they experience strong negative consequence‐based emotions toward the risks from energy projects.
A Brief Survey on Oracle-based Test Adequacy Metrics

Code coverage is a popular and widespread test adequacy metric that measures the percentage of program codes executed by a test suite. Despite its popularity, code coverage has several limitations. One of the major limitations is that it does not provide any insights into the quality or quantity of test oracles, a core component of testing. Due to this limitation, several studies have suggested that coverage is a poor test adequacy metric; therefore, it should not be used as an indicator of a test suite's fault detection effectiveness. To address this limitation, researchers have proposed extensions to traditional structural code coverage to explicitly consider the quality of test oracles. We refer to these extensions as oracle-based code coverage. This survey paper studies oracle-based coverage techniques published since their inception in 2007. We discuss each metric's definition, methodology, experimental studies, and research findings. Even though oracle-based coverage metrics are proven to be more effective than traditional coverage in detecting faults, they have received little attention in the software engineering community. We present all existing oracle-based adequacy metrics in this paper and compare the critical features against each other. We observe that different oracle-based adequacy metrics operate on different coverage domains and use diverse underlying analysis techniques, enabling a software tester to choose the appropriate metric based on the testing requirements. Our paper provides valuable information regarding the limitations of oracle-based methods, addressing which may help their broader adoption in software testing automation.
Dynamics of an almost periodic competitor-competitor-mutualist Lotka-Volterra systems with time delays

By using Mawhin's continuation theorem of coincidence degree theory and constructing a suitable Lyapunov functional, a set of easily verifiable conditions are obtained for the existence and global asymptotical stability of a unique positive almost periodic solution of competitor-competitor-mutualist Lotka-Volterra systems with time delays. An example and simulations are employed to illustrate the main results of this paper.
Approximate Dynamic Programming for Dynamic Quantile-Based Risk Measures

In this paper, we consider a finite-horizon Markov decision process (MDP) for which the objective at each stage is to minimize a quantile-based risk measure (QBRM) of the sequence of future costs (we call the overall objective a dynamic quantile-based risk measure (DQBRM)). In particular, we consider optimizing dynamic risk measures constructed using one-step risk measures that are a convex combination of the expectation and a QBRM, a class of risk measures that includes the popular value at risk (VaR) and the conditional value at risk (CVaR). Although there is considerable theoretical development of risk-averse MDPs in the literature, the computational challenges have not been explored as thoroughly. We propose a simulation-based approximate dynamic programming (ADP) algorithm to solve the risk-averse sequential decision problem. In addition, we address the issue of inefficient sampling in risk applications and present a procedure, based on importance sampling, to direct samples toward the "risky region" as the ADP algorithm progresses. Finally, we show numerical results of applying our algorithms in the context of an energy storage and bidding application.