Miracle-dz/UniFAR-FTUs huggingface dataset:
Influenza Epidemics in the United States, France, and Australia, 1972–1997

Influenza epidemics occur once a year during the winter in temperate areas. Little is known about the similarities between epidemics at different locations. We have analyzed pneumonia and influenza deaths from 1972 to 1997 in the United States, France, and Australia to examine the correlation over space and time between the three countries. We found a high correlation in both areas between France and the United States (correlation in impact, Spearman’s ρ = 0.76, p < 0.001, and test for synchrony in timing of epidemics, p < 0.001). We did not find a similar correlation between the United States and Australia or between France and Australia, when considering a systematic half-year lead or delay of influenza epidemics in Australia as compared with those in the United States or France. These results support a high correlation at the hemisphere level and suggest that the global interhemispheric circulation of epidemics follows an irregular pathway with recurrent changes in the leading hemisphere.
Exploration of Natural Alignment Scoring Rules and Clustering Thresholds for Bacterial Core/Pan Genome Analysis

Bacterial adaptation through gene loss and acquisition are the fundamental mechanisms that determine the structure of the core and pan genomes. One of the challenges in identifying homologous genes required for the description of core and pan genomes is the absence of appropriate alignment scoring rules and clustering thresholds. In this work, we present new methods to establish appropriate alignment scoring rules and clustering thresholds.
Proposal for a New Tool to Evaluate Drug Interaction Cases

The assessment of causation for a potential drug interaction requires thoughtful consideration of the properties of both the object and precipitant drugs, patient-specific factors, and the possible contribution of other drugs that the patient may be taking. The Naranjo nomogram was designed to evaluate single-drug adverse events, not drug–drug interactions. Several of the questions on the Naranjo nomogram do not apply to potential drug–drug interactions, while others do not specify object or precipitant drug. Nevertheless, it has been inappropriately used to evaluate drug–drug interactions. The Drug Interaction Probability Scale (DIPS) was developed to provide a guide to evaluating drug interaction causation in a specific patient. It is intended to be used to assist practitioners in the assessment of drug interaction–induced adverse outcomes. The DIPS uses a series of questions relating to the potential drug interaction to estimate a probability score. An accurate assessment using the DIPS requires knowledge of the pharmacologic properties of both the object and precipitant drugs. Inadequate knowledge of either the drugs involved or the basic mechanisms of interaction will be a limitation for some users. The DIPS can also serve as a guide in the preparation of articles describing case reports of drug interactions, as well as in the evaluation of published case reports.
The impact of the roll-out of rapid molecular diagnostic testing for tuberculosis on empirical treatment in Cape Town, South Africa

Abstract Objective To investigate the impact of introducing a rapid test as the first-line diagnostic test for drug-sensitive tuberculosis in Cape Town, South Africa. Methods Xpert® MTB/RIF (Xpert®), an automated polymerase-chain-reaction-based assay, was rolled out between 2011 and 2013. Data were available on 102 007 adults treated for pulmonary tuberculosis between 2010 and 2014. Tuberculosis notification rates per 100 000 population were calculated for each calendar year and for each year relative to the test roll-out locally, overall and by bacteriological confirmation. Empirical treatment was defined as treatment given without bacteriological confirmation by Xpert®, sputum smear microscopy or sputum culture. Findings Between 2010 and 2014, the proportion of human immunodeficiency virus (HIV)-negative patients treated empirically for tuberculosis declined from 23% (2445/10 643) to 11% (1149/10 089); in HIV-positive patients, it declined from 42% (4229/9985) to 27% (2364/8823). The overall tuberculosis notification rate decreased by 12% and 19% among HIV-negative and HIV-positive patients, respectively; the rate of bacteriologically confirmed cases increased by 1% and 3%, respectively; and the rate of empirical treatment decreased by 56% and 49%, respectively. These changes occurred gradually following the test’s introduction and stabilized after 3 years. Conclusion Roll-out of the rapid test in a setting with a high prevalence of pulmonary tuberculosis and HIV infection was associated with a halving of empirical treatment that occurred gradually after the test’s introduction, possibly reflecting the time needed for full implementation. More than a quarter of HIV-positive patients with tuberculosis were still treated empirically, highlighting the diagnostic challenge in these patients.
Ensuring operating system kernel integrity with OSck

Kernel rootkits that modify operating system state to avoid detection are a dangerous threat to system security. This paper presents OSck, a system that discovers kernel rootkits by detecting malicious modifications to operating system data. OSck integrates and extends existing techniques for detecting rootkits, and verifies safety properties for large portions of the kernel heap with minimal overhead. We deduce type information for verification by analyzing unmodified kernel source code and in-memory kernel data structures. High-performance integrity checks that execute concurrently with a running operating system create data races, and we demonstrate a deterministic solution for ensuring kernel memory is in a consistent state. We introduce two new classes of kernel rootkits that are undetectable by current systems, motivating the need for the OSck API that allows kernel developers to conveniently specify arbitrary integrity properties.
Impaired functional capacity in potential liver transplant candidates predicts short‐term mortality before transplantation

Liver transplantation (LT) is a lifesaving treatment. Because of the shortage of donor organs, some patients will not survive long enough to receive a transplant. The identification of LT candidates at increased risk of short‐term mortality without transplantation may affect listing decisions. Functional capacity, determined with cardiopulmonary exercise testing (CPET), is a measure of cardiorespiratory reserve and predicts perioperative outcomes. This study examined the association between functional capacity and short‐term survival before LT and the potential for CPET to predict 90‐day mortality without transplantation. A total of 176 patients who were assessed for nonacute LT underwent CPET. Ninety days after the assessment, 10 of the 164 patients who had not undergone transplantation were deceased (mortality rate = 6.1%). According to a comparison of survivors and nonsurvivors, the Model for End‐Stage Liver Disease score, UK Model for End‐Stage Liver Disease (UKELD) score, age, anaerobic threshold, and peak oxygen uptake (VO2) were significant univariate predictors of 90‐day mortality without transplantation, but only the UKELD score and peak VO2 retained significance in a multivariate analysis. The mean peak VO2 was significantly lower for nonsurvivors versus survivors (15.2 ± 3.3 versus 21.2 ± 5.3 mL/minute/kg, P < 0.001). According to a receiver operating characteristic (ROC) curve analysis, peak VO2 performed well as a diagnostic test (area under the ROC curve = 0.84, 95% confidence interval = 0.76‐0.92, sensitivity = 0.90, specificity = 0.74, P < 0.001). The optimal cutoff value for predicting mortality was ≤17.6 mL/minute/kg. The positive predictive value of a peak VO2 ≤ 17.6 mL/minute/kg for 90‐day mortality was greatest for patients with high UKELD scores: 38% of the patients with a UKELD score ≥ 57 and a peak VO2 ≤ 17.6 mL/minute/kg died, whereas only 6% of the patients with a UKELD score ≥ 57 and a peak VO2 > 17.6 mL/minute/kg died (P = 0.03). In conclusion, patients assessed for LT with an impaired functional capacity have poorer short‐term survival; this is particularly true for individuals with worse liver disease severity. Liver Transpl 20:1081–1088, 2014. © 2014 AASLD.
DGFIndex for Smart Grid: Enhancing Hive with a Cost-Effective Multidimensional Range Index

In Smart Grid applications, as the number of deployed electric smart meters increases, massive amounts of valuable meter data is generated and collected every day. To enable reliable data collection and make business decisions fast, high throughput storage and high-performance analysis of massive meter data become crucial for grid companies. Considering the advantage of high efficiency, fault tolerance, and price-performance of Hadoop and Hive systems, they are frequently deployed as underlying platform for big data processing. However, in real business use cases, these data analysis applications typically involve multidimensional range queries (MDRQ) as well as batch reading and statistics on the meter data. While Hive is high-performance at complex data batch reading and analysis, it lacks efficient indexing techniques for MDRQ. In this paper, we propose DGFIndex, an index structure for Hive that efficiently supports MDRQ for massive meter data. DGFIndex divides the data space into cubes using the grid file technique. Unlike the existing indexes in Hive, which stores all combinations of multiple dimensions, DGFIndex only stores the information of cubes. This leads to smaller index size and faster query processing. Furthermore, with pre-computing user-defined aggregations of each cube, DGFIndex only needs to access the boundary region for aggregation query. Our comprehensive experiments show that DGFIndex can save significant disk space in comparison with the existing indexes in Hive and the query performance with DGFIndex is 2-50 times faster than existing indexes in Hive and HadoopDB for aggregation query, 2-5 times faster than both for non-aggregation query, 2-75 times faster than scanning the whole table in different query selectivity.
Best-Arm Identification in Linear Bandits

We study the best-arm identification problem in linear bandit, where the rewards of the arms depend linearly on an unknown parameter θ* and the objective is to return the arm with the largest reward. We characterize the complexity of the problem and introduce sample allocation strategies that pull arms to identify the best arm with a fixed confidence, while minimizing the sample budget. In particular, we show the importance of exploiting the global linear structure to improve the estimate of the reward of near-optimal arms. We analyze the proposed strategies and compare their empirical performance. Finally, as a by-product of our analysis, we point out the connection to the G-optimality criterion used in optimal experimental design.
Health impact and cost-effectiveness of a domestically-produced rotavirus vaccine in India: A model based analysis

Background Currently, Indian officials are incorporating a domestically manufactured rotavirus vaccine (based on the 116E rotavirus strain) into the country’s universal immunization program; this vaccine will cost significantly less than western rotavirus vaccines. Here, we examine the public health impact, cost, and cost-effectiveness of universal vaccination in India using the 116E vaccine. This work will allow comparison of universal 116E vaccination with other approaches to child mortality reduction, shed light on the future burden of rotavirus disease in India, and help stakeholders understand future resource needs. Methods Using information from published literature, we developed a dynamic simulation model of rotavirus transmission, natural history, and related utilization among Indian infants followed until age five. Infection risk depended on the degree of viral shedding in the population. Infection risk and severity were influenced by age, number of previous infections, and vaccination history. Probabilities of inpatient and outpatient health services utilization depended on symptom severity. With the model, we compared a strategy of nationwide 116E vaccination to one of no vaccination. Costs were considered from the perspective of all payers (including families) and from the societal perspective. Results We estimated that an established 116E vaccination program would reduce symptomatic rotavirus infection by 13.0%, while reducing population-wide rotavirus mortality by 34.6% (over 34,000 lives annually). Rotavirus outpatient visits would decline by 21.3%, and hospitalization would decline by 28.1%. The cost per disability-adjusted life year (DALY) averted was estimated at 3,429 Rupees (approximately $56). Predicted mortality reduction in children born during the first five years of vaccination implementation was nearly identical to that in children born in later years (34.4% versus 34.6%). Conclusions 116E vaccination of Indian infants would likely substantially reduce rotavirus-related morbidity, mortality, and utilization at a cost considered highly cost-effective by standard criteria. Nearly the entire mortality reduction benefit of vaccination was attributable to direct protection of those vaccinated, as opposed to indirect “herd immunity” effects.
Mechanism-specific effects of adenosine on atrial tachycardia.

BACKGROUND Recent reports suggest that adenosine, in addition to terminating supraventricular tachycardia involving the atrioventricular (AV) node, may have antiarrhythmic effects on atrial tachycardia. The electrophysiological effects of adenosine on supraventricular tissue include shortening of action potential duration in atrial myocytes mediated by the potassium current, IKACh,Ado; shortening of action potential duration and hyperpolarization in sinus node cells; and anti-adrenergic electrophysiological effects resulting from inhibition of adenylyl cyclase. We therefore hypothesized that the response of atrial tachycardia to adenosine would be mechanism specific, with termination of atrial tachycardia due to sinus node reentry or cAMP-mediated triggered activity, transient suppression of automatic atrial tachycardia, and an absence of antiarrhythmic effect on tachycardia due to intraatrial reentry. METHODS AND RESULTS Adenosine (mean +/- SD, 143 +/- 54 micrograms/kg IV) was administered to 27 patients (55 +/- 19 years) in atrial tachycardia whose mechanism was confirmed by electrophysiological study. Adenosine terminated sinus node reentrant tachycardia in 6 of 6 patients and terminated atrial tachycardia due to triggered activity in the 1 patient in whom it was identified. Adenosine transiently suppressed automatic atrial tachycardia in 7 of 7 patients and had no effect in 13 patients with intra-atrial reentrant tachycardia, including 8 patients with atrial flutter. CONCLUSIONS These findings demonstrate that adenosine's effects on atrial tachycardia are mechanism specific and can be used to differentiate between reentrant tachycardia confined to the region of the sinus node or atria and between nonreentrant atrial tachycardia due to either triggered activity or automaticity.
Enhanced Antihypertensive Activity of Candesartan Cilexetil Nanosuspension: Formulation, Characterization and Pharmacodynamic Study

The objective of the present investigation was to enhance the oral bioavailability of practically insoluble Candesartan cilexetil [CC] by preparing nanosuspension. The nanosuspension was prepared by media milling using zirconium oxide beads and converted to solid state by spray drying. The spray dried nanosuspension of CC [SDCN] was evaluated for particle size, zeta potential, saturation solubility, crystallanity, surface morphology and dissolution behavior. SDCN showed particle size of 223.5±5.4 nm and zeta potential of −32.2±0.6 mV while saturation solubility of bulk CC and SDCN were 125±6.9 μg/ml and 2805±29.5 μg/ml respectively, showing more than 20 times increase in solubility. Differential Scanning Calorimetry [DSC] and X-ray diffraction [XRD] analysis showed that crystalline state of CC remained unchanged in SDCN. Dissolution studies in phosphate buffer pH 6.5 containing 0.7% Tween 20 showed that 53±5% of bulk drug dissolved in 15 min whereas SDCN was almost completely dissolved exhibiting higher dissolution velocity and solubility. Transmission electron microscopy [TEM] revealed that nanocrystals were not of uniform size, and approximately of oval shape. Pharmacodynamic study based on deoxycorticosterone acetate [DOCA] salt model was performed in rats to evaluate in-vivo performance, which showed 26.75±0.33% decrease in systolic blood pressure for nanosuspension while plain drug suspension showed 16.0±0.38% reduction, indicating that increase in dissolution velocity and saturation solubility leads to enhancement of bioavailability of SDCN when compared to bulk CC suspension. Thus, the results conclusively demonstrated a significant enhancement in antihypertensive activity of candesartan when formulated as nanosuspension.
Membrane Phospholipid Augments Cytochrome P4501a Enzymatic Activity by Modulating Structural Conformation during Detoxification of Xenobiotics

Cytochrome P450 is a superfamily of membrane-bound hemoprotein that gets involved with the degradation of xenobiotics and internal metabolites. Accumulated body of evidence indicates that phospholipids play a crucial role in determining the enzymatic activity of cytochrome P450 in the microenvironment by modulating its structure during detoxification; however, the structure-function relationship of cytochrome P4501A, a family of enzymes responsible for degrading lipophilic aromatic hydrocarbons, is still not well defined. Inducibility of cytochrome P4501A in cultured catfish hepatocytes in response to carbofuran, a widely used pesticide around the world, was studied earlier in our laboratory. In this present investigation, we observed that treating catfish with carbofuran augmented total phospholipid in the liver. We examined the role of phospholipid on the of cytochrome P4501A-marker enzyme which is known as ethoxyresorufin-O-deethylase (EROD) in the context of structure and function. We purified the carbofuran-induced cytochrome P4501A protein from catfish liver. Subsequently, we examined the enzymatic activity of purified P4501A protein in the presence of phospholipid, and studied how the structure of purified protein was influenced in the phospholipid environment. Membrane phospholipid appeared to accelerate the enzymatic activity of EROD by changing its structural conformation and thus controlling the detoxification of xenobiotics. Our study revealed the missing link of how the cytochrome P450 restores its enzymatic activity by changing its structural conformation in the phospholipid microenvironment.
Cross-sectional study of factors associated with community health centre use in a recently urbanised community in Chengdu, China

Objectives Public investment in community health centres (CHCs) has been increasing as a response to rapid urbanisation in China. The objectives of this study were: (1) to examine factors associated with CHC use among residents from a recently urbanised community in western China and (2) to describe satisfaction with CHC among users. Design Cross-sectional design. Setting A community recently converted to urban status with a newly constructed CHC in Southwest China. Participants A random sample of 2259 adults in the Hezuo community in Chengdu, China, completed the survey in 2013. Outcome measures Trained staff interviewed study participants in their homes using structured questionnaires. The survey included questions regarding sociodemographics, health status, access to and usage of healthcare, health behaviours and CHC use. The Andersen’s behavioural model of health service use was used to guide multivariable logistic regression modelling in identifying predisposing, enabling and need factors associated with the likelihood of using CHC. Descriptive statistics were used to describe residents’ satisfaction with the CHC. Results A total of 71.8% of the respondents reported using the CHC during the past year. Factors influencing adults’ CHC use included: gender, marital status, education level and knowledge of one’s blood pressure (predisposing factors); annual household per capita income and walking time to the CHC (enabling factors) and self-rated health as well as physical activities (need factors). CHC users reported modest satisfaction across various aspects of the CHC. Conclusions Neighbourhood CHC in urban areas provides important services to these residents living in a recently urbanised community. All three categories of factors in the Andersen model help explain the likelihood of CHC use. There is much room for improvement in CHC to enhance customer satisfaction. Future research is needed to improve access to CHCs and promote their use in urbanised populations with low to modest education.
Self‐Organization and Vegetation Collapse in Salt Marsh Ecosystems

Complexity theory predicts that local feedback processes may strongly affect the organization of ecosystems on larger spatial scales. Whether complexity leads to increased resilience and stability or to increased vulnerability and criticality remains one of the dominant questions in ecology. We present a combined theoretical and empirical study of complex dynamics in mineralogenic salt marsh ecosystems that emerge from a positive feedback between clay accumulation and plant growth. Positive feedback induces self‐organizing within the ecosystem, which buffers for the strong physical gradient that characterizes the marine‐terrestrial boundary, and improves plant growth along the gradient. However, as a consequence of these self‐organizing properties, salt marshes approach a critical state as the edge of the salt marsh and the adjacent intertidal flat becomes increasingly steep and vulnerable to wave attack. Disturbance caused, for instance, by a storm may induce a cascade of vegetation collapse and severe erosion on the cliff edge, leading to salt marsh destruction. Our study shows that on short timescales, self‐organization improves the functioning of salt marsh ecosystems. On long timescales, however, self‐organization may lead to destruction of salt marsh vegetation.
Light and Scanning Electron Microscopic Study of the Tongue in the Estuarine Dolphin (Sotalia guianensis van Bénéden, 1864)

The importance of the tongue during feeding, and the limited information on the tongue of most aquatic mammals led us to investigate its morphological aspects in sexually immature and mature Sotalia guianensis. Six tongues were measured and photo-documented after their removal from the oral cavity. The samples were divided into rostral, middle, and caudal regions, and examined using light microscopy and scanning electron microscopy (S.E.M.). Sotalia guianensis tongue presented lateral grooves from the apex to the middle portion, while the anterolateral region presented marginal papillae. Histological characteristics revealed the presence of a keratinized stratified epithelium, salivary glands in the middle and caudal portions of the tongue, and filiform papillae in the caudal region. S.E. M. images revealed the presence of filiform papillae and ducts of salivary glands in the middle and caudal portions of the tongue. We can conclude that the characteristics found in this study may reflect an adaptation to changes in diet after weaning.