Miracle-dz/UniFAR-FTUs huggingface dataset:
Management of drug resistance in the population: influenza as a case study

The rise of drug resistance remains a major impediment to the treatment of some diseases caused by fast-evolving pathogens that undergo genetic mutations. Models describing the within-host infectious dynamics suggest that the resistance is unlikely to emerge if the pathogen-specific immune responses are maintained above a certain threshold during therapy. However, emergence of resistance in the population involves both within-host and between-host infection mechanisms. Here, we employ a mathematical model to identify an effective treatment strategy for the management of drug resistance in the population. We show that, in the absence of pre-existing immunity, the population-wide spread of drug-resistant pathogen strains can be averted if a sizable portion of susceptible hosts is depleted before drugs are used on a large scale. The findings, based on simulations for influenza infection as a case study, suggest that the initial prevalence of the drug-sensitive strain under low pressure of drugs, followed by a timely implementation of intensive treatment, can minimize the total number of infections while preventing outbreaks of drug-resistant infections.
Nocardia cyriacigeogica from Bovine Mastitis Induced In vitro Apoptosis of Bovine Mammary Epithelial Cells via Activation of Mitochondrial-Caspase Pathway

Nocardia is one of the causing agents of bovine mastitis and increasing prevalence of nocardial mastitis in shape of serious outbreaks has been reported from many countries. However, the mechanisms by which this pathogen damages the bovine mammary epithelial cells (bMECs) is not yet studied. Therefore, this study was designed with the aim to evaluate the apoptotic effects elicited by Nocardia and to investigate the pathway by which the Nocardia induce apoptosis in bMECs. Clinical Nocardia cyriacigeorgica strain from bovine mastitis was used to infect the bMECs for different time intervals, viz. 1, 3, 6, 12, and 18 h, and then the induced effects on bMECs were studied using adhesion and invasion assays, release of lactate dehydrogenase (LDH), apoptosis analysis by annexin V and propidium iodide (PI) double staining, morphological, and ultrastructural observations under scanning electron microscope (SEM) and transmission electron microscope (TEM), mitochondrial transmembrane potential (ΔΨm) assay using flow cytometry, and the protein quantification of mitochondrial cytochrome c and caspase-9 and caspase-3 by western blotting. The results of this study showed that N. cyriacigeorgica possessed the abilities of adhesion and invasion to bMECs. N. cyriacigeorgica was found to collapse mitochondrial transmembrane potential, significantly (p < 0.05) release mitochondrial cytochrome c and ultimately induce cell apoptosis. Additionally, it promoted casepase-9 (p < 0.01) and casepase-3 (p < 0.05) levels, significantly (p < 0.01) increased the release of LDH and promoted DNA fragmentation which further confirmed the apoptosis. Furthermore, N. cyriacigeorgica induced apoptosis/necrosis manifested specific ultrastructure features under TEM, such as swollen endoplasmic reticulum, cristae degeneration, and swelling of mitochondria, vesicle formation on the cell surface, rupturing of cell membrane and nuclear membrane, clumping, fragmentation, and margination of chromatin. The present study is the first comprehensive insight into patho-morphological ultrastructural features of apoptosis/necrosis induced by N. cyriacigeorgica, which concluded that the clinical N. cyriacigeorgica induced apoptotic changes in the bMECs through mitochondrial-caspase dependent apoptotic pathway.
Closed-form posterior Cramer-Rao bounds for bearings-only tracking

We address the classical bearings-only tracking problem (BOT) for a single object, which belongs to the general class of nonlinear filtering problems. Recently, algorithms based on sequential Monte-Carlo methods (particle filtering) have been proposed. As far as performance analysis is concerned, the posterior Cramer-Rao bound (PCRB) provides a lower bound on the mean square error. Classically, under a technical assumption named "asymptotic unbiasedness assumption", the PCRB is given by the inverse Fisher information matrix (FIM). The latter is computed using Tichavsky's recursive formula via Monte-Carlo methods. Two major problems are studied here. First, we show that the asymptotic unbiasedness assumption can be replaced by an assumption which is more meaningful. Second, an exact algorithm to compute the PCRB is derived via Tichavsky's recursive formula without using Monte-Carlo methods. This result is based on a new coordinate system named logarithmic polar coordinate (LPC) system. Simulation results illustrate that PCRB can now be computed accurately and quickly, making it suitable for sensor management applications
Variability in Migration Routes Influences Early Marine Survival of Juvenile Salmon Smolts

Variability in animal migratory behavior is expected to influence fitness, but few empirical examples demonstrating this relationship exist. The initial marine phase in the migration of juvenile salmon smolts has been identified as a potentially critical life history stage to overall population productivity, yet how fine-scale migration routes may influence survival are unknown. Large-scale acoustic telemetry studies have estimated survival rates of outmigrant Pacific salmon smolts through the Strait of Georgia (SOG) along the British Columbian coastline to the Pacific Ocean, but these data have not been used to identify and characterize fine-scale movements. Data collected on over 850 sockeye salmon (Oncorhynchus nerka) and steelhead (Oncorhynchus mykiss) smolts detected at an array in the Strait of Georgia in 2004–2008 and 2010–2013 were analyzed to characterize migration routes and link movements to subsequent survival at an array 250 km further along the marine migration pathway. Both species exhibited disproportionate use of the most eastern route in the Strait of Georgia (Malaspina Strait). While many smolts moved across the northern Strait of Georgia acoustic array with no indication of long-term milling or large-scale east-to-west movements, large proportions (20–40% of sockeye and 30–50% of steelhead) exhibited a different behavior, apparently moving in a westward or counterclockwise pattern. Variability in migratory behavior for both species was linked to subsequent survival through the Strait of Georgia. Survival for both species was influenced by initial east-to-west location, and sockeye were further influenced by migration timing and duration of time spent near the northern Strait of Georgia array. Westward movements result in a net transport of smolts from Malaspina Strait to the Strait of Georgia, particularly for steelhead. Counterclockwise movements may be due to the currents in this area during the time of outmigration, and the higher proportion of steelhead smolts exhibiting this counterclockwise behavior may reflect a greater exposure to wind-altered currents for the more surface-oriented steelhead. Our results provide an empirical example of how movements can affect migration survival, for which examples remain rare in movement ecology, confirming that variability in movements themselves are an important part of the migratory process.
Assessing the impacts of Light Rail Transit on urban land in Manila

is paper presents an assessment of impacts of Light Rail Transit Line 1 (LRT1) in terms of accessibility and distance as they relate to variables such as land values, land uses, and population densities in Manila, Philippines. Using correlations and regressions, these variables are analyzed against an accessibility index and network distances obtained from a model built within a Geographic Information System (GIS). Land values, land uses, and population densities are in uenced in a limited, though consistent, way by the accessibility provided by LRT1 and the distance to it. e analysis of impacts a er the construction of LRT1 found that accessibility and distance were only consistent in uences for residential land values, with marginal results for the rest of the variables. ese results, when contrasted with the urban con guration of Manila and the studies reviewed, show that the limited impacts may be a consequence of good accessibility before LRT1 and the lack of complementary planning and policies for taking advantage of its in uence.
Music and Leadership : the Role of the Conductor

Leadership is a social competence linked to the figure of the conductor of a music group (choir, orchestra, gospel, and big-band). In the case of leadership, this is a skill you can develop, as you can learn to be a good director. This paper presents a series of reflections that link leadership and musical conducting, establishing different types of music conductors and their functions within a band or a choir –in rehearsals and concerts, such as personal dimensions, verbal level, legitimacy, emotional self-awareness, social awareness (empathy, organizational awareness, social skill (inspirational leadership, influence, conflict management, teamwork and collaboration) and self-management (emotional self-control, adaptability, achievement orientation and positive attitude). The paper also speaks about different styles of leadership (analyzed by the psychological and social models) applied to many kind of musical activities, such as authoritarian, semi-authoritarian, laissez-faire, democratic, visionary, organizer, affiliative, and coach leader.
THE SIZE, SHAPE, AND ORIENTATION OF COSMOLOGICAL VOIDS IN THE SLOAN DIGITAL SKY SURVEY

We present a detailed description of our void finding algorithm which is an extension of the prescription by Hoyle and Vogeley. We include a discussion of the reproducibility and robustness of the algorithm as well as the statistical significance of the detected voids. We apply our void finder to the Data Release 5 of the Sloan Digital Sky Survey and identify 232 cosmological voids. A void catalog which contains the most salient properties of the detected voids is created. We present a statistical analysis of the distribution of the size, shape, and orientation of our identified cosmological voids. We also investigate possible trends with redshift for 0.04 ⩽ z ⩽ 0.16. We compare our results to those from an identical analysis of a mock catalog based on the ΛCDM model and find reasonable agreement. However, some statistically significant differences in the overall orientation of cosmological voids are exhibited and will have to be reconciled by further refinement of the simulations.
Rank Tests at Jump Events

We propose a test for the rank of a cross-section of processes at a set of jump events. The jump events are either specific known times or are random and associated with jumps of some process. The test is formed from discretely sampled data on a fixed time interval with asymptotically shrinking mesh. In the first step, we form nonparametric estimates of the jump events via thresholding techniques. We then compute the eigenvalues of the outer product of the cross-section of increments at the identified jump events. The test for rank r is based on the asymptotic behavior of the sum of the squared eigenvalues excluding the largest r. A simple resampling method is proposed for feasible testing. The test is applied to financial data spanning the period 2007–2015 at the times of stock market jumps. We find support for a one-factor model of both industry portfolio and Dow 30 stock returns at market jump times. This stands in contrast with earlier evidence for higher-dimensional factor structure of stock returns during “normal” (nonjump) times. We identify the latent factor driving the stocks and portfolios as the size of the market jump.
Understanding the Risk Factors and Long-Term Consequences of Cisplatin-Associated Acute Kidney Injury: An Observational Cohort Study

Acute kidney injury (AKI) is a well-known complication of cisplatin-based chemotherapy; however, its impact on long-term patient survival is unclear. We sought to determine the incidence and risk factors for development of cisplatin-associated AKI and its impact on long-term renal function and patient survival. We identified 233 patients who received 629 cycles of high-dose cisplatin (99±9mg/m2) for treatment of head and neck cancer between 2005 and 2011. These subjects were reviewed for development of AKI. Cisplatin nephrotoxicity (CN) was defined as persistent rise in serum creatinine, with a concomitant decline in serum magnesium and potassium, in absence of use of nephrotoxic agents and not reversed with hydration. All patients were hydrated per protocol and none had baseline glomerular filtration rate (GFR) via CKD-EPI<60mL/min/1.73m2. The patients were grouped based on development of AKI and were staged for levels of injury, per KDIGO-AKI definition. Renal function was assessed via serum creatinine and estimated glomerular filtration rate (eGFR) via CKD-EPI at baseline, 6- and 12-months. Patients with AKI were screened for the absence of nephrotoxic medication use and a temporal decline in serum potassium and magnesium levels. Logistic regression models were constructed to determine risk factors for cisplatin-associated AKI. Twelve-month renal function was compared among groups using ANOVA. Kaplan-Maier curves and Cox proportional hazard models were constructed to study its impact on patient survival. Of 233 patients, 158(68%) developed AKI; 77 (49%) developed stage I, 55 (35%) developed stage II, and 26 (16%) developed stage III AKI. Their serum potassium and magnesium levels correlated negatively with level of injury (p<0.05). African American race was a significant risk factor for cisplatin-associated AKI, OR 2.8 (95% CI 1.3 to 6.3) and 2.8 (95% CI 1.2 to 6.7) patients with stage III AKI had the lowest eGFR value at 12 months (p = 0.05) and long-term patient survival (HR 2.1; p<0.01) than patients with no or lower grades of AKI. Most common causes of death were recurrent cancer (44%) or secondary malignancy elsewhere (40%). Cisplatin-associated severe AKI occurs in 20% of the patients and has a negative impact on long-term renal function and patient survival. PEG tube placement may be protective and should be considered in high risk-patients.
Programming in the Kitchen

In this paper we discuss issues for the integration of computing power in mundane artefacts. We do so with reference to a recent project with a manufacturer of ovens for larger kitchens and catering services. We introduce three levels of obstacles when integrating computers into mundane tools and point out how organisational issues are a source of interface problems. We conclude that the design of computer-based interfaces to mundane tools should encompass broader studies of the context of use and the history of the considered artefact.
Eigenvalue curves of asymmetric tridiagonal random matrices

Random Schrodinger operators with imaginary vector potentials are studied in di- mension one. These operators are non-Hermitian and their spectra lie in the complex plane. We consider the eigenvalue problem on nite intervals of length n with periodic boundary conditions and describe the limit eigenvalue distribution when n ! 1 . We prove that this limit distribu- tion is supported by curves in the complex plane. We also obtain equations for these curves and for the corresponding eigenvalue density in terms of the Lyapunov exponent and the integrated density of states of a \reference" symmetric eigenvalue problem. In contrast to these results, the spectrum of the limit operator in l 2 (Z) is a two dimensional set which is not approximated by the spectra of the nite-interval operators.
Postpartum airway responsiveness and exacerbation of asthma during pregnancy – a pilot study

Background Airway responsiveness and inflammation are associated with the clinical manifestations of asthma and the response to pharmacological therapy. Objective To investigate if airway responsiveness and inflammatory characteristics are related to asthma exacerbations during pregnancy. Materials and methods In women with asthma who were prescribed controller medication and monitored closely during pregnancy, the risk of exacerbations was analyzed in relation to postpartum measures of fractional exhaled nitric oxide (FENO), skin prick test reactivity, static and dynamic lung volumes, diffusing capacity for carbon monoxide, bronchial responsiveness to inhaled mannitol, and inflammatory characteristics in induced sputum. Obtained data were analyzed in relation to exacerbation status during pregnancy. The PD15 is defined as the cumulative administered dose causing a 15% decline in forced expiratory volume in the first second (FEV1). Results Fifty women (mean age ± standard deviation of 32±5 years) were enrolled over an 11-month period and examined on average 4 months postpartum. During pregnancy, 13 women had a total of 16 exacerbations (8 mild and 8 severe). Women with asthma exacerbation during pregnancy had more pronounced airway responsiveness to inhaled mannitol (geometric mean PD15 82 vs 171 mg, p=0.04) and were less likely to be atopic (62% vs 86%, respectively; p=0.04) than the non-exacerbators. No statistically significant difference was found between the 2 groups of women with regard to type of airway inflammation in sputum and fractional exhaled nitric oxide (FENO). Conclusion More pronounced airway hyperresponsiveness together with nonatopic status appears to characterize women at high risk of exacerbation of asthma during pregnancy.
Non-saturated performance analysis of IEEE 802.11 broadcast in 2-D mobile ad hoc networks

The non-saturated performance of the IEEE 802.11 broadcast scheme in the two-dimensional (2-D) mobile ad hoc networks is studied in this paper. A simplified yet reasonable system model is built to derive the closed-form expressions of average packet reception probability, non-saturated throughput, and average queuing delay. Compared with the existing work in the literature, the proposed system model takes into account the effect of arbitrary transmission queue length. Moreover, our analysis considers both the impact of concurrent transmissions caused by identical backoff interval selection and that of hidden nodes caused by limited sensing range on an observed transmitter. All the analysis results are validated by extensive simulations.
Dynamic analyses reveal cytoprotection by RPE melanosomes against non-photic stress

Purpose Isolated melanosomes are known to have antioxidant properties but whether the granules perform an antioxidant function within cells is unclear. The aim of this study was to determine whether retinal pigment epithelium (RPE) melanosomes are competent to protect cultured cells against non-photic oxidative stress induced by treatment with H2O2. Methods Porcine melanosomes, either untreated or irradiated with visible light to simulate age-related melanin photobleaching, were introduced by phagocytosis into ARPE-19 cells. Cells were treated with H2O2 using two delivery methods: as a pulse, or by continuous generation following addition of glucose oxidase to the medium. Cell survival in melanosome-containing cells was compared to survival in cells containing phagocytosed control latex beads using two real-time cell death assays. Results Following H2O2 delivery by either method, greater resistance to critical concentrations of H2O2 was seen for cells containing melanosomes than for cells containing beads. Melanosome-mediated protection manifested as a delay in the time of onset of cell death and a slower rate of cell death over time. Photobleaching diminished the stress resistance conferred by the pigment granules. Individual cells in co-cultures were differentially sensitive to oxidative stress depending upon their particle content. Additional features of the time course of the cell death response were revealed by the dynamic analyses conducted over hours post oxidant treatment. Conclusions The results show, for the first time, that melanosomes perform a cytoprotective function within cultured cells by acting as an antioxidant. The outcomes imply that melanosomes perform functions within RPE cells aside from those related to light irradiation, and also suggest that susceptibility to ubiquitous pro-oxidizing agents like H2O2 is partly determined by discrete features of individual RPE cells such as their granule content.
Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons

Animals must respond selectively to specific combinations of salient environmental stimuli in order to survive in complex environments. A task with these features, biconditional discrimination, requires responses to select pairs of stimuli that are opposite to responses to those stimuli in another combination. We investigate the characteristics of synaptic plasticity and network connectivity needed to produce stimulus-pair neural responses within randomly connected model networks of spiking neurons trained in biconditional discrimination. Using reward-based plasticity for synapses from the random associative network onto a winner-takes-all decision-making network representing perceptual decision-making, we find that reliably correct decision making requires upstream neurons with strong stimulus-pair selectivity. By chance, selective neurons were present in initial networks; appropriate plasticity mechanisms improved task performance by enhancing the initial diversity of responses. We find long-term potentiation of inhibition to be the most beneficial plasticity rule by suppressing weak responses to produce reliably correct decisions across an extensive range of networks.
Gene–gene interaction between 14‐3‐3 zeta and butyrylcholinesterase modulates Alzheimer′s disease risk

A loss in the regulatory mechanism that controls tau phosphorylation in normal brain is suggested to cause tau hyperphosphorylation in Alzheimer′s disease (AD) brain and the development of neurofibrillary tangles (NFT). 14‐3‐3 zeta protein and butyrylcholinesterase (BCHE) are associated with NFT in AD brain and stimulate tau phosphorylation. In a case–control study in 231 AD patients and 221 healthy controls, we examined whether the combined effects between 14‐3‐3 zeta (rs964917 and rs983583) and BCHE (K variant) polymorphisms might be responsible for susceptibility to AD. Subjects carrying both the BCHE K allele and the 14‐3‐3 zeta rs964917 G/G genotype (OR = 0.44, 95% CI = 0.20–0.95, P = 0.03), or 14‐3‐3 zeta rs983583 G/G genotype (OR = 0.46, 95% CI = 0.21–1.00, P = 0.05) had a lower risk of developing AD than subjects without these risk genotypes. Considering synergistic effects between polymorphisms in tau phosphorylation relate‐genes may help in determining the risk profile for AD.