Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between immunotoxicants and parasite stress: implications for host health

Many organisms face a wide variety of biotic and abiotic stressors which reduce individual survival, interacting synergistically to further reduce fitness. Here we studied the effects of two such synergistically interacting stressors; immunotoxicant exposure and parasite infection. We model the dynamics of a within-host infection and the associated immune response of an individual. We consider both the indirect sub-lethal effects on immunosuppression and the direct effects on health and mortality of individuals exposed to toxicants. We demonstrate that sub-lethal exposure to toxicants can promote infection through the suppression of the immune system. This happens through the depletion of the immune response which causes rapid proliferation in parasite load. In addition, high toxicant exposure can alter cellular regulation and cause the breakdown of normal healthy tissue, from which we infer higher mortality risk of the host. We classify this breakdown into three phases of increasing toxicant stress, and demonstrate the range of conditions under which toxicant exposure causes failure at the within-host level. These phases are determined by the relationship between the immunity status, overall cellular health and the level of toxicant exposure. We discuss the implications of our model in the context of individual honey bee health. Our model provides an assessment of how pesticide stress and infection interact to cause the synergistic breakdown of the within-host dynamics of individual honey bees.
Impact of BPR critical success factors on inter-organizational functions: an empirical study

This research paper investigates the impact of critical success factors for business process reengineering (BPR) on two internal organizational factors: business process efficiency (BPE) and process conflict. The paper further examines how these internal organizational factors affect the financial and nonfinancial performances of employees. Structured questionnaires were distributed among the employees of three recently privatized companies. The sample size was 300 companies, and we used a stratified random sampling method in the study. The research model was tested using AMOS version 16.This research finds that critical success factors of BPR increase business process efficiency (BPE) by reducing cost, cycle time, delays and duplications. These factors also affect the financial and nonfinancial performances of employees positively. But no relationship was found between BPR critical success factors and process conflict. This paper is one of the few empirical studies that investigate the relationship between BPR critical success factors and BPE. Our study further contributes to the existing literature by studying the consequences of BPR critical success factors on process conflicts and the effects of these factors on the performances of employees.
Influenza Pathogenesis in Genetically Defined Resistant and Susceptible Murine Strains  

The murine infection model is a cornerstone for influenza virus research and includes aspects such as disease pathogenesis, immunobiology, and vaccine and antiviral drug development. One compelling feature of the murine model is the availability of inbred mouse strains, each with a unique genetic makeup and potential for variable responses to influenza infection. Using highly controlled infection studies, the response to influenza virus infection is classified on a spectrum from susceptible to resistant, reflecting severe morbidity and high mortality, to limited or no morbidity and no mortality. Although there have been a variety of studies establishing disparate pathogenesis amongst various murine strains, thus far, there is no consensus regarding the determinants of the outcome of infection. The goal of this review is to explore and discuss the differences in pathogenesis, as well as the innate and adaptive immune responses to influenza infection that have been described in susceptible and resistant mouse strains. Understanding how host genetics influences the response to influenza infection provides valuable insight into the variable responses seen in vaccine or drug efficacy studies, as well as indicates possible mechanisms contributing to increased disease severity in humans infected with influenza virus with no known risk factors.
Detecting Video Saliency via Local Motion Estimation

In the last decades, saliency detection was extensively studied. The number of computational models that help to detect salient regions in still images is increasing, whereas, detecting salient regions in videos is in its early stages. In this paper we propose a video saliency detection method using local motion estimation. Starting from a patch, the problem of saliency detection is modeled as a growing region starting from a region which contains the higher motion information to the background. Local saliency is measured by combining local motion estimation and local surrounding contrast which leads to the construction of foreground and background patches. Experiments have proved that The proposed method outperforms state-of-the-art methods over two benchmark datasets.
Climate and Landscape Factors Associated with Buruli Ulcer Incidence in Victoria, Australia

Background Buruli ulcer (BU), caused by Mycobacterium ulcerans (M. ulcerans), is a necrotizing skin disease found in more than 30 countries worldwide. BU incidence is highest in West Africa; however, cases have substantially increased in coastal regions of southern Australia over the past 30 years. Although the mode of transmission remains uncertain, the spatial pattern of BU emergence in recent years seems to suggest that there is an environmental niche for M. ulcerans and BU prevalence. Methodology/Principal Findings Network analysis was applied to BU cases in Victoria, Australia, from 1981–2008. Results revealed a non-random spatio-temporal pattern at the regional scale as well as a stable and efficient BU disease network, indicating that deterministic factors influence the occurrence of this disease. Monthly BU incidence reported by locality was analyzed with landscape and climate data using a multilevel Poisson regression approach. The results suggest the highest BU risk areas occur at low elevations with forested land cover, similar to previous studies of BU risk in West Africa. Additionally, climate conditions as far as 1.5 years in advance appear to impact disease incidence. Warmer and wetter conditions 18–19 months prior to case emergence, followed by a dry period approximately 5 months prior to case emergence seem to favor the occurrence of BU. Conclusions/Significance The BU network structure in Victoria, Australia, suggests external environmental factors favor M. ulcerans transmission and, therefore, BU incidence. A unique combination of environmental conditions, including land cover type, temperature and a wet-dry sequence, may produce habitat characteristics that support M. ulcerans transmission and BU prevalence. These findings imply that future BU research efforts on transmission mechanisms should focus on potential vectors/reservoirs found in those environmental niches. Further, this study is the first to quantitatively estimate environmental lag times associated with BU outbreaks, providing insights for future transmission investigations.
Functionalization of carbon nanotube scanning probes for advanced studies of ferroic thin films

Ferroic materials at the nanoscale reveal new properties and functionalities as such they are recognized as extremely promising materials from both fundamental and application point of view. One of the major tool used to advance studies of ferroic thin films is the atomic force probe microscopy (AFM). In the present work, we study the synthesis, fabrication, processing, and characterization of carbon nanotube (CNT) scanning probes with a further application to ferroic thin film. Our main results include both experimental and theoretical studies of ultra-high resolution magnetic force microscopy imaging of spin nanostructures of soft magnetic materials with ferromagnetically-coated CNT probes, transport measurements of dielectric-coated-CNT AFM probes, and piezoresponse force microscopy studies of switching dynamics in ferroelectric thin films. Notably, we performed the non-perturbative imaging of spin nanostructures with a resolution higher than that of X-ray microscopy, and at ambient conditions.
Using iMCFA to Perform the CFA, Multilevel CFA, and Maximum Model for Analyzing Complex Survey Data

To construct CFA, MCFA, and maximum MCFA with LISREL v.8 and below, we provide iMCFA (integrated Multilevel Confirmatory Analysis) to examine the potential multilevel factorial structure in the complex survey data. Modeling multilevel structure for complex survey data is complicated because building a multilevel model is not an infallible statistical strategy unless the hypothesized model is close to the real data structure. Methodologists have suggested using different modeling techniques to investigate potential multilevel structure of survey data. Using iMCFA, researchers can visually set the between- and within-level factorial structure to fit MCFA, CFA and/or MAX MCFA models for complex survey data. iMCFA can then yield between- and within-level variance-covariance matrices, calculate intraclass correlations, perform the analyses and generate the outputs for respective models. The summary of the analytical outputs from LISREL is gathered and tabulated for further model comparison and interpretation. iMCFA also provides LISREL syntax of different models for researchers' future use. An empirical and a simulated multilevel dataset with complex and simple structures in the within or between level was used to illustrate the usability and the effectiveness of the iMCFA procedure on analyzing complex survey data. The analytic results of iMCFA using Muthen's limited information estimator were compared with those of Mplus using Full Information Maximum Likelihood regarding the effectiveness of different estimation methods.
Overfishing of Small Pelagic Fishes Increases Trophic Overlap between Immature and Mature Striped Dolphins in the Mediterranean Sea

The interactions among diet, ecology, physiology, and biochemistry affect N and C stable isotope signatures in animal tissues. Here, we examined if ecological segregation among animals in relation to sex and age existed by analyzing the signatures of δ15N and δ13C in the muscle of Western Mediterranean striped dolphins. Moreover, we used a Bayesian mixing model to study diet composition and investigated potential dietary changes over the last two decades in this population. For this, we compared isotope signatures in samples of stranded dolphins obtained during two epizootic events occurring in 1990 and 2007–2008. Mean δ13C values for females and males were not significantly different, but age-related variation indicated δ13C enrichment in both sexes, suggesting that females and males most likely fed in the same general areas, increasing their consumption of benthic prey with age. Enrichment of δ15N was only observed in females, suggesting a preference for larger or higher trophic level prey than males, which could reflect different nutritional requirements. δ13C values showed no temporal variation, although the mean δ15N signature decreased from 1990 to 2007–2008, which could indicate a dietary shift in the striped dolphin over the last two decades. The results of SIAR indicated that in 1990, hake and sardine together contributed to 60% on the diet of immature striped dolphins, and close to 90% for mature striped dolphins. Conversely, the diet of both groups in 2007–2008 was more diverse, as hake and sardine contributed to less than 40% of the entire diet. These results suggest a dietary change that was possibly related to changes in food availability, which is consistent with the depletion of sardine stocks by fishing.
Simultaneous modeling of initial conditions and time heterogeneity in dynamic networks: An application to Foreign Direct Investments

Abstract In dynamic networks, the presence of ties are subject both to endogenous network dependencies and spatial dependencies. Current statistical models for change over time are typically defined relative to some initial condition, thus skirting the issue of where the first network came from. Additionally, while these longitudinal network models may explain the dynamics of change in the network over time, they do not explain the change in those dynamics. We propose an extension to the longitudinal exponential random graph model that allows for simultaneous inference of the changes over time and the initial conditions, as well as relaxing assumptions of time-homogeneity. Estimation draws on recent Bayesian approaches for cross-sectional exponential random graph models and Bayesian hierarchical models. This is developed in the context of foreign direct investment relations in the global electricity industry in 1995–2003. International investment relations are known to be affected by factors related to: (i) the initial conditions determined by the geographical locations; (ii) time-dependent fluctuations in the global intensity of investment flows; and (iii) endogenous network dependencies. We rely on the well-known gravity model used in research on international trade to represent how spatial embedding and endogenous network dependencies jointly shape the dynamics of investment relations.
Advanced numerical modeling of semiconductor material properties and their device performances

With the renewed concept of “Materials by Design” attracting particular attentions from the engineering communities in recent years, numerical methods that can reliably predict the optical and electrical properties of materials is highly preferable. Since the growth or the synthesis of a “designed” material and the ensuing devices is usually prohibitively expensive and time-consuming, numerical simulation tools that predict the properties of a proposed material together with its device performance before production is especially important and cost-effective. Furthermore, as the technology advances, semiconductor devices have been pushed to operate at their material limits, which requires a thorough understanding of the materials’ microscopic processes under different conditions. Therefore, developing numerical models that are capable of investigating the semiconductor properties from material level to device level is highly desirable. This dissertation develops a suite of numerical models in which optical absorption and Auger recombination in semiconductor materials are studied and simulated
Attitudes towards psychiatric treatment and people with mental illness: changes over two decades

Background Over the past decades, psychiatry, as a science and a clinical discipline, has witnessed profound changes. Aims To examine whether these changes are reflected in changes in the public's conceptualisation of mental disorders, the acceptance of mental health treatment and attitudes towards people with mental illness. Method In 1990 and 2011, population surveys were conducted in Germany on public attitudes about schizophrenia, depression and alcohol dependence. Results Although the public has become more inclined to endorse a biological causation of schizophrenia, the opposite trend was observed with the other two disorders. The public's readiness to recommend help-seeking from mental health professionals and using psychotherapy and psychotropic medication has increased considerably. Attitudes towards people with schizophrenia worsened, whereas for depression and alcohol dependence no or inconsistent changes were found. Conclusions The growing divide between attitudes towards schizophrenia and other mental disorders should be of particular concern to future anti-stigma campaigns.
Cyclosporine for the treatment of lupus nephritis in patients with systemic lupus erythematosus.

AIMS This study aimed to assess retrospectively the efficacy and safety of cyclosporin A (CsA) therapy in patients with lupus nephritis (LN). MATERIALS AND METHODS From September 2005 to August 2015, eligible patients with LN undergoing CsA treatment were enrolled in the study. Medical charts as well as clinical and laboratory data were retrospectively reviewed. The data were evaluated at 0, 1, 6, 12 month(s) after the start of CsA. Serum creatinine (SCr), estimated glomerular filtration rate (eGFR), urine protein/creatinine ratio (uPCR), complement components C3, C4, and anti-double stranded DNA antibody (anti-dsDNA) titers were recorded. Renal response to CsA (complete response (CR) and partial response (PR)) and relapse after stopping CsA were set as primary endpoint, and adverse events, progression to end-stage renal disease (ESRD), and all-cause mortality as secondary endpoint. RESULTS Among 60 patients enrolled, 11.7%, 20%, 25% achieved CR and 65.0%, 51.7%, 40% achieved PR at 1, 6, and 12 months, respectively. The SCr and eGFR remained stable during follow-up. After 1 year, CsA led to a decrease in median uPCR (3.79 to 0.51, p < 0.001) and anti-dsDNA (10.1 to 5.7 IU/mL, p = 0.011), an increase in mean C3 (75.9 to 88.5 mg/dL, p < 0.001) and C4 (15.9 to 19.5 mg/dL, p < 0.001) as well as a decrease in glucocorticoid dose. There were no deaths or progression to ESRD originating from adverse events in our study. CONCLUSION CsA is an effective and safe treatment for patients with LN. Further randomized controlled trials are needed.
Evaluation of Telavancin Activity versus Daptomycin and Vancomycin against Daptomycin-Nonsusceptible Staphylococcus aureus in an In Vitro Pharmacokinetic/Pharmacodynamic Model

ABSTRACT Daptomycin-nonsusceptible (DNS) Staphylococcus aureus strains have been reported over the last several years. Telavancin is a lipoglycopeptide with a dual mechanism of action, as it inhibits peptidoglycan polymerization/cross-linking and disrupts the membrane potential. Three clinical DNS S. aureus strains, CB1814, R6212, and SA-684, were evaluated in an in vitro pharmacokinetic/pharmacodynamic (PK/PD) model with simulated endocardial vegetations (starting inoculum, 108.5 CFU/g) for 120 h. Simulated regimens included telavancin at 10 mg/kg every 24 h (q24h; peak, 87.5 mg/liter; t1/2, 7.5 h), daptomycin at 6 mg/kg q24h (peak, 95.7 mg/liter; t1/2, 8 h), and vancomycin at 1 g q12h (peak, 30 mg/liter; t1/2, 6 h). Differences in CFU/g between regimens at 24 through 120 h were evaluated by analysis of variance with a Tukey's post hoc test. Bactericidal activity was defined as a ≥3-log10 CFU/g decrease in colony count from the initial inoculum. MIC values were 1, 0.25, and 0.5 mg/liter (telavancin), 4, 2, and 2 mg/liter (daptomycin), and 2, 2, and 2 mg/liter (vancomycin) for CB1814, R6212, and SA-684, respectively. Telavancin displayed bactericidal activities against R6212 (32 to 120 h; −4.31 log10 CFU/g), SA-684 (56 to 120 h; −3.06 log10 CFU/g), and CB1814 (48 to 120 h; −4.9 log10 CFU/g). Daptomycin displayed initial bactericidal activity followed by regrowth with all three strains. Vancomycin did not exhibit sustained bactericidal activity against any strain. At 120 h, telavancin was significantly better at reducing colony counts than vancomycin against all three tested strains and better than daptomycin against CB1814 (P < 0.05). Telavancin displayed bactericidal activity in vitro against DNS S. aureus isolates.
Improvement of Sidewall Roughness of Submicron SOI Waveguides by Hydrogen Plasma and Annealing

We report the successful fabrication of low-loss submicrometric silicon-on-insulator strip waveguides for on-chip links. Postlithography treatment and postetching hydrogen annealing have been used to smoothen the waveguide sidewalls, as roughness is the major source of transmission losses. An extremely low silicon line-edge roughness of 0.75 nm is obtained with the optimized process flow. As a result, record-low optical losses of less than 0.5 dB/cm are measured at 1310 nm for strip waveguide dimensions exceeding 500 nm. They range from 1.2 to 0.8 dB/cm for 300–400-nm-wide waveguides. Those results are to our knowledge the best ever published for a 1310-nm wavelength. These results are compared to modeling based on Payne and Lacey equations.
DUAL-PHASE STEELS MODELLING - A STRAIN GRADIENT APPROACH - PART II

To obtain the behaviour of dual-phase microstructures, a three dimensional (3D) strain gradient finite element model has been developed. The effect of grain size on flow stress has been investigated in polycristalline dualphase steels. A strong size-dependence of plastic deformation in the micron range is observed. To describe the work hardening process in polycrystalline materials, two models, a gradient-one-internal-variable model and a gradienttotal dislocation density evolution model, constructed in the basis of the Kocks-Mecking model are proposed. Results demonstrate that more dislocations are stored in specimens with finer grains and that the total dislocation density is not a single function of strain. Ferrite and martensite individual mechanical behaviour calculated into the dual-phase composite structure are presented. The effect of plastic deformation gradients imposed by the microstructure are clearly observed. An attempt is made to determine the mathematical expressions which best describe the strain hardening behaviour of crystalline materials in uniaxial deformation.
Complete mitochondrial genome and the phylogenetic position of the brown-spotted grouper Epinephelus chlorostigma (Perciformes: Epinephelidae)

Abstract The complete mitogenome of the brown-spotted grouper Epinephelus chlorostigma was determined in this study. It is 16,894 bp in length, containing 37 genes with the typical order and transcriptional direction in the vertebrates. The overall nucleotide composition is: 28.7% A; 28.0% C; 16.3% G and 27.0% T. The lengths of 22 transfer RNA (tRNA) genes range from 67 (tRNA-Cys) to 76 (tRNA-Leu1) bp. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were found in the protein-coding genes. The nodes of phylogenetic tree were strongly supported based on the complete mitogenomes of available groupers. The phylogenetic results suggested E. chlorostigma is the closest to E. areolatus within the genus Epinephelus.
The roles of injury and nonsteroidal anti-inflammatory drugs in the development and outcomes of severe group A streptococcal soft tissue infections

Purpose of review This review summarizes clinical and basic science evidence linking trauma and nonsteroidal anti-inflammatory drug (NSAID) use to initiation and progression of severe group A streptococcal (GAS) soft tissue infection. Recent findings New evidence includes recent clinical series and controlled studies that lend support to an NSAID/GAS association, basic science studies that demonstrate unique roles for nonpenetrating injury and NSAID administration in initiation of cryptogenic GAS infection and experimental studies showing that nonselective NSAIDs accelerate disease progression and limit antibiotic efficacy in established GAS soft tissue infections. Potential mechanisms for these processes are discussed. Summary NSAIDs are important anti-inflammatory and analgesic drugs; however, new experimental data suggest that nonselective NSAIDs do more than simply mask the signs and symptoms of developing GAS infection. A more thorough understanding of the triadic interplay of injury-triggered immune signaling, GAS soft tissue infection and NSAIDs is of significant clinical importance and could shift the current paradigm of pain management to avert the consequences of such devastating infections.