Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of the Combination of Tobramycin and a Macrolide in an InVitroPseudomonas aeruginosa Mature Biofilm Model

ABSTRACT Respiratory disease is the main cause of morbidity and mortality in patients with cystic fibrosis (CF). In particular, patients suffer from chronic infection due to biofilm formation by opportunistic Pseudomonas aeruginosa (32). Therefore, there is an urgent need to develop alternative ways to treat biofilm-associated clinical infections. The aim of this study was to compare the antimicrobial effects in vitro of the combinations tobramycin-clarithromycin and tobramycin-azithromycin against five P. aeruginosa biofilms and to establish the most effective combination. We performed a kinetic study over a period of 28 days of a twice-daily coadministration of the combinations tobramycin-clarithromycin and tobramycin-azithromycin on 12-day-old, mature P. aeruginosa biofilms formed on microplate pegs for 4 clinical isolates and one laboratory strain (PAO1) to simulate the treatment of CF patients with tobramycin inhalation solution (TOBI) through aerosolization. A synergy between tobramycin and clarithromycin was recorded for 3/5 biofilms, with a bacterial decrease of more than 5 log. Conversely, we found an antagonistic activity when 4 μg/ml tobramycin was administered with azithromycin at 2 μg/ml for P. aeruginosa PAO1 and with azithromycin at 2, 20, 50, 100, and 200 μg/ml for P. aeruginosa PYO1. Treatment with tobramycin at 4 μg/ml combined with clarithromycin at 200 μg/ml eradicated all five biofilms, while tobramycin-azithromycin at the same concentrations eradicated only three biofilms. Results of this study suggest that local administration of tobramycin and clarithromycin into the respiratory tract represents a better strategy than the combination tobramycin-azithromycin for the treatment of P. aeruginosa-associated pulmonary infections.
Toxicity of aqueous fullerene in adult and larval Fundulus heteroclitus

Aqueous suspensions of fullerene aggregates (aqua‐nC60) were used to investigate the movement of carbon‐based nanomaterials in a marine water column and to determine their effects on different life stages of a marine teleost. Fullerene aggregates formed precipitates as a result of mixing in natural seawater, and levels of aqua‐nC60 were significantly increased in bottom waters after 24 h. Exposure of Fundulus heteroclitus embryos, larvae, and adults to increasing concentrations of aqua‐nC60 resulted in very little mortality, and no median lethal concentrations could be calculated at ≤ 10 mg/L. Aggregates of aqua‐nC60 did adhere to the chorion but did not affect development of the embryos or their hatching success. Movements of aqua‐nC60 through the chorion and into the embryo tended to increase with higher exposure levels; however, the concentrations were extremely low and did not differ significantly. Larvae exposed to increasing concentrations of aqua‐nC60 exhibited a significant dose‐dependent increase in total glutathione (GSH). This was accompanied by a decreasing trend in lipid peroxidation (LPO), but LPO was not statistically different between treatments. Adult F. heteroclitus exposed to increasing concentrations of aqua‐nC60 exhibited an increase in total GSH in liver tissue but not in the gill. No significant effects on LPO were observed in either tissue. Thus, we conclude that aqua‐nC60 affects the oxidative stress response of F. heteroclitus and that increased antioxidant defenses provide some physiological tolerance for these materials. Environmental factors influencing uptake, metabolism, and physiological response following exposure, however, need further investigation.
Trauma mortality patterns in three nations at different economic levels: implications for global trauma system development.

BACKGROUND Whereas organized trauma care systems have decreased trauma mortality in the United States, trauma system design has not been well addressed in developing nations. We sought to determine areas in greatest need of improvement in the trauma systems of developing nations. METHODS We compared outcome of all seriously injured (Injury Severity Score > or = 9 or dead), nontransferred, adults managed over 1 year in three cities in nations at different economic levels: (1) Kumasi, Ghana: low income, gross national product (GNP) per capita of $310, no emergency medical service (EMS); (2) Monterrey, Mexico: middle income, GNP $3,900, basic EMS; and (3) Seattle, Washington: high income, GNP $25,000, advanced EMS. Each city had one main trauma hospital, from which hospital data were obtained. Annual budgets (in US$) per bed for these hospitals were as follows: Kumasi, $4,100; Monterrey, $68,000; and Seattle, $606,000. Data on prehospital deaths were obtained from vital statistics registries in Monterrey and Seattle, and by an epidemiologic survey in Kumasi. RESULTS Mean age (34 years) and injury mechanisms (79% blunt) were similar in all locations. Mortality declined with increased economic level: Kumasi (63% of all seriously injured persons died), Monterrey (55%), and Seattle (35%). This decline was primarily due to decreases in prehospital deaths. In Kumasi, 51% of all seriously injured persons died in the field; in Monterrey, 40%; and in Seattle, 21%. Mean prehospital time declined progressively: Kumasi (102 +/- 126 minutes) > Monterrey (73 +/- 38 minutes) > Seattle (31 +/- 10 minutes). Percent of trauma patients dying in the emergency room was higher for Monterrey (11%) than for either Kumasi (3%) or Seattle (6%). CONCLUSIONS The majority of deaths occur in the prehospital setting, indicating the importance of injury prevention in nations at all economic levels. Additional efforts for trauma care improvement in both low-income and middle-income developing nations should focus on prehospital and emergency room care. Improved emergency room care is especially important in middle-income nations which have already established a basic EMS.
Poor Diet Quality Is Associated With Low CD4 Count and Anemia and Predicts Mortality Among Antiretroviral Therapy–Naive HIV-Positive Adults in Uganda

Background:We assessed the association between dietary diversity and CD4 count, moderate anemia, and mortality among 876 antiretroviral therapy–naive people living with HIV/AIDS infection (PLHIV) in Uganda. Methods:Participants were interviewed and followed for an average of 21.6 months. Dietary diversity was measured using the Individual Dietary Diversity Score (IDDS) (range, 0–12) and summarized into an overall measure and disaggregated into nutrient-rich food groups (range, 0–7), cereals, roots, and tubers (range, 0\x{2013} 2); and oils, fats, sugars, and condiments (range, 0\x{2013} 3). We determined the cross-sectional associations between dietary diversity and (1) immunosuppression (CD4 count ⩽ 350 cells/&mgr;L) and (2) moderate anemia (hemoglobin < 10 g/dL) at baseline with logistic regression. We assessed the association between IDDS and mortality using Cox proportional hazards regression. Results:The mean IDDS score was 6.3 (SD 1.7) food groups per day, with a mean of 2.7 (SD 1.1) nutrient-rich food groups per day. Each additional nutrient-rich food group consumed was associated with a 16% reduction in the likelihood of having a CD4 count ⩽350 cells/&mgr;L [adjusted odds ratio, 0.84; 95% confidence interval (CI): 0.72 to 0.97] at baseline. Among those with >350 CD4 cells per microliter, but not those with CD4 count ⩽350 cells per microliter, consumption of nutrient-rich food groups was associated with a lower odds of moderate anemia (adjusted odds ratio, 0.57; 95% CI: 0.34 to 0.96). During follow-up, 48 participants (5.6%) died (mortality rate of 3.1 per 100 person-years). IDDS was inversely associated with mortality [adjusted hazard ratio, 0.76; 95% CI: 0.63 to 0.91]. Conclusion:These results suggest that diet quality is an important determinant of HIV disease severity and mortality in antiretroviral therapy–naive PLHIV.
Use of mental health services by veterans with PTSD after the terrorist attacks of September 11.

OBJECTIVE Community surveys have demonstrated significant psychological distress since the terrorist attacks of Sept. 11, 2001. Since people with posttraumatic stress disorder (PTSD) and other mental illnesses are especially vulnerable to stressful events, the authors examined the use of PTSD treatment services and other mental health services at Department of Veterans Affairs (VA) medical centers in New York City and elsewhere after the attacks. METHOD Analysis of variance was used to compare changes in average daily service use in the 6 months before and the 6 months after September 11, with changes in service use across the same months in the 2 previous years. Chi-square tests were used to examine differences from previous years in the proportion of new patients (i.e., who had not received treatment in the previous 6 months) entering treatment after September 11. RESULTS There was no significant increase in the use of VA services for the treatment of PTSD or other mental disorders or in visits to psychiatric or nonpsychiatric clinics in New York City after September 11 and no significant change in the pattern of service use from previous years. Nor was there a significant increase in PTSD treatment in the greater New York area, Washington, D.C., or Oklahoma City or in the proportion of new patients. CONCLUSIONS No increase was observed in the use of mental health services among VA patients with PTSD or other mental illnesses in response to the terrorist attacks of September 11.
Tracking Using Multiple Linear Searches and Motion Direction Sampling

Recent work in visual tracking has focussed on modelling target appearance, while using comparatively simple search methods to match those models to image data. Knowledge of the target's likely motion can both significantly reduce the search space and support more effective search strategies. We propose a new approach to target location which utilises sparse estimates of motion direction derived from local features to guide the generation of particles by a Markov Chain Monte Carlo (MCMC) based particle filter. The standard two-dimensional random walk is replaced by a series of one-dimensional searches in directions determined by the distribution of local feature motions. Two algorithms based on this approach are presented and evaluated. Experiments on both artificial and publically available, real image sequences show that the highest accuracy is obtained by sampling motion direction. The resulting algorithm successfully handles motion variations and reduces the likelihood that the tracker will be trapped in local extrem a when the target moves close to or is partially occluded by similar objects.
Analysis, simulation and circuit implementation of a precise high-output impedance analog current mirror

The decision for most the appropriate current mirror topology when designing a circuit is a matter of trade-offs between impedance, current transfer ratio, area on chip, power consumption and voltage-headroom, expandability etc. Current mirrors are mainly used for biasing, for transferring current from one part of the circuit to another or as load for amplifier stages. This paper presents the theoretical analysis, the simulation and the circuit built of a current mirror with excellent performance characteristics compared to conventional designs at the expense of voltage-headroom. Great emphasis in the analysis of the circuit has been paid on the current transfer ratio and the output impedance of the configuration.
probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

probeBase http://www.probebase. net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.
[Estimation of passive smoking during pregnancy by cotinine measurement and its effect on fetal growth].

Maternal cigarette smoking has been associated with some complications of pregnancy, including low birth weight and increased morbidity. Recently, it has been reported that maternal passive smoking also affects the fetal environment and causes fetal growth disturbance. In this study, we aimed to investigate the effects of maternal passive smoking on pregnant women and their fetuses by measuring cotinine concentrations in maternal urine and umbilical cord blood. The results were as follows: 1) Among 259 pregnant women, 17 cases (6.6%) were active smokers. The women who were not aware of passive smoking at all, were only 39 cases (15.1%). More than 80% of the pregnant women smoked either passively or actively each day. 2) Cotinine concentrations in both maternal urine and umbilical cord blood increased with the increase in passive smoking. Those in maternal serum, however, did not correlate with the increase in passive smoking. 3) The relative birth weight (R.B.W.) of the newborn infants delivered by the mothers whose cotinine concentration was more than 9.0ng/ml (This value represented the mean +1.5SD of the cotinine concentration in the urine from the mother who did not passively or actively smoke) was significantly lower than that of the mothers whose cotinine concentration was less than 9.0ng/ml. It is concluded that the measurement of the cotinine concentration in maternal urine or umbilical cord blood is very useful in estimating the effects of passive smoking on pregnant women. And passive smoking as well as active smoking also has a harmful effect on the fetal growth mechanism.
Numerical simulation in electrical cardiometry

This study is concerned with the direct problem of Electro Cardiometry (ECM) technique, and the associated thoracic electrical bioimpedance (TEB). We present a mathematical model for the hemodynamic of the aorta, the change in the electrical conductivity of the blood, and the electrical field problem equivalent to the ECM procedure. Having in view that anatomy plays a key role in investigating the ECM-TEB problem we used a 3D computational domain produced by medical image based reconstruction techniques. The mathematical model is solved by numerical simulation in the finite element method (FEM) technique. Analytic formulae for the electrical conductivity of the blood are available, however, when investigating the hemodynamic of the aorta flow considering an anatomically realistic computational domain, these results are difficult (if possible) to use as such. To circumvent this difficulty we defined an equivalent conductivity based on analytic results, by averaging techniques that outline the sensitivity of TEB to the aorta blood flow dynamics. The work reported here addresses the direct problem of ECM-TEB, aiming at assessing the sensitivity of TEB to the flow parameters. Its solution opens the path to the inverse EMC-TEB problem, with the objective of deciphering the flow dynamics out of EMC-TEB experimental data.
Subcellular localization and distribution of the breast cancer resistance protein transporter in normal human tissues.

High expression of the Breast Cancer Resistance Protein (BCRP) gene has been shown to be involved in resistance to chemotherapeutic drugs. Knowledge of the localization of BCRP protein in normal tissues may help unravel the normal function of this protein. Therefore, we characterized the tissue distribution and cellular localization of BCRP in frozen sections of normal human tissues. For this purpose, we used the recently described monoclonal antibody BXP-34 and another independently developed monoclonal antibody directed against BCRP, BXP-21. Both monoclonal antibodies show specific BCRP plasma membrane staining on cytospins obtained from topotecan- or mitoxantrone-selected cell lines, as well as from BCRP-transfected cell lines. Immunoprecipitation experiments using either BXP-21 or BXP-34 yielded a clear M(r) 72,000 BCRP band from BCRP-overexpressing tumor cells. In the topotecan-selected T8 and mitoxantrone-selected MX3 tumor cell lines, BCRP turned out to be differentially glycosylated. In contrast to BXP-34, BXP-21 is able to detect the M(r) 72,000 BCRP protein on immunoblots and is reactive with BCRP in formalin-fixed, paraffin-embedded tissues. Using BXP-21 and BXP-34, prominent staining of BCRP was observed in placental syncytiotrophoblasts, in the epithelium of the small intestine and colon, in the liver canalicular membrane, and in ducts and lobules of the breast. Furthermore, BCRP was present in veinous and capillary endothelium, but not in arterial endothelium in all of the tissues investigated. In the tissues studied, the mRNA levels of BCRP were assessed using reverse transcription-PCR, and these corresponded with the levels of BCRP protein estimated from immunohistochemical staining. The presence of BCRP at the placental syncytiotrophoblasts is consistent with the hypothesis of a protective role of BCRP for the fetus. The apical localization in the epithelium of the small intestine and colon indicates a possible role of BCRP in the regulation of the uptake of p.o. administered BCRP substrates by back-transport of substrate drugs entering from the gut lumen. Therefore, it may be useful to attempt to modulate the uptake of p.o. delivered BCRP substrates, e.g., topotecan or irinotecan, by using a BCRP inhibitor. Clinical trials testing this hypothesis have been initiated in our institute.
Case Report: Persistent cytomegalovirus (CMV) infection after haploidentical hematopoietic stem cell transplantation using in vivo alemtuzumab: emergence of resistant CMV due to mutations in the UL97 and UL54 genes

Addition of in vivo alemtuzumab to the conditioning regimen enabled 2‐ or 3‐locus‐mismatched hematopoietic stem cell transplantation with an acceptable incidence of graft‐versus‐host‐disease. However, the procedure was associated with a high incidence of cytomegalovirus (CMV) reactivation. Although preemptive therapy with ganciclovir prevented successfully severe CMV diseases and CMV‐related mortality, a patient developed persistent positive CMV antigenemia for more than 1 year after transplantation and CMV disease, despite the use of ganciclovir and foscarnet. The in vitro susceptibility assay showed that the clinical isolate was resistant to foscarnet, moderately resistant to ganciclovir, but sensitive to cidofovir. Therefore, cidofovir was administered. CMV antigenemia became negative within 2 weeks and never developed again. Nucleotide sequence of the UL54 and UL97 of the clinical isolate showed 4 amino acid substitutions (V11L, Q578H, S655L, and G874R) in UL54 and 2 mutations (A140V and A594V) in UL97 compared with the Towne and AD169 strains. Ganciclovir resistance was suspected to be caused by both A594V of UL97 and Q578H of UL54, whereas foscarnet resistance was due mainly to Q578H of UL54. In conclusion, the in vitro susceptibility assay as well as nucleotide sequence of clinical isolate is important to choose appropriate antiviral agents for patients who have persistent CMV reactivation after stem cell transplantation. J. Med. Virol. 80:1769–1775, 2008. © 2008 Wiley‐Liss, Inc.
Genetically determined interferon-gamma production influences the histological phenotype of lupus nephritis.

OBJECTIVE To clarify whether the interferon-gamma (IFN-gamma) gene (IFNG) is associated with the histological phenotype of lupus nephritis. METHOD We analysed microsatellite polymorphisms located within the first intron of the IFNG gene to determine the genotypes of patients with lupus nephritis WHO class IV (n=24), patients with WHO class V (n=12) and healthy controls (n=61). We used flow cytometric detection of intracellular cytokines to identify CD4(+) T cells producing IFN-gamma. Production of IFN-gamma by peripheral blood mononuclear cells after stimulation with phytohaemagglutinin was evaluated with an enzyme-linked immunosorbent assay. RESULT The frequency of the IFNG allele 114 was significantly greater in WHO class V patients than in WHO class IV patients. Furthermore, the IFNG 114 +/+ genotype was more frequent in WHO class V than in WHO class IV patients. The level of IFN-gamma and the percentage of IFN-gamma-producing CD4(+) T cells were lower in individuals with genotype 114 +/+ than in individuals with genotype 114 -/-. CONCLUSION The IFN-gamma gene is associated with the histological phenotype in lupus nephritis.
The impact of farming systems on soil biology and soilborne diseases: examples from the Australian sugar and vegetable industries — the case for better integration of sugarcane and vegetable production and implications for future research

A sugarcane farming system based on residue retention, minimum tillage, a leguminous rotation crop and controlled traffic using global positioning system guidance is currently being adopted by the Australian sugar industry because it improves sugar yields, reduces costs and provides additional income from crops such as soybean and peanut. This paper discusses the soil health improvements that are being obtained with this new farming system, particularly its beneficial effects on soil carbon levels and soil biological properties. It also summarises research showing that breaking the sugarcane monoculture with a soybean or peanut crop reduces populations of lesion nematode (Pratylenchus zeae) and root-knot nematode (Meloidogyne javanica), the two most important nematode pests of sugarcane. The role of minimum tillage and inputs of organic matter in enhancing the natural biological control mechanisms that suppress these nematodes is also discussed. The paper then considers the farming system currently used for vegetable crops such as tomato, capsicum and rockmelon, where inadequate crop rotation, excessive tillage, low organic inputs and the fallowing and solarisation effect of covering beds with plastic leads to a situation where soil fumigation is seen as the only option for reducing losses from soilborne pests and pathogens. Since the sugar industry coexists with the vegetable industry in some areas of Australia, the paper argues the case for developing minimum tillage practices for vegetable production and integrating them into the sugarcane farming system. It concludes that a farming system of this nature would improve profitability in both industries, produce better environmental outcomes at a landscape level and provide more sustainable solutions to nematode and soilborne disease problems.