Miracle-dz/UniFAR-FTUs huggingface dataset:
Absence of PmrAB-Mediated Phosphoethanolamine Modifications of Citrobacter rodentium Lipopolysaccharide Affects Outer Membrane Integrity

ABSTRACT The PmrAB two-component system of enterobacteria regulates a number of genes whose protein products modify lipopolysaccharide (LPS). The LPS is modified during transport to the bacterial outer membrane (OM). A subset of PmrAB-mediated LPS modifications consists of the addition of phosphoethanolamine (pEtN) to lipid A by PmrC and to the core by CptA. In Salmonella enterica, pEtN modifications have been associated with resistance to polymyxin B and to excess iron. To investigate putative functions of pEtN modifications in Citrobacter rodentium, ΔpmrAB, ΔpmrC, ΔcptA, and ΔpmrC ΔcptA deletion mutants were constructed. Compared to the wild type, most mutant strains were found to be more susceptible to antibiotics that must diffuse across the LPS layer of the OM. All mutant strains also showed increased influx rates of ethidium dye across their OM, suggesting that PmrAB-regulated pEtN modifications affect OM permeability. This was confirmed by increased partitioning of the fluorescent dye 1-N-phenylnaphthylamine (NPN) into the OM phospholipid layer of the mutant strains. In addition, substantial release of periplasmic β-lactamase was observed for the ΔpmrAB and ΔpmrC ΔcptA strains, indicating a loss of OM integrity. This study attributes a new role for PmrAB-mediated pEtN LPS modifications in the maintenance of C. rodentium OM integrity.
Barcelona Consensus on Biomarker-Based Immunosuppressive Drugs Management in Solid Organ Transplantation

Abstract: With current treatment regimens, a relatively high proportion of transplant recipients experience underimmunosuppression or overimmunosuppression. Recently, several promising biomarkers have been identified for determining patient alloreactivity, which help in assessing the risk of rejection and personal response to the drug; others correlate with graft dysfunction and clinical outcome, offering a realistic opportunity for personalized immunosuppression. This consensus document aims to help tailor immunosuppression to the needs of the individual patient. It examines current knowledge on biomarkers associated with patient risk stratification and immunosuppression requirements that have been generally accepted as promising. It is based on a comprehensive review of the literature and the expert opinion of the Biomarker Working Group of the International Association of Therapeutic Drug Monitoring and Clinical Toxicology. The quality of evidence was systematically weighted, and the strength of recommendations was rated according to the GRADE system. Three types of biomarkers are discussed: (1) those associated with the risk of rejection (alloreactivity/tolerance), (2) those reflecting individual response to immunosuppressants, and (3) those associated with graft dysfunction. Analytical aspects of biomarker measurement and novel pharmacokinetic–pharmacodynamic models accessible to the transplant community are also addressed. Conventional pharmacokinetic biomarkers may be used in combination with those discussed in this article to achieve better outcomes and improve long-term graft survival. Our group of experts has made recommendations for the most appropriate analysis of a proposed panel of preliminary biomarkers, most of which are currently under clinical evaluation in ongoing multicentre clinical trials. A section of Next Steps was also included, in which the Expert Committee is committed to sharing this knowledge with the Transplant Community in the form of triennial updates.
The Comparative Validity and Reproducibility of a Diet Quality Index for Adults: The Australian Recommended Food Score

Adult diet quality indices are shown to predict nutritional adequacy of dietary intake as well as all-cause morbidity and mortality. This study describes the reproducibility and validity of a food-based diet quality index, the Australian Recommended Food Score (ARFS). ARFS was developed to reflect alignment with the Australian Dietary Guidelines and is modelled on the US Recommended Food Score. Dietary intakes of 96 adult participants (31 male, 65 female) age 30 to 75 years were assessed in two rounds, five months apart. Diet was assessed using a 120-question semi-quantitative food frequency questionnaire (FFQ). The ARFS diet quality index was derived using a subset of 70 items from the full FFQ. Reproducibility of the ARFS between round one and round two was confirmed by the overall intraclass correlation coefficient of 0.87 (95% CI 0.83, 0.90), which compared favourably to that for the FFQ at 0.85 (95% CI 0.80, 0.89). ARFS was correlated with FFQ nutrient intakes, particularly fiber, vitamin A, beta-carotene and vitamin C (0.53, 95% CI 0.37–0.67), and with mineral intakes, particularly calcium, magnesium and potassium (0.32, 95% CI 0.23–0.40). ARFS is a suitable brief tool to evaluate diet quality in adults and reliably estimates a range of nutrient intakes.
Potential clinical and economic effects of homocyst(e)ine lowering.

BACKGROUND Elevated total homocyst(e)ine levels (>/=11 micromol/L) have been identified as a potential risk factor for coronary heart disease. However, the benefits expected from lowering homocyst(e)ine levels with folic acid and vitamin B(12) supplementation have yet to be demonstrated in clinical trials. SUBJECTS AND METHODS We constructed a decision analytic model to estimate the clinical benefits and economic costs of 2 homocyst(e)ine-lowering strategies: (1) "treat all"-no screening, daily supplementation with folic acid (400 microg) and vitamin B(12) (cyanocobalamin; 500 microg) for all; (2) "screen and treat"-screening, followed by daily supplementation with folic acid and vitamin B(12) for individuals with elevated homocyst(e)ine levels. Simulated cohorts of 40-year-old men and 50-year-old women in the general population were evaluated. In the base-case analysis, we assumed that lowering elevated levels would reduce excess coronary heart disease risk by 40%; however, this assumption and others were evaluated across a broad range of potential values using sensitivity analysis. Primary outcomes were discounted costs per life-year saved. RESULTS Although the treat-all strategy was slightly more effective overall, the screen and treat strategy resulted in a much lower cost per life-year saved ($13,600 in men and $27,500 in women) when compared with no intervention. Incremental cost-effectiveness ratios for the treat-all strategy compared with the screen and treat strategy were more than $500,000 per life-year saved in both cohorts. Sensitivity analysis showed that cost-effectiveness ratios for the screen and treat strategy remained less than $50,000 per life-year saved under several unfavorable scenarios, such as when effective homocyst(e)ine lowering was assumed to reduce the relative risk of coronary heart disease-related death by only 11% in men or 23% in women. CONCLUSIONS Homocyst(e)ine lowering with folic acid and vitamin B(12) supplementation could result in substantial clinical benefits at reasonable costs. If homocyst-(e)ine lowering is considered, a screen and treat strategy is likely to be more cost-effective than universal supplementation. Arch Intern Med. 2000;160:3406-3412.
Collective Content Selection for Concept-to-Text Generation

A content selection component determines which information should be conveyed in the output of a natural language generation system. We present an efficient method for automatically learning content selection rules from a corpus and its related database. Our modeling framework treats content selection as a collective classification problem, thus allowing us to capture contextual dependencies between input items. Experiments in a sports domain demonstrate that this approach achieves a substantial improvement over context-agnostic methods.
A study of TH01 and IGF2-INS-TH haplotypes in relation to smoking initiation in three independent surveys

Objectives Recent studies suggest an association between a microsatellite locus (TH01) located in intron 1 of the tyrosine hydroxylase gene (TH) and nicotine dependence. We aimed here to study whether both TH01 and haplotypes of the wider IGF2-INS-TH region influence initiation of regular smoking in current smokers. Methods A total of 3637 individuals from three independent studies (two of adults and one of adolescents) were analysed in relation to the age of first regular smoking (AFRS). Haplotypes and genotypes were obtained for the polymorphisms TH01, IGF2 ApaI, INS HphI and DRD4 VNTR (48 bp)n. Association between IGF2-INS-TH haplotypes and AFRS was tested by a regression model. A genotype-based genetic model assuming additivity was followed in order to estimate the effect of individual loci. Results Overall, no significant associations were found after correcting for multiple tests. However, an IGF2-INS-TH haplotype (*5) was found to be nominally associated with AFRS at younger ages in adult smokers. Analyses of individual loci points to TH01 as a possible candidate influencing initiation of regular smoking. An AFRS-lowering trend nominally associated with allele 9 in a dosage-dependent manner was identified in both adult cohorts. TH01 did not show association or trend with age of initiation (first puff) either in adolescents or in the adolescents smoking regularly at age 18. Conclusion This study adds to the genetic evaluation of the associations of TH01 with smoking predisposition. Differences between historical and prospective surveys, different biological pathways and possible functional roles of this microsatellite in smoking initiation are discussed.
Erbium:YAG laser radiation interaction with dental tissue

The ablative mechanism associated with the interaction of erbium:YAG laser radiation with dental tissue has been studied. The rates of ablation in dentine and enamel of extracted human teeth were determined and compared to a theoretical model. Ablative threshold energy densities were 10 +/- 2 and 25 +/- 8 J cm-2 and effective absorption coefficients were 380 +/- 30 and 240 +/- 40 cm-1, for dentine and enamel respectively. Using an optical probe beam, the dynamics of the ejected plume has been investigated in dentine. The mean velocity of the plume was 350 +/- 60 m s-1. Histological sections of ablations were also produced, and the extent of secondary thermal damage assessed. The implications of these results for laser ablation of dental tissue are discussed.
LSU Digital Commons LSU Digital Commons AS ABOVE, so BELOW: EXPLOITING MASS SCALING in BLACK AS ABOVE, so BELOW: EXPLOITING MASS SCALING in BLACK HOLE ACCRETION to BREAK DEGENERACIES in SPECTRAL HOLE ACCRETION to BREAK DEGENERACIES in SPECTRAL INTERPRETATION INTERPRETATION

Over the past decade, evidence has mounted that several aspects of black hole ( BH ) accretion physics proceed in a mass-invariant way. One of the best examples of this scaling is the empirical “ fundamental plane of BH accretion ” relation linking mass, radio, and X-ray luminosity over eight orders of magnitude in BH mass. The currently favored theoretical interpretation of this relation is that the physics governing power output in weakly accreting BHs depends more on relative accretion rate than on mass. In order to test this theory, we explore whether a mass-invariant approach can simultaneously explain the broadband spectral energy distributions from two BHs at opposite ends of the mass scale but that are at similar Eddington accretion fractions. We ﬁ nd that the same model, with the same value of several ﬁ tted physical parameters expressed in mass-scaling units to enforce self-similarity, can provide a good description of two data sets from V404 Cyg and M81 * , a stellar and supermassive BH, respectively. Furthermore, only one of several potential emission scenarios for the X-ray band is successful, suggesting it is the dominant process driving the fundamental plane relation at this accretion rate. This approach thus holds promise for breaking current degeneracies in the interpretation of BH high-energy spectra and for constructing better prescriptions of BH accretion for use in various local and cosmological feedback applications.
20-fs 1.6-mJ Pulses from a cw-Diode-Pumped Single-Stage 1-kHz Yb Amplifier

200-fs 2.5-mJ pulses from a fiber-oscillator-seeded DPSS Yb:CaF2 MOPA are spectrally broadened in Ar and recompressed to 20 fs using a pair of LAK14 prisms. Multi-millijoule 12-fs pulses are feasible upon higher-order spectral phase correction.
A Machinability Study of Granite Using Abrasive Waterjet Cutting Technology

Abrasive waterjet (AWJ) machining is one of the non-traditional machining processes which have been used extensively in various industries. It offers some advantages like narrow kerf width, reduced waste material and flexibility to machining process in different shapes. In this study, abrasive waterjet machining of the granite was experimentally investigated for various process parameters in terms of the cut depth and kerf width. The design philosophy of Taguchi was followed to conduct experiments. Analysis of variance was used to evaluate data obtained statistically. Major significant process factors affecting the cut depth and kerf width were determined. Additionally, effects of the process parameters on the cut depth and kerf width were presented by mean responses in detail. As a result of the study, it was determined that the highly effective parameters on the cut depth were the traverse speed, the abrasive flow rate and the abrasive size, although all the process parameters were found to be highly effective on the kerf width of the granite.
Atmospheric correction of visible to middle-infrared EOS-MODIS data over land surfaces: Background, operational algorithm and validation

The NASA moderate resolution imaging spectroradiometer (MODIS) instrument will provide a global and improved source of information for the study of land surfaces with a spatial resolution of up to 250 m. Prior to the derivation of various biophysical parameters based on surface reflectances, the top of the atmosphere signals need to be radiometrically calibrated and corrected for atmospheric effects. The present paper describes in detail the state of the art techniques that will be used for atmospheric correction of MODIS bands 1 through 7, centered at 648, 858, 470, 555, 1240, 1640, and 2130 nm, respectively. Previous operational correction schemes have assumed a standard atmosphere with zero or constant aerosol loading and a uniform, Lambertian surface. The MODIS operational atmospheric correction algorithm, reported here, uses aerosol and water vapor information derived from the MODIS data, corrects for adjacency effects and takes into account the directional properties of the observed surface. This paper also describes the operational implementation of these techniques and its optimization. The techniques are applied to remote sensing data from the Landsat Thematic Mapper (TM), the NOAA advanced very high resolution radiometer (AVHRR), and the MODIS airborne simulator (MAS) and validated against ground-based measurements from the Aerosol Robotic Network (AERONET).
Persistent pain and sensory disturbances after treatment for breast cancer: six year nationwide follow-up study

Objective To examine the development of persistent pain after treatment for breast cancer and to examine risk factors associated with continuing pain. Design Repeated cross sectional study in a previously examined nationwide cohort. All eligible women who underwent surgery for primary breast cancer in Denmark in 2005 and 2006 and were examined in 2008 were surveyed again with the same questionnaire. Setting Surgical centres in Denmark. Main outcome measures Prevalence, location, and severity of persistent pain after treatment for breast cancer in well defined treatment groups and changes in pain reporting and sensory disturbances from 2008 to 2012. Participants In 2012, 2828 women were eligible in our database, and 108 were excluded. Exclusion criteria were death; new, recurrent, or other cancer; reconstructive breast surgery; and emigration. Results 2411 (89%) women returned the questionnaire. Prevalence of persistent pain after treatment for breast cancer ranged from 22% to 53% depending on treatment. In 2012, 903 (37%) women reported such pain, a fall from 45% in 2008. Of these, 378 (16%) reported pain of ≥4 on a numerical rating scale (scale 0-10), a fall from 19%. Among women reporting pain in 2008, 36% no longer reported it in 2012. In contrast, 15% of the women who did not report pain in 2008 reported it in 2012. Risk factors for having pain were axillary lymph node dissection rather than sentinel lymph node biopsy (odds ratio 2.04, 95% confidence interval 1.60 to 2.61; P<0.001) and age ≤49 (1.78, 1.25 to 2.54; P<0.001). No particular method of treatment or age was associated with an increase in pain from 2008 to 2012. Conclusions Persistent pain after treatment for breast cancer remains an important problem five to seven years later. The problem is not static as it can either progress or regress with time. Trial registration Clinicaltrials.gov NCT No 01543711.
A robust metallo‐oxidase from the hyperthermophilic bacterium Aquifex aeolicus

The gene, Aquifex aeolicus AAC07157.1, encoding a multicopper oxidase (McoA) and localized in the genome as part of a putative copper‐resistance determinant, has been cloned, over‐expressed in Escherichia coli and the recombinant enzyme purified to homogeneity. The purified enzyme shows spectroscopic and biochemical characteristics typical of the well‐characterized multicopper oxidase family of enzymes. McoA presents higher specificity (kcat/Km) for cuprous and ferrous ions than for aromatic substrates and is therefore designated as a metallo‐oxidase. Addition of copper is required for maximal catalytic efficiency. A comparative model structure of McoA has been constructed and a striking structural feature is the presence of a methionine‐rich region (residues 321–363), reminiscent of those found in copper homeostasis proteins. The kinetic properties of a mutant enzyme, McoAΔP321‐V363, deleted in the methionine‐rich region, provide evidence for the key role of this region in the modulation of the catalytic mechanism. McoA has an optimal temperature of 75 °C and presents remarkable heat stability at 80 and 90 °C, with activity lasting for up to 9 and 5 h, respectively. McoA probably contributes to copper and iron homeostasis in A. aeolicus.
Ideal Cardiovascular Health in Childhood and Cardiometabolic Outcomes in Adulthood: The Cardiovascular Risk in Young Finns Study

Background— The American Heart Association (AHA) defined a new concept, cardiovascular health, and determined metrics needed to monitor it over time as part of its 2020 Impact Goal definition. Ideal cardiovascular health is defined by the presence of both ideal health behaviors and ideal health factors. The applicability of this concept to a cohort of children and its relationship with cardiometabolic outcomes in adulthood has not been reported. Methods and Results— The sample comprised 856 participants aged 12 to 18 years (mean age 15.0 years) from the Cardiovascular Risk in Young Finns Study cohort. Participants were followed up for 21 years since baseline (1986) and had data available concerning health factors and behaviors in childhood and cardiometabolic outcomes in adulthood (2007). The number of ideal cardiovascular health metrics present in childhood was associated with reduced risk of hypertension (odds ratio [95% confidence interval] 0.66 [0.52–0.85], P<0.001), metabolic syndrome (0.66 [0.52–0.77], P<0.001), high low-density lipoprotein cholesterol (0.66 [0.52–0.85], P=0.001), and high-risk carotid artery intima-media thickness (0.75 [0.60–0.94], P=0.01) in adulthood. All analyses were age and sex adjusted, and the results were not altered after additional adjustment with socioeconomic status. Conclusions— The number of ideal cardiovascular health metrics present in childhood predicts subsequent cardiometabolic health in adulthood. Our findings suggest that pursuit of ideal cardiovascular health in childhood is important to prevent cardiometabolic outcomes in adulthood.
Anti‐inflammatory and Antinociceptive Effects in Rodents of the Essential Oil of Croton cajucara Benth

The plant Croton cajucara Benth. (Euphorbiaceae) is widely used in Amazonian folk medicine for the treatment of a wide range of illnesses. In this investigation the analgesic and anti‐inflammatory properties of the essential oil from the bark of C. cajucara Benth. , administered orally, were determined in several standard rodent models of pain and inflammation.
Immunomagnetic isolation and in vitro expansion of human uveal melanoma cell lines

Purpose Uveal melanoma (UM) is the most common intra-ocular tumor in adults. Despite advances in diagnosis and treatment, the survival rate of UM has not increased in the last several decades. Approximately 50% of patients will die as a consequence of metastatic disease with the majority of metastases localized to the liver. Due to the lack of lymphatics in the eye, hematogenous dissemination is the predominant means by which UM cells escape the primary site. Our laboratory has recently demonstrated the presence of circulating malignant cells (CMCs) in the blood using both animal models and clinical trails involving UM patients. Current data suggests that all UM patients will be positive for CMCs after diagnosis. Furthermore, some of the phenotypic changes that are necessary for metastatic growth may occur while the cells are circulating in the blood. In this study, we evaluated the efficiency of a panel of antibodies to immunomagnetically isolate CMCs for the purpose of in vitro expansion and genetic, immunological, and phenotypic characterization. Methods In this study, five human uveal melanoma cell lines (92.1, MKT-BR, OCM-1, SP6.5, and UW-1) were immunostained with a panel of antibodies against known melanoma cell surface markers. Staining with monoclonal antibodies PAL M2, NKI C3, NKI/Beteb, and 9.2. 27 permitted the generation of a cell surface expression profile in these cell lines. The five human UM cell lines and 92.1 transfected with GFP were subsequently spiked into human blood at concentrations ranging from 1x106 cells/ml to 10 cells/ml. Cells were immuno-magnetically isolated at concentrations as low as 10 cells/ml. Results Immunomagnetic isolation of all five human UM cell lines tested at concentrations down to 10 cells/ml human blood was achieved only when antibodies were used in combination. Individually, the antibodies did not permit isolation of cells at physiologically relevant concentrations. Conclusions The immunomagnetic isolation method presented in this study can be used to isolate CMCs at physiologically relevant concentrations and at sensitivities comparable to those seen in polymerase chain reactions (PCR). In addition, our data suggests that our method is more efficient and reliable for the isolation of CMCs in UM than the methods currently used.