Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Arabidopsis to Study Shoot Branching in Biomass Willow1[C][W][OA]

Knowledge and assays from Arabidopsis axillary meristem biology can be successfully applied to Salix spp. and can increase the understanding of a fundamental aspect of SRC biomass production, allowing more targeted breeding. The success of the short-rotation coppice system in biomass willow (Salix spp.) relies on the activity of the shoot-producing meristems found on the coppice stool. However, the regulation of the activity of these meristems is poorly understood. In contrast, our knowledge of the mechanisms behind axillary meristem regulation in Arabidopsis (Arabidopsis thaliana) has grown rapidly in the past few years through the exploitation of integrated physiological, genetic, and molecular assays. Here, we demonstrate that these assays can be directly transferred to study the control of bud activation in biomass willow and to assess similarities with the known hormone regulatory system in Arabidopsis. Bud hormone response was found to be qualitatively remarkably similar in Salix spp. and Arabidopsis. These similarities led us to test whether Arabidopsis hormone mutants could be used to assess allelic variation in the cognate Salix spp. hormone genes. Allelic differences in Salix spp. strigolactone genes were observed using this approach. These results demonstrate that both knowledge and assays from Arabidopsis axillary meristem biology can be successfully applied to Salix spp. and can increase our understanding of a fundamental aspect of short-rotation coppice biomass production, allowing more targeted breeding.
Beyond The Ivory Tower The Frontiers Of Public And Private Science

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Exposure measurement in the association between periodontal disease and prematurity/low birth weight.

AIM To compare the use of different definitions for exposure measurement in cases of association between periodontal disease (PD) and prematurity and/or low birth weight (PLBW). MATERIAL AND METHODS A database from a previous case-control study was used to compare four different definitions for periodontitis: at least one site with probing depth > or =4 mm (1); at least one site with clinical attachment loss (CAL)> or =3 mm (2); at least four teeth with one or more sites presenting probing depth > or =4 mm, with CAL> or =3 mm at the same site (3); and at least four teeth with one or more sites with probing depth > or =4 mm, with CAL> or =3 mm at the same site and presence of bleeding on probing (4). The PD frequency, diagnostic values and adjusted association measurements were calculated. RESULTS PD frequency ranged from 33.1% to 94.7%. Odds ratio(adjusted) varied slightly according to the exposure measurement used. CONCLUSIONS The association between PD and PLBW weight was consistent, except for exposure measurement 1, i.e. using at least one site with CAL> or =3 mm for periodontitis diagnosis, while the magnitude of this varied according to the definition established.
Cluster detection diagnostics for small area health data: with reference to evaluation of local likelihood models

The focus of this paper is the development of a range of cluster detection diagnostics that can be used to assess the degree to which a clustering method recovers the true clustering behaviour of small area data. The diagnostics proposed range from individual region specific diagnostics to neighbourhood diagnostics, and assume either individual region risk as focus, or concern areas of maps defined to be clustered and the recovery ability of methods. A simulation‐based comparison is made between a small set of count data models: local likelihood, BYM and Lawson and Clark. It is found that local likelihood has good performance across a range of criteria when a CAR prior is assumed for the lasso parameter. Copyright © 2006 John Wiley & Sons, Ltd.
Overload‐induced skeletal muscle extracellular matrix remodelling and myofibre growth in mice lacking IL‐6

Aim: Overloading healthy skeletal muscle produces myofibre hypertrophy and extracellular matrix remodelling, and these processes are thought to be interdependent for producing muscle growth. Inflammatory cytokine interleukin‐6 (IL‐6) gene expression is induced in overloaded skeletal muscle, and the loss of this IL‐6 induction can attenuate the hypertrophic response to overload (OV). Although the OV induction of IL‐6 in skeletal muscle may be an important regulator of inflammatory processes and satellite cell proliferation, less is known about its role in the regulation of extracellular matrix remodelling. The purpose of the current study was to examine if OV‐induced extracellular matrix remodelling, muscle growth, and associated gene expression were altered in mice that lack IL‐6, when compared with wild‐type mice.
Validation of the Neighborhood Environment Walkability Scale (NEWS) items using geographic information systems.

BACKGROUND Concurrent validity of Neighborhood Environment Walkability Scale (NEWS) items was evaluated with objective measures of the built environment using geographic information systems (GIS). METHODS A sample of 878 parents of children 10 to 16 years old (mean age 43.5 years, SD = 6.8, 34.8% non-White, 63.8% overweight) completed NEWS and the International Physical Activity Questionnaire. GIS was used to develop 1-mile street network buffers around participants' residences. GIS measures of the built environment within participants' buffers included percent of commercial and institutional land uses; number of schools and colleges, recreational facilities, parks, transit stops, and trees; land topography; and traffic congestion. RESULTS Except for trees and traffic, concordance between the NEWS and GIS measures were significant, with weak to moderate effect sizes (r = -0.09 to -0.36, all P < or = 01). After participants were stratified by physical activity level, stronger concordance was observed among active participants for some measures. A sensitivity analysis of self-reported distance to 15 neighborhood destinations found a 20-minute (compared with 10- or 30-minute) walking threshold generally had the strongest correlations with GIS measures. CONCLUSIONS These findings provide evidence of the concurrent validity of self-reported built environment items with objective measures. Physically active adults may be more knowledgeable about their neighborhood characteristics.
Essays on transportation infrastructure, urbanisation and economic growth: evidence from China.

China’s spectacular economic growth during the reform era from 1978 to 2008 has captivated much attention both in academia and in the policy arena. This thesis looks at this period of Chinese economic reforms and the consequences for China’s economic growth, urbanisation, and income inequality, in which transportation infrastructure plays a pivotal role. Among many contributors to the economic growth in China, as measured by GDP per capita growth, recent studies shed light on the importance of transportation infrastructure. Therefore, a comprehensive understanding of the function of transportation infrastructure in the context of China and an accurate quantification of its contribution are desired. Accompanying the GDP per capita growth, China also experienced a rapid process of urbanisation during 1978–2008. However, whether the GDP per capita growth causes urbanisation is not yet clear. After the accession to the WTO in 2001, China became an important player in world trade. For example, China’s exports increased from USD 0.27 trillion in 2001 to USD 1.43 trillion in 2008, which has resulted in massive income growth nation-wide. However, the income has been unequally distributed among wage earners. Since urban wage earners are more likely to work in exporting sectors, it is important to analyse the impact of accessibility to international markets, as measured by length of current transport routes from origin city to its nearest major seaport, on income inequality in urban China. This thesis explores three major areas and improves upon existing methodology. First, it delineates the effect of changes in the density of transportation infrastructure, as measured by length of highways and railroads per square kilometre, on short-run and long-run GDP per capita
Effect of exercise on total and intra-abdominal body fat in postmenopausal women: a randomized controlled trial.

CONTEXT The increasing prevalence of obesity is a major public health concern. Physical activity may promote weight and body fat loss. OBJECTIVE To examine the effects of exercise on total and intra-abdominal body fat overall and by level of exercise. DESIGN Randomized controlled trial conducted from 1997 to 2001. SETTING AND PARTICIPANTS A total of 173 sedentary, overweight (body mass index > or =24.0 and >33% body fat), postmenopausal women aged 50 to 75 years who were living in the Seattle, Wash, area. INTERVENTION Participants were randomly assigned to an intervention consisting of exercise facility and home-based moderate-intensity exercise (n = 87) or a stretching control group (n = 86). MAIN OUTCOME MEASURE Changes in body weight and waist and hip circumferences at 3 and 12 months; total body, intra-abdominal, and subcutaneous abdominal fat at 12 months. RESULTS Twelve-month data were available for 168 women. Women in the exercise group participated in moderate-intensity sports/recreational activity for a mean (SD) of 3.5 (1.2) d/wk for 176 (91) min/wk. Walking was the most frequently reported activity. Exercisers showed statistically significant differences from controls in baseline to 12-month changes in body weight (-1.4 kg; 95% confidence interval [CI], -2.5 to -0.3 kg), total body fat (-1.0%; 95% CI, -1.6% to -0.4%), intra-abdominal fat (-8.6 g/cm2; 95% CI, -17.8 to 0.9 g/cm2), and subcutaneous abdominal fat (-28.8 g/cm2); 95% CI, -47.5 to -10.0 g/cm2). A significant dose response for greater body fat loss was observed with increasing duration of exercise. CONCLUSIONS Regular exercise such as brisk walking results in reduced body weight and body fat among overweight and obese postmenopausal women.
Are typical starting doses of the selective serotonin reuptake inhibitors sub-optimal? A meta-analysis of randomized, double-blind, placebo-controlled, dose-finding studies in major depressive disorder

The purpose of this meta-analysis is to examine the relationship between selective serotonin reuptake inhibitor (SSRI) starting dose and treatment outcome in major depressive disorder (MDD). Medline/Pubmed, EMBASE, the Cochrane database, as well as a number of online clinical trial registries were searched for double-blind, placebo-controlled, fixed-dose trials comparing different starting doses of SSRIs for MDD. Data from nine trials (n=2340) were combined using a random-effects model. Patients randomized to receive the usual starting dose (10 mg escitalopram; 20 mg fluoxetine, paroxetine, citalopram; 50 mg sertraline and fluvoxamine) were less likely to respond than patients who received higher starting doses (RR=0.9; P=0.04; response rate 50.8 vs. 54.8%). The rate of discontinuation due to adverse events was lower among the usual starting dose group (9.8%) compared to the higher starting dose group (16.5%). Initiating treatment with SSRIs at doses higher than those typically used in clinical trials/settings is associated with higher response rates but also higher rates of discontinuation due to intolerance. Developing treatment strategies allowing clinicians to deliver higher initial SSRI doses while enhancing the tolerability of treatment may represent an alternative approach to improving the efficacy of treatment of MDD.
Comparative evaluation of laboratory-scale silages using standard glass jar silages or vacuum-packed model silages.

BACKGROUND The objective of this study was to compare the fermentation variables of laboratory-scale silages made in glass preserving jars (GLASS) and vacuum-packed plastic bags (Rostock model silages, ROMOS). Silages were prepared from perennial ryegrass (fresh and wilted, 151 g kg(-1) and 286 g kg(-1) dry matter (DM), respectively) and remoistened coarsely ground rye grain (650 g kg(-1) DM) either with or without the addition of a lactic acid bacteria inoculant (3×10(5) colony forming units (cfu) g(-1) , LAB). Quintuplicate silos were opened on days 2, 4, 8, 49 and 90. RESULTS Silage pH (P=0.073), acetic acid content (P=0.608) and ethanol content (P=0.223) were not influenced by the ensiling method. The contents of DM (P<0.001) and propionic acid (P=0.008) were affected by the ensiling method, but mean differences were only marginal. In ROMOS the concentration of lactic acid was increased (P=0.007) whereas butyric acid was produced less (P=0.001) when compared to GLASS. This suggested slightly better ensiling conditions for ROMOS. CONCLUSIONS ROMOS represents a reasonable alternative to glass jar silages and opens the possibility for further investigations, e.g. studying the impact of packing density as well as the quantitative and qualitative analysis of fermentation gases.
Conventional High-resolution CT Versus Contiguous Multidetector CT in the Detection of Bronchiolitis Obliterans Syndrome in Lung Transplant Recipients

Objective To compare the detection rate of pulmonary abnormalities between conventional high-resolution computed tomography (HRCT) and high-resolution multidetector computed tomography (MDCT) in lung transplant recipients and to correlate a composite computed tomography (CT) score with bronchiolitis obliterans syndrome (BOS) stage. Methods Twenty-four lung transplant recipients (12 single/12 double lung transplants, 13 males/11 females, mean age: 53 y, range: 28 to 71) underwent contiguous 16-slice high-resolution MDCT of the lungs at maximal inspiration and maximal expiration. Eight reformatted image sets were reconstructed: (i) contiguous 1-mm slice MDCT image set in the transverse, sagittal, and coronal image planes at maximal inspiration; (ii) contiguous 1-mm slice MDCT image set in the transverse, sagittal, and coronal image planes at maximal expiration; (iii) conventional HRCT image set of 1-mm slices every 10 mm at maximal inspiration; and (iv) conventional expiratory HRCT of 1-mm slices at 3 selected levels at maximal expiration. Individual pulmonary abnormalities were added to give a composite CT score. Individual abnormalities and the composite CT score were correlated with BOS stage, as based on functional testing of airflow obstruction, for each of the 8 image sets. Results Transverse, sagittal, and coronal MDCT correlated significantly with BOS stage (R=0.46, 0.49, 0.52, respectively), whereas conventional HRCT did not. Multiple regression analysis demonstrated that transverse MDCT was the only independent predictor of BOS stage (R2=0.33, P<0.01). Interobserver agreement for composite CT scores for HRCT, transverse, sagittal, and coronal MDCT were R=0.89, 0.87, 0.83 and 0.80, respectively. Interobserver agreement for individual abnormalities was better with MDCT than with conventional HRCT. Conclusions In lung transplant recipients, high-resolution MDCT detects significantly more pulmonary abnormalities and has better interobserver agreement than conventional HRCT and is an independent predictor of BOS stage.
Access and outcomes of elderly patients enrolled in managed care.

OBJECTIVE To determine differences in access to care and medical outcomes for Medicare patients with an acute or a chronic symptom who were enrolled in health maintenance organizations (HMOs) compared with similar fee-for-service (FFS) nonenrollees. DESIGN A 1990 household telephone survey of Medicare beneficiaries who reported joint pain or chest pain during the previous 12 months. SAMPLE Stratified random sample of HMO enrollees (n = 6476) and comparable sample of FFS Medicare beneficiaries (n = 6381). ACCESS AND OUTCOME MEASURES: Care-seeking behavior, physician visits, diagnostic procedures performed, therapeutic interventions prescribed, follow-up recommended by a physician, and symptom response to treatment. RESULTS After controlling for demographic factors, health and functional status, and health behavior characteristics, HMO enrollees with joint pain (n = 2243) were more likely than nonenrollees (n = 2009) to have a physician visit (odds ratio [OR], 1.19; 95% confidence interval [CI], 1.03 to 1.38) and medication prescribed (OR, 1.35; 95% CI, 1.14 to 1.60). Patients with chest pain who were enrolled in HMOs (n = 556) were less likely than nonenrollees (n = 524) to have a physician visit (OR, 0.50; 95% CI, 0.30 to 0.82). For both joint and chest pain, HMO enrollees were less likely to see a specialist for care, have follow-up recommended, or have their progress monitored. There were no differences in complete elimination of symptoms, but HMO enrollees with continued joint pain reported less symptomatic improvement than nonenrollees (OR, 0.72; 95% CI, 0.59 to 0.86). CONCLUSIONS Reduced utilization of services for patients with specific ambulatory conditions was observed in HMOs with Medicare risk contracts, with less symptomatic improvement in one of the four outcomes studied.
Is the Renminbi a Safe Haven?

We investigate the relationship between market uncertainty and the relative value of the Renminbi in the offshore market against currencies that the safe haven literature typically considers as the traditional safe haven currency candidates. Our sample spans the February 2011 to May 2017 period. Band spectral regression models enable us to capture that the relationship between market uncertainty and the relative value of the Renminbi is frequency dependent. While we find evidence of some degree of safe haven currency behavior of the Renminbi during the early part of our sample, our findings do not support the suggestion that the Renminbi is currently a safe haven currency or that the Renminbi is progressing towards safe haven currency status.
Immunization with Th-CTL Fusion Peptide and Cytosine-Phosphate-Guanine DNA in Transgenic HLA-A2 Mice Induces Recognition of HIV-Infected T Cells and Clears Vaccinia Virus Challenge 1

We evaluated immunogenicity of a novel Th-CTL fusion peptide composed of the pan DR Th epitope and a CTL epitope derived from HIV-pol in two transgenic HLA-A*0201/Kb mouse models. The immunogenicity of peptides of this structure is highly dependent on coadministered cytosine-phosphate-guanine DNA. Initial evaluations of peptide-specific immunity are based on results of chromium release assay, intracellular cytokine, and tetramer staining. Significant cytotoxic T cell responses are found upon a single immunization with as low as 0.1 nmol both peptide and cytosine-phosphate-guanine DNA. Splenocytes from immunized mice recognize naturally processed HIV-pol expressed from vaccinia virus (pol-VV). Translation of immunologic criteria into more relevant assays was pursued using systemic challenge of immunized mice with pol-VV. Only mice receiving both peptide and DNA together successfully cleared upward of 6 logs of virus from ovaries, compared with controls. Challenge with pol-VV by intranasal route of intranasal immunized mice showed a significant reduction in the levels of VV in lung compared with naive mice. A convincing demonstration of the relevance of these vaccines is the robust lysis of HIV-infected Jurkat T cells (JA2/R7/Hyg) by immune splenocytes from peptide- and DNA-immunized mice. This surprisingly effective immunization merits consideration for clinical evaluation, because it succeeded in causing immune recognition and lysis of cells infected with its target virus and reduction in titer of highly pathogenic VV.
Essays on asset pricing and optimal policy under limited asset market participation

Models based on the representative agent assumption cannot rationalize observed equity premia. In response to this, exchange economy models have introduced agents heterogeneity, typically in the form of bond and equity holders. We reconsider the issue introducing Limited Asset Market Participation in an otherwise standard medium scale DSGE model. Our model ts nancial and macroeconomic data well. We obtain that the correlation between asset holders consumption and nancial returns strongly increases in the share of agents excluded from nancial markets participation, The predicted unconditional equity premium is therefore large. Further, the strong correlation between dividends and Ricardian households consumption unambiguously increases precautionary savings and reduces the riskless rate. Jel codes: E32 G12
Tenofovir Diphosphate and Emtricitabine Triphosphate Concentrations in Blood Cells Compared With Isolated Peripheral Blood Mononuclear Cells: A New Measure of Antiretroviral Adherence?

Background:The active metabolites of tenofovir (TFV) and emtricitabine (FTC) in peripheral blood mononuclear cells (PBMCs) have been used as markers of long-term antiretroviral (ARV) adherence. However, the process of isolating PBMCs is expensive, complex, and not feasible in many settings. We compared concentrations of TFV-diphosphate (TFV-DP) and FTC-triphosphate (FTC-TP) in the upper layer packed cells (ULPCs) obtained after whole blood centrifugation to isolated PBMCs as a possible alternative marker of adherence. Methods:Ten HIV+ adults with HIV RNA <50 copies/mL on a TDF/FTC-containing regimen provided 5 paired PBMC and ULPC samples over 6 hours. TFV-DP and FTC-TP concentrations were analyzed by liquid chromatography/mass spectrometry. Partial areas under the curve were calculated using noncompartmental methods and Spearman Rank Correlations (rho) between PBMC and ULPC were determined. Results:The median (25th–75th percentile) concentration of TFV-DP in PBMCs was 143 (103–248) fmol/106 cells and in ULPC was 227 (160–394) fmol/106 cells (rho = 0.65; P < 0.0001). The concentration of FTC-TP in PBMCs was 6660 (5650–10,000) fmol/106 cells and in ULPC was 19.0 (12.0–27.8) fmol/106 cells (rho = 0.55; P < 0.0001). Compared to PBMCs, ULPC TFV-DP was 64% higher and FTC-TP was 99.7% lower. ULPC concentrations of TFV-DP and FTC-TP in one additional subject receiving a single dose of TDF/FTC were only 0.05% and 25%, of the other 10 subjects, respectively. Conclusions:ULPC concentrations significantly correlated with PBMC concentrations. Preliminary single-dose data suggest some discrimination between intermittent versus consistent dosing. ULPC concentrations of TFV-DP and FTC-TP should be further investigated as a simply collected surrogate measure of ARV adherence.