Circulating cell-free DNA undergoes significant decline in yield after prolonged storage time in both plasma and purified form.

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Circulating DNA (cirDNA) is generally purified from plasma that has been biobanked for variable lengths of time. In long-term experiments or clinical trials, the plasma can be stored frozen for up to several years. Therefore, it is crucial to determine the stability of cirDNA to ensure confidence in sample quality upon analysis. Our main objective was to determine the effect of storage for up to 2years on cirDNA yield and fragmentation. We stored frozen EDTA plasma and purified cirDNA from 10 healthy female donors, then quantified cirDNA yield at baseline, and at regular intervals for up to 2years, by qPCR and Qubit. We also compared cirDNA levels in non-haemolysed and haemolysed blood samples after 16months of storage and tested the effect of varying DNA extraction protocol parameters. Storage up to two years caused an annual cirDNA yield decline of 25.5% when stored as plasma and 23% when stored as purified DNA, with short fragments lost more rapidly than long fragments. Additionally, cirDNA yield was impacted by plasma input and cirDNA elution volumes, but not by haemolysis. The design of long-term cirDNA-based studies and clinical trials should factor in the deterioration of cirDNA during storage.

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  • Research Article
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  • 10.3390/d13070317
Effects of Continuous Cropping of Codonopsis tangshen on Rhizospheric Soil Bacterial Community as Determined by Pyrosequencing
  • Jul 12, 2021
  • Diversity
  • Meide Zhang + 6 more

Codonopsis tangshen, a perennial herbaceous, has been shown to be affected by continuous cropping, with significant decline in both yield and quality. In this study, we studied the effect of continuous cropping on the abundance and composition of rhizospheric soil bacterial community. Results showed that continuous cropping causes a significant decline in both yield and quality. The nutrient content in continuous cropping soil was higher than that of soil in main cropping. Pyrosequencing analyses revealed Proteobacteria and Acidobacteria as the main phyla in two types of soils. Relative abundance of Acidobacteria, Nitrospirae, TM7, and AD3 phyla was observed to be high in continuous cropping soils, whereas Chloroflexi, Bacteroidetes, and Planctomycetes phyla were richer in main cropping soils. At the genus level, high relative abundance of Pseudomonas (γ-Proteobacteria), Rhodanobacter, Candidatus Koribacter, and Candidatus were observed in continuous cropping soil. Different patterns of bacterial community structure were observed between different soils. Redundancy analysis indicated that organic matter content and available nitrogen content exhibited the strongest effect on bacterial community structure in the continuous cropping soil. Taken together, continuous cropping led to a significant decline in yield and quality, decrease in rhizospheric soil bacterial abundance, and alteration of rhizospheric soil microbial community structure, thereby resulting in poor growth of C. tangshen in the continuous cropping system.

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  • 10.1111/j.2517-6161.1989.tb01434.x
Discussion of the Paper by Jennison and Turnbull
  • Jul 1, 1989
  • Journal of the Royal Statistical Society Series B: Statistical Methodology

Discussion of the Paper by Jennison and Turnbull

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  • Cite Count Icon 231
  • 10.1016/s0378-4290(00)00075-7
How widespread are yield declines in long-term rice experiments in Asia?
  • Apr 7, 2000
  • Field Crops Research
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How widespread are yield declines in long-term rice experiments in Asia?

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  • 10.1111/bjd.12583
The interpretation of long-term trials of biologic treatments for psoriasis: trial designs and the choices of statistical analyses affect ability to compare outcomes across trials
  • Dec 1, 2013
  • British Journal of Dermatology
  • R.G Langley + 1 more

Psoriasis is a chronic disease requiring long-term therapy, which makes finding treatments with favourable long-term safety and efficacy profiles crucial. The goal of this review is to provide the background needed to evaluate properly long-term studies of biologic treatments for psoriasis. Firstly, important elements of design and analysis strategies are described. Secondly, data from published trials of biologic therapies for psoriasis are reviewed in light of the design and analysis choices implemented in the studies. Published reports of clinical trials of biologic treatments (adalimumab, alefacept, etanercept, infliximab or ustekinumab) that lasted 33 weeks or longer and included efficacy results and statistical analysis were reviewed. Study designs and statistical analyses were evaluated and summarized, emphasizing patient follow-up methods and handling of missing data. Various trial designs and data handling methods are used in long-term studies of biologic psoriasis treatments. Responder analyses in long-term trials can be conducted in responder enrichment, re-treated nonresponder or intent-to-treat trials. Missing data can be handled in four ways, including, from most to least conservative, nonresponder imputation, last-observation-carried-forward, as-observed analysis and anytime analysis. Long-term clinical trials have shown that adalimumab, alefacept, etanercept, infliximab and ustekinumab are efficacious for psoriasis treatment; however, without common standards for these trials, direct comparisons of these agents are difficult. Understanding differences in trial design and data handling is essential to make informed treatment decisions.

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  • 10.1177/153331750602100206
Treating Alzheimer's disease: do clinical trial methods produce unnecessary practitioner dilemmas?
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  • American Journal of Alzheimer's Disease & Other Dementias®
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Recent clinical trials and critical reviews of Alzheimer's disease (AD) research discourage already relatively sparing clinical uses of cholinesterase inhibitors (ChEIs) considering the prevalence of AD. As evidence against use of this class of drugs, detractors cite critical reviews of ChEIs and lack of long-term health benefits found in one long-term clinical trial. This paper describes the use of standard error of measurement to allow investigators to design clinical trials that address these issues. The new clinical trial procedures afford sufficient precision for two purposes. First, practitioners can assess individual patients with precision and certainty in their observations. Second, clinical trial researchers can study how short-term drug effects on individual patients predict long-term benefits from continued treatment. With these more clinically informative clinical trial designs, investigators would be able to avoid uncertainties currently raised by conflicts between short- and long-term AD clinical trials.

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Epigenetic Modulators in Anti-Aging Skincare: Unraveling Molecular Mechanisms and Advancing Patient Applications
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A comprehensive evaluation of metaproterenol, a new bronchodilator.
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Metaproterenol (Alupent), a new bronchodilator, was administered in oral and metered aerosol forms to 134 patients with bronchial asthma in three separate studies: (1) a placebo-controlled trial of single doses of aerosol, (2) a long-term uncontrolled clinical trial of the aerosol, and (3) a long-term uncontrolled clinical trial of the oral tablet. In the first study, statistical analysis of results in 31 patients showed that a single dose of metaproterenol aerosol was significantly superior to placebo aerosol in improving the pulmonary function as measured by forced expiratory volume (P less than 0.01) and maximum mid-expiratory flow rate (P less than 0.05). In the two uncontrolled, long-term clinical trials, 37 patients were treated with metaproterenol aerosol for an average of about four months, and 66 other patients received the drug orally for an average of about three weeks, respectively. The daily dose was one or two doses of aerosol, approximately 0.65 mg. per dose, taken as required several times daily; or 20 to 80 mg. of metaproterenol tablets daily orally. Satisfactory clinical response was seen in 29 (78.4 per cent) of the patients on aerosol and in 45 (68.2 per cent) of the patients on oral therapy. On the aerosol, nine patients (24.3 per cent) experienced mild tachycardia. On oral medication, side effects developed in 16 patients (24.2 per cent). Reactions, mostly nervousness and tachycardia, were mild and usually could be controlled by reducing the dosage. Only two patients (3 per cent) discontinued the drug. Laboratory tests carried out during the aerosol trial and at the end of the oral study revealed no drug-related abnormalities.(ABSTRACT TRUNCATED AT 250 WORDS)

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  • Cite Count Icon 1
  • 10.1111/all.15231
Novel adaptive design for allergen immunotherapy clinical trials.
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  • Research Article
  • Cite Count Icon 83
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Analysis of Yield Trends of the Rice-Wheat System in North-Western India
  • Dec 1, 2000
  • Outlook on Agriculture
  • P.K Aggarwal + 5 more

The north-western region of India is extremely important for food security and has contributed substantially to the country's past agricultural growth. This has been possible largely because the region is endowed with good natural resources such as soils and water, and is relatively well developed in respect of markets and infrastructure. Rice and wheat are now commonly grown in double-cropping rotation and their average productivity varies from 2 to 5 t/ha. This needs to be increased substantially to meet growing demands due to the increasing population, urbanization and income growth. Concerns have been expressed lately that the rice–wheat system is causing environmental degradation in the region, and that there is a stagnation/decline in its productivity threatening food security. In this paper, the authors analyse the historical trends in yields of rice and wheat crops using regional statistics, long-term fertility experiments, other conventional field experiments and crop simulation models. Rice yields showed a very modest decline in many districts in the region, as well as in field experiments. The simulated yields showed a similar decline. Wheat yields of normally sown crops showed an increasing trend in most districts due to a greater application of fertilizers. Long-term experiments conducted elsewhere in the Indo-Gangetic plains also showed a large decline in rice yields and a small or no decline in wheat yields during the same period. The simulation results indicated that the rate of decline was related to the initial yield of crops. A significant annual yield decline was shown only when yield levels were high. It is concluded that the evidence of a yield decline in north-western India is not very strong at present. The yield trends may be partly related to the gradual change in weather conditions during the last two decades in selected research centres located in and around urban areas. The relationship of these trends to changes in nutrient use efficiencies, water use, insects and disease prevalence is discussed. Results indicate that there are only limited management options for increasing yields of rice and wheat crops in north-western India.

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