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An increasing emphasis on understanding the dynamics of microbial communities in various settings has led to the proliferation of longitudinal metagenomic sampling studies. Data from whole metagenomic shotgun sequencing and marker-gene survey studies have characteristics that drive novel statistical methodological development for estimating time intervals of differential abundance. In designing a study and the frequency of collection prior to a study, one may wish to model the ability to detect an effect, e.g., there may be issues with respect to cost, ease of access, etc. Additionally, while every study is unique, it is possible that in certain scenarios one statistical framework may be more appropriate than another. Here, we present a simulation paradigm implemented in the R Bioconductor software package microbiomeDASim available at http//bioconductor.org/packages/microbiomeDASim microbiomeDASim. microbiomeDASim allows investigators to simulate longitudinal differential abundant microbiome features with a variety of known functional forms with flexible parameters to control desired signal-to-noise ratio. We present metrics of success results on one particular method called metaSplines. Copyright © 2020 Williams J et al.Background To obtain accurate measurements of cortisol (C) and testosterone (T) in Aceh cattle, commercial enzyme-linked immunosorbent assay (ELISA) kits need to be carefully validated. Moreover, repeated freeze-thaw cycles during the storage of the samples may affect the stability of the hormones in the serum. Here, the reliability of C and T concentration measurements in the serum of Aceh cattle, was tested using commercial C and T ELISA kits designed to measure human C and T concentrations. Further, the effect of repeated freeze-thaw cycles on the stability of C and T concentrations in the serum was evaluated. Methods Commercial C (Cat. no. EIA-1887) and T (Cat. no. EIA-1559) ELISA kits from DRG Instruments GmbH were validated through an analytical validation test (i.e., parallelism, accuracy, and precision) and a biological validation test (for C effect of transportation on the C excretion; for T the concentrations of T between bulls and cows). To test the effects of freeze-thaw cycles, cattle serum was subjected to the following treatments (i) remained frozen at -20 OC (control group); (ii) exposed to freeze-thaw cycles for two, four, six, and eight times (test groups). Results Parallelism, accuracy, and precision tests showed that both C and T ELISA kits adequately measured C and T in the serum of Aceh cattle. Concentrations of C post-transportation were significantly higher than pre-transportation (p0.05). Conclusions Commercial C (EIA-1887) and T (EIA-1559) ELISA kits are reliable assays for measuring serum C and T, respectively, in Aceh cattle. Repeated freeze-thaw cycles significantly affected the stability of serum C, but did not for T. Copyright © 2020 Gholib G et al.Background The Portfolio-To-Impact (P2I) P2I model is a recently developed product portfolio tool that enables users to estimate the funding needs to move a portfolio of candidate health products, such as vaccines and drugs, along the product development path from late stage preclinical to phase III clinical trials, as well as potential product launches over time. In this study we describe the use of this tool for analysing the vaccine portfolio of the European Vaccine Initiative (EVI). This portfolio includes vaccine candidates for various diseases of poverty and emerging infectious diseases at different stages of development. Methods Portfolio analyses were conducted using the existing assumptions integrated in the P2I tool, as well as modified assumptions for costs, cycle times, and probabilities of success based on EVI's own internal data related to vaccine development. Results According to the P2I tool, the total estimated cost to move the 18 candidates currently in the EVI portfolio along the pipeline to launch would be about US $470 million, and there would be 0.69 expected launches across all six diseases in EVI's portfolio combined during the period 2019-2031. Running of the model using EVI-internal parameters resulted in a significant increase in the expected product launches. Conclusions Not all the assumptions underlying the P2I tool could be tested in our study due to limited amount of data available. Nevertheless, we expect that the accelerated clinical testing of vaccines (and drugs) based on the use of controlled human infection models that are increasingly available, as well as the accelerated approval by regulatory authorities that exists for example for serious conditions, will speed up product development and result in significant cost reduction. Project findings as well as potential future modifications of the P2I tool are discussed with the aim to improve the underlying methodology of the P2I model. Copyright © 2020 Gunn A et al.Background Self-harm and suicide in children and adolescents are of serious consequence and increase during the adolescent years. Consequently, there is need for interventions that prevent such behaviour. The objective of this paper to evaluate the effects of interventions preventing self-harm and suicide in children and adolescents in an overview of systematic reviews. Methods We conducted an overview of systematic reviews (OoO). We included reviews evaluating any preventive or therapeutic intervention. The methodological quality of the included reviews was assessed independently, and data was extracted by two reviewers. We report the review findings descriptively. The certainty of evidence was assessed using Grading of Recommendations Assessment, Development and Evaluation (GRADE). Results Moderate certainty evidence suggests that school-based interventions prevent suicidal ideation and attempts short term, and possibly suicide attempts long term. The effects of community-based interventions following suiciles, and studies on conditions associated with self-harm and/or suicidality, such as depression and psychosis. PROSPERO registration CRD42019117942 08/02/19. Copyright © 2020 Morken IS et al.Background The 2014-2015 Ebola outbreak in Sierra Leone led the Ministry of Health and Sanitation to set minimum standards of staffing (medical/non-medical) at the district level for the provision of basic essential health services (BPEHS). In one of the worst Ebola affected districts in Sierra Leone, we assessed staffing levels measured against these stipulated standards before, during, and 16 months after the Ebola outbreak. Methods The study population included all health workers in 83 health facilities. We assessed staffing levels at three points in time pre-Ebola (April 2014); the end of the outbreak (November 2015); and 16 months post-Ebola (March 2017). April 2014 was immediately prior to the Ebola outbreak and thus representative of the human resource situation before the outbreak. November 2015 was the month when Sierra Leone was declared Ebola-free, and thus reflects the end-situation after Ebola. March 2017 was two years since the launch of the BPEHS, and some progress should be expected. Results Against recommended medical staff numbers during pre-, intra- and post-Ebola periods, deficits were 67%, 65% and 60% respectively. Similarly, against recommended non-medical staff numbers during pre-, intra- and post-Ebola periods, the deficit remained at 92% throughout. In the post-Ebola period, there was a deficit of 73% against 1,389 recommended health worker positions. Conclusions Nothing has really changed in the state of human resources for health, and urgent measures are needed to rectify the situation and prevent a déjà vu in the advent of a new Ebola outbreak. Copyright © 2020 Squire JS et al.Circadian rhythm is an endogenous oscillation of about 24-h period in many physiological processes and behaviors. This daily oscillation is maintained by the molecular clock machinery with transcriptional-translational feedback loops mediated by clock genes including Period2 (Per2) and Bmal1. Recently, it was revealed that gut microbiome exerts a significant impact on the circadian physiology and behavior of its host; however, the mechanism through which it regulates the molecular clock has remained elusive. 3-(4-hydroxyphenyl)propionic acid (4-OH-PPA) and 3-phenylpropionic acid (PPA) are major metabolites exclusively produced by Clostridium sporogenes and may function as unique chemical messengers communicating with its host. In the present study, we examined if two C. sporogenes-derived metabolites can modulate the oscillation of mammalian molecular clock. Interestingly, 4-OH-PPA and PPA increased the amplitude of both PER2 and Bmal1 oscillation in a dosedependent manner following their administration immediately after the nadir or the peak of their rhythm. The phase of PER2 oscillation responded differently depending on the mode of administration of the metabolites. In addition, using an organotypic slice culture ex vivo, treatment with 4-OH-PPA increased the amplitude and lengthened the period of PER2 oscillation in the suprachiasmatic nucleus and other tissues. In summary, two C. sporogenes-derived metabolites are involved in the regulation of circadian oscillation of Per2 and Bmal1 clock genes in the host's peripheral and central clock machineries.BACKGROUND Hemophilia B (HB) is a coagulation disorder with an X-linked recessive inheritance pattern, caused by plasma FIX deficiency. In Colombia, HB is considered a rare and high-cost disease, with 362 males reported in 2017. METHODS Here, we characterized 20 HB apparently unrelated families by PCR amplification and Sanger sequencing. RESULTS Fourteen unique variants were identified seven missense, three nonsense, one variant in the 3' UTR region, two large deletions >50 bp, and one intronic substitution that affects splicing c.520+13A>G that was present in 7/20 patients (35%). All these variants have been previously reported in the literature, except for exons 3 and 4, deletions, present in one patient. The genotype-phenotype association correlates with the reported in the literature, with the exception of one patient. CONCLUSION This molecular analysis allowed us to establish the causal variant of HB in 100% of patients, to provide the appropriate genetic counseling to each of the families, and to propose a more cost-effective carrier analysis. Here, we reported the first variants in Colombian population with Hemophilia B, finding a new variant and one intron recurrent variant present in 35% of patients. © 2020 The Authors. Pitstop 2 Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.BACKGROUND Radioresistance in tumors limits the curative effect of the radiotherapy. Mimetic compounds of second mitochondria-derived activator of caspase (Smac) are potential new tumor radiation-sensitizing drugs because they can increase radiation-induced tumor cell apoptosis. Here, we observed the radiosensitization effect of a new Smac mimetic Antennapedia protein (ANTP)-SmacN7 fusion peptide in A549 cells and investigated the underlying mechanisms behind the effects of this protein on tumor cells. METHODS The ANTP-SmacN7 fusion peptide was synthesized and linked with fluorescein isothiocyanate to observe the protein's ability to penetrate cells. A549 cells were divided into the control, radiation-only, ANTP-SmacN7-only and ANTP-SmacN7 + radiation groups. The cells were exposed to 0, 2, 4 and 6 Gy, with 20 μmol/L of ANTP-SmacN7. The radiation-sensitizing effects of the ANTP-SmacN7 fusion proteins were observed via clonogenic assay. Apoptosis was detected using flow cytometry. A comet assay was used to assess DNA damage.
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