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Journal, Genetic Engineering &... Nov 2023Factorial design is a simple, yet elegant method to investigate the effect of multiple factors and their interaction on a specific response simultaneously. Hence, this...
BACKGROUND
Factorial design is a simple, yet elegant method to investigate the effect of multiple factors and their interaction on a specific response simultaneously. Hence, this type of study design reaches the best optimization conditions of a process. Although the interaction between the variables is widely prevalent in cell culture procedures, factorial design per se is infrequently utilized in improving cell culture output. Therefore, we aim to optimize the experimental conditions for generating mature bone marrow-derived dendritic cells (BMDCs). Two different variables were investigated, including the concentrations of the inducing factors and the starting density of the bone marrow mononuclear cells. In the current study, we utilized the design of experiments (DoE), a statistical approach, to systematically assess the impact of factors with varying levels on cell culture outcomes. Herein, we apply a two-factor, two-level (2) factorial experiment resulting in four conditions that are run in triplicate. The two variables investigated here are cytokines combinations with two levels, granulocyte-macrophage colony-stimulating factor (GM-CSF) alone or with interleukin-4 (IL4). The other parameter is cell density with two different concentrations, 2 × 10 and 4 × 10 cells/mL. Then, we measured cell viability using the trypan blue exclusion method, and a flow cytometer was used to detect the BMDCs expressing the markers FITC-CD80, CD86, CD83, and CD14. BMDC marker expression levels were calculated using arbitrary units (AU) of the mean fluorescence intensity (MFI).
RESULTS
The current study showed that the highest total viable cells and cells yield obtained were in cell group seeded at 2 × 10 cells/mL and treated with GM-CSF and IL-4. Importantly, the expression of the co-stimulatory molecules CD83 and CD80/CD86 were statistically significant for cell density of 2 × 10 cells/mL (P < 0.01, two-way ANOVA). Bone marrow mononuclear cells seeded at 4 × 10 in the presence of the cytokine mix less efficiently differentiated and matured into BMDCs. Statistical analysis via two-way ANOVA revealed an interaction between cell density and cytokine combinations.
CONCLUSION
The analysis of this study indicates a substantial interaction between cytokines combinations and cell densities on BMDC maturation. However, higher cell density is not associated with optimizing DC maturation. Notably, applying DoE in bioprocess designs increases experimental efficacy and reliability while minimizing experiments, time, and process costs.
PubMed: 38017248
DOI: 10.1186/s43141-023-00597-4 -
Nutrients Oct 2023A drinking strategy aiming to replace a given percentage of the sweat losses incurred during exercise should result in reproducible fluid intake volume and, hence, fluid...
A drinking strategy aiming to replace a given percentage of the sweat losses incurred during exercise should result in reproducible fluid intake volume and, hence, fluid balance from one exercise session to the other performed under similar scenarios. Whether this may also be the case with ad libitum drinking during exercise is unclear. We characterized the repeatability of ad libitum water intake during repeated 1 h exercise sessions and examined its effect over time on fluid balance and selected physiological functions and perceptual sensations. Twelve (3 women) healthy individuals participated in this study. At weekly intervals, they completed four 2 × 30 min walking/jogging exercise bouts (55% V˙O, 40 °C, 20-30% relative humidity) interspersed by a 3 min recovery period. During exercise, participants consumed water (20 °C) ad libitum. There were no significant differences among the four exercise sessions for absolute water intake volume (~1000 mL·h), percent body mass loss (~0.4%), sweat rate (~1300 mL·h) and percent of sweat loss replaced by water intake (~80%). Heart rate, rectal temperature, and perceived thirst and heat stress did not differ significantly between the first and fourth exercise sessions. Perceived exertion was significantly lower during the fourth vs. the first exercise session, but the difference was trivial (<1 arbitrary unit). In conclusion, ad libitum water intake during four successive identical 1 h walking/jogging sessions conducted in the heat will result in similar water intake volumes and perturbations in fluid balance, heart rate, rectal temperature, and perceived thirst, heat stress and exertion.
Topics: Female; Humans; Dehydration; Drinking; Hot Temperature; Jogging; Osmolar Concentration; Walking; Water-Electrolyte Balance; Male
PubMed: 37960153
DOI: 10.3390/nu15214500 -
Sensors and Actuators. B, Chemical Jul 2023The COVID-19 pandemic has highlighted the need to monitor important correlates of immunity on a population-wide level. To this end, we have developed a competitive assay...
The COVID-19 pandemic has highlighted the need to monitor important correlates of immunity on a population-wide level. To this end, we have developed a competitive assay to assess neutralizing antibody (NAb) titer on the giant magnetoresistive (GMR) biosensor platform. We compared the clinical performance of our biosensor with established techniques such as Ortho's VITROS Anti-SARS-CoV-2 IgG Quantitative Antibody test. Results obtained between the VITROS test and the GMR assay showed correlation ( = -0.93). We then validated the assay with patient plasma samples that had been tested using focus reduction neutralization testing (FRNT). The results obtained from our GMR assay exhibit a previously identified trend of increased NAb titers 2 weeks post-vaccination. We further evaluated NAb titers 6 months post-vaccination and observed waning neutralizing antibody titers over that time in vaccinated patients. In addition, we calibrated our assay to an arbitrary unit (IU/mL) using World Health Organization (WHO) reference plasma provided by the National Institute of Biological Standards and Control (NIBSC). Our biosensor provides highly specific and sensitive results in serum and plasma with analytical, clinical, and point-of-care (POC) applications due to quick turnaround times on samples and the cost-effectiveness of the platform.
PubMed: 37056483
DOI: 10.1016/j.snb.2023.133773 -
Experimental and Clinical... Mar 2024Management of potential organ donors is crucial in the donation process, considering that hemodynamic instability is quite common. (Observational Study)
Observational Study
OBJECTIVES
Management of potential organ donors is crucial in the donation process, considering that hemodynamic instability is quite common.
MATERIALS AND METHODS
In the this single-center retrospective observational study, we analyzed 87 utilized brain death donors consecutively admitted to our intensive care unit from January 1, 2019, to December 31, 2022. We assessed the achievement of donor management goals during the observation period, and we also evaluated whether the achieve-ment of donor goals differed between younger and older donors (arbitrary age cutoff of 65 years).
RESULTS
In our series, mean age of donors was 67 ± 18 y, and organ-per-donor ratio was 2.3. The number of donor goals significantly increased during the 6-hour observation period (P < .001) and all donor goals were achieved in most donors (84/87) at the end of the observation period with no changes in the use and dose of vasoactive drugs. With respect to age, the number of donor goals was significantly higher in older donors at first evaluation, but goals significantly increased in both age subgroups of donors at the end of the 6-hour observation period.
CONCLUSIONS
Our data strongly suggested that a strict hemodynamic monitoring schedule allows the achievement of donor goals both in older and in younger brain death donors. We confirmed our previous findings that hemodynamic management in brain death donors is influenced by age. A strict hemodynamic monitoring schedule of brain death donors is useful to consistently achieve donor goals.
Topics: Humans; Brain Death; Retrospective Studies; Middle Aged; Male; Female; Tissue Donors; Aged; Time Factors; Age Factors; Hemodynamics; Adult; Aged, 80 and over; Donor Selection; Risk Factors
PubMed: 38695586
DOI: 10.6002/ect.2024.0030 -
Sports Medicine (Auckland, N.Z.) Feb 2024Publication bias refers to a systematic deviation from the truth in the results of a meta-analysis due to the higher likelihood for published studies to be included in... (Meta-Analysis)
Meta-Analysis Review
Publication bias refers to a systematic deviation from the truth in the results of a meta-analysis due to the higher likelihood for published studies to be included in meta-analyses than unpublished studies. Publication bias can lead to misleading recommendations for decision and policy making. In this education review, we introduce, explain, and provide solutions to the pervasive misuses and misinterpretations of publication bias that afflict evidence syntheses in sport and exercise medicine, with a focus on the commonly used funnel-plot based methods. Publication bias is more routinely assessed by visually inspecting funnel plot asymmetry, although it has been consistently deemed unreliable, leading to the development of statistical tests to assess publication bias. However, most statistical tests of publication bias (i) cannot rule out alternative explanations for funnel plot asymmetry (e.g., between-study heterogeneity, choice of metric, chance) and (ii) are grossly underpowered, even when using an arbitrary minimum threshold of ten or more studies. We performed a cross-sectional meta-research investigation of how publication bias was assessed in systematic reviews with meta-analyses published in the top two sport and exercise medicine journals throughout 2021. This analysis highlights that publication bias is frequently misused and misinterpreted, even in top tier journals. Because of conceptual and methodological problems when assessing and interpreting publication bias, preventive strategies (e.g., pre-registration, registered reports, disclosing protocol deviations, and reporting all study findings regardless of direction or magnitude) offer the best and most efficient solution to mitigate the misuse and misinterpretation of publication bias. Because true publication bias is very difficult to determine, we recommend that future publications use the term "risk of publication bias".
Topics: Humans; Publication Bias; Cross-Sectional Studies; Systematic Reviews as Topic; Bias
PubMed: 37684502
DOI: 10.1007/s40279-023-01927-9 -
The Lancet. Rheumatology Jun 2024The humoral and T-cell responses to booster COVID-19 vaccine types in multidisease immunocompromised individuals who do not generate adequate antibody responses to two... (Randomized Controlled Trial)
Randomized Controlled Trial
Immunogenicity of third dose COVID-19 vaccine strategies in patients who are immunocompromised with suboptimal immunity following two doses (OCTAVE-DUO): an open-label, multicentre, randomised, controlled, phase 3 trial.
BACKGROUND
The humoral and T-cell responses to booster COVID-19 vaccine types in multidisease immunocompromised individuals who do not generate adequate antibody responses to two COVID-19 vaccine doses, is not fully understood. The OCTAVE DUO trial aimed to determine the value of third vaccinations in a wide range of patients with primary and secondary immunodeficiencies.
METHODS
OCTAVE-DUO was a prospective, open-label, multicentre, randomised, controlled, phase 3 trial investigating humoral and T-cell responses in patients who are immunocompromised following a third vaccine dose with BNT162b2 or mRNA-1273, and of NVX-CoV2373 for those with lymphoid malignancies. We recruited patients who were immunocompromised from 11 UK hospitals, aged at least 18 years, with previous sub-optimal responses to two doses of SARS-CoV-2 vaccine. Participants were randomly assigned 1:1 (1:1:1 for those with lymphoid malignancies), stratified by disease, previous vaccination type, and anti-spike antibody response following two doses. Individuals with lived experience of immune susceptibility were involved in the study design and implementation. The primary outcome was vaccine-specific immunity defined by anti-SARS-CoV-2 spike antibodies (Roche Diagnostics UK and Ireland, Burgess Hill, UK) and T-cell responses (Oxford Immunotec, Abingdon, UK) before and 21 days after the third vaccine dose analysed by a modified intention-to-treat analysis. The trial is registered with the ISRCTN registry, ISRCTN 15354495, and the EU Clinical Trials Register, EudraCT 2021-003632-87, and is complete.
FINDINGS
Between Aug 4, 2021 and Mar 31, 2022, 804 participants across nine disease cohorts were randomly assigned to receive BNT162b2 (n=377), mRNA-1273 (n=374), or NVX-CoV2373 (n=53). 356 (45%) of 789 participants were women, 433 (55%) were men, and 659 (85%) of 775 were White. Anti-SARS-CoV-2 spike antibodies measured 21 days after the third vaccine dose were significantly higher than baseline pre-third dose titres in the modified intention-to-treat analysis (median 1384 arbitrary units [AU]/mL [IQR 4·3-7990·0] compared with median 11·5 AU/mL [0·4-63·1]; p<0·001). Of participants who were baseline low responders, 380 (90%) of 423 increased their antibody concentrations to more than 400 AU/mL. Conversely, 166 (54%) of 308 baseline non-responders had no response after the third dose. Detectable T-cell responses following the third vaccine dose were seen in 494 (80%) of 616 participants. There were 24 serious adverse events (BNT612b2 eight [33%] of 24, mRNA-1273 12 [50%], NVX-CoV2373 four [17%]), two (8%) of which were categorised as vaccine-related. There were seven deaths (1%) during the trial, none of which were vaccine-related.
INTERPRETATION
A third vaccine dose improved the serological and T-cell response in the majority of patients who are immunocompromised. Individuals with chronic renal disease, lymphoid malignancy, on B-cell targeted therapies, or with no serological response after two vaccine doses are at higher risk of poor response to a third vaccine dose.
FUNDING
Medical Research Council, Blood Cancer UK.
Topics: Humans; Female; Male; COVID-19; Middle Aged; Immunocompromised Host; SARS-CoV-2; COVID-19 Vaccines; Immunogenicity, Vaccine; Aged; BNT162 Vaccine; Antibodies, Viral; Prospective Studies; Immunization, Secondary; 2019-nCoV Vaccine mRNA-1273; Adult; T-Lymphocytes; United Kingdom; ChAdOx1 nCoV-19
PubMed: 38734019
DOI: 10.1016/S2665-9913(24)00065-1 -
PloS One 2024The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary developed by the U.S. National Library of Medicine (NLM) for classifying journal articles. It is...
The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary developed by the U.S. National Library of Medicine (NLM) for classifying journal articles. It is increasingly used by researchers studying medical innovation to classify text into disease areas and other categories. Although this process was once manual, human indexers are now assisted by algorithms that automate some of the indexing process. NLM has made one of their algorithms, the Medical Text Indexer (MTI), available to researchers. MTI can be used to easily assign MeSH descriptors to arbitrary text, including from document types other than publications. However, the reliability of extending MTI to other document types has not been studied directly. To assess this, we collected text from grants, patents, and drug indications, and compared MTI's classification to expert manual classification of the same documents. We examined MTI's recall (how often correct terms were identified) and found that MTI identified 78% of expert-classified MeSH descriptors for grants, 78% for patents, and 86% for drug indications. This high recall could be driven merely by excess suggestions (at an extreme, all diseases being assigned to a piece of text); therefore, we also examined precision (how often identified terms were correct) and found that most MTI outputs were also identified by expert manual classification: precision was 53% for grant text, 73% for patent text, and 64% for drug indications. Additionally, we found that recall and precision could be improved by (i) utilizing ranking scores provided by MTI, (ii) excluding long documents, and (iii) aggregating to higher MeSH categories. For simply detecting the presence of any disease, MTI showed > 94% recall and > 87% precision. Our overall assessment is that MTI is a potentially useful tool for researchers wishing to classify texts from a variety of sources into disease areas.
Topics: United States; Humans; Reproducibility of Results; Abstracting and Indexing; Medical Subject Headings; Algorithms; National Library of Medicine (U.S.)
PubMed: 38478542
DOI: 10.1371/journal.pone.0297526 -
The Lancet. Child & Adolescent Health Apr 2024Touch interventions such as massage and skin-to-skin contact relieve neonatal pain. The Parental touch trial (Petal) aimed to assess whether parental stroking of their... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
Touch interventions such as massage and skin-to-skin contact relieve neonatal pain. The Parental touch trial (Petal) aimed to assess whether parental stroking of their baby before a clinically required heel lance, at a speed of approximately 3 cm/s to optimally activate C-tactile nerve fibres, provides effective pain relief.
METHODS
Petal is a multicentre, randomised, parallel-group interventional superiority trial conducted in the John Radcliffe Hospital (Oxford University Hospitals NHS Foundation Trust, Oxford, UK) and the Royal Devon and Exeter Hospital (Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK). Neonates without neurological abnormalities who were born at 35 weeks gestational age or more and required a blood test via a heel lance in the first week of life were randomly assigned (1:1) to receive parental touch for 10 s either before (intervention group) or after (control group) the clinically required heel lance. Randomisation was managed at the Oxford site using a web-based minimisation algorithm with allocation concealment. The primary outcome measure was the magnitude of noxious-evoked brain activity in response to the heel lance measured with electroencephalography (EEG). Secondary outcome measures were Premature Infant Pain Profile-Revised (PIPP-R) score, development of tachycardia, and parental anxiety score. For all outcomes, the per-protocol effect was estimated via complier average causal effect analysis on the full analysis set. The trial is registered on ISRCTN (ISRCTN14135962) and ClinicalTrials.gov (NCT04901611).
FINDINGS
Between Sept 1, 2021, and Feb 7, 2023, 159 parents were approached to participate in the study, and 112 neonates were included. 56 neonates were randomly assigned to the intervention group of parental stroking before the heel lance and 56 to the control group of parental stroking after the heel lance. The mean of the magnitude of the heel lance-evoked brain activity was 0·85 arbitrary units (a.u.; SD 0·70; n=39; a scaled magnitude of 1 a.u. represents the expected mean response to a heel lance in term-aged neonates) in the intervention group and 0·91 a.u. (SD 0·76; n=43) in the control group. Therefore, the primary outcome did not differ significantly between groups, with a mean difference of -0·11 a.u. (lower in intervention group; SD 0·77; 95% CI -0·42 to 0·20; p=0·38; n=82). No significant difference was observed across secondary outcomes. The PIPP-R difference in means was 1·10 (higher in intervention group, 95% CI -0·42 to 2·61; p=0·15; n=100); the odds ratio of becoming tachycardic was 2·08 (95% CI 0·46 to 9·46; p=0·34, n=105) in the intervention group with reference to the control group; and the difference in parental State-Trait Anxiety Inventory-State score was -0·44 (higher in control group; SD 6·85; 95% CI -2·91 to 2·02; p=0·72; n=106). One serious adverse event (desaturation) occurred in a neonate randomly assigned to the control group, which was not considered to be related to the study.
INTERPRETATION
Parental stroking delivered at an optimal speed to activate C-tactile fibres for a duration of 10 s before the painful procedure did not significantly change neonates' magnitude of pain-related brain activity, PIPP-R score, or development of tachycardia. The trial highlighted the challenge of translating an experimental researcher-led tactile intervention into a parent-led approach, and the value of involving parents in their baby's pain management.
FUNDING
Wellcome Trust and Bliss.
Topics: Humans; Infant, Newborn; Pain; Pain, Procedural; Tachycardia; Touch; United Kingdom
PubMed: 38373429
DOI: 10.1016/S2352-4642(23)00340-1 -
Cureus Oct 2023To compare the doses calculated by the analytical anisotropic algorithm (AAA) and two dose reporting modes of Acuros XB (AXB(D) and AXB(D)) with varied CT values on the...
BACKGROUND
To compare the doses calculated by the analytical anisotropic algorithm (AAA) and two dose reporting modes of Acuros XB (AXB(D) and AXB(D)) with varied CT values on the Eclipse (Varian Medical Systems, Palo Alto, CA).
MATERIALS AND METHODS
Virtual phantoms with a central layer of heterogeneous material (thickness = 2 or 5 cm) were created with Eclipse. Using single or opposed fields, the field sizes were 5 x 5 cm or 10 x 10 cm. The photon energies were 6 or 10 MV, and the source-to-target distance was 100 cm. The relative doses at the center of the heterogeneous material layer were evaluated with varied CT values, from -1000 to 3000 HU. Values were normalized with the dose at 0 HU (100%) for comparative analysis.
RESULTS
The results obtained from continuous data for a single field, 6 MV, 5 x 5 cm, and the heterogeneous material 5 cm, where the differences between algorithms were most pronounced, were as follows. In the low-density region (-1000 HU and -800 HU), the dose differences for AXB with reference to AAA were, respectively, -54.5% and +4.6% (AXB(D)) and -47.0% and +3.5% (AXB(D)), and in the high-density regions (1000 HU and 3000 HU) were -5.7% and -8.8% (AXB(D)) and +7.4% and +3.5% (AXB(D)), respectively. Consequently, dose differences at arbitrary CT values could be obtained.
CONCLUSION
Dose differences between these algorithms were clarified for heterogeneous materials. The risk of dose reduction or escalation in clinical use was clearly visible between CT values from -1000 to 3000 HU.
PubMed: 37954761
DOI: 10.7759/cureus.46805 -
Briefings in Bioinformatics May 2024Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal...
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
Topics: Humans; Colorectal Neoplasms; Mutation; Computational Biology; Workflow; Cell Line, Tumor; Exome Sequencing; Female; Algorithms
PubMed: 38783705
DOI: 10.1093/bib/bbae249