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There is no microbiological gold standard for childhood tuberculosis (TB) diagnosis. The paucibacillary nature of the disease, challenges in sample collection in young children, and the limitations of currently available microbiological tests restrict microbiological confirmation of intrathoracic TB to the minority of children. Recent WHO guidelines recommend the use of novel rapid molecular assays as initial diagnostic tests for TB and endorse alternative sample collection methods for children. However, the uptake of these tools in high-endemic settings remains low. In this review, we appraise historic and new microbiological tests and sample collection techniques that can be used for the diagnosis of intrathoracic TB in children. We explore challenges and possible ways to improve diagnostic yield despite limitations, and identify research gaps to address in order to improve the microbiological diagnosis of intrathoracic TB in children.

A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies. Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

The aim of the present study was to assess whether individual Sarcoptes mites collected from frozen skin (‘postponed isolation’ method) are suitable sources of PCR-quality genomic DNA, and to test the effectiveness of this method in comparison with the ‘direct isolation’ method, often used through force of habit. Hundreds of single Sarcoptes scabiei samples, resulting from direct (live) or postponed (post-frozen) isolation, were tested using a ~450 bp product (ITS-2) and multi-locus 10× genotyping with microsatellite markers. No statistical difference in yield of soluble DNA was found between the two isolation methods. Nevertheless, 19% of the reactions were classified as failed preparations in the direct isolation method, whereas the rate of unsuccessful reactions was 34% in the postponed isolation method. Consequently, post-frozen isolation is suitable and recommendable for Sarcoptes mite gDNA preparation, particularly when performing a balancing act among safety, practicability and profitability. These results have implications for mite collection for DNA extraction, and hence the needed wider leap of Sarcoptes into the genetic era.

Aerosols are emitted into the workplace atmosphere and the ambient environment through a variety of processes. Aerosol particles are known to have significant effects on both human health and the ambient environment. For this reason, monitoring aerosol concentrations in the atmosphere by aerosol sampling is undertaken in workplace and ambient environments. A wide range of aerosol sampling methods using different collection mechanisms has been used for collecting representative aerosol samples using either a collecting or sensing medium. This paper shows the existing and commonly used aerosol sampling methods based on aerosol collection and real-time measurements. The method of choice for aerosol sampling will ultimately depend on a variety of factors, such as purpose of sampling, type of aerosol, analysis requirements, and available budget.

For measuring water content and density, this chapter discusses the sample collection method, and method without sample collection. The frying pan method of measuring water content is carried out on site. The oven‐dry method is carried out in a laboratory and is subject to a standard. Measuring dry density using a membrane densitometer is carried out in situ with a membrane densitometer or a sample of soil on a core taken from the soil. In both cases, a wet density is measured and then converted into a dry density. Methods that use the radioactive sources are y rays are provided by a radioactive source of radium, beryllium or cesium 137, and rays from fast neutrons. Measurements are taken from backscatter or surface transmission, from drilling, or between two boreholes. The device is calibrated beforehand for reference materials whose compactness or water content is known.

Mechanical Turk (MTurk) is a common source of research participants within the academic community. Despite MTurk's utility and benefits over traditional subject pools some researchers have questioned whether it is sustainable. Specifically, some have asked whether MTurk workers are too familiar with manipulations and measures common in the social sciences, the result of many researchers relying on the same small participant pool. Here, we show that concerns about non-naivete on MTurk are due less to the MTurk platform itself and more to the way researchers use the platform. Specifically, we find that there are at least 250,000 MTurk workers worldwide and that a large majority of US workers are new to the platform each year and therefore relatively inexperienced as research participants. We describe how inexperienced workers are excluded from studies, in part, because of the worker reputation qualifications researchers commonly use. Then, we propose and evaluate an alternative approach to sampling on MTurk that allows researchers to access inexperienced participants without sacrificing data quality. We recommend that in some cases researchers should limit the number of highly experienced workers allowed in their study by excluding these workers or by stratifying sample recruitment based on worker experience levels. We discuss the trade-offs of different sampling practices on MTurk and describe how the above sampling strategies can help researchers harness the vast and largely untapped potential of the Mechanical Turk participant pool.

Background Choosing a suitable sample size in qualitative research is an area of conceptual debate and practical uncertainty. That sample size principles, guidelines and tools have been developed to enable researchers to set, and justify the acceptability of, their sample size is an indication that the issue constitutes an important marker of the quality of qualitative research. Nevertheless, research shows that sample size sufficiency reporting is often poor, if not absent, across a range of disciplinary fields. Methods A systematic analysis of single-interview-per-participant designs within three health-related journals from the disciplines of psychology, sociology and medicine, over a 15-year period, was conducted to examine whether and how sample sizes were justified and how sample size was characterised and discussed by authors. Data pertinent to sample size were extracted and analysed using qualitative and quantitative analytic techniques. Results Our findings demonstrate that provision of sample size justifications in qualitative health research is limited; is not contingent on the number of interviews; and relates to the journal of publication. Defence of sample size was most frequently supported across all three journals with reference to the principle of saturation and to pragmatic considerations. Qualitative sample sizes were predominantly – and often without justification – characterised as insufficient (i.e., ‘small’) and discussed in the context of study limitations. Sample size insufficiency was seen to threaten the validity and generalizability of studies’ results, with the latter being frequently conceived in nomothetic terms. Conclusions We recommend, firstly, that qualitative health researchers be more transparent about evaluations of their sample size sufficiency, situating these within broader and more encompassing assessments of data adequacy . Secondly, we invite researchers critically to consider how saturation parameters found in prior methodological studies and sample size community norms might best inform, and apply to, their own project and encourage that data adequacy is best appraised with reference to features that are intrinsic to the study at hand. Finally, those reviewing papers have a vital role in supporting and encouraging transparent study-specific reporting.

BackgroundIn Turkey, paediatric emergency departments often lack the specialised environments required for invasive procedures on neonates. Given their developmental vulnerability, it is crucial to use interventions that reduce discomfort and support physiological stability. This study introduces the portable therapeutic baby nest (PTBN), designed to provide developmentally supportive care aligned with the principles of the Newborn Individualized Developmental Care and Assessment Program.MethodsThis two-phase study included 80 term neonates (40 per group). First, the PTBN was developed from February to April 2022. Second, its effectiveness was evaluated through a randomized controlled trial conducted from May to September 2022. The experimental group underwent venous blood sampling in the PTBN, and the control group on a standard stretcher. All procedures were video-recorded and assessed by two blinded nurses using the Physiological Parameter Monitoring Form, COMFORTneo and Neonatal Infant Pain Scale (NIPS).ResultsBaseline characteristics were similar across groups (p>0.05). During and after sampling, the PTBN group had significantly lower heart and respiratory rates, higher oxygen saturation and lower NIPS and COMFORTneo scores compared with controls (p<0.05).ConclusionThe PTBN improved physiological stability, comfort and pain outcomes during venous sampling in neonates.Trial registration numberNCT05442619.

In-depth interviews are a common method of qualitative data collection, providing rich data on individuals' perceptions and behaviors that would be challenging to collect with quantitative methods. Researchers typically need to decide on sample size a priori. Although studies have assessed when saturation has been achieved, there is no agreement on the minimum number of interviews needed to achieve saturation. To date, most research on saturation has been based on in-person data collection. During the COVID-19 pandemic, web-based data collection became increasingly common, as traditional in-person data collection was possible. Researchers continue to use web-based data collection methods post the COVID-19 emergency, making it important to assess whether findings around saturation differ for in-person versus web-based interviews. We aimed to identify the number of web-based interviews needed to achieve true code saturation or near code saturation. The analyses for this study were based on data from 5 Food and Drug Administration-funded studies conducted through web-based platforms with patients with underlying medical conditions or with health care providers who provide primary or specialty care to patients. We extracted code- and interview-specific data and examined the data summaries to determine when true saturation or near saturation was reached. The sample size used in the 5 studies ranged from 30 to 70 interviews. True saturation was reached after 91% to 100% (n=30-67) of planned interviews, whereas near saturation was reached after 33% to 60% (n=15-23) of planned interviews. Studies that relied heavily on deductive coding and studies that had a more structured interview guide reached both true saturation and near saturation sooner. We also examined the types of codes applied after near saturation had been reached. In 4 of the 5 studies, most of these codes represented previously established core concepts or themes. Codes representing newly identified concepts, other or miscellaneous responses (eg, \"in general\"), uncertainty or confusion (eg, \"don't know\"), or categorization for analysis (eg, correct as compared with incorrect) were less commonly applied after near saturation had been reached. This study provides support that near saturation may be a sufficient measure to target and that conducting additional interviews after that point may result in diminishing returns. Factors to consider in determining how many interviews to conduct include the structure and type of questions included in the interview guide, the coding structure, and the population under study. Studies with less structured interview guides, studies that rely heavily on inductive coding and analytic techniques, and studies that include populations that may be less knowledgeable about the topics discussed may require a larger sample size to reach an acceptable level of saturation. Our findings also build on previous studies looking at saturation for in-person data collection conducted at a small number of sites.

Raman microspectroscopy is useful for the analysis of biological samples, because chemical and structural information can be obtained without using labels. This protocol brings together practical guidelines from expert research groups. Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.