Sequence-Based Characterization of Intratumoral Bacteria-A Guide to Best Practice.
Ontology highlight
ABSTRACT:
SUBMITTER: Walker SP
PROVIDER: S-EPMC7046755 | biostudies-literature | 2020
REPOSITORIES: biostudies-literature
Publications
Sequence-Based Characterization of Intratumoral Bacteria-A Guide to Best Practice.
Walker Sidney P SP Tangney Mark M Claesson Marcus J MJ
Frontiers in oncology 20200221
Tumors are hospitable environments to bacteria and several recent studies on cancer patient samples have introduced the concept of an endogenous tumor microbiome. For a variety of reasons, this putative tumor microbiome is particularly challenging to investigate, and a failure to account for the various potential pitfalls will result in erroneous results and claims. Before this potentially extremely medically-significant habitat can be accurately characterized, a clear understanding of all poten ...[more]
Similar Datasets
Project description:It is well established that treatment regime compliance is linked to the acceptability of a pharmaceutical formulation, and hence also to therapeutic outcomes. To that end, acceptability must be assessed during the development of all pharmaceutical products and especially for those intended for paediatric patients. Although acceptability is a multifaceted concept, poor sensory characteristics often contribute to poor patient acceptability. In particular, poor taste is often cited as a major reason for many patients, especially children, to refuse to take their medicine. It is thus important to understand and, as far as possible, optimise the sensory characteristics and, in particular, the taste/flavour/mouthfeel of the formulation throughout the development of the product. Sensory analysis has been widely practiced, providing objective data concerning the sensory aspects of food and cosmetic products. In this paper, we present proposals concerning how the well-established principles of sensory analysis can best be applied to pharmaceutical product development, allowing objective, scientifically valid, sensory data to be obtained safely. We briefly discuss methodologies that may be helpful in reducing the number of samples that may need to be assessed by human volunteers. However, it is only possible to be sure whether or not the sensory characteristics of a pharmaceutical product are non-aversive to potential users by undertaking sensory assessments in human volunteers. Testing is also required during formulation assessment and to ensure that the sensory characteristics remain acceptable throughout the product shelf life. We provide a risk assessment procedure to aid developers to define where studies are low risk, the results of a survey of European regulators on their views concerning such studies, and detailed guidance concerning the types of sensory studies that can be undertaken at each phase of product development, along with guidance about the practicalities of performing such sensory studies. We hope that this guidance will also lead to the development of internationally agreed standards between industry and regulators concerning how these aspects should be measured and assessed throughout the development process and when writing and evaluating regulatory submissions. Finally, we hope that the guidance herein will help formulators as they seek to develop better medicines for all patients and, in particular, paediatric patients.
| S-EPMC10535428 | biostudies-literature
Project description:BackgroundThis is a practice guide for the evaluation tool specifically created to objectively evaluate longitudinal faculty development programs (FDP) using the "5×2 -D backward planning faculty development model". It was necessary to create this tool as existing evaluation methods are designed to evaluate linear faculty development models with a specific endpoint. This backward planning approach is a cyclical model without an endpoint, consisting of 5 dynamic steps that are flexible and interchangeable, therefore can be a base for an evaluation tool that is objective and takes into account all the domains of the FDP in contrast to the existing, traditional, linear evaluation tools which focus on individual aspects of the program. The developed tool will target evaluation of longitudinal faculty development programs regardless of how they were planned.MethodologyDeductive qualitative grounded theory approach was used. Evaluation questions were generated and tailored based on the 5 × 2-D model followed by 2 Delphi rounds to finalize them. Based on the finalized evaluation questions from the results of the Delphi rounds, two online focus group discussions (FGDs) were conducted to deduce the indicators, data sources and data collection method.ResultsBased on the suggested additions, the authors added 1 new question to domains B, with a total of 42 modifications, such as wording changes or discarding or merging questions. Some domains received no comments, therefore, were not included in round 2. For each evaluation question, authors generated indicators, data sources and data collection methods during the FGD.ConclusionThe methodology used to develop this tool takes into account expert opinions. Comprehensiveness of this tool makes it an ideal evaluation tool during self-evaluation or external quality assurance for longitudinal FDP. After its validation and testing, this practice guide can be used worldwide, along with the provided indicators which can be quantified and used to suit the local context.
| S-EPMC8898439 | biostudies-literature
Project description:Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
| S-EPMC8592384 | biostudies-literature
Project description:Cherubism is a skeletal dysplasia characterized by bilateral and symmetric fibro-osseous lesions limited to the mandible and maxilla. In most patients, cherubism is due to dominant mutations in the SH3BP2 gene on chromosome 4p16.3. Affected children appear normal at birth. Swelling of the jaws usually appears between 2 and 7 years of age, after which, lesions proliferate and increase in size until puberty. The lesions subsequently begin to regress, fill with bone and remodel until age 30, when they are frequently not detectable.Fibro-osseous lesions, including those in cherubism have been classified as quiescent, non-aggressive and aggressive on the basis of clinical behavior and radiographic findings. Quiescent cherubic lesions are usually seen in older patients and do not demonstrate progressive growth. Non-aggressive lesions are most frequently present in teenagers. Lesions in the aggressive form of cherubism occur in young children and are large, rapidly growing and may cause tooth displacement, root resorption, thinning and perforation of cortical bone.Because cherubism is usually self-limiting, operative treatment may not be necessary. Longitudinal observation and follow-up is the initial management in most cases. Surgical intervention with curettage, contouring or resection may be indicated for functional or aesthetic reasons. Surgical procedures are usually performed when the disease becomes quiescent. Aggressive lesions that cause severe functional problems such as airway obstruction justify early surgical intervention.
| S-EPMC3359956 | biostudies-literature
Project description:Intravascular lithotripsy (IVL) is a novel approach to lesion preparation of severely calcified plaques in coronary and peripheral vessels. Lithotripsy is delivered by vaporising fluid to create an expanding bubble that generates sonic pressure waves that interact with arterial calcification. Available data indicate that IVL leads to increased vessel compliance before stent implantation with high efficacy and an excellent safety profile. Since it gained the CE mark in 2017, and with improved operator experience, the use of IVL has expanded into more complex clinical situations. This review focuses on the best practice for IVL use in the cath lab, based on 3 years of experience with the technology and the latest scientific data from the Disrupt CAD clinical trials.
| S-EPMC8826142 | biostudies-literature
Project description:The nutritional status of hospitalised patients is often at risk or compromised and predisposed to further deterioration after discharge, leading to poor clinical outcomes, high healthcare costs, and poor quality of life. This paper aims to provide evidence-based best-practice recommendations to address this, supported by a national survey of healthcare professionals in Singapore and reviewed by a multidisciplinary expert panel under the Sarcopenia Interest Group of Society of Parenteral and Enteral Nutrition Singapore (SingSPEN). We advocate screening all patients with a validated tool which includes a disease activity/burden component, an easily accessible dietitian referral pathway for patients at risk of malnutrition, and an individualised nutrition care plan formulated and delivered using a multidisciplinary team approach for patients at risk or with malnutrition. A comprehensive team would include not only dietitians but also physicians, nurses, physiotherapists, speech therapists, and medical social workers working together towards a common goal. Information on why nutrition is important for good health and how it can be achieved should also be provided to all patients and their caregivers before and after hospital discharge. With the above recommendations, we seek to improve upon the current nutrition care processes at discharge for healthcare institutions in Singapore.
| S-EPMC10650134 | biostudies-literature
Project description:Coastal marine ecosystems can be managed by actions undertaken both on the land and in the ocean. Quantifying and comparing the costs and benefits of actions in both realms is therefore necessary for efficient management. Here, we quantify the link between terrestrial sediment runoff and a downstream coastal marine ecosystem and contrast the cost-effectiveness of marine- and land-based conservation actions. We use a dynamic land- and sea-scape model to determine whether limited funds should be directed to 1 of 4 alternative conservation actions-protection on land, protection in the ocean, restoration on land, or restoration in the ocean-to maximise the extent of light-dependent marine benthic habitats across decadal timescales. We apply the model to a case study for a seagrass meadow in Australia. We find that marine restoration is the most cost-effective action over decadal timescales in this system, based on a conservative estimate of the rate at which seagrass can expand into a new habitat. The optimal decision will vary in different social-ecological contexts, but some basic information can guide optimal investments to counteract land- and ocean-based stressors: (1) marine restoration should be prioritised if the rates of marine ecosystem decline and expansion are similar and low; (2) marine protection should take precedence if the rate of marine ecosystem decline is high or if the adjacent catchment is relatively intact and has a low rate of vegetation decline; (3) land-based actions are optimal when the ratio of marine ecosystem expansion to decline is greater than 1:1.4, with terrestrial restoration typically the most cost-effective action; and (4) land protection should be prioritised if the catchment is relatively intact but the rate of vegetation decline is high. These rules of thumb illustrate how cost-effective conservation outcomes for connected land-ocean systems can proceed without complex modelling.
| S-EPMC5587113 | biostudies-literature
Project description:BackgroundEvidence-based practice in nursing is challenging and relies on the sources of information used by nurses to inform clinical practice. An integrative review from 2008 revealed that nurses more frequently relied on information from colleagues than information from high-level sources such as systematic reviews and evidence-based clinical practice guidelines.AimsTo describe the information sources used by registered nurses to inform their clinical practice.MethodsAn integrative review was conducted according to the PRISMA guidelines, based on empirical research studies published from January 2007 until June 2021. The included studies were appraised, following which the identified sources of information from quantitative studies were compiled and ranked. Finally, the qualitative text data were summarized into categories.ResultsFifty-two studies from various countries were included. The majority of studies employed a quantitative design and used original instruments. Peers were ranked as the number one source of information to inform nurses' clinical practice. However, computers and reference materials are now ranked among the top four most used information sources.Linking evidence to actionImprovement in computer and information searching skills, as well as the availability of computerized decision support tools, may contribute to nurses' frequent use of digital sources and reference material to inform clinical practice. This review shows that nurses' most frequently reported peer nurses as their source of information in clinical practice. Information sources such as computers and reference materials were ranked higher, and information from patients was ranked lower than in the 2008 review. Developing and standardizing instruments and ensuring high-quality study design is critical for further research on nurses' sources of information for clinical practice.
| S-EPMC9790517 | biostudies-literature
Project description:Journal peer review is a gatekeeper in the scientific process, determining which papers are published in academic journals. It also supports authors in improving their papers before they go to press. Training for early-career researchers on how to conduct a high-quality peer review is scarce, however, and there are concerns about the quality of peer review in the health sciences. Standardized training and guidance may help reviewers to improve the quality of their feedback. In this paper, we approach peer review as a staged writing activity and apply writing process best practices to help early-career researchers and others learn to create a comprehensive and respectful peer-review report. The writing stages of reading, planning and composing are reflected in our three-step peer-review process. The first step involves reading the entire manuscript to get a sense of the paper as a whole. The second step is to comprehensive evaluate the paper. The third step, of writing the review, emphasizes a respectful tone, providing feedback that motivates revision as well as balance in pointing out strengths and making suggestions. Detailed checklists that are provided in the Supplementary material (available as Supplementary data at IJE online) aid in the paper evaluation process and examples demonstrate points about writing an effective review.
| S-EPMC11580681 | biostudies-literature
Project description:Background and aimsDrug-related impairment is persistently stigmatized delaying and preventing treatment engagement. To reduce stigma, various medical terms (e.g. 'chronically relapsing brain disease', 'disorder') have been promoted in diagnostic systems and among national health agencies, yet some argue that over-medicalization of drug-related impairment lowers prognostic optimism and reduces personal agency. While intensely debated, rigorous empirical study is lacking. This study investigated whether random exposure to one of six common ways of describing drug-related impairment induces systematically different judgments.Design, setting and participantsCross-sectional survey, US general population, among a nationally representative non-institutionalized sample (n = 3635; 61% response rate; December 2019-January 2020).InterventionTwelve vignettes (six terms × gender) describing someone treated for opioid-related impairment depicted in one of six ways as a(n): 'chronically relapsing brain disease', 'brain disease', 'disease', 'illness', 'disorder' or 'problem'.MeasurementsMulti-dimensional stigma scale assessing: blame; social exclusion; prognostic optimism, continuing care, and danger (a = 0.70-0.83).FindingsUS adults [mean age = 47.81, confidence interval (CI) = 47.18-48.44; 52.4% female; 63.14% white] rated the same opioid-impaired person differently across four of five stigma dimensions depending on which of six terms they were exposed to. 'Chronically relapsing brain disease' induced the lowest stigmatizing blame attributions (P < 0.05); at the same time, this term decreased prognostic optimism [mean difference (MD) = 0.18, 95% CI = 0.05, 0.30] and increased perceived need for continuing care (MD = -0.26, 95% CI = -0.43, -0.09) and danger (MD = -0.13, 95% CI = -0.25, -0.02) when compared with 'problem'. Compared with a man, a woman was blamed more for opioid-related impairment (MD = -0.08, 95% CI = -0.15, -0.01); men were viewed as more dangerous (MD = 0.13, 95% CI = 0.06, 0.19) and to be socially excluded (MD = 0.16, 95% CI = 0.09, 0.23).ConclusionsThere does not appear to be one single medical term for opioid-related impairment that can meet all desirable clinical and public health goals. To reduce stigmatizing blame, biomedical 'chronically relapsing brain disease' terminology may be optimal; to increase prognostic optimism and decrease perceived danger/social exclusion use of non-medical terminology (e.g. 'opioid problem') may be optimal.
| S-EPMC8124079 | biostudies-literature