Predicting responses to chemotherapy in the context that matters - the patient.
Ontology highlight
ABSTRACT:
SUBMITTER: Moreno-Gonzalez A
PROVIDER: S-EPMC4845209 | biostudies-other | 2016 Jan
REPOSITORIES: biostudies-other
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Project description:BackgroundUnderstanding public attitudes to genomic data sharing is widely seen as key in shaping effective governance. However, empirical research in this area often fails to capture the contextual nuances of diverse sharing practices and regulatory concerns encountered in real-world genomic data sharing. This study aimed to investigate factors affecting public attitudes to data sharing through responses to diverse genomic data sharing scenarios.MethodsA set of seven empirically validated genomic data sharing scenarios reflecting a range of current practices in Australia was used in an open-ended survey of a diverse sample of the Australian public (n = 243). Qualitative responses were obtained for each of the scenarios. Respondents were each allocated one scenario and asked five questions on: whether (and why/not) they would share data; what sharing would depend on; benefits and risks of sharing; risks they were willing to accept if sharing was certain to result in benefits; and what could increase their comfort about sharing and any potential risk. A thematic analysis was used to examine responses, coded and validated by two blinded coders.ResultsParticipants indicated an overall high willingness to share genomic information, although this willingness varied considerably between different scenarios. A strong perception of benefits was reported as the foremost explanation for willingness to share across all scenarios. The high degree of convergence in the perception of benefits and the types of benefits identified by participants across all the scenarios suggests that the differentiation in intention to share may lie in perceptions of risk, which showed distinct patterns within and between the different scenarios. Some concerns were shared strongly across all scenarios, particularly benefit sharing, future use, and privacy.ConclusionsQualitative responses provide insight into popular assumptions regarding existing protections, conceptions of privacy, and which trade-offs are generally acceptable. Our results indicate that public attitudes and concerns are heterogeneous and influenced by the context in which sharing takes place. The convergence of key themes such as benefits and future uses point to core concerns that must be centred in regulatory responses to genomic data sharing.
| S-EPMC10068139 | biostudies-literature
Project description:Many flavoenzymes--oxidases and monooxygenases--react faster with oxygen than free flavins do. There are many ideas on how enzymes cause this. Recent work has focused on the importance of a positive charge near N5 of the reduced flavin. Fructosamine oxidase has a lysine near N5 of its flavin. We measured a rate constant of 1.6 × 10(5) M(-1) s(-1) for its reaction with oxygen. The Lys276Met mutant reacted with a rate constant of 291 M(-1) s(-1), suggesting an important role for this lysine in oxygen activation. The dihydroorotate dehydrogenases from E. coli and L. lactis also have a lysine near N5 of the flavin. They react with O(2) with rate constants of 6.2 × 10(4) and 3.0 × 10(3) M(-1) s(-1), respectively. The Lys66Met and Lys43Met mutant enzymes react with rate constants that are nearly the same as those for the wild-type enzymes, demonstrating that simply placing a positive charge near N5 of the flavin does not guarantee increased oxygen reactivity. Our results show that the lysine near N5 does not exert an effect without an appropriate context; evolution did not find only one mechanism for activating the reaction of flavins with O(2).
| S-EPMC3203534 | biostudies-literature
Project description:BackgroundThere is a growing number of older adults with cognitive impairment (CI) that require inpatient rehabilitation, and as such patient centred rehabilitation models have been developed. However, implementing evidence-based models without attending to the fit of the model to the new context could lead to an unsuccessful outcome. Researchers collaborated with administrators and staff in one rural site to adapt a patient centred rehabilitation model of care in the Canadian province of Ontario. This paper reports on the contextual factors that influenced the implementation of the model of care.MethodsThe study takes a case study approach. One rural facility was purposefully selected for its interest in offering rehabilitation to persons with CI. Four focus group discussions were conducted to explore healthcare professionals' perceptions on the contextual factors that could affect the implementation of the rehabilitation model of care in the facility. Twenty-seven professionals with various backgrounds were purposively sampled using a maximum diversity sampling strategy. A hybrid inductive-deductive approach was used to analyze the data using the Context and Implementation of Complex Interventions (CICI) Framework.ResultsAcross the domains of the CICI framework, three domains (political, epidemiological, and geographical) and seven corresponding sub-domains of the context were found to have a major influence on the implementation process. Key elements within the political domain included effective teamwork, facilitation, adequate resources, effective communication strategies, and a vision for change. Within the epidemiological domain, a key element was knowing how to tailor rehabilitation approaches for persons with CI. Infrastructure, an aspect of the geographical domain, focused on the facility's physical layout that required attention.ConclusionsThe CICI framework was a useful guide to identify key factors within the context that existed and were required to fully support the implementation of the model of care in a new environment. The findings suggest that when implementing a new program of care, strong consideration should be paid to the political, epidemiological, and geographical domains of the context and how they interact and influence one another.
| S-EPMC7937255 | biostudies-literature
Project description:PurposeA setting-sensitive instrument for assessing Quality of Life (QoL) in Telemedicine (TM) was unavailable. To close this gap, a content-valid "add-on" measure was developed. In parallel, a brief index was derived featuring six items that summarise the main content of the multidimensional assessment. After pre- and pilot-testing, the psychometric performance of the final measures was investigated in an independent validation study.MethodsThe questionnaires were applied along with other standardised instruments of similar concepts as well as associated, yet disparate concepts for validation purposes. The sample consisted of patients with depression or heart failure, with or without TM (n = 200). Data analyses were aimed at calculating descriptive statistics and testing the psychometric performance on item, scale, and instrument level, including different types of validity and reliability.ResultsThe proposed factor structure of the multidimensional Tele-QoL measure has been confirmed. Reliability coefficients for internal consistency, split-half, and test-retest reliability of the subscales and index reached sufficient values. The Tele-QoL subscales and the index demonstrated Rasch scalability. Validity of both instruments can be assumed. Evidence for discriminant construct validity was provided. Known-groups validity was indicated by respective score differences for various classes of disease severity.ConclusionBoth measures show convincing psychometric properties. The final multidimensional Tele-QoL assessment consists of six outcome scales and two impact scales assessing (un-)intended effects of TM on QoL. In addition, the Tele-QoL index provides a short alternative for outcome assessment. The Tele-QoL measures can be used as complementary modules to existing QoL instruments capturing healthcare-related aspects of QoL from the patients' perspective.
| S-EPMC10522723 | biostudies-literature
Project description:Progress in understanding childhood disease using next-generation sequencing (NGS) portends vast improvements in the nature and quality of patient care. However, ethical questions surrounding the disclosure of incidental findings (IFs) persist, as NGS and other novel genomic technologies become the preferred tool for clinical genetic testing. Thus, the need for comprehensive management plans and multidisciplinary discussion on the return of IFs in pediatric research has never been more immediate. The aim of this study is to explore the views of investigators concerning the return of IFs in the pediatric oncology research context. Our findings reveal at least four contextual themes underlying the ethics of when, and how, IFs could be disclosed to participants and their families: clinical significance of the result, respect for individual, scope of professional responsibilities, and implications for the healthcare/research system. Moreover, the study proposes two action items toward anticipatory governance of IF in genetic research with children. The need to recognize the multiplicity of contextual factors in determining IF disclosure practices, particularly as NGS increasingly becomes a centerpiece in genetic research broadly, is heightened when children are involved. Sober thought should be given to the possibility of discovering IF, and to proactive discussions about disclosure considering the realities of young participants, their families, and the investigators who recruit them.
| S-EPMC4062531 | biostudies-other
Project description:The selection of effective genes that accurately predict chemotherapy responses might improve cancer outcomes. We compare optimized gene signatures for cisplatin, carboplatin, and oxaliplatin responses in the same cell lines and validate each signature using data from patients with cancer. Supervised support vector machine learning is used to derive gene sets whose expression is related to the cell line GI50 values by backwards feature selection with cross-validation. Specific genes and functional pathways distinguishing sensitive from resistant cell lines are identified by contrasting signatures obtained at extreme and median GI50 thresholds. Ensembles of gene signatures at different thresholds are combined to reduce the dependence on specific GI50 values for predicting drug responses. The most accurate gene signatures for each platin are: cisplatin: BARD1, BCL2, BCL2L1, CDKN2C, FAAP24, FEN1, MAP3K1, MAPK13, MAPK3, NFKB1, NFKB2, SLC22A5, SLC31A2, TLR4, and TWIST1; carboplatin: AKT1, EIF3K, ERCC1, GNGT1, GSR, MTHFR, NEDD4L, NLRP1, NRAS, RAF1, SGK1, TIGD1, TP53, VEGFB, and VEGFC; and oxaliplatin: BRAF, FCGR2A, IGF1, MSH2, NAGK, NFE2L2, NQO1, PANK3, SLC47A1, SLCO1B1, and UGT1A1. Data from The Cancer Genome Atlas (TCGA) patients with bladder, ovarian, and colorectal cancer were used to test the cisplatin, carboplatin, and oxaliplatin signatures, resulting in 71.0%, 60.2%, and 54.5% accuracies in predicting disease recurrence and 59%, 61%, and 72% accuracies in predicting remission, respectively. One cisplatin signature predicted 100% of recurrence in non-smoking patients with bladder cancer (57% disease-free; N?=?19), and 79% recurrence in smokers (62% disease-free; N?=?35). This approach should be adaptable to other studies of chemotherapy responses, regardless of the drug or cancer types.
| S-EPMC6329797 | biostudies-literature
Project description:Neoadjuvant chemoradiotherapy (CRT) is used in locally advanced rectal cancer when tumours threaten the circumferential resection margin. A variable response to treatment remains, notwithstanding potentially significant morbidity, and no clinically routinely used predictive biomarkers guide decision making. This experimental study aimed to identify significantly differentially expressed proteins between patients responding or not to CRT, using novel temporal proteomic profiling, and to validate any proteins of interest.
2018-03-12 | PXD008436 | Pride
Project description:Bacteria-phage symbioses are ubiquitous in nature and serve as valuable biological models. Historically, the ecology and evolution of bacteria-phage systems have been studied in either very simple or very complex communities. Although both approaches provide insight, their shortcomings limit our understanding of bacteria and phages in multispecies contexts. To address this gap, here we synthesize the emerging body of bacteria-phage experiments in medium-complexity communities, specifically those that manipulate bacterial community presence. Generally, community presence suppresses both focal bacterial (phage host) and phage densities, while sometimes altering bacteria-phage ecological interactions in diverse ways. Simultaneously, community presence can have an array of evolutionary effects. Sometimes community presence has no effect on the coevolutionary dynamics of bacteria and their associated phages, whereas other times the presence of additional bacterial species constrains bacteria-phage coevolution. At the same time, community context can alter mechanisms of adaptation and interact with the pleiotropic consequences of (co)evolution. Ultimately, these experiments show that community context can have important ecological and evolutionary effects on bacteria-phage systems, but many questions still remain unanswered and ripe for additional investigation.
| S-EPMC8528888 | biostudies-literature
Project description:During sleep, recently acquired episodic memories (i.e., autobiographical memories for specific events) are strengthened and transformed, a process termed consolidation. These memories are contextual in nature, with details of specific features interwoven with more general properties such as the time and place of the event. In this study, we hypothesized that the context in which a memory is embedded would guide the process of consolidation during sleep. To test this idea, we used a spatial memory task and considered changes in memory over a 10-h period including either sleep or wake. In both conditions, participants (N = 62) formed stories that contextually bound four objects together and then encoded the on-screen spatial position of all objects. Results showed that the changes in memory over the sleep period were correlated among contextually linked objects, whereas no such effect was identified for the wake group. These results demonstrate that context-binding plays an important role in memory consolidation during sleep.
| S-EPMC9987156 | biostudies-literature
Project description:Even in V1, where neurons have well characterized classical receptive fields (CRFs), it has been difficult to deduce which features of natural scenes stimuli they actually respond to. Forward models based upon CRF stimuli have had limited success in predicting the response of V1 neurons to natural scenes. As natural scenes exhibit complex spatial and temporal correlations, this could be due to surround effects that modulate the sensitivity of the CRF. Here, instead of attempting a forward model, we quantify the importance of the natural scenes surround for awake macaque monkeys by modeling it non-parametrically. We also quantify the influence of two forms of trial to trial variability. The first is related to the neuron's own spike history. The second is related to ongoing mean field population activity reflected by the local field potential (LFP). We find that the surround produces strong temporal modulations in the firing rate that can be both suppressive and facilitative. Further, the LFP is found to induce a precise timing in spikes, which tend to be temporally localized on sharp LFP transients in the gamma frequency range. Using the pseudo R(2) as a measure of model fit, we find that during natural scene viewing the CRF dominates, accounting for 60% of the fit, but that taken collectively the surround, spike history and LFP are almost as important, accounting for 40%. However, overall only a small proportion of V1 spiking statistics could be explained (R(2)?5%), even when the full stimulus, spike history and LFP were taken into account. This suggests that under natural scene conditions, the dominant influence on V1 neurons is not the stimulus, nor the mean field dynamics of the LFP, but the complex, incoherent dynamics of the network in which neurons are embedded.
| S-EPMC3389039 | biostudies-literature