Qualitative research within the Deaf community in Northern Ireland: A multilingual approach

In this methodology article, the authors illustrate how they conducted multilingual qualitative research in an exploration of the barriers that Deaf people in Northern Ireland face when attempting to access the system of justice. The authors’ research practices are informed, to the extent possible, by the principles of community-based participatory research (CBPR). They explore the challenges of conducting research in American Sign Language (ASL), British Sign Language (BSL), and Irish Sign Language (ISL), and spoken English, facilitated by sign language interpreters fluent in BSL and ISL. Centering the research on the lived experiences of Deaf people who navigate the system of justice, the authors implemented CBPR-informed research methods, which ultimately led to sustained discussion and joint action by the authors and members of the Northern Ireland Deaf community aimed at the removal of barriers that Deaf people face when interacting with the justice system. By writing about their methodological approach in Northern Ireland, the authors wish to be transparent about their work in the hope that other researchers can replicate their successes and avoid the limitations of conducting this work in partnership with members of the Deaf community in other countries.     

How accurate is Invisalign in nonextraction cases? Are predicted tooth positions achieved?

Objective:To evaluate the accuracy of Invisalign technology in achieving predicted tooth positions with respect to tooth type and direction of tooth movement.Materials and Methods:The posttreatment models of 30 patients who had nonextraction Invisalign treatment were digitally superimposed on their corresponding virtual treatment plan models using best-fit surface-based registration. The differences between actual treatment outcome and predicted outcome were computed and tested for statistical significance for each tooth type in mesial-distal, facial-lingual, and occlusal-gingival directions, as well as for tip, torque, and rotation. Differences larger than 0.5 mm for linear measurements and 2° for angular measurements were considered clinically relevant.Results:Statistically significant differences (P < .05) between predicted and achieved tooth positions were found for all teeth except maxillary lateral incisors, canines, and first premolars. In general, anterior teeth were positioned more occlusally than predicted, rotation of rounded teeth was incomplete, and movement of posterior teeth in all dimensions was not fully achieved. However, except for excess posttreatment facial crown torque of maxillary second molars, these differences were not large enough to be clinically relevant.Conclusions:Although Invisalign is generally able to achieve predicted tooth positions with high accuracy in nonextraction cases, some of the actual outcomes may differ from the predicted outcomes. Knowledge of dimensions in which the final tooth position is less consistent with the predicted position enables clinicians to build necessary compensations into the virtual treatment plan.     

Chapter 12: Systematic Review of Prognostic Tests

A number of new biological markers are being studied as predictors of disease or adverse medical events among those who already have a disease. Systematic reviews of this growing literature can help determine whether the available evidence supports use of a new biomarker as a prognostic test that can more accurately place patients into different prognostic groups to improve treatment decisions and the accuracy of outcome predictions. Exemplary reviews of prognostic tests are not widely available, and the methods used to review diagnostic tests do not necessarily address the most important questions about prognostic tests that are used to predict the time-dependent likelihood of future patient outcomes. We provide suggestions for those interested in conducting systematic reviews of a prognostic test. The proposed use of the prognostic test should serve as the framework for a systematic review and to help define the key questions. The outcome probabilities or level of risk and other characteristics of prognostic groups are the most salient statistics for review and perhaps meta-analysis. Reclassification tables can help determine how a prognostic test affects the classification of patients into different prognostic groups, hence their treatment. Review of studies of the association between a potential prognostic test and patient outcomes would have little impact other than to determine whether further development as a prognostic test might be warranted.     

Cytoplasmic TRADD Confers a Worse Prognosis in Glioblastoma

Tumor necrosis factor receptor 1 (TNFR1)-associated death domain protein (TRADD) is an important adaptor in TNFR1 signaling and has an essential role in nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and survival signaling. Increased expression of TRADD is sufficient to activate NF-κB. Recent studies have highlighted the importance of NF-κB activation as a key pathogenic mechanism in glioblastoma multiforme (GBM), the most common primary malignant brain tumor in adults.We examined the expression of TRADD by immunohistochemistry (IHC) and find that TRADD is commonly expressed at high levels in GBM and is detected in both cytoplasmic and nuclear distribution. Cytoplasmic IHC TRADD scoring is significantly associated with worse progression-free survival (PFS) both in univariate and multivariate analysis but is not associated with overall survival (n = 43 GBMs). PFS is a marker for responsiveness to treatment. We propose that TRADD-mediated NF-κB activation confers chemoresistance and thus a worse PFS in GBM. Consistent with the effect on PFS, silencing TRADD in glioma cells results in decreased NF-κB activity, decreased proliferation of cells, and increased sensitivity to temozolomide. TRADD expression is common in glioma-initiating cells. Importantly, silencing TRADD in GBM-initiating stem cell cultures results in decreased viability of stem cells, suggesting that TRADD may be required for maintenance of GBM stem cell populations. Thus, our study suggests that increased expression of cytoplasmic TRADD is both an important biomarker and a key driver of NF-κB activation in GBM and supports an oncogenic role for TRADD in GBM.     

Safety assessment of food and feed from biotechnology-derived crops employing RNA-mediated gene regulation to achieve desired traits: A scientific review

Gene expression can be modulated in plants to produce desired traits through agricultural biotechnology. Currently, biotechnology-derived crops are compared to their conventional counterparts, with safety assessments conducted on the genetic modification and the intended and unintended differences. This review proposes that this comparative safety assessment paradigm is appropriate for plants modified to express mediators of RNA-mediated gene regulation, including RNA interference (RNAi), a gene suppression mechanism that naturally occurs in plants and animals. The molecular mediators of RNAi, including long double-stranded RNAs (dsRNA), small interfering RNAs (siRNA), and microRNAs (miRNA), occur naturally in foods; therefore, there is an extensive history of safe consumption. Systemic exposure following consumption of plants containing dsRNAs that mediate RNAi is limited in higher organisms by extensive degradation of ingested nucleic acids and by biological barriers to uptake and efficacy of exogenous nucleic acids. A number of mammalian RNAi studies support the concept that a large margin of safety will exist for any small fraction of RNAs that might be absorbed following consumption of foods from biotechnology-derived plants that employ RNA-mediated gene regulation. Food and feed derived from these crops utilizing RNA-based mechanisms is therefore expected to be as safe as food and feed derived through conventional plant breeding.     

Stem water cryogenic extraction biases estimation in deuterium isotope composition of plant source water

The hydrogen isotope ratio of water cryogenically extracted from plant stem samples (δ²H_{stem_CVD}) is routinely used to aid isotope applications that span hydrological, ecological, and paleoclimatological research. However, an increasing number of studies have shown that a key assumption of these applications—that δ²H_{stem_CVD} is equal to the δ²H of plant source water (δ²H_source)—is not necessarily met in plants from various habitats. To examine this assumption, we purposedly designed an experimental system to allow independent measurements of δ²H_{stem_CVD}, δ²H_source, and δ²H of water transported in xylem conduits (δ²H_xylem) under controlled conditions. Our measurements performed on nine woody plant species from diverse habitats revealed a consistent and significant depletion in δ²H_{stem_CVD} compared with both δ²H_source and δ²H_xylem. Meanwhile, no significant discrepancy was observed between δ²H_source and δ²H_xylem in any of the plants investigated. These results cast significant doubt on the long-standing view that deuterium fractionation occurs during root water uptake and, alternatively, suggest that measurement bias inherent in the cryogenic extraction method is the root cause of δ²H_{stem_CVD} depletion. We used a rehydration experiment to show that the stem water cryogenic extraction error could originate from a dynamic exchange between organically bound deuterium and liquid water during water extraction. In light of our finding, we suggest caution when partitioning plant water sources and reconstructing past climates using hydrogen isotopes, and carefully propose that the paradigm-shifting phenomenon of ecohydrological separation (“two water worlds”) is underpinned by an extraction artifact.

The analysis of the stable isotope ratios of plant source water (δ_source) is a powerful tool enabling the elucidation of a range of plant physiological, ecological, and hydrological processes from scales ranging from individual plants to the planet. δ_source provides a foundation on which to form isotope signals of transpired water vapor and plant-derived biomarkers (i.e., cellulose and lipids) and thus is of high relevance to studies of terrestrial water fluxes (1, 2) and paleoclimate reconstructions (3, 4). δ_source also contains information on the spatial and temporal origins of water used by plants and so is commonly used for investigating plant water uptake patterns under natural conditions (5, 6). Moreover, dual-isotope (δ²H and δ¹⁸O) analysis of δ_source was critical in formulating the paradigm-shifting “two water worlds” (TWW) hypothesis, whereby ecohydrological separation exists between plant-accessible soil water pools and those recharging streams and groundwater (7, 8).Elucidation of the foregoing processes rest on the assumption that water extracted from plant stems is isotopically identical to water taken up by plant roots. Plant stem water is typically extracted with the cryogenic-vacuum distillation technique; δ generated with this method is hereinafter referred as δ_{stem_CVD} (9). For δ_{stem_CVD} to be an accurate indicator of δ_source (i.e., δ_{stem_CVD} = δ_source), two prerequisites must be met: 1) isotope change does not occur during root uptake and/or xylem transport of the source water (prerequisite I) and 2) stem water cryogenic extraction is a robust approach toward isotope recovery of xylem water (prerequisite II). The “δ_{stem_CVD} = δ_source” assumption is generally valid for oxygen isotopes of water, but numerous studies have used hydrogen isotopes to assess source water, and here this assumption has faced scrutiny, as multiple studies have reported significant depletion in δ²H_{stem_CVD} compared with δ²H_source in plants from various habitats (10–18).A frequently invoked explanation for the observed δ²H_{stem_CVD} depletion is a violation of prerequisite I, as it is believed that symplastic uptake of source water into the root xylem can give rise to hydrogen isotope fractionation (10, 11, 13, 19). The available evidence (10, 11) in support of such an explanation is largely peripheral, because direct, unambiguous confirmation of water uptake/transport-related fractionation would require a comparison of deuterium in source water and water transported within xylem conduits (δ²H_xylem). However, this type of comparison is difficult owing to the technical challenges in obtaining targeted measurements of δ²H_xylem in most plants. Intriguingly, in a field-grown riparian tree species (Populus euphratica) in which δ²H_xylem measurement was made possible with the aid of a syringe-aided xylem sap bleeding technique, no significant difference was observed between δ²H_xylem and δ²H_source (12). This led to the suggestion that, at least for the investigated species, δ²H_{stem_CVD} depletion arises not from a violation of prerequisite I, but rather from a violation of prerequisite II. The violation of prerequisite II has been deemed possible (12, 17) based on the argument that hydrogen isotope heterogeneity could be present within the bulk stem water (i.e., the outside xylem water may carry a metabolism-induced, more-depleted δ²H signature compared with the xylem water), potentially causing the stem water extraction technique to artifactually underestimate δ²H_xylem.Given the controvertible state of knowledge regarding the mechanism driving δ²H_{stem_CVD} depletion, it is imperative for us to build a better and more comprehensive understanding of the isotopic relationships among cryogenic extracted bulk stem water, source water, and xylem water in different plants, so as to put the application of the stem water cryogenic extraction technique in diverse fields on firmer ground. In this context, it should be pointed out that the xylem water direct sampling technique (12) is applicable only to a few riparian tree species. Recently, a new method relying on laser-enabled isotope measurement of water vapor in equilibrium with xylem water has demonstrated potential for in situ continuous monitoring of xylem isotope signatures in trees (20, 21); however, the method needs further development before it becomes broadly applicable to different plant types. Thus, a more generally applicable method is needed for determining xylem water signature across diverse plant types.Toward this goal, and capitalizing on the well-recognized mass balance-dictated principle that the isotopic composition of steady-state (SS) plant transpiration is identical to that of the xylem water supplying the plant canopy, we custom-designed a measurement system to enable independent quantification of xylem water isotope composition through isotope measurement of SS plant transpiration. This measurement system conferred the ability to compare values of δ_{stem_CVD}, δ_source, and δ_xylem across a number of plant species of varying native habitats. The data allowed us to confirm the common presence of δ²H_{stem_CVD} depletion across all plant types measured, and also to demonstrate that this phenomenon is caused by cryogenic extraction-associated artifact and not by water uptake/transport-related fractionation. We also performed a rehydration experiment to illustrate that the extraction artifact is unrelated to within-stem isotope heterogeneity as has been recently suggested, but rather is more likely linked to a deuterium-exchange process that occurs dynamically during cryogenic extraction. Using the TWW hypothesis as an example, we further discuss the ramifications for ecological/hydrological queries that rely on accurate isotopic information on plant source/xylem water.