A concise patient reported outcome measure for people with aphasia: the aphasia impact questionnaire 21

Background: There are many validated and widely used assessments within aphasiology. Few, however, describe language and life with aphasia from the perspective of the person with aphasia. Across healthcare, patient experience and user involvement are increasingly acknowledged as fundamental to person-centred care. As part of this movement, Patient Reported Outcome Measures (PROMs) are being used in service evaluation and planning. Aims: This paper reports the quantitative aspects of a mixed methods study that developed and validated a concise PROM, the Aphasia Impact Questionnaire (AIQ), co-produced with People with Aphasia (PWA). Methods & Procedures: The AIQ was developed within the social model of disability and all stages of the development of the AIQ were performed in partnership with PWA. It was adapted from a pre-existing and lengthier PROM for PWA, the Communication Disability Profile. The first iterations of the AIQ focused on domains of communication, participation and well-being/emotional state. Subsequently the AIQ was extended to include additional items relating to reading and writing (AIQ-21). The research design was iterative. Initially, concurrent validity, internal consistency, and sensitivity of the AIQ-prototype were obtained. The AIQ-prototype was modified to become the AIQ-21. Statistical testing with a new group of PWA was performed, investigating internal consistency and concurrent validity of the AIQ-21. Outcomes & Results: Results for both the AIQ-prototype and AIQ-21 showed statistically significant concurrent validity and good internal consistency. Repeated measurement using the AIQ-prototype demonstrated statistically significant change after PWA accessed a community intervention. Conclusions: The AIQ-21 is a PROM that has great potential to be one of the core set of aphasia tests for clinical and research use. Results can be used alongside language assessment to enable person-centred goal setting and partnership working for people with aphasia

Alcohol Consumption is associated with Increased CEA Levels in Male Patients with Stage IV Colorectal Cancer- A Single-Institution Retrospective Analysis

Introduction: Alcohol use is an independent risk factor for liver metastasis, a major cause of morbidity and mortality in colorectal cancer (CRC) patients. Serum CEA level is an established prognostic indicator in CRC, yet the correlation with behavioral factors such as alcohol use remains to be defined. In a single-center review, we evaluated alcohol use, gender, and CEA levels in predicting advanced disease in CRC patients. Methods: Retrospective analysis of UNMC patients diagnosed with CRC as the primary cancer between 2012-2019, stages I-IV, and age \u3e19 with documentation of alcohol use. Univariable statistics were performed using Chi-Square and non-parametric tests. Associations between stage, gender, and alcohol use (some vs. none) and the log-transformed CEA outcome (either initial or rate of change) were assessed using linear regressions. Results: Alcohol use was found to be reported in 333 of 1243 CRC patients. The cohort was comprised of 192 male and 141 female subjects. Elevated CEA levels at CRC diagnosis were associated with increased all-cause mortality (33.0% for CEA \u3e 3.4ng/ml vs 10.4% for CEA \u3c 3.4ng/ml). Model analysis found that stage IV male alcohol users showed an increase in serial CEA levels compared to males who did not use alcohol, but this pattern was not observed among stage IV females. Conclusions: Males with a history of alcohol use may be at risk for advanced CRC disease suggesting the utility of serial serum CEA monitoring in these patients. A detailed alcohol use history should be obtained in all patients with CRC as it has prognostic value and may allow for early intervention. This analysis was limited by missing alcohol use data for the majority (73.2%) of CRC patients evaluated. A prospective study is warranted to define the implications of alcohol use and risk of CRC liver metastasis

Microtubules gate tau condensation to spatially regulate microtubule functions.

Tau is an abundant microtubule-associated protein in neurons. Tau aggregation into insoluble fibrils is a hallmark of Alzheimer's disease and other types of dementia1, yet the physiological state of tau molecules within cells remains unclear. Using single-molecule imaging, we directly observe that the microtubule lattice regulates reversible tau self-association, leading to localized, dynamic condensation of tau molecules on the microtubule surface. Tau condensates form selectively permissible barriers, spatially regulating the activity of microtubule-severing enzymes and the movement of molecular motors through their boundaries. We propose that reversible self-association of tau molecules, gated by the microtubule lattice, is an important mechanism of the biological functions of tau, and that oligomerization of tau is a common property shared between the physiological and disease-associated forms of the molecule

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Surface Reconstruction of Maltese Cisterns Using ROV Sonar Data for Archeological Study

Abstract. We present a methodology and algorithm for the reconstruc tion of three dimensional geometric models of ancient Maltese water stor age systems, i.e. cisterns, from sonar data. This project was conducted as a part of a four week expedition on the islands of Malta and Gozo. During this expedition, investigators used underwater robot systems ca pable of mapping ancient underwater cisterns and tunnels. The mapping included probabilistic algorithms for constructing the maps of the sonar data and computer graphics for surface reconstruction and visualization. This paper presents the general methodology for the data acquisition and the novel application of algorithms from computer graphics for surface reconstruction to this new data setting. In addition to reconstructing the geometry of the cisterns, the visualization system includes methods to enhance the understanding of the data by visualizing water level and texture detail either through the application of real image data via pro jective textures or by more standard texture mapping techniques. The resulting surface reconstructions and visualizations can be used by ar chaeologists for educational purposes and to help understand the shape and history of such water receptacles

The philosopher of ambiguity: exploring stories of spirituality of people with aphasia through the lens of Merleau-Ponty

Spirituality as a concept has only recently begun to be considered in speech and language therapy research and practice, and phenomenology as a research methodology is also not widely used in SLT research. Yet, concepts propounded by the phenomenologist Maurice Merleau-Ponty arguably offer a useful theoretical framework from which to view certain aspects of SLT including the concept of spirituality and how this is expressed by people with a communication difficulty. In this project, eight people with aphasia were interviewed about their spirituality. The interviews were transcribed, themes identified and stories created. These stories were viewed using one of the concepts propounded by Merleau-Ponty, namely ambiguity

Coupling of kinesin ATP turnover to translocation and microtubule regulation: one engine, many machines

The cycle of ATP turnover is integral to the action of motor proteins. Here we discuss how variation in this cycle leads to variation of function observed amongst members of the kinesin superfamily of microtubule associated motor proteins. Variation in the ATP turnover cycle among superfamily members can tune the characteristic kinesin motor to one of the range of microtubule-based functions performed by kinesins. The speed at which ATP is hydrolysed affects the speed of translocation. The ratio of rate constants of ATP turnover in relation to association and dissociation from the microtubule influence the processivity of translocation. Variation in the rate-limiting step of the cycle can reverse the way in which the motor domain interacts with the microtubule producing non-motile kinesins. Because the ATP turnover cycle is not fully understood for the majority of kinesins, much work remains to show how the kinesin engine functions in such a wide variety of molecular machines

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution

A Simple Method for Analyzing Exome Sequencing Data Shows Distinct Levels of Nonsynonymous Variation for Human Immune and Nervous System Genes

To measure the strength of natural selection that acts upon single nucleotide variants (SNVs) in a set of human genes, we calculate the ratio between nonsynonymous SNVs (nsSNVs) per nonsynonymous site and synonymous SNVs (sSNVs) per synonymous site. We transform this ratio with a respective factor f that corrects for the bias of synonymous sites towards transitions in the genetic code and different mutation rates for transitions and transversions. This method approximates the relative density of nsSNVs (rdnsv) in comparison with the neutral expectation as inferred from the density of sSNVs. Using SNVs from a diploid genome and 200 exomes, we apply our method to immune system genes (ISGs), nervous system genes (NSGs), randomly sampled genes (RSGs), and gene ontology annotated genes. The estimate of rdnsv in an individual exome is around 20% for NSGs and 30–40% for ISGs and RSGs. This smaller rdnsv of NSGs indicates overall stronger purifying selection. To quantify the relative shift of nsSNVs towards rare variants, we next fit a linear regression model to the estimates of rdnsv over different SNV allele frequency bins. The obtained regression models show a negative slope for NSGs, ISGs and RSGs, supporting an influence of purifying selection on the frequency spectrum of segregating nsSNVs. The y-intercept of the model predicts rdnsv for an allele frequency close to 0. This parameter can be interpreted as the proportion of nonsynonymous sites where mutations are tolerated to segregate with an allele frequency notably greater than 0 in the population, given the performed normalization of the observed nsSNV to sSNV ratio. A smaller y-intercept is displayed by NSGs, indicating more nonsynonymous sites under strong negative selection. This predicts more monogenically inherited or de-novo mutation diseases that affect the nervous system

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

Allele frequency differences across populations can provide valuable information both for studying population structure and for identifying loci that have been targets of natural selection. Here, we examine the relationship between recombination rate and population differentiation in humans by analyzing two uniformly-ascertained, whole-genome data sets. We find that population differentiation as assessed by inter-continental FST shows negative correlation with recombination rate, with FST reduced by 10% in the tenth of the genome with the highest recombination rate compared with the tenth of the genome with the lowest recombination rate (P≪10−12). This pattern cannot be explained by the mutagenic properties of recombination and instead must reflect the impact of selection in the last 100,000 years since human continental populations split. The correlation between recombination rate and FST has a qualitatively different relationship for FST between African and non-African populations and for FST between European and East Asian populations, suggesting varying levels or types of selection in different epochs of human history