Translating Ultrasound into Clinical Practice for the Assessment of Swallowing and Laryngeal Function: A Speech and Language Pathology-Led Consensus Study

Ultrasound (US) has an emerging evidence base for the assessment of swallowing and laryngeal function. Accessibility and technological advances support the use of US as a clinical assessment tool; however, there is insufficient evidence to support its translation into clinical practice. This study aimed to establish consensus on the priorities for translation of US into clinical practice for the assessment of swallowing and laryngeal function. Nominal Group Technique (NGT) was used as a formal method of consensus development. Clinicians and academics, all members of an international US working group, were invited to participate in the study. Two NGT meetings were held, where participants silently generated and then shared ideas. Participants anonymously ranked items. Rankings were aggregated before participants re-ranked items in order of priority. Discussions regarding rankings were recorded and transcribed to inform analysis. Member-checking with participants informed the final analysis. Participants (n = 15) were speech and language pathologists, physiotherapists and sonographers representing six countries. Fifteen items were identified and prioritised 1–13 (including two equally ranked items). Reliability, validity and normative data emerged as key areas for research while development of training protocols and engagement with stakeholders were considered vital to progressing US into practice. Analysis revealed common themes that might be addressed together in research, in addition to the ranked priority. A measured approach to the translation of US into clinical practice will enable effective implementation of this tool. Priorities may evolve as clinical and professional contexts shift, but this study provides a framework to advance research and clinical practice in this field

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

Translating ultrasound into clinical practice for the assessment of swallowing and laryngeal function: A speech and language pathology-led consensus study

Joan Ma - ORCID: 0000-0003-2051-8360 https://orcid.org/0000-0003-2051-8360Ultrasound (US) has an emerging evidence base for the assessment of swallowing and laryngeal function. Accessibility and technological advances support the use of US as a clinical assessment tool; however, there is insufficient evidence to support its translation into clinical practice. This study aimed to establish consensus on the priorities for translation of US into clinical practice for the assessment of swallowing and laryngeal function. Nominal Group Technique (NGT) was used as a formal method of consensus development. Clinicians and academics, all members of an international US working group, were invited to participate in the study. Two NGT meetings were held, where participants silently generated and then shared ideas. Participants anonymously ranked items. Rankings were aggregated before participants re-ranked items in order of priority. Discussions regarding rankings were recorded and transcribed to inform analysis. Member-checking with participants informed the final analysis. Participants (n = 15) were speech and language pathologists, physiotherapists and sonographers representing six countries. Fifteen items were identified and prioritised 1–13 (including two equally ranked items). Reliability, validity and normative data emerged as key areas for research while development of training protocols and engagement with stakeholders were considered vital to progressing US into practice. Analysis revealed common themes that might be addressed together in research, in addition to the ranked priority. A measured approach to the translation of US into clinical practice will enable effective implementation of this tool. Priorities may evolve as clinical and professional contexts shift, but this study provides a framework to advance research and clinical practice in this field.Jodi Allen receives part-funding from the National Institute of Health Research (NIHR) Pre-Clinical Academic Fellowship Award. Gemma Clunie receives funding from the National Institute for Health Research (NIHR) Integrated Clinical Academic Clinical Doctoral Fellowship Programme and acknowledges the support and infrastructure provided by the NIHR Imperial Biomedical Research Centre. Anna Volkmer receives funding from the NIHR via a Development and Skills Award. Soren Lowell receives funding from the National Institute of Health (NIH) Research Enhancement Award (R15).https://doi.org/10.1007/s00455-022-10413-9aheadofprintaheadofprin

Translating Ultrasound into Clinical Practice for the Assessment of Swallowing and Laryngeal Function: A Speech and Language Pathology-Led Consensus Study

From Springer Nature via Jisc Publications RouterHistory: received 2021-11-09, accepted 2022-01-19, registration 2022-01-20, pub-electronic 2022-02-24, online 2022-02-24, pub-print 2022-12Acknowledgements: Acknowledgements: The authors would like to thank the members of the international ultrasound group who participated in this project: Jemma Haines (UK), Becca Hammond (NZ), Lisa Hayward (UK), Professor Maggie-Lee Huckabee (New Zealand), Marloes Lagarde (Netherlands), Corinne Mossey-Gaston (UK), Claire Slinger (UK) and Sarah Wallace (UK).Publication status: PublishedFunder: Research Trainees Coordinating Centre; doi: http://dx.doi.org/10.13039/501100000659; Grant(s): Pre-Clinical Academic Fellowship, Clinical Doctoral Research Fellowship, Development and Skills AwardFunder: National Institutes of Health; doi: http://dx.doi.org/10.13039/100000002; Grant(s): Research Enhancement Award (R15)Ultrasound (US) has an emerging evidence base for the assessment of swallowing and laryngeal function. Accessibility and technological advances support the use of US as a clinical assessment tool; however, there is insufficient evidence to support its translation into clinical practice. This study aimed to establish consensus on the priorities for translation of US into clinical practice for the assessment of swallowing and laryngeal function. Nominal Group Technique (NGT) was used as a formal method of consensus development. Clinicians and academics, all members of an international US working group, were invited to participate in the study. Two NGT meetings were held, where participants silently generated and then shared ideas. Participants anonymously ranked items. Rankings were aggregated before participants re-ranked items in order of priority. Discussions regarding rankings were recorded and transcribed to inform analysis. Member-checking with participants informed the final analysis. Participants (n = 15) were speech and language pathologists, physiotherapists and sonographers representing six countries. Fifteen items were identified and prioritised 1–13 (including two equally ranked items). Reliability, validity and normative data emerged as key areas for research while development of training protocols and engagement with stakeholders were considered vital to progressing US into practice. Analysis revealed common themes that might be addressed together in research, in addition to the ranked priority. A measured approach to the translation of US into clinical practice will enable effective implementation of this tool. Priorities may evolve as clinical and professional contexts shift, but this study provides a framework to advance research and clinical practice in this field

The genome sequence of <i>Trypanosoma brucei gambiense</i>, causative agent of chronic Human African Trypanosomiasis

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; &lt;i&gt;Trypanosoma brucei gambiense&lt;/i&gt; is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a &lt;i&gt;T. b. brucei&lt;/i&gt; isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between &lt;i&gt;T. b. gambiense&lt;/i&gt; and the reference genome. We sought to identify features that were uniquely associated with &lt;i&gt;T. b. gambiense&lt;/i&gt; and its ability to infect humans.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and findings:&lt;/b&gt; An improved high-quality draft genome sequence for the group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with &lt;i&gt;T. b. brucei&lt;/i&gt; showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972. A comparison of the variant surface glycoproteins (VSG) in &lt;i&gt;T. b. brucei&lt;/i&gt; with all &lt;i&gt;T. b. gambiense&lt;/i&gt; sequence reads showed that the essential structural repertoire of VSG domains is conserved across &lt;i&gt;T. brucei&lt;/i&gt;.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study provides the first estimate of intraspecific genomic variation within &lt;i&gt;T. brucei&lt;/i&gt;, and so has important consequences for future population genomics studies. We have shown that the &lt;i&gt;T. b. gambiense&lt;/i&gt; genome corresponds closely with the reference, which should therefore be an effective scaffold for any &lt;i&gt;T. brucei&lt;/i&gt; genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in &lt;i&gt;T. b. brucei&lt;/i&gt;, no &lt;i&gt;T. b. gambiense&lt;/i&gt;-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.&lt;/p&gt

Polymorphisms in the SAA1/2 Gene Are Associated with Carotid Intima Media Thickness in Healthy Han Chinese Subjects: The Cardiovascular Risk Survey

BACKGROUND: Serum amyloid A protein (SAA) is not only an inflammatory factor, but also an apolipoprotein that can replace apolipoprotein A1 (apoA1) as the major apolipoprotein of high-density lipoprotein (HDL), which has been linked to atherosclerosis. However, the relationship between genetic polymorphisms of SAA and the intima-media thickness (IMT) of the common carotid artery in healthy subjects remains unclear. We investigated the role of SAA1 and SAA2 gene polymorphisms with IMT in a cohort of healthy subjects participating in the Cardiovascular Risk Survey (CRS) study. METHODOLOGY/PRINCIPAL FINDINGS: Anthropometric and B-mode ultrasound of the carotid IMT were measured in 1914 subjects (849 men; 1065 women) recruited from seven cities in Xinjiang province, (western China). Four SNPs (rs12218, rs2229338, rs1059559, and rs2468844) were genotyped by use of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The SNP rs12218 was associated with carotid IMT by analyses of a dominate model (P<0.001) and additive model (P = 0.003), and the difference remained significant after multivariate adjustment (P = 0.008, P<0.001, respectively). This relationship was also observed in rs2468844 after multivariate adjustment by recessive model analysis (P = 0.011) but this was not observed in rs2229338 and rs1059559 before and after multivariate adjustment. These associations were not modified by serum HDL concentration. Furthermore, there were significant interactions between rs2468844 and rs12218 (interaction P<0.001) and rs2229338 (interaction P = 0.001) on carotid IMT. CONCLUSION/SIGNIFICANCE: Both rs12218 of the SAA1 gene and rs2468844 of SAA2 gene are associated with carotid IMT in healthy Han Chinese subjects

Identification of spinal circuits involved in touch-evoked dynamic mechanical pain

Mechanical hypersensitivity is a debilitating symptom associated with millions of chronic pain patients. It exists in distinct forms, including brush-evoked dynamic and filament-evoked punctate. Here we report that dynamic mechanical hypersensitivity induced by nerve injury or inflammation was compromised in mice with ablation of spinal VT3Lbx1 neurons defined by coexpression of VGLUT3Cre and Lbx1Flpo, as indicated by the loss of brush-evoked nocifensive responses and conditional place aversion. Electrophysiological recordings show that VT3Lbx1 neurons form morphine-resistant polysynaptic pathways relaying inputs from low-threshold Aβ mechanoreceptors to lamina I output neurons. Meanwhile, the subset of somatostatin (SOM) lineage neurons preserved in VT3Lbx1 neuron-ablated mice is largely sufficient to mediate von Frey filament-evoked punctate mechanical hypersensitivity, including both morphine-sensitive and morphine-resistant forms. Furthermore, acute silencing of VT3Lbx1 neurons attenuated pre-established dynamic mechanical hypersensitivity induced by nerve injury, suggesting these neurons as a potential cellular target for treating this form of neuropathic pain

An Unexpected Role for the Clock Protein Timeless in Developmental Apoptosis

Background: Programmed cell death is critical not only in adult tissue homeostasis but for embryogenesis as well. One of the earliest steps in development, formation of the proamniotic cavity, involves coordinated apoptosis of embryonic cells. Recent work from our group demonstrated that c-Src protein-tyrosine kinase activity triggers differentiation of mouse embryonic stem (mES) cells to primitive ectoderm-like cells. In this report, we identified Timeless (Tim), the mammalian ortholog of a Drosophila circadian rhythm protein, as a binding partner and substrate for c-Src and probed its role in the differentiation of mES cells. Methodology/Principal Findings: To determine whether Tim is involved in ES cell differentiation, Tim protein levels were stably suppressed using shRNA. Tim-defective ES cell lines were then tested for embryoid body (EB) formation, which models early mammalian development. Remarkably, confocal microscopy revealed that EBs formed from the Tim-knockdown ES cells failed to cavitate. Cells retained within the centers of the failed cavities strongly expressed the pluripotency marker Oct4, suggesting that further development is arrested without Tim. Immunoblots revealed reduced basal Caspase activity in the Tim-defective EBs compared to wild-type controls. Furthermore, EBs formed from Tim-knockdown cells demonstrated resistance to staurosporine-induced apoptosis, consistent with a link between Tim and programmed cell death during cavitation. Conclusions/Significance: Our data demonstrate a novel function for the clock protein Tim during a key stage of early development. Specifically, EBs formed from ES cells lacking Tim showed reduced caspase activity and failed to cavitate. As a consequence, further development was halted, and the cells present in the failed cavity remained pluripotent. These findings reveal a new function for Tim in the coordination of ES cell differentiation, and raise the intriguing possibility that circadian rhythms and early development may be intimately linked. © 2011 O'Reilly et al