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European Journal of Translational... Jan 2022This article was not intended to be a complete review of the electromyography of pathological muscle states, but it was written to illustrate how the "Coletti Method of...
This article was not intended to be a complete review of the electromyography of pathological muscle states, but it was written to illustrate how the "Coletti Method of EMG ChemoDenervation" (CMECD®) protocol for the treatment of chronic pain resulting from chronic muscle spasm was developed and established. That process led to an unexpected understanding of the underlying pathophysiology of chronic muscle spasm, which represents a paradigm shift in our understanding and ultimately in our treatment of muscle spasm-induced chronic pain. Other investigators had brought to light the presence of spontaneous electrical activity (SEA) in states of muscle spasm. Those findings were all but ignored by standard EMG/Nerve conduction studies in clinical practice. Starting with a simple EMG device I experimented with various medications to treat patients with chronic pain associated with chronic muscle spasm. Suppression of SEA with long-acting medications resolved both the chronic spasm and chronic pain. A successful protocol using phenoxybenzamine was established and clinical outcomes were followed. More than 200 patients were successfully treated during last 12 years. Correlating known exercise muscle physiology with the development of the pathological state of chronic muscle spasm as seen by electromyography led to the postulation of the ischemic model of chronic muscle spasm. Light microscopy pathophysiologic supportive findings are presented and discussed. Predictions from this model to various aspects of treatment were supportive. Implications regarding treatment by the CMECD procedure, as well as other standard therapies, are discussed. Application of the ischemic model to other pain conditions was explored with implications of therapeutic modification. Recommendations for changes in rehabilitation therapy are discussed.
PubMed: 35044134
DOI: 10.4081/ejtm.2022.10323 -
BMC Medicine May 2020Individuals with co-occurring hyperactivity disorder/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) can have complex presentations that may complicate...
BACKGROUND
Individuals with co-occurring hyperactivity disorder/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) can have complex presentations that may complicate diagnosis and treatment. There are established guidelines with regard to the identification and treatment of ADHD and ASD as independent conditions. However, ADHD and ASD were not formally recognised diagnostically as co-occurring conditions until the Diagnostic and Statistical Manual of Mental Disorders 5 (DSM-5) was published in 2013. Hence, awareness and understanding of both conditions when they co-occur is less established and there is little guidance in the clinical literature. This has led to uncertainty among healthcare practitioners when working with children, young people and adults who present with co-existing ADHD and ASD. The United Kingdom ADHD Partnership (UKAP) therefore convened a meeting of professional experts that aimed to address this gap and reach expert consensus on the topic that will aid healthcare practitioners and allied professionals when working with this complex and vulnerable population.
METHOD
UK experts from multiple disciplines in the fields of ADHD and ASD convened in London in December 2017. The meeting provided the opportunity to address the complexities of ADHD and ASD as a co-occurring presentation from different perspectives and included presentations, discussion and group work. The authors considered the clinical challenges of working with this complex group of individuals, producing a consensus for a unified approach when working with male and female, children, adolescents and adults with co-occurring ADHD and ASD. This was written up, circulated and endorsed by all authors.
RESULTS
The authors reached a consensus of practical recommendations for working across the lifespan with males and females with ADHD and ASD. Consensus was reached on topics of (1) identification and assessment using rating scales, clinical diagnostic interviews and objective supporting assessments; outcomes of assessment, including standards of clinical reporting; (2) non-pharmacological interventions and care management, including psychoeducation, carer interventions/carer training, behavioural/environmental and Cognitive Behavioural Therapy (CBT) approaches; and multi-agency liaison, including educational interventions, career advice, occupational skills and training, and (3) pharmacological treatments.
CONCLUSIONS
The guidance and practice recommendations (Tables 1, 4, 5, 7, 8 and 10) will support healthcare practitioners and allied professionals to meet the needs of this complex group from a multidisciplinary perspective. Further research is needed to enhance our understanding of the diagnosis, treatment and management of individuals presenting with comorbid ADHD and ASD.
Topics: Adolescent; Adult; Attention Deficit Disorder with Hyperactivity; Autism Spectrum Disorder; Child; Consensus; Diagnostic and Statistical Manual of Mental Disorders; Female; Humans; Male; Young Adult
PubMed: 32448170
DOI: 10.1186/s12916-020-01585-y -
Proceedings of the National Academy of... Jan 2022Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic...
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
Topics: Animals; Base Sequence; Biodiversity; Biological Evolution; Ecology; Ecosystem; Eukaryota; Genome; Genomics; Humans; Phylogeny
PubMed: 35042801
DOI: 10.1073/pnas.2115636118 -
Bioinformatics (Oxford, England) Oct 2023Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages...
SUMMARY
Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be "anchored" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.
AVAILABILITY AND IMPLEMENTATION
PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.
Topics: Humans; Genome; Software; Eukaryota; Documentation; Sequence Analysis, DNA
PubMed: 37846049
DOI: 10.1093/bioinformatics/btad621 -
Bioinformatics (Oxford, England) May 2023Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford...
SUMMARY
Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.
AVAILABILITY AND IMPLEMENTATION
The cramino, chopper, kyber, and phasius tools are written in Rust and available as executable binaries without requiring installation or managing dependencies. Binaries build on musl are available for broad compatibility. NanoPlot and NanoComp are written in Python3. Links to the separate tools and their documentation can be found at https://github.com/wdecoster/nanopack. All tools are compatible with Linux, Mac OS, and the MS Windows Subsystem for Linux and are released under the MIT license. The repositories include test data, and the tools are continuously tested using GitHub Actions and can be installed with the conda dependency manager.
Topics: Humans; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing; Nanopores; Documentation
PubMed: 37171891
DOI: 10.1093/bioinformatics/btad311 -
AMIA ... Annual Symposium Proceedings.... 2021Working with scribes can reduce provider documentation time, but few studies have examined how scribes affect clinical notes. In this retrospective cross-sectional...
Working with scribes can reduce provider documentation time, but few studies have examined how scribes affect clinical notes. In this retrospective cross-sectional study, we examine over 50,000 outpatient progress notes written with and without scribe assistance by 70 providers across 27 specialties in 2017-2018. We find scribed notes were consistently longer than those written without scribe assistance, with most additional text coming from note templates. Scribed notes were also more likely to contain certain templated lists, such as the patient's medications or past medical history. However, there was significant variation in how working with scribes affected a provider's mix of typed, templated, and copied note text, suggesting providers adapt their documentation workflows to varying degrees when working with scribes. These results suggest working with scribes may contribute to note bloat, but that providers' individual documentation workflows, including their note templates, may have a large impact on scribed note contents.
Topics: Cross-Sectional Studies; Documentation; Electronic Health Records; Humans; Outpatients; Retrospective Studies
PubMed: 35309010
DOI: No ID Found -
Rural and Remote Health Jul 2022Communication is the foundation of informed consent in research. This article relays the reflections of an American urogynecology fellow and researcher in Kenya on the...
Communication is the foundation of informed consent in research. This article relays the reflections of an American urogynecology fellow and researcher in Kenya on the topic of informed consent. After learning of how a previous foreign researcher's presence in the community had violated the trust that women placed in women's health research, she reflects on how the standard eurocentric approach to obtaining written informed consent in research may sow breakdowns in communication and also perpetuate distrust in research. Particularly for settings in which the language is primarily spoken, or where there are varying literacy levels, the standard research consent should be reimagined to make the informed consent process more equitable and less of an exercise in documentation. Communication of research study information to patients must take into account the diverse and evolving ways in which patients best consume information, and in such a way that it ultimately enhances their autonomy.
Topics: Animals; Communication; Female; Humans; Informed Consent; Kenya; Language; Swine; Trust
PubMed: 35882376
DOI: 10.22605/RRH7370 -
Advances in Medicine 2023Ineffective nursing documentation practices have been reported to negatively impact patient outcomes and health professional efficiency. On the prevalence of nurses'... (Review)
Review
BACKGROUND
Ineffective nursing documentation practices have been reported to negatively impact patient outcomes and health professional efficiency. On the prevalence of nurses' documentation practices in Ethiopia, several separate studies have been carried out. However, there is no pooled prevalence of nurses' documentation practice. Therefore, this systematic review and meta-analysis aimed to assess the overall prevalence of nursing care documentation practice and related factors in Ethiopia.
METHODS AND MATERIALS
This review only included articles that were published. The main databases were Medline/PubMed, Web of Science, Google Scholar, Scopus, Ethiopian University Repository Online, and the Cochrane Library. Cross-sectional studies that satisfy the criteria and are written in English are included in the review. Using a random effects model, the pooled prevalence of nurses' documentation practices was determined. The funnel plot and the Eggers test were also used to look into publication bias. All statistical analyses were done with STATA version 14.
RESULT
This review included nine studies with a total of 2,900 participants. The pooled prevalence of nurses' documentation practice in Ethiopia was 50.01% (95% CI: 42.59 and 57.18; = 93.8%; and ≤ 0.001). In terms of subgroup analysis, Addis Ababa had the highest prevalence of nurses' documentation practice at 84% (95% CI: 77.18 and 90.82), while Southern Ethiopia had the lowest at 40.00% (95% CI: 38.10 and 44.90). Nursing documentation practices were statistically associated with the availability of nursing documentation formats, adequate nurse-to-patient ratio, motivation, and training.
CONCLUSION
This review showed that one in two nurses practiced poor documentation of their daily activities in Ethiopia. Therefore, strict monitoring, evaluation, and supervision of nursing care documentation services are highly recommended for all stakeholders. We strongly recommend improving the identified factors by arranging training for nurses, motivating them, providing adequate documentation formats, and maintaining a nurse-to-patient ratio.
PubMed: 37965424
DOI: 10.1155/2023/5565226 -
Statistics in Medicine Nov 2021The world is becoming increasingly complex, both in terms of the rich sources of data we have access to and the statistical and computational methods we can use on data....
The world is becoming increasingly complex, both in terms of the rich sources of data we have access to and the statistical and computational methods we can use on data. These factors create an ever-increasing risk for errors in code and the sensitivity of findings to data preparation and the execution of complex statistical and computing methods. The consequences of coding and data mistakes can be substantial. In this paper, we describe the key steps for implementing a code quality assurance (QA) process that researchers can follow to improve their coding practices throughout a project to assure the quality of the final data, code, analyses, and results. These steps include: (i) adherence to principles for code writing and style that follow best practices; (ii) clear written documentation that describes code, workflow, and key analytic decisions; (iii) careful version control; (iv) good data management; and (v) regular testing and review. Following these steps will greatly improve the ability of a study to assure results are accurate and reproducible. The responsibility for code QA falls not only on individual researchers but institutions, journals, and funding agencies as well.
Topics: Humans; Mathematical Computing
PubMed: 34486156
DOI: 10.1002/sim.9169 -
Journal of Medical Internet Research Nov 2022Topic modeling approaches allow researchers to analyze and represent written texts. One of the commonly used approaches in psychology is latent Dirichlet allocation... (Review)
Review
BACKGROUND
Topic modeling approaches allow researchers to analyze and represent written texts. One of the commonly used approaches in psychology is latent Dirichlet allocation (LDA), which is used for rapidly synthesizing patterns of text within "big data," but outputs can be sensitive to decisions made during the analytic pipeline and may not be suitable for certain scenarios such as short texts, and we highlight resources for alternative approaches. This review focuses on the complex analytical practices specific to LDA, which existing practical guides for training LDA models have not addressed.
OBJECTIVE
This scoping review used key analytical steps (data selection, data preprocessing, and data analysis) as a framework to understand the methodological approaches being used in psychology research using LDA.
METHODS
A total of 4 psychology and health databases were searched. Studies were included if they used LDA to analyze written words and focused on a psychological construct or issue. The data charting processes were constructed and employed based on common data selection, preprocessing, and data analysis steps.
RESULTS
A total of 68 studies were included. These studies explored a range of research areas and mostly sourced their data from social media platforms. Although some studies reported on preprocessing and data analysis steps taken, most studies did not provide sufficient detail for reproducibility. Furthermore, the debate surrounding the necessity of certain preprocessing and data analysis steps is revealed.
CONCLUSIONS
Our findings highlight the growing use of LDA in psychological science. However, there is a need to improve analytical reporting standards and identify comprehensive and evidence-based best practice recommendations. To work toward this, we developed an LDA Preferred Reporting Checklist that will allow for consistent documentation of LDA analytic decisions and reproducible research outcomes.
Topics: Humans; Reproducibility of Results; Big Data; Documentation; Databases, Factual
PubMed: 36346659
DOI: 10.2196/33166