Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional ...post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user's desired dataset can vary from hours to days depending on factors such as dataset size or input parameters.
AI and immunology Germain, Ronald N.; Van Allen, Eliezer M.; Trynka, Gosia ...
Immunity,
06/2024, Letnik:
57, Številka:
6
Journal Article
Recenzirano
Odprti dostop
AI is rapidly becoming part of many aspects of daily life, with an impact that reaches all fields of research. We asked investigators to share their thoughts on how AI is changing immunology ...research, what is necessary to move forward, the potential and the pitfalls, and what will remain unchanged as the field journeys into a new era.
AI is rapidly becoming part of many aspects of daily life, with an impact that reaches all fields of research. We asked investigators to share their thoughts on how AI is changing immunology research, what is necessary to move forward, the potential and the pitfalls, and what will remain unchanged as the field journeys into a new era.
Objectives: To determine the psychometric properties of the Chinese version of the work and social adjustment scale (CWSAS) in outpatients with common mental disorders, and to evaluate the ...correlations of CWSAS with Physical Health Questionnaire-9 (PHQ-9), General Anxiety Disorder-7 (GAD-7), World Health Organization Five Well-being Index (WHO-5), and Chinese version of the Perceived Stress Scale- 10 (CPSS-10).
Methods: Forward and backward translations of the CWSAS was performed. Between October 2018 and March 2020, 252 outpatients with a common mental disorder who had a job or a job plan were recruited from two psychiatric centres in Hong Kong. Participants were asked to complete the CWSAS, PHQ-9, GAD-7, WHO-5, and CPSS-10. Classical test theory and Rasch analysis were undertaken to determine the psychometric properties of the CWSAS and its correlations with other tools.
Results: Principal component analysis revealed that the CWSAS was a one-factor structure and showed adequate convergent and discriminant validities, internal consistency, item-total correlation, and interitem correlation. There was a significant group difference in terms of employment status. CPSS-10 and PHQ-9 were predictors for CWSAS score. The CWSAS was a distinct factor among other outcome measures. Rasch analysis indicated that the CWSAS was well-targeted and unidimensional. The CWSAS had an adequate person separation index, item separation index, person reliability, and item reliability. No categorical disordering was found, whereas inadequate adjacent threshold distance was reported. The item of ability to work indicated a noticeable differential item functioning in employment status and main source of finance.
Conclusion: The CWSAS is psychometrically appropriate to measure functional outcomes in outpatients with common mental disorders.
Pathology in Practice Swan, Melissa P; Hooser, Stephen B; Lin, Tsang-Long
Journal of the American Veterinary Medical Association,
2022-May-20, Letnik:
259, Številka:
S2
Journal Article
Recenzirano
Odprti dostop
In collaboration with the American College of Veterinary Pathologists.
•While bronchoscopic biopsy methods result in fewer biopsy-related complications, percutaneous core-needle biopsy (PT-CNB) is superior in its ability to obtain more tissue.•Rebiopsies characterizing ...resistance mutations in patients with non-small cell lung cancer (NSCLC) can guide personalized medicine and improve overall survival rates.•Percutaneous core-needle lung biopsies obtain adequate samples for molecular characterization of the acquired resistance mutation T790M in patients with NSCLC.
Rebiopsies characterizing resistance mutations in patients with non-small cell lung cancer (NSCLC) can guide personalized medicine and improve overall survival rates. In this systematic review, we examine the suitability of percutaneous core-needle biopsy (PT-CNB) to obtain adequate samples for molecular characterization of the acquired resistance mutation T790M. This review provides evidence that PT-CNB can obtain samples with high adequacy, with a mutation detection rate that is in accordance with prior literature.
Non-small cell lung cancer (NSCLC) comprises 85% of all lung cancers and has seen improved survival rates with the rise of personalized medicine. Resistance mutations to first-line therapies, such as T790M, however, render first-line therapies ineffective. Rebiopsies characterizing resistance mutations inform therapeutic decisions, which result in prolonged survival. Given the high efficacy of percutaneous core-needle biopsy (PT-CNB), we conducted the first systematic review to analyze the ability of PT-CNB to obtain samples of high adequacy in order to characterize the acquired resistance mutation T790M in patients with NSCLC.
We performed a comprehensive literature search across PubMed, Embase, and CENTRAL. Search terms related to “NSCLC,” “rebiopsy,” and “PT-CNB” were used to obtain results. We included all prospective and retrospective studies that satisfied our inclusion and exclusion criteria. A random effects model was utilized to pool adequacy and detection rates of the chosen articles. We performed a systematic review, meta-analysis, and meta-regression to investigate the adequacy and T790M detection rates of samples obtained via PT-CNB.
Out of the 173 studies initially identified, 5 studies met the inclusion and exclusion criteria and were chosen for our final cohort of 436 patients for meta-analysis. The pooled adequacy rate of samples obtained via PT-CNB was 86.92% (95% CI: 79.31%, 92.0%) and the pooled T790M detection rate was 46.0% (95% CI: 26.6%, 66.7%). There was considerable heterogeneity among studies (I2 > 50%) in both adequacy and T790M detection rates.
PT-CNB can obtain adequate samples for T790M molecular characterization in NSCLC lung cancer patients. Additional prospective studies are needed to corroborate the results in this review.
Thieme congratulates Dr. Eric M. Genden on being chosen by New York magazine for its prestigious 'Best Doctors 2018' list!
Head and Neck Cancer: Management and Reconstruction, 2nd Edition by Eric M. ...Genden masterfully blends two lauded Thieme books, Reconstruction of the Head and Neck, focusing on defect repair, and Head and Neck Cancer, a multidisciplinary, evidence-based approach to treatment. A significant increase in the incidence of oropharyngeal cancer in the U.S. and other countries, especially among men, is attributed to high-risk subtypes of the human papillomavirus (HPV). HPV associated tonsillar cancer and base of tongue cancer account for 90% of all oropharyngeal squamous cell carcinoma. Internationally renowned authors share the latest knowledge on HPV and other causes of head and neck cancers, from diagnosis to cutting-edge treatments.
Thirty richly illustrated chapters feature open and endoscopic ablative techniques for treating a full spectrum of carcinomas and associated defects of the buccal, mandible and composite, laryngeal, hypopharyngeal, and parotid. The book encompasses the nuances of each pathology, step-by-step procedural guidance, clinical pearls, and the latest reconstructive techniques such as 3-D. For each disease, the authors discuss management concepts followed by principles of reconstruction and functional rehabilitation. Special topics include patient surveillance, monoclonal antibodies and immunotherapy, microvascular reconstruction, and minimizing wound complications.
We present a New Frontiers class mission concept of a Jupiter system observatory located at the Sun-Jupiter L1 point focusing on time-domain sciences to study Jupiter, its Galilean moons, and ...irregular satellites and address fundamental solar system sciences with broad implications and synergy to planetary missions and astrophysics studies.
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