tbuckley/cabot-search huggingface dataset:
An implementation science approach to evaluating pathogen whole genome sequencing in public health
Authors: Angeline S. Ferdinand, Margaret Kelaher, Courtney R. Lane, Anders Gonçalves da Silva, Norelle L. Sherry, Susan A. Ballard, Patiyan Andersson, Tuyet Hoang, Justin T. Denholm, Marion Easton, Benjamin P. Howden, Deborah A. Williamson
Journal: Genome Medicine (2021)

Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease surveillance, outbreak investigation and infection prevention and control. However, to date, there are limited data regarding (i) the optimal models for integration of genomic data into epidemiological investigations and (ii) how to quantify and evaluate public health impacts resulting from genomic epidemiological investigations.We developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2.The framework utilises an adaptable whole-of-system approach towards understanding how interconnected elements in the public health application of pathogen genomics contribute to public health processes and outcomes. The three phases of the PG-PHASE Framework are designed to support understanding of WGS laboratory processes, analysis, reporting and data sharing, and how genomic data are utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing to the use of sequence data in public health surveillance, investigation and decision-making. Importantly, the phases can be used separately or in conjunction, depending on the need of the evaluator. Subsequent to conducting evaluation underpinned by the framework, avenues may be developed for strategic investment or interventions to improve utilisation of whole genome sequencing.Comprehensive evaluation is critical to support health departments, public health laboratories and other stakeholders to successfully incorporate microbial genomics into public health practice. The PG-PHASE Framework aims to assist public health laboratories, health departments and authorities who are either considering transitioning to whole genome sequencing or intending to assess the integration of WGS in public health practice, including the capacity to detect and respond to outbreaks and associated costs, challenges and facilitators in the utilisation of microbial genomics and public health impacts.
Haploflow: strain-resolved de novo assembly of viral genomes
Authors: Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmueller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn, Alice Carolyn McHardy
Journal: Genome biology (2021)

Abstract With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assess Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. We show Haploflow reconstructs viral strain genomes from patient HCMV samples and SARS-CoV-2 wastewater samples identical to clinical isolates.
Endoscopic ultrasound-guided gallbladder drainage: a backdoor for biliary decompression?
Authors: Mihai Rimbaș, Stefano Francesco Crinò, Gianenrico Rizzatti, Alberto Larghi
Journal: Endoscopy (2021)

See also: Endoscopic ultrasound-guided gallbladder drainage as a rescue therapy for unresectable malignant biliary obstruction: a multicenter experience Endoscopy 2021; 53(08): 827-831DOI: 10.1055/a-1259-0349
Data Comparison and Software Design for Easy Selection and Application of CRISPR-Based Genome Editing Systems in Plants
Authors: Yi Wang, Fatma Lecourieux, Rui Zhang, Zhanwu Dai, David Lecourieux, Shaohua Li, Zhenchang Liang
Journal: Genomics Proteomics & Bioinformatics (2021)

Abstract CRISPR-based genome editing systems have been successfully and effectively used in many organisms. However, only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications. Although many web-based toolkits are available, there is still a shortage of comprehensive, user-friendly, and plant-specific CRISPR databases and desktop software. In this study, we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif (PAM) sites, the effects of GC content, optimal proto-spacer length, potential universality within the plant kingdom, PAM-rich region (PARR) inhibiting ratio, and the effects of G-quadruplex (G-Q) structures. Using this information, we built a comprehensive CRISPR database (including 138 plant genome data sources, www.grapeworld.cn/pc/index.html), which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems. We also developed a desktop software on the basis of the Perl/Tk tool, which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows platform. Therefore, this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.
Construction of multifunctional hydrogel based on the tannic acid-metal coating decorated MoS2 dual nanozyme for bacteria-infected wound healing
Authors: Yang Li, Rongzhan Fu, Zhiguang Duan, Chenhui Zhu, Daidi Fan
Journal: Bioactive Materials (2021)

Bacterial infection, tissue hypoxia and inflammatory response can hinder the infected wound repair process. To mitigate the above issues, tannic acid-chelated Fe-decorated molybdenum disulfide nanosheets (MoS2@TA/Fe NSs) with dual enzyme activities were developed and anchored to a multifunctional hydrogel. The hydrogel exhibited excellent antibacterial ability owing to the combined effects of photothermal therapy (PTT), glutathione (GSH) loss, and the peroxidase (POD)-like activity (catalyse H2O2 into ·OH under acid condition) of MoS2@TA/Fe NSs. Benefitting from the catalase (CAT)-like activity, the hydrogel could decompose H2O2 into O2 at neutral pH to relieve hypoxia and supply adequate O2. POD-like activity was mainly attributed to MoS2 NSs, while CAT-like activity was primarily due to TA/Fe complex. Moreover, MoS2@TA/Fe NSs endowed the hydrogel with outstanding anti-oxidant ability to scavenge redundant reactive oxygen species (ROS) and reactive nitrogen species (RNS) under neutral environment to maintain the balance of antioxidant systems and prevent inflammation. In addition, the hydrogel could inhibit the release of inflammatory factors for the anti-inflammatory property of TA. TA retained partial phenolic hydroxyl groups, which cross-linked the nanosheets to the network structure of the hydrogel and promoted the adhesion of hydrogels. Due to the dynamic boron ester bonds between polyvinyl alcohol (PVA), dextran (Dex), MoS2@TA/Fe, and borax, the hydrogel demonstrated fast self-healing and rapid shape adaptability. This shape-adaptable adhesive hydrogel could fill the whole wound and closely contact the wound, ensuring that it achieved its functions with maximum efficiency. The MoS2@TA/Fe nanozyme-anchored multifunctional hydrogel showed high potential for bacteria-infected wound healing.
Abstract 19429: Fractal Dimension as an Index of Left Ventricular Trabeculation: Normal Values in Healthy Subjects, and Association With Age
Authors: Philip J Ostrowski, Antonio de Marvao, Marina Quinlan, Jiashen Cai, Pawel F Tokarczuk, Declan P O’Regan, Stuart A Cook
Journal: Circulation (2016)

Background: Evaluation of left ventricular non-compaction (LVNC) is an increasingly common indication for cardiac magnetic resonance imaging (MRI). Fractal dimension (FD) is a unitless measure of g...
Estimated impact of increased diagnosis, treatment, and control of diabetes mellitus among low- and middle-income countries: a microsimulation model
Authors: Sanjay Basu, David Flood, Pascal Geldsetzer, Michaela Theilmann, Maja-Emilia Marcus, Cara Ebert, Mary T Mayige, Roy Wong-McClure, Farshad Farzadfar, Sahar Saeedi Moghaddam, Kokou Agoudavi, Bolormaa Norov, Corine Houehanou, Glennis Andall-Brereton, Mongal Singh Gurung, Garry Brian, Pascal Bovet, Joao S Martins, Rifat Atun, Till Bärnighausen, Sebastian Vollmer, Jennifer Manne-Goehler, Justine Davies
Journal: The Lancet Global Health (2021)
From Crime to Care — On the Front Lines of Decarceration
Authors: Nathaniel P. Morris
Journal: New England Journal of Medicine (2021)

Interview with Dr. Nathaniel Morris on the role of clinicians in programs that provide alternatives to incarceration. (16:18)Download Many clinicians are working on the front lines of decarceration, supporting and treating patients who might once have been incarcerated. Models for decarceration involving problem-solving courts and treatment are not perfect, but they allow physicians to do their part.
MESENTERIC VASCULAR INSUFFICIENCY
Authors: A M LANSING, T D McLARTY
Journal: JAMA (1961)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Modeling PNPLA3‐Associated NAFLD Using Human‐Induced Pluripotent Stem Cells
Authors: Samantha G. Tilson, Carola M. Morell, An‐Sofie Lenaerts, Seung Bum Park, Zongyi Hu, Benjamin Jenkins, Albert Koulman, T. Jake Liang, Ludovic Vallier
Journal: Hepatology (2021)

NAFLD is a growing public health burden. However, the pathogenesis of NAFLD has not yet been fully elucidated, and the importance of genetic factors has only recently been appreciated. Genomic studies have revealed a strong association between NAFLD progression and the I148M variant in patatin-like phospholipase domain-containing protein 3 (PNPLA3). Nonetheless, very little is known about the mechanisms by which this gene and its variants can influence disease development. To investigate these mechanisms, we have developed an in vitro model that takes advantage of the unique properties of human-induced pluripotent stem cells (hiPSCs) and the CRISPR/CAS9 gene editing technology.
Explainable artificial intelligence (XAI) in deep learning-based medical image analysis
Authors: Bas H.M. van der Velden, Hugo J. Kuijf, Kenneth G.A. Gilhuijs, Max A. Viergever
Journal: Medical Image Analysis (2022)

With an increase in deep learning-based methods, the call for explainability of such methods grows, especially in high-stakes decision making areas such as medical image analysis. This survey presents an overview of eXplainable Artificial Intelligence (XAI) used in deep learning-based medical image analysis. A framework of XAI criteria is introduced to classify deep learning-based medical image analysis methods. Papers on XAI techniques in medical image analysis are then surveyed and categorized according to the framework and according to anatomical location. The paper concludes with an outlook of future opportunities for XAI in medical image analysis.
Coastal areas need more doctors, says England’s chief medical officer
Authors: Gareth Iacobucci
Journal: BMJ (2021)

Medical staff shortages in coastal areas must be tackled to help narrow stark health inequalities, England’s chief medical officer has recommended.

In his annual report1 for 2021 focusing on health in coastal communities, Chris Whitty highlighted that people living in coastal areas of England have some of the worst health outcomes in the country, with low life expectancy and high rates of many major diseases.

“If we do not tackle the health problems of coastal communities vigorously and systematically there will be a long tail of preventable ill health which will get worse as current populations age,” Whitty said.

The report includes case …
P4-7 A review of adjuvant chemotherapy for rectal cancer in our department, focusing on one-year administration of S-1
Authors: Kazuma Kobayashi, Ayaka Sato, Takuro Fujita, Shinichiro Ito, Yusuke Inoue, Satomi Okada, Sayaka Kuba, Michi Morita, Shinichiro Kobayashi, Yasuhiro Maruya, Masayuki Fukumoto, Taiichiro Kosaka, Akihiko Soyama, Minoru Fukuda, Takuya Honda, Tomohiko Adachi, Masaaki Hidaka, Kengo Kanetaka, Susumu Eguchi
Journal: Annals of Oncology (2021)
Publisher Correction: A systems approach identifies HIPK2 as a key regulator of kidney fibrosis
Authors: Yuanmeng Jin, Krishna Ratnam, Peter Y. Chuang, Ying Fan, Yifei Zhong, Yan Dai, Amin R. Mazloom, Edward Y. Chen, Vivette D’Agati, Huabao Xiong, Michael J. Ross, Nan Chen, Avi Ma’ayan, John Cijiang He
Journal: Nature Medicine (2021)
Duration of Adjuvant Aromatase-Inhibitor Therapy in Postmenopausal Breast Cancer
Authors: Michael Gnant, Florian Fitzal, Gabriel Rinnerthaler, Guenther G. Steger, Sigrun Greil-Ressler, Marija Balic, Dietmar Heck, Raimund Jakesz, Josef Thaler, Daniel Egle, Diether Manfreda, Vesna Bjelic-Radisic, Ursula Wieder, Christian F. Singer, Elisabeth Melbinger-Zeinitzer, Ferdinand Haslbauer, Paul Sevelda, Harald Trapl, Viktor Wette, Kerstin Wimmer, Simon P. Gampenrieder, Rupert Bartsch, Stephanie Kacerovsky-Strobl, Christoph Suppan, Christine Brunner, Christine Deutschmann, Lidija Soelkner, Christian Fesl, Richard Greil
Journal: New England Journal of Medicine (2021)

For postmenopausal women with hormone-receptor-positive breast cancer, the most effective duration for adjuvant therapy with an aromatase inhibitor remains unclear.In this prospective, phase 3 trial, we randomly assigned postmenopausal women with hormone-receptor-positive breast cancer who had received 5 years of adjuvant endocrine therapy to receive the aromatase inhibitor anastrozole for an additional 2 years (2-year group, receiving a total of 7 years) or an additional 5 years (5-year group, receiving a total of 10 years). The primary end point was disease-free survival. The primary analysis included all the patients who were still participating in the trial and who had no recurrence 2 years after randomization (i.e., when treatment in the 2-year group had ended). Secondary end points were overall survival, contralateral breast cancer, second primary cancer, and clinical bone fracture.Among the 3484 women who were enrolled in the trial, 3208 remained in the trial without disease progression after the first 2 years of extended anastrozole treatment following randomization. Among these women, disease progression or death occurred in 335 women in each treatment group in the primary-analysis set at 8 years (hazard ratio, 0.99; 95% confidence interval [CI], 0.85 to 1.15; P = 0.90). No between-group differences occurred in most secondary end points, and subgroup analyses did not indicate differences in any particular subgroup. The risk of clinical bone fracture was higher in the 5-year group than in the 2-year group (hazard ratio, 1.35; 95% CI, 1.00 to 1.84).In postmenopausal women with hormone-receptor-positive breast cancer who had received 5 years of adjuvant endocrine therapy, extending hormone therapy by 5 years provided no benefit over a 2-year extension but was associated with a greater risk of bone fracture. (Funded by AstraZeneca and the Austrian Breast and Colorectal Cancer Study Group; ABCSG-16/SALSA ClinicalTrials.gov number, NCT00295620.).
Treating symptoms and reversing remodelling: clinical and echocardiographic <scp>1‐year</scp> outcomes with percutaneous mitral annuloplasty for mild to moderate secondary mitral regurgitation
Authors: Klaus K. Witte, David M. Kaye, Janusz Lipiecki, Tomasz Siminiak, Steven L. Goldberg, Ralph S. von Bardeleben, Horst Sievert, Wayne C. Levy, Randall C. Starling
Journal: European Journal of Heart Failure (2021)

To determine the effects of percutaneous mitral annuloplasty on symptoms, walk distance and left ventricular (LV) structure and function in patients with mild or moderate secondary mitral regurgitation (SMR).
Will Some Adolescents and Young Adults Forgo Adherence to COVID-19 Prevention Methods in Favor of Romantic Relationships?
Authors: Yzette Lanier
Journal: JAMA Pediatrics (2021)

effect of maternal COVID-19 infection on social determinants of health, growth and development, milestones, and biomarkers, such as blood glucose, lipids, viral antibodies, and inflammatory markers.However, intensive follow-up is considerably more resource intensive and risks losing participants to follow-up; methods to mitigate such risks are needed for any long-term study.Some registries, such as the Pregnancy Coronavirus Outcomes (PRIORITY) Registry and Mother-ToBaby Registry, are already studying short-term outcomes in infants born to mothers who have had COVID-19, including the effect on breastfeeding.This is invaluable research and provides a framework for which longer-term study can be initiated to investigate lifecourse effects.However, any long-term study faces challenges from the large number of patients with unrecognized COVID-19 infection.The presence of such patients must be considered in recruiting patient cohorts.Furthermore, as the COVID-19 pandemic has not equally affected all populations, any study should be undertaken with consideration toward the particular health risks faced by these populations where COVID-19 has been more prevalent.Maternal COVID-19 infection has resulted in elevated rates of preterm birth and low birth weight.However, it has yet to be determined if children born to mothers infected with COVID-19 face deleterious long-term health outcomes.The prevalence of perinatal complications already observed combined with observations from life-course studies in past pandemics suggests that these children face potential risk of long-term health outcomes and should be followed up with for observation of those outcomes.The rise in perinatal complications, such as prematurity in children born to mothers infected with COVID-19, not only poses a risk for negative longterm outcomes by itself-particularly to late-maturing organs, such as the kidneys-but also indicates that in utero exposure could have broader implications than are initially apparent.Just as children born during the 1918 pandemic faced differing risks of future negative outcomes depending on when in utero they faced the peaks of the pandemic, the timing of maternal COVID-19 infection may too present higher risk for certain outcomes in these children.As such, these children could be observed for development of negative health outcomes.Registries like the PRIORITY and MotherToBaby registries are already studying short-term effects, but such large-scale databases are needed to examine effects in the longer term as well to determine if these children face a higher relative risk than their counterparts born at a similar time to mothers who were not infected with COVID-19.
Distinction between the effects of parental and fetal genomes on fetal growth
Authors: Thorhildur Juliusdottir, Valgerdur Steinthorsdottir, Lilja Stefansdottir, Gardar Sveinbjornsson, Erna V. Ivarsdottir, Rosa B. Thorolfsdottir, Jon K. Sigurdsson, Vinicius Tragante, Kristjan E. Hjorleifsson, Anna Helgadottir, Michael L. Frigge, Gudmundur Thorgeirsson, Rafn Benediktsson, Emil L. Sigurdsson, David O. Arnar, Thora Steingrimsdottir, Ingileif Jonsdottir, Hilma Holm, Daniel F. Gudbjartsson, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Kari Stefansson
Journal: Nature Genetics (2021)
Microbiome dysbiosis and epigenetic modulations in lung cancer: From pathogenesis to therapy
Authors: Faizan Haider Khan, Basharat Ahmad Bhat, Bashir Ahmad Sheikh, Lubna Tariq, Roshan Padmanabhan, Jay Prakash Verma, Amritesh Chandra Shukla, Afshin Dowlati, Ata Abbas
Journal: Seminars in Cancer Biology (2021)
Translational evidence for RRM2 as a prognostic biomarker and therapeutic target in Ewing sarcoma
Authors: Shunya Ohmura, Aruna Marchetto, Martin F. Orth, Jing Li, Susanne Jabar, Andreas Ranft, Endrit Vinca, Katharina Ceranski, Martha J. Carreño-Gonzalez, Laura Romero-Pérez, Fabienne S. Wehweck, Julian Musa, Felix Bestvater, Maximilian M. L. Knott, Tilman L. B. Hölting, Wolfgang Hartmann, Uta Dirksen, Thomas Kirchner, Florencia Cidre-Aranaz, Thomas G. P. Grünewald
Journal: Molecular Cancer (2021)
Biocompatible Micron‐Scale Silk Fibers Fabricated by Microfluidic Wet Spinning
Authors: Arne Lüken, Matthias Geiger, Lea Steinbeck, Anna‐Christin Joel, Angelika Lampert, John Linkhorst, Matthias Wessling
Journal: Advanced Healthcare Materials (2021)

For successful material deployment in tissue engineering, the material itself, its mechanical properties, and the microscopic geometry of the product are of particular interest. While silk is a widely applied protein-based tissue engineering material with strong mechanical properties, the size and shape of artificially spun silk fibers are limited by existing processes. This study adjusts a microfluidic spinneret to manufacture micron-sized wet-spun fibers with three different materials enabling diverse geometries for tissue engineering applications. The spinneret is direct laser written (DLW) inside a microfluidic polydimethylsiloxane (PDMS) chip using two-photon lithography, applying a novel surface treatment that enables a tight print-channel sealing. Alginate, polyacrylonitrile, and silk fibers with diameters down to 1 µm are spun, while the spinneret geometry controls the shape of the silk fiber, and the spinning process tailors the mechanical property. Cell-cultivation experiments affirm bio-compatibility and showcase an interplay between the cell-sized fibers and cells. The presented spinning process pushes the boundaries of fiber fabrication toward smaller diameters and more complex shapes with increased surface-to-volume ratio and will substantially contribute to future tailored tissue engineering materials for healthcare applications.
Validation of the International Myeloma Working Group standard response criteria in the PETHEMA/GEM2012MENOS65 study: are these times of change?
Authors: Ana Jiménez-Ubieto, Bruno Paiva, Noemi Puig, Maria-Teresa Cedena, Joaquín Martínez-López, Albert Oriol, María-Jesús Blanchard, Rafael Ríos, Jesús Martin, Rafael Martínez, Anna Sureda, Miguel-Teodoro Hernández, Javier de la Rubia, Isabel Krnisk, Valentín Cabañas, Luis Palomera, José María Sánchez-Pina, Joan Bargay, María-Victoria Mateos, Laura Rosiñol, Joan Blade, Jesús San Miguel, Juan José Lahuerta
Journal: Blood (2021)