tbuckley/cabot-search huggingface dataset:
Assessment of Community-Level Vulnerability and Access to Medications for Opioid Use Disorder
Authors: Paul J. Joudrey, Marynia Kolak, Qinyun Lin, Susan Paykin, Vidal Anguiano, Emily A. Wang
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Given that COVID-19 and recent natural disasters exacerbated the shortage of medication for opioid use disorder (MOUD) services and were associated with increased opioid overdose mortality, it is important to examine how a community's ability to respond to natural disasters and infectious disease outbreaks is associated with MOUD access. <h3>Objective</h3> To examine the association of community vulnerability to disasters and pandemics with geographic access to each of the 3 MOUDs and whether this association differs by urban, suburban, or rural classification. <h3>Design, Setting, and Participants</h3> This cross-sectional study of zip code tabulation areas (ZCTAs) in the continental United States excluding Washington, DC, conducted a geospatial analysis of 2020 treatment location data. <h3>Exposures</h3> Social vulnerability index (US Centers for Disease Control and Prevention measure of vulnerability to disasters or pandemics). <h3>Main Outcomes and Measures</h3> Drive time in minutes from the population-weighted center of the ZCTA to the ZCTA of the nearest treatment location for each treatment type (buprenorphine, methadone, and extended-release naltrexone). <h3>Results</h3> Among 32 604 ZCTAs within the continental US, 170 within Washington, DC, and 20 without an urban-rural classification were excluded, resulting in a final sample of 32 434 ZCTAs. Greater social vulnerability was correlated with longer drive times for methadone (correlation, 0.10; 95% CI, 0.09 to 0.11), but it was not correlated with access to other MOUDs. Among rural ZCTAs, increasing social vulnerability was correlated with shorter drive times to buprenorphine (correlation, –0.10; 95% CI, –0.12 to –0.08) but vulnerability was not correlated with other measures of access. Among suburban ZCTAs, greater vulnerability was correlated with both longer drive times to methadone (correlation, 0.22; 95% CI, 0.20 to 0.24) and extended-release naltrexone (correlation, 0.15; 95% CI, 0.13 to 0.17). <h3>Conclusions and Relevance</h3> In this study, communities with greater vulnerability did not have greater geographic access to MOUD, and the mismatch between vulnerability and medication access was greatest in suburban communities. Rural communities had poor geographic access regardless of vulnerability status. Future disaster preparedness planning should match the location of services to communities with greater vulnerability to prevent inequities in overdose deaths.
Helen Salisbury: Open doors and open windows
Authors: Helen Salisbury
Journal: BMJ (2022)

Our practice has finally reverted to its pre-pandemic appointment system.Patients can book by telephone, online, or in person for either a face-to-face or a telephone appointment, according to what they think they need.They can also submit e-consultation forms.When we had to use telephone triage for all appointments earlier in the pandemic it reduced our efficiency: if, after a five minute conversation with a patient, you decided that you couldn't safely manage them or sort out their problem without an examination, another appointment was needed.The conversion rate of telephone to face-to-face appointments varied between clinicians, but we all shared a sense of work being postponed or incomplete.We'd try to book face-to-face follow-ups with the same doctor, but this wasn't always possible in a suitable timeframe, so a second clinician had to pick up where the first one left off.In this situation you can either take the history again from scratch (which is inefficient) or rely on what your colleague has written, which will inevitably leave out some of the nuances around what was said.This loss of continuity isn't just about information-it also affects rapport, which you need to establish afresh if you take over midway.In theory, a written e-consultation might take the place of the original phone appointment, but in practice this often just turns a two stage process into a three stage one, with a form to read, a phone call to clarify, and a face-to-face appointment to examine.We're not completely back to normal.We're still wearing scrubs-not because there's any evidence of fomite transmission of SARS-CoV-2 but as a visual reminder to our patients that the pandemic's not over.We wear FFP2 masks for all patient contacts, and we expect our patients to wear masks too.We also open the windows wide after each consultation, to change the air.Very occasionally, patients decline to wear masks, in which case my window stays open throughout.This was fine during the brief spell of warm weather in mid-March and less fun when snow was blowing in over my desk last week, but, given that I was doing an extra surgery to cover for a colleague absent with covid, I was in no mood to compromise.It's still early days for our "new normal," and we don't yet know how well it will work, although we expect that more patients than before will choose the telephone for simple, transactional appointments.However, we're also aware that although no physical examination may be needed, some people find that being in the same room as the doctor contributes significantly to feeling heard and understood.As a doctor who is trained to use all of my senses and not just my ears, this is less stressful for me, and I'm more confident when I can see, touch-and occasionally even smell-my patients.
<i>Campylobacter jejuni</i> induces autoimmune peripheral neuropathy via Sialoadhesin and Interleukin-4 axes
Authors: Ankit Malik, Jean M. Brudvig, Barbie J. Gadsden, Alexander D. Ethridge, Linda S. Mansfield
Journal: Gut Microbes (2022)

is a leading cause of gastroenteritis that has been causally linked with development of the autoimmune peripheral neuropathy Guillain Barré Syndrome (GBS). Previously, we showed that
An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses
Authors: Lihong Liu, Sho Iketani, Yicheng Guo, Eswar R. Reddem, Ryan G. Casner, Manoj S. Nair, Jian Yu, Jasper F.-W. Chan, Maple Wang, Gabriele Cerutti, Zhiteng Li, Nicholas C. Morano, Candace D. Castagna, Laura Corredor, Hin Chu, Shuofeng Yuan, Vincent Kwok-Man Poon, Chris Chun-Sing Chan, Zhiwei Chen, Yang Luo, Marcus Cunningham, Alejandro Chavez, Michael T. Yin, David S. Perlin, Moriya Tsuji, Kwok-Yung Yuen, Peter D. Kwong, Zizhang Sheng, Yaoxing Huang, Lawrence Shapiro, David D. Ho
Journal: Science Translational Medicine (2022)

The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)–directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.
Altered purine metabolism at reperfusion affects clinical outcome in lung transplantation
Authors: Cristina Baciu, Jason Shin, Michael Hsin, Marcelo Cypel, Shaf Keshavjee, Mingyao Liu
Journal: Thorax (2022)

Introduction Lung transplantation is an established treatment for patients with end-stage lung disease. However, ischaemia reperfusion injury remains a barrier to achieving better survival outcomes. Here, we aim to investigate the metabolomic and transcriptomic profiles in human lungs before and after reperfusion, to identify mechanisms relevant to clinical outcome. Methods We analysed 67 paired human lung tissue samples collected from 2008 to 2011, at the end of cold preservation and 2 hours after reperfusion. Gene expression analysis was performed with R. Pathway analysis was conducted with Ingenuity Pathway Analysis. MetaboAnalyst and OmicsNet were used for metabolomics analysis and omics data integration, respectively. Association of identified metabolites with transplant outcome was investigated with Kaplan-Meier estimate and Cox proportional hazard models. Results Activation of energy metabolism and reduced antioxidative biochemicals were found by metabolomics. Upregulation of genes related to cytokines and inflammatory mediators, together with major signalling pathways were revealed by transcriptomics. Purine metabolism was identified as the most significantly enriched pathway at reperfusion, based on integrative analysis of the two omics data sets. Elevated expression of purine nucleoside phosphorylase ( PNP ) could be attributed to activation of multiple transcriptional pathways. PNP catabolised reactions were evidenced by changes in related metabolites, especially decreased levels of inosine and increased levels of uric acid. Multivariable analyses showed significant association of inosine and uric acid levels with intensive care unit length of stay and ventilation time. Conclusion Oxidative stress, especially through purine metabolism pathway, is a major metabolic event during reperfusion and may contribute to the ischaemia reperfusion injury of lung grafts.
Integrated fecal microbiome–metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome
Authors: Zlatan Mujagic, Melpomeni Kasapi, Daisy MAE Jonkers, Isabel Garcia-Perez, Lisa Vork, Zsa Zsa R.M. Weerts, Jose Ivan Serrano-Contreras, Alexandra Zhernakova, Alexander Kurilshikov, Jamie Scotcher, Elaine Holmes, Cisca Wijmenga, Daniel Keszthelyi, Jeremy K Nicholson, Joram M Posma, Ad AM Masclee
Journal: Gut Microbes (2022)

To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome–metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome–metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome–metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.
A Phenome-Wide Association Study and the Discovery of a New Clinical Spectrum of Hereditary Cancer Genes
Authors: Kailin Yang, Jacob G. Scott
Journal: JAMA Oncology (2022)

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 Oncology HomeNew OnlineCurrent IssueFor Authors Podcast 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 Oncology journal
Validation of artificial intelligence prediction models for skin cancer diagnosis using dermoscopy images: the 2019 International Skin Imaging Collaboration Grand Challenge
Authors: Marc Combalia, Noel Codella, Veronica Rotemberg, Cristina Carrera, Stephen Dusza, David Gutman, Brian Helba, Harald Kittler, Nicholas R Kurtansky, Konstantinos Liopyris, Michael A Marchetti, Sebastian Podlipnik, Susana Puig, Christoph Rinner, Philipp Tschandl, Jochen Weber, Allan Halpern, Josep Malvehy
Journal: The Lancet Digital Health (2022)
Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer
Authors: Min Liu, Nabihah Tayob, Livius Penter, MacLean Sellars, Anna Tarren, Vipheaviny Chea, Isabel Carulli, Teddy Huang, Shuqiang Li, Su-Chun Cheng, Phuong Le, Laura Frackiewicz, Julia Fasse, Courtney Qi, Joyce F. Liu, Elizabeth H. Stover, Jennifer Curtis, Kenneth J. Livak, Donna Neuberg, Guanglan Zhang, Ursula A. Matulonis, Catherine J. Wu, Derin B. Keskin, Panagiotis A. Konstantinopoulos
Journal: Clinical Cancer Research (2022)

Although local tissue-based immune responses are critical for elucidating direct tumor-immune cell interactions, peripheral immune responses are increasingly recognized as occupying an important role in anticancer immunity. We evaluated serial blood samples from patients with advanced epithelial ovarian cancer (EOC) undergoing standard-of-care neoadjuvant carboplatin and paclitaxel chemotherapy (including dexamethasone for prophylaxis of paclitaxel-associated hypersensitivity reactions) to characterize the evolution of the peripheral immune cell function and composition across the course of therapy.Serial blood samples from 10 patients with advanced high-grade serous ovarian cancer treated with neoadjuvant chemotherapy (NACT) were collected before the initiation of chemotherapy, after the third and sixth cycles, and approximately 2 months after completion of chemotherapy. T-cell function was evaluated using ex vivo IFNγ ELISpot assays, and the dynamics of T-cell repertoire and immune cell composition were assessed using bulk and single-cell RNA sequencing (RNAseq).T cells exhibited an improved response to viral antigens after NACT, which paralleled the decrease in CA125 levels. Single-cell analysis revealed increased numbers of memory T-cell receptor (TCR) clonotypes and increased central memory CD8+ and regulatory T cells throughout chemotherapy. Finally, administration of NACT was associated with increased monocyte frequency and expression of HLA class II and antigen presentation genes; single-cell RNAseq analyses showed that although driven largely by classical monocytes, increased class II gene expression was a feature observed across monocyte subpopulations after chemotherapy.NACT may alleviate tumor-associated immunosuppression by reducing tumor burden and may enhance antigen processing and presentation. These findings have implications for the successful combinatorial applications of immune checkpoint blockade and therapeutic vaccine approaches in EOC.
Longitudinal Analysis of Substance Use Disorder Symptom Severity at Age 18 Years and Substance Use Disorder in Adulthood
Authors: Sean Esteban McCabe, John E. Schulenberg, Ty S. Schepis, Vita V. McCabe, Philip T. Veliz
Journal: JAMA Network Open (2022)

<h3>Importance</h3> Although more than 1 in every 3 US individuals will develop a substance use disorder (SUD) in their lifetime, relatively little is known about the long-term sequelae of SUD symptoms from adolescence through adulthood. <h3>Objective</h3> To evaluate the longitudinal associations between adolescents' SUD symptom severity with later medical use of prescription drugs (ie, opioids, sedatives, and tranquilizers), prescription drug misuse (PDM), and SUD symptoms at ages 35 to 50 years. <h3>Design, Setting, and Participants</h3> Eleven cohorts of US 12th grade students were followed longitudinally from age 18 years (1976-1986) to age 50 years (2008-2018) in the Monitoring the Future (MTF) study. Baseline surveys were self-administered in classrooms, and follow-ups were conducted by mail. Data were analyzed from June 2021 to February 2022. <h3>Exposure</h3> Response to MTF study between 1976 and 2018. <h3>Main Outcomes and Measures</h3> Sociodemographic variables were measured at baseline. All bivariate and multivariate analyses use attrition weights to adjust for attrition by age 50 years within the sample. SUD symptoms, prescription drug use, and PDM were measured at baseline and every follow-up. <h3>Results</h3> The sample of 5317 individuals was 51.2% female (2685 participants; 95% CI, 49.6%-52.6%) and 77.9% White (4222 participants; 95% CI, 77.6%-79.1%). Participants were surveyed beginning at age 18 years and ending at age 50 years. The baseline response rate ranged from 77% to 84%, and the 32-year retention rate was 53%. Most adolescents with most severe SUD symptoms at age 18 years had 2 or more SUD symptoms in adulthood (316 participants [61.6%]; 95% CI, 55.7%-66.9%), and this association held for baseline alcohol, cannabis, and other drug use disorder symptoms. Adolescents with the highest SUD symptom severity at age 18 years had the highest adjusted odds of prescription drug use and PDM in adulthood (4-5 symptoms, adjusted odds ratio, 1.56; 95% CI, 1.06-2.32; ≥6 symptoms, adjusted odds ratio, 1.55; 95% CI, 1.11-2.16). The majority of adults using prescribed opioids, sedatives, or tranquilizers (568 participants [52.2%]; 95% CI, 48.4%-55.9%) in the past year had multiple SUD symptoms at age 18 years. <h3>Conclusions and Relevance</h3> These findings suggest that most adolescents with severe SUD symptoms do not transition out of symptomatic substance use, and the long-term sequelae for adolescents with more severe SUD symptoms are more deleterious than those for adolescents with no or low severity. Prescribers should be aware that many adults prescribed opioids, sedatives, or tranquilizers had multiple SUD symptoms during adolescence and require careful assessment and monitoring.
Determinants of long-term outcomes of splenectomy in pediatric autoimmune cytopenias
Authors: Thomas Pincez, Nathalie Aladjidi, Sébastien Héritier, Nathalie Garnier, Mony Fahd, Wadih Abou Chahla, Helder Fernandes, Claire Dichamp, Stéphane Ducassou, Marlène Pasquet, Sophie Bayart, Despina Moshous, Nathalie Cheikh, Catherine Paillard, Dominique Plantaz, Eric Jeziorski, Caroline Thomas, Corinne Guitton, Marianna Deparis, Aude Marie Cardine, Jean-Louis Stephan, Isabelle Pellier, Eric Doré, Joy Benadiba, Claire Pluchart, Claire Briandet, Vincent Barlogis, Guy Leverger, Thierry Leblanc
Journal: Blood (2022)
Amorphous silica fiber matrix biomaterials: An analysis of material synthesis and characterization for tissue engineering
Authors: Hyun S. Kim, Sangamesh G. Kumbar, Syam P. Nukavarapu
Journal: Bioactive Materials (2022)

Silica biomaterials including Bioglass offer great biocompatibility and bioactivity but fail to provide pore and degradation features needed for tissue engineering. Herein we report on the synthesis and characterization of novel amorphous silica fiber matrices to overcome these limitations. Amorphous silica fibers were fused by sintering to produce porous matrices. The effects of sacrificial polymer additives such as polyvinyl alcohol (PVA) and cellulose fibers (CF) on the sintering process were also studied. The resulting matrices formed between sintering temperatures of 1,350-1,550 °C retained their fiber structures. The matrices presented pores in the range of 50-200 μm while higher sintering temperatures resulted in increased pore diameter. PVA addition to silica significantly reduced the pore diameter and porosity compared with silica matrices with or without the addition of CF. The PVA additive morphologically appeared to fuse the silica fibers to a greater extent and resulted in significantly higher compressive modulus and strength than the rest of the matrices synthesized. These matrices lost roughly 30% of their original mass in an in vitro degradation study over 40 weeks. All matrices absorbed 500 wt% of water and did not change in their overall morphology, size, or shape with hydration. These fiber matrices supported human mesenchymal stem cell adhesion, proliferation, and mineralized matrix production. Amorphous silica fiber biomaterials/matrices reported here are biodegradable and porous and closely resemble the native extracellular matrix structure and water absorption capacity. Extending the methodology reported here to alter matrix properties may lead to a variety of tissue engineering, implant, and drug delivery applications.
Immunity and lifespan: answering long-standing questions with comparative genomics
Authors: Emily A. O’Connor, Charlie K. Cornwallis
Journal: Trends in Genetics (2022)

Long life requires individuals to defend themselves against pathogens over prolonged periods of time whilst minimising damage to themselves. In vertebrates, pathogen defence is provided by two integrated systems, innate and adaptive immunity. Innate immunity is relatively nonspecific, resulting in collateral damage to hosts, and does not involve canonical immunological memory. In contrast, adaptive immunity is highly specific and confers long-lasting memory, which are features that are predicted to facilitate long life. However, there is long-standing debate over the general importance of adaptive immunity for the evolution of extended lifespans, partly because this is difficult to test. We highlight how recent improvements in whole genome assemblies open the door to immunogenomic comparative analyses that enable the coevolution of longevity and specific immune traits to be disentangled.