tbuckley/cabot-search huggingface dataset:
Meta-criteria to formulate criteria of consciousness
Authors: Boris Kotchoubey
Journal: Behavioral and Brain Sciences (2022)

Any neurobiological model claiming explanation of a complex human phenomenon should start with an explicit definition of the explanandum. If a classical intensional definition is impossible, we can use a descriptive definition by listing necessary criteria (e.g., of consciousness). This commentary suggests four meta-criteria that different proposed criteria of consciousness should fulfill: phenomenological consensus, empirical evidence, domain specificity, and non-circularity.
Classification of Visual Field Abnormalities in Highly Myopic Eyes without Pathologic Change
Authors: Fengbin Lin, Shida Chen, Yunhe Song, Fei Li, Wei Wang, Zhenni Zhao, Xinbo Gao, Peiyuan Wang, Ling Jin, Yuhong Liu, Meiling Chen, Xiaohong Liang, Bin Yang, Guili Ning, Ching-Yu Cheng, Paul R. Healey, Ki Ho Park, Linda M. Zangwill, Tin Aung, Kyoko Ohno-Matsui, Jost B. Jonas, Robert N. Weinreb, Xiulan Zhang, Yizhi Liu, Lin Lv, David Friedman, Kai Gao, Bingqian Liu, Neil M. Bressler, Mingguang He, Xiang Chen, Guangxian Tang
Journal: Ophthalmology (2022)
The public finance cost of covid-19
Authors: John Appleby
Journal: BMJ (2022)

<h3>Background</h3> Consultations for self-limiting infections in children are increasing. It has been proposed that digital technology could be used to enable parents' decision making in terms of self-care and treatment seeking. <h3>Aim</h3> To evaluate the evidence that digital interventions facilitate parents deciding whether to self-care or seek treatment for acute illnesses in children. <h3>Design and setting</h3> Systematic review of studies undertaken worldwide. <h3>Method</h3> Searches of MEDLINE and EMBASE were made to identify studies (of any design) published between database inception and January 2019 that assessed digital interventions for parents of children (from any healthcare setting) with acute illnesses. The primary outcome of interest was whether the use of digital interventions reduced the use of urgent care services. <h3>Results</h3> Three studies were included in the review. They assessed two apps and one website: Children's On-Call — a US advice-only app; Should I See a Doctor? — a Dutch self-triage app for any acute illness; and Strategy for Off-Site Rapid Triage (SORT) for Kids — a US self-triage website for influenza-like illness. None of the studies involved parents during intervention development and it was shown that many parents did not find the two apps easy to use. The sensitivity of self-triage interventions was 84% for Should I See a Doctor? compared with nurse triage, and 93.3% for SORT for Kids compared with the need for emergency-department intervention; however, both had lower specificity (74% and 13%, respectively). None of the interventions demonstrated reduced use of urgent-care services. <h3>Conclusion</h3> There is little evidence to support the use of digital interventions to help parent and/or carers looking after children with acute illness. Future research should involve parents during intervention development, and adequately powered trials are needed to assess the impact of such interventions on health services and the identification of children who are seriously ill.
Endoscopic submucosal dissection of a solitary gastric plasmacytoma: “third space oddity”
Authors: Gertjan Rasschaert, Paraskevas Gkolfakis, Pierre Eisendrath, Laurine Verset, Jacques Devière, Arnaud Lemmers
Journal: Endoscopy (2022)

Although well established for classic indications [1] [2] [3], the use of endoscopic submucosal dissection (ESD) can help to solve rare clinical situations [4] [5].
PHISDetector: A Tool to Detect Diverse <i>In Silico</i> Phage–Host Interaction Signals for Virome Studies
Authors: Fengxia Zhou, Rui Gan, Fan Zhang, Chunyan Ren, Ling Yu, Yu Si, Zhiwei Huang
Journal: Genomics Proteomics & Bioinformatics (2022)

Phage-microbe interactions are appealing systems to study coevolution, and have also been increasingly emphasized due to their roles in human health, disease, and the development of novel therapeutics. Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences, defined as phage-host interaction signals (PHISs), which include clustered regularly interspaced short palindromic repeats (CRISPR) targeting, prophage, and protein-protein interaction signals. In the present study, we developed a novel tool phage-host interaction signal detector (PHISDetector) to predict phage-host interactions by detecting and integrating diverse in silico PHISs, and scoring the probability of phage-host interactions using machine learning models based on PHIS features. We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases. When tested on a dataset of 758 annotated phage-host pairs, PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels, respectively, outperforming other phage-host prediction tools. When applied to on 125,842 metagenomic viral contigs (mVCs) derived from 3042 geographically diverse samples, a detection rate of 54.54% could be achieved. Furthermore, PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant (MDR) bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health (NIH) Human Microbiome Project (HMP). The PHISDetector can be run either as a web server (http://www.microbiome-bigdata.com/PHISDetector/) for general users to study individual inputs or as a stand-alone version (https://github.com/HIT-ImmunologyLab/PHISDetector) to process massive phage contigs from virome studies.
Country-specific approaches to latent tuberculosis screening targeting migrants in EU/EEA* countries: A survey of national experts, September 2019 to February 2020
Authors: Ioana Margineanu, Kieran Rustage, Teymur Noori, Dominik Zenner, Christina Greenaway, Manish Pareek, Onno Akkerman, Sally Hayward, Jon S Friedland, Delia Goletti, Ymkje Stienstra, Sally Hargreaves
Journal: Eurosurveillance (2022)

BackgroundMigrants in low tuberculosis (TB) incidence countries in the European Union (EU)/European Economic Area (EEA) are an at-risk group for latent tuberculosis infection (LTBI) and are increasingly included in LTBI screening programmes.AimTo investigate current approaches and implement LTBI screening in recently arrived migrants in the EU/EEA and Switzerland.MethodsAt least one TB expert working at a national level from the EU/EEA and one TB expert from Switzerland completed an electronic questionnaire. We used descriptive analyses to calculate percentages, and framework analysis to synthesise free-text responses.ResultsExperts from 32 countries were invited to participate (30 countries responded): 15 experts reported an LTBI screening programme targeting migrants in their country; five reported plans to implement one in the near future; and 10 reported having no programme. LTBI screening was predominantly for asylum seekers (n = 12) and refugees (n = 11). Twelve countries use 'country of origin' as the main eligibility criteria. The countries took similar approaches to diagnosis and treatment but different approaches to follow-up. Six experts reported that drop-out rates in migrants were higher compared with non-migrant groups. Most of the experts (n = 22) called for a renewed focus on expanding efforts to screen for LTBI in migrants arriving in low-incidence countries.ConclusionWe found a range of approaches to LTBI screening of migrants in the EU/EEA and Switzerland. Findings suggest a renewed focus is needed to expand and strengthen efforts to meaningfully include migrants in these programmes, in order to meet regional and global elimination targets for TB.
mRNA-1273 and BNT162b2 COVID-19 vaccines elicit antibodies with differences in Fc-mediated effector functions
Authors: Paulina Kaplonek, Deniz Cizmeci, Stephanie Fischinger, Ai-ris Collier, Todd Suscovich, Caitlyn Linde, Thomas Broge, Colin Mann, Fatima Amanat, Diana Dayal, Justin Rhee, Michael de St. Aubin, Eric J. Nilles, Elon R. Musk, Anil S. Menon, Erica Ollmann Saphire, Florian Krammer, Douglas A. Lauffenburger, Dan H. Barouch, Galit Alter
Journal: Science Translational Medicine (2022)

The successful development of several coronavirus disease 2019 (COVID-19) vaccines has substantially reduced morbidity and mortality in regions of the world where the vaccines have been deployed. However, in the wake of the emergence of viral variants that are able to evade vaccine-induced neutralizing antibodies, real-world vaccine efficacy has begun to show differences across the two approved mRNA platforms, BNT162b2 and mRNA-1273; these findings suggest that subtle variation in immune responses induced by the BNT162b2 and mRNA-1273 vaccines may confer differential protection. Given our emerging appreciation for the importance of additional antibody functions beyond neutralization, we profiled the postboost binding and functional capacity of humoral immune responses induced by the BNT162b2 and mRNA-1273 vaccines in a cohort of hospital staff. Both vaccines induced robust humoral immune responses to wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to variants of concern. However, differences emerged across epitope-specific responses, with higher concentrations of receptor binding domain (RBD)- and N-terminal domain-specific IgA observed in recipients of mRNA-1273. Antibodies eliciting neutrophil phagocytosis and natural killer cell activation were also increased in mRNA-1273 vaccine recipients as compared to BNT162b2 recipients. RBD-specific antibody depletion highlighted the different roles of non-RBD-specific antibody effector functions induced across the mRNA vaccines. These data provide insights into potential differences in protective immunity conferred by these vaccines.
ESCAPE CAPTURE BIGEMINY FOLLOWING CONVERGENT ABLATION IN A PATIENT WITH LONG STANDING PERSISTENT ATRIAL FIBRILLATION
Authors: Jakrin Kewcharoen, Rahul Bhardwaj, Kamal M. Kotak, Tahmeed Contractor, Ravi Mandapati, Bruce M. Toporoff, Jalaj Garg
Journal: Journal of the American College of Cardiology (2022)
mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 omicron variant
Authors: Venkata-Viswanadh Edara, Kelly E. Manning, Madison Ellis, Lilin Lai, Kathryn M. Moore, Stephanie L. Foster, Katharine Floyd, Meredith E. Davis-Gardner, Grace Mantus, Lindsay E. Nyhoff, Sarah Bechnak, Ghina Alaaeddine, Amal Naji, Hady Samaha, Matthew Lee, Laurel Bristow, Matthew Gagne, Jesmine Roberts-Torres, Amy R. Henry, Sucheta Godbole, Arash Grakoui, Marybeth Saxton, Anne Piantadosi, Jesse J. Waggoner, Daniel C. Douek, Nadine Rouphael, Jens Wrammert, Mehul S. Suthar
Journal: Cell Reports Medicine (2022)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant emerged in November 2021 and consists of several mutations within the spike. We use serum from mRNA-vaccinated individuals to measure neutralization activity against omicron in a live-virus assay. At 2-4 weeks after a primary series of vaccinations, we observe a 30-fold reduction in neutralizing activity against omicron. Six months after the initial two-vaccine doses, sera from naive vaccinated subjects show no neutralizing activity against omicron. In contrast, COVID-19-recovered individuals 6 months after receiving the primary series of vaccinations show a 22-fold reduction, with the majority of the subjects retaining neutralizing antibody responses. In naive individuals following a booster shot (third dose), we observe a 14-fold reduction in neutralizing activity against omicron, and over 90% of subjects show neutralizing activity. These findings show that a third dose is required to provide robust neutralizing antibody responses against the omicron variant.
LONG-TERM OUTCOMES OF TRANSCATHETER AORTIC VALVE REPLACEMENT IN PATIENTS WITH END-STAGE RENAL DISEASE ON DIALYSIS
Authors: Denny Joseph, Abiodun Adeuti, Areeba Ali, Graviss A. Edward, Duc Nguyen, Stephen Henry Little, Nadeen Nader Faza, Moritz C. Wyler von Ballmoos, Marvin Atkins, Neal S. Kleiman, Michael J. Reardon, Sachin Goel
Journal: Journal of the American College of Cardiology (2022)
Abstract P3-14-10: Breast cancer patterns, behavior and survival among American Indians in the west north central region and the other regions of the U.S.
Authors: Anu G Gaba, Li Cao, Rebecca Renfrew, Deann Witte, Janet Wernisch, Denise Lutkemeier, Kristi Egland, Ross Crosby
Journal: Cancer Research (2022)

Abstract Purpose: American Indians (AIs) constitute the single largest racial minority in North Dakota and South Dakota. There are no studies looking at what sociodemographic or biological factors may play a role in affecting outcomes and mortality of breast cancer (BC) among AIs in the United States. Our study compared the BC patterns, behavior, and survival of AIs living in the West North Central Region (WNCR) of the U.S (which includes ND, SD, MN, NE, IO, KS, MO) to the AI BC patients in the remainder of the country. Methods: We used the records of all AI BC patients diagnosed between the years 2004-2016 from The National Cancer Database participant user files. All analyses were conducted using SPSS software (version 25). Results: Records were available for 6,466 AI BC patients, 798 were in the WNCR. There was no difference between WNCR and other regions in the stage distribution, mean age at diagnosis, morphology, hormonal/HER2 status, tumor size, lymph node status, or second cancers. The WNCR patients had less private insurance, lived in zip codes with lower median income, had more co-morbidities, and traveled longer distances for care (p&amp;lt;0.001 for each). They had higher grade cancers (p&amp;lt;0.001) at diagnosis. The WNCR patients were less likely to have received radiation therapy (p=0.015) but more likely to have received chemotherapy (p&amp;lt;0.001) and hormonal therapy (p=0.009) and had longer inpatient stay days after surgery (p&amp;lt;0.001). Time to first treatment and first treatment within 90 days (88.0% vs. 79.7%, p&amp;lt;0.001) was significantly better in the WNCR than in other regions of the country. Five year mortality rate was higher (16.3% vs. 11.1%, p&amp;lt;0.001) and cumulative survival was lower (p&amp;lt;0.001) in the WNCR as compared to AIs in other regions of the country. Univariate/multivariate analysis failed to identify variables that could explain the differences in 5 year mortality or cumulative survival between WNCR and other regions. Conclusion:AIs with BC in the WNCR had worse 5 year mortality and cumulative survival as compared to AIs in other regions in the US. Our analysis could not identify variables that explained the differences in mortality or cumulative survival between WNCR and other regions. Citation Format: Anu G Gaba, Li Cao, Rebecca Renfrew, Deann Witte, Janet Wernisch, Denise Lutkemeier, Kristi Egland, Ross Crosby. Breast cancer patterns, behavior and survival among American Indians in the west north central region and the other regions of the U.S. [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-14-10.
Machine Learning Quantitative Analysis of FDG PET Images of Medial Temporal Lobe Epilepsy Patients
Authors: Yen-Cheng Shih, Tse-Hao Lee, Hsiang-Yu Yu, Chien-Chen Chou, Cheng-Chia Lee, Po-Tso Lin, Syu-Jyun Peng
Journal: Clinical Nuclear Medicine (2022)

Purpose 18 F-FDG PET is widely used in epilepsy surgery. We established a robust quantitative algorithm for the lateralization of epileptogenic foci and examined the value of machine learning of 18 F-FDG PET data in medial temporal lobe epilepsy (MTLE) patients. Patients and Methods We retrospectively reviewed patients who underwent surgery for MTLE. Three clinicians identified the side of MTLE epileptogenesis by visual inspection. The surgical side was set as the epileptogenic side. Two parcellation paradigms and corresponding atlases (Automated Anatomical Labeling and FreeSurfer aparc + aseg) were used to extract the normalized PET uptake of the regions of interest (ROIs). The lateralization index of the MTLE-associated regions in either hemisphere was calculated. The lateralization indices of each ROI were subjected for machine learning to establish the model for classifying the side of MTLE epileptogenesis. Result Ninety-three patients were enrolled for training and validation, and another 11 patients were used for testing. The hit rate of lateralization by visual analysis was 75.3%. Among the 23 patients whose MTLE side of epileptogenesis was incorrectly determined or for whom no conclusion was reached by visual analysis, the Automated Anatomical Labeling and aparc + aseg parcellated the associated ROIs on the correctly lateralized MTLE side in 100.0% and 82.6%. In the testing set, lateralization accuracy was 100% in the 2 paradigms. Conclusions Visual analysis of 18 F-FDG PET to lateralize MTLE epileptogenesis showed a lower hit rate compared with machine-assisted interpretation. While reviewing 18 F-FDG PET images of MTLE patients, considering the regions associated with MTLE resulted in better performance than limiting analysis to hippocampal regions.
Heart failure quality of care and <scp>in‐hospital</scp> outcomes during the <scp>COVID</scp>‐19 pandemic: findings from the Get With The <scp>Guidelines‐Heart</scp> Failure registry
Authors: Neil Keshvani, Anurag Mehta, Heather M. Alger, Christine Rutan, Joseph Williams, Shuiaqi Zhang, Rebecca Young, Brooke Alhanti, Karen Chiswell, Stephen J. Greene, Adam D. DeVore, Clyde W. Yancy, Gregg C. Fonarow, Ambarish Pandey
Journal: European Journal of Heart Failure (2022)
Safety of mRNA vaccines administered during the initial 6 months of the US COVID-19 vaccination programme: an observational study of reports to the Vaccine Adverse Event Reporting System and v-safe
Authors: Hannah G Rosenblum, Julianne Gee, Ruiling Liu, Paige L Marquez, Bicheng Zhang, Penelope Strid, Winston E Abara, Michael M McNeil, Tanya R Myers, Anne M Hause, John R Su, Lauri E Markowitz, Tom T Shimabukuro, David K Shay
Journal: The Lancet Infectious Diseases (2022)
Protection and antibody levels 35 years after primary series with hepatitis B vaccine and response to a booster dose
Authors: Michael G. Bruce, Dana Bruden, Debby Hurlburt, Julie Morris, Sara Bressler, Gail Thompson, Danielle Lecy, Karen Rudolph, Lisa Bulkow, Thomas Hennessy, Brenna C. Simons, Mark K. Weng, Noele Nelson, Brian J. McMahon
Journal: Hepatology (2022)

Abstract Background and Aims The duration of protection from hepatitis B vaccination in children and adults is not known. In 1981, we used three doses of plasma‐derived hepatitis B vaccine to immunize a cohort of 1578 Alaska Native adults and children from 15 Alaska communities who were ≥6 months old. Approach and Results We tested persons for antibody to hepatitis B surface antigen (anti‐HBs) levels 35 years after receiving the primary series. Those with levels &lt;10 mIU/ml received one booster dose of recombinant hepatitis B vaccine 2–4 weeks later and were then evaluated on the basis of anti‐HBs measurements 30 days postbooster. Among the 320 recruited, 112 persons had not participated in the 22‐ or 30‐year follow‐up study (group 1), and 208 persons had participated but were not given an HBV booster dose (group 2). Among the 112 persons in group 1 who responded to the original primary series, 53 (47.3%) had an anti‐HBs level ≥10 mIU/ml. Among group 1, 73.7% (28 of 38) of persons available for a booster dose responded to it with an anti‐HBs level ≥10 mIU/ml at 30 days. Initial anti‐HBs level after the primary series was correlated with higher anti‐HBs levels at 35 years. Among 8 persons who tested positive for antibody to hepatitis B core antigen, none tested positive for HBsAg or HBV DNA. Conclusions Based on anti‐HBs level ≥10 mIU/ml at 35 years and a 73.7% booster dose response, we estimate that 86% of participants had evidence of protection 35 years later. Booster doses are not needed in the general population at this time.
Issue Information
Journal: American Journal of Hematology (2022)

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Global, regional, and national burden of diseases and injuries for adults 70 years and older: systematic analysis for the Global Burden of Disease 2019 Study
Journal: BMJ (2022)

To use data from the Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019) to estimate mortality and disability trends for the population aged ≥70 and evaluate patterns in causes of death, disability, and risk factors.
Robot-assisted Prostate-specific Membrane Antigen–radioguided Salvage Surgery in Recurrent Prostate Cancer Using a DROP-IN Gamma Probe: The First Prospective Feasibility Study
Authors: Hilda A de Barros, Matthias N van Oosterom, Maarten L Donswijk, Jeroen J M A Hendrikx, André N Vis, Tobias Maurer, Fijs W B van Leeuwen, Henk G van der Poel, Pim J van Leeuwen
Journal: European Urology (2022)
PREDICTIVE VALUE OF INDEX OF MICROVASCULAR RESISTANCE MEASURED AFTER PRIMARY PERCUTANEOUS CORONARY INTERVENTION ON MYOCARDIAL SCARRING ON CARDIAC MAGNETIC RESONANCE AND LONG-TERM OUTCOMES IN PATIENTS WITH ST-ELEVATION MYOCARDIAL INFARCTION
Authors: Andie Hartanto Djohan, Ping Chai, Stephanie Marchesseau, Lieng Hsi Ling, Li-Ling Tan, Mark Richards, Siew Pang Chan, Mark Y.Y. Chan, Adrian Low
Journal: Journal of the American College of Cardiology (2022)
INCREMENTAL PROGNOSTIC VALUE OF LEFT ATRIAL STRAIN IN PREDICTING CARDIOTOXICITY AFTER CHEMOTHERAPY: SUB-ANALYSIS FROM THE SUCCOUR STUDY
Authors: Christopher Yu, Tomoko Negishi, Paaladinesh Thavendiranathan, Martin Penicka, Marc-André Côté, Richard Massey, Sakiko Miyazaki, Mitra Gh Shirazi, Ciro Santoro, Goo-Yeong Cho, Bogdan A. Popescu, Dragos Vinereanu, Wojciech Kosmala, Thomas H. Marwick, Kazuaki Negishi
Journal: Journal of the American College of Cardiology (2022)
Generalizable design parameters for soluble T cell receptor-based T cell engagers
Authors: Karen J Froning, Arlene Sereno, Flora Huang, Stephen J Demarest
Journal: Journal for ImmunoTherapy of Cancer (2022)

While most biological and cellular immunotherapies recognize extracellular targets, T cell receptor (TCR) therapeutics are unique in their ability to recognize the much larger pool of intracellular antigens found on virus-infected or cancerous cells. Recombinant T cell receptor (rTCR)-based therapeutics are gaining momentum both preclinically and clinically highlighted by recent positive phase III human clinical trial results for a TCR/CD3 bifunctional protein in uveal melanoma. Unlike antibody-based T cell engagers whose molecular formats have been widely and extensively evaluated, little data exist describing the putative activities of varied bifunctional formats using rTCRs. Here we generate rTCR/anti-CD3 bifunctionals directed toward NY-ESO-1 or MAGE-A3 with a variety of molecular formats. We show that inducing strong redirected lysis activity against tumors displaying either NY-ESO-1 or MAGE-A3 is highly restricted to small, tandem binding formats with an rTCR/antiCD3 Fab demonstrating the highest potency, rTCR/anti-CD3 single chain variable domain fragment showing similar but consistently weaker potency, and IgG-like or IgG-Fc-containing molecules demonstrating poor activity. We believe this is a universal trait of rTCR bifunctionals, given the canonical TCR/human leukocyte antigen structural paradigm.