tbuckley/cabot-search huggingface dataset:
Distortion and instability compensation with deep learning for rotational scanning endoscopic optical coherence tomography
Authors: Guiqiu Liao, Oscar Caravaca-Mora, Benoit Rosa, Philippe Zanne, Diego Dall’Alba, Paolo Fiorini, Michel de Mathelin, Florent Nageotte, Michalina J. Gora
Journal: Medical Image Analysis (2022)

Optical Coherence Tomography (OCT) is increasingly used in endoluminal procedures since it provides high-speed and high resolution imaging. Distortion and instability of images obtained with a proximal scanning endoscopic OCT system are significant due to the motor rotation irregularity, the friction between the rotating probe and outer sheath and synchronization issues. On-line compensation of artefacts is essential to ensure image quality suitable for real-time assistance during diagnosis or minimally invasive treatment. In this paper, we propose a new online correction method to tackle both B-scan distortion, video stream shaking and drift problem of endoscopic OCT linked to A-line level image shifting. The proposed computational approach for OCT scanning video correction integrates a Convolutional Neural Network (CNN) to improve the estimation of azimuthal shifting of each A-line. To suppress the accumulative error of integral estimation we also introduce another CNN branch to estimate a dynamic overall orientation angle. We train the network with semi-synthetic OCT videos by intentionally adding rotational distortion into real OCT scanning images. The results show that networks trained on this semi-synthetic data generalize to stabilize real OCT videos, and the algorithm efficacy is demonstrated on both ex vivo and in vivo data, where strong scanning artifacts are successfully corrected.
Attenuated response to fourth dose SARS-CoV-2 vaccination in patients with autoimmune disease: a case series
Authors: Mayan Teles, Caoilfhionn M Connolly, Sarah Frey, Teresa Po-Yu Chiang, Jennifer J Alejo, Brian J Boyarsky, Ami A Shah, Jemima Albayda, Lisa Christopher-Stine, William A Werbel, Dorry L Segev, Julie J Paik
Journal: Annals of the Rheumatic Diseases (2022)
Final results of a prospective, randomized controlled trial assessing the impact of early Dorsal Venous Complex (eDVC) ligation on urinary continence recovery after robot-assisted radical prostatectomy
Authors: F. Montorsi, C.A. Bravi, G. Gandaglia, N. Fossati, A. Stabile, E. Mazzone, G. Rosiello, G. Sorce, F. Pellegrino, L. Nocera, G. Cirulli, F. Barletta, S. Scuderi, A. Salonia, A. Gallina, M. Moschini, A. Briganti
Journal: European Urology (2021)
Racial Discrimination and Resting-State Functional Connectivity of Salience Network Nodes in Trauma-Exposed Black Adults in the United States
Authors: E. Kate Webb, Claire M. Bird, Terri A. deRoon-Cassini, Carissa N. Weis, Ashley A. Huggins, Jacklynn M. Fitzgerald, Tara Miskovich, Kenneth Bennett, Jessica Krukowski, Lucas Torres, Christine L. Larson
Journal: JAMA Network Open (2022)

<h3>Importance</h3> For Black US residents, experiences of racial discrimination are still pervasive and frequent. Recent empirical work has amplified the lived experiences and narratives of Black people and further documented the detrimental effects of racial discrimination on both mental and physical health; however, there is still a need for further research to uncover the mechanisms connecting experiences of racial discrimination with adverse health outcomes. <h3>Objective</h3> To examine neurobiological mechanisms that may offer novel insight into the association of racial discrimination with adverse health outcomes. <h3>Design, Setting, and Participants</h3> This cross-sectional study included 102 Black adults who had recently experienced a traumatic injury. In the acute aftermath of the trauma, participants underwent a resting-state functional magnetic resonance imaging scan. Individuals were recruited from the emergency department at a Midwestern level 1 trauma center in the United States between March 2016 and July 2020. Data were analyzed from February to May 2021. <h3>Exposures</h3> Self-reported lifetime exposure to racial discrimination, lifetime trauma exposure, annual household income, and current posttraumatic stress disorder (PTSD) symptoms were evaluated. <h3>Main Outcomes and Measures</h3> Seed-to-voxel analyses were conducted to examine the association of racial discrimination with connectivity of salience network nodes (ie, amygdala and anterior insula). <h3>Results</h3> A total of 102 individuals were included, with a mean (SD) age of 33 (10) years and 58 (57%) women. After adjusting for acute PTSD symptoms, annual household income, and lifetime trauma exposure, greater connectivity between the amygdala and thalamus was associated with greater exposure to discrimination (<i>t</i><sub>(97)</sub> = 6.05; false discovery rate (FDR)–corrected<i>P</i> = .03). Similarly, racial discrimination was associated with greater connectivity between the insula and precuneus (<i>t</i><sub>(97)</sub> = 4.32; FDR-corrected<i>P</i> = .02). <h3>Conclusions and Relevance</h3> These results add to the mounting literature that racial discrimination is associated with neural correlates of vigilance and hyperarousal. The study findings extend this theory by showing that this association is apparent even when accounting for socioeconomic position, lifetime trauma, and symptoms of psychological distress related to an acute trauma.
Lung Cancer Screening in Persons Who Never Smoked Has to be Evaluated—A Response to Letter to the Editor
Authors: Anna Kerpel-Fronius, Martin C Tammemägi, Milena Cavic, Rudolf M Huber, Dawei Yang, Javier Zulueta, Lucia Viola, Anant Mohan, Choon-Taek Lee, Milena Cavic, Heidi Schmidt, Ella Kazerooni, Ricardo Sales Dos Santos, Anna Kerpel-Fronius, Claudia Henschke, Luigi Ventura, Long Jiang, Gabriella Sozzi, Martin Tammemägi, Stephen Lam, Rudolf Huber
Journal: Journal of Thoracic Oncology (2022)
Renal mass size and presence of synchronous lung metastasis at time of diagnosis: Implications for chest imaging
Authors: M. Jamil, R. Hanna, A. Sood, N. Nicholas Corsi, D. Daniele Modonutti, J. Jacob Keeley, G. Giacomo Novara, A. Amit Patel, C. Craig Rogers, F. Firas Abdollah
Journal: European Urology (2021)
Disease severity during SARS-COV-2 reinfection: a nationwide study
Authors: Anna A. Mensah, Joanne Lacy, Julia Stowe, Giulia Seghezzo, Ruchira Sachdeva, Ruth Simmons, Antoaneta Bukasa, Shennae O'Boyle, Nick Andrews, Mary Ramsay, Helen Campbell, Kevin Brown
Journal: Journal of Infection (2022)

We aimed to look at the burden of disease caused by SARS-COV-2 reinfections and identified potential risk factors for disease severity.We used national surveillance data to collect information on all SARS-CoV-2 primary infection and suspected reinfection cases between January 2020 until early May 2021. Reinfection cases were positive COVID-19 PCR or antigen test, 90 days after their first COVID-19 positive test. We collected information on case demographics, hospital and ICU admission, immunisation status and if individuals were at risk of complication for COVID-19.Deaths reported within 28 days of testing positive were 61% (95% confidence interval: 56% to 65%) lower in suspected COVID-19 reinfection than primary infection cases. In the unvaccinated cohort, reinfections were associated with 49% (37% to 58%) lower odds of hospital admission in cases aged 50 to 65 years in the population not identified at risk of complication for COVID-19, and 34% (17% to 48%) in those at risk. ICU admission at reinfection compared to primary infection decreased 76% (55% to 87%). Individuals at risk and those aged below 50 years, who received at least 1 dose of vaccine against COVID-19, were 62% (39% to 74%) and 58% (24% to 77%) less likely to get admitted to hospital at reinfection, respectively.Prior SARS-CoV-2 infection was associated with lower odds of dying, and both prior infection and immunisation showed a protective effect against severe disease in selected populations. Older age, sex and underlying comorbidities appeared as principal risk factors for illness severity at reinfection.PHE/UKHSA.
Cutaneous Squamous Cell Carcinoma: The Frontier of Cancer Immunoprevention
Authors: Michael S. Chang, Marjan Azin, Shadmehr Demehri
Journal: Annual Review of Pathology Mechanisms of Disease (2022)

Cutaneous squamous cell carcinoma (cSCC) is the second most common cancer, with its incidence rising steeply. Immunosuppression is a well-established risk factor for cSCC, and this risk factor highlights the critical role of the immune system in regulating cSCC development and progression. Further highlighting the nature of cSCC as an immunological disorder, substantial evidence demonstrates a tight association between cSCC risk and age-related immunosenescence. Besides the proven efficacy of immune checkpoint blockade therapy for advanced cSCC, novel immunotherapy that targets cSCC precursor lesions has shown efficacy for cSCC prevention. Furthermore, the appreciation of the interplay between keratinocytes, commensal papillomaviruses, and the immune system has revealed the possibility for the development of a preventive cSCC vaccine. cSCC shares fundamental aspects of its origin and pathogenesis with mucosal SCCs. Therefore, advances in the field of cSCC immunoprevention will inform our approach to the management of mucosal SCCs and potentially other epithelial cancers.
Salvage versus primary robot-assisted radical prostatectomy: A propensity-matched comparative effectiveness study from a high-volume tertiary center
Authors: A. Nathan, M. Fricker, R. De Groote, A. Arora, Y. Phuah, K. Flora, N. Pavan, V. Kasivisvanathan, J. Collins, A. Kelkar, A. Sridhar, G. Shaw, P. Rajan, J. Kelly, T. Briggs, P. Sooriakumaran, S. Nathan
Journal: European Urology (2021)
Impact of preexisting opioid-dependence on morbidity, length of stay, and inpatient cost of urologic oncologic surgery
Authors: S. Arora, C. Bronkema, B. Ranasinghe, H. Wurst, J. Keeley, A. Sood, D. Modonutti, G. Novara, M. Menon, C.G. Rogers, F. Abdollah
Journal: European Urology (2021)
COVID-19 Incidence and Death Rates Among Unvaccinated and Fully Vaccinated Adults with and Without Booster Doses During Periods of Delta and Omicron Variant Emergence — 25 U.S. Jurisdictions, April 4–December 25, 2021
Authors: Amelia G. Johnson, Avnika B. Amin, Akilah R. Ali, Brooke Hoots, Betsy L. Cadwell, Shivani Arora, Tigran Avoundjian, Abiola O. Awofeso, Jason Barnes, Nagla S. Bayoumi, Katherine Busen, Carolyn Chang, Mike Cima, Molly Crockett, Alicia Cronquist, Sherri Davidson, Elizabeth Davis, Janelle Delgadillo, Vajeera Dorabawila, Cherie Drenzek, Leah Eisenstein, Hannah E. Fast, Ashley Gent, Julie Hand, Dina Hoefer, Corinne Holtzman, Amanda Jara, Amanda Jones, Ishrat Kamal-Ahmed, Sarah Kangas, FNU Kanishka, Ramandeep Kaur, Saadiah Khan, Justice King, Samantha Kirkendall, Anna Klioueva, Anna Kocharian, Frances Y. Kwon, Jacqueline Logan, B. Casey Lyons, Shelby Lyons, Andrea May, Donald McCormick, Erica Mendoza, Lauren Milroy, Allison O’Donnell, Melissa Pike, Sargis Pogosjans, Amy Saupe, Jessica Sell, Elizabeth Smith, Daniel M. Sosin, Emma Stanislawski, Molly K. Steele, Meagan Stephenson, Allen Stout, Kyle Strand, Buddhi P. Tilakaratne, Kathryn Turner, Hailey Vest, Sydni Warner, Caleb Wiedeman, Allison Zaldivar, Benjamin J. Silk, Heather M. Scobie
Journal: MMWR Morbidity and Mortality Weekly Report (2022)

Previous reports of COVID-19 case, hospitalization, and death rates by vaccination status
Trail running injury risk factors: a living systematic review
Authors: Carel Viljoen, Dina C (Christa) Janse van Rensburg, Willem van Mechelen, Evert Verhagen, Bruno Silva, Volker Scheer, Manuela Besomi, Rubén Gajardo-Burgos, Sérgio Matos, Marlene Schoeman, Audrey Jansen van Rensburg, Nicol van Dyk, Susan Scheepers, Tanita Botha
Journal: British Journal of Sports Medicine (2022)

Objective To review and frequently update the available evidence on injury risk factors and epidemiology of injury in trail running. Design Living systematic review. Updated searches will be done every 6 months for a minimum period of 5 years. Data sources Eight electronic databases were searched from inception to 18 March 2021. Eligibility criteria Studies that investigated injury risk factors and/or reported the epidemiology of injury in trail running. Results Nineteen eligible studies were included, of which 10 studies investigated injury risk factors among 2 785 participants. Significant intrinsic factors associated with injury are: more running experience, level A runner and higher total propensity to sports accident questionnaire (PAD-22) score. Previous history of cramping and postrace biomarkers of muscle damage is associated with cramping. Younger age and low skin phototypes are associated with sunburn. Significant extrinsic factors associated with injury are neglecting warm-up, no specialised running plan, training on asphalt, double training sessions per day and physical labour occupations. A slower race finishing time is associated with cramping, while more than 3 hours of training per day, shade as the primary mode of sun protection and being single are associated with sunburn. An injury incidence range 0.7–61.2 injuries/1000 hours of running and prevalence range 1.3% to 90% were reported. The lower limb was the most reported region of injury, specifically involving blisters of the foot/toe. Conclusion Limited studies investigated injury risk factors in trail running. Our review found eight intrinsic and nine extrinsic injury risk factors. This review highlighted areas for future research that may aid in designing injury risk management strategies for safer trail running participation. PROSPERO registration number CRD42021240832.
Ecologists and Ecologians
Journal: JAMA (1971)

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Screening for Atrial Fibrillation
Authors: Leila C. Kahwati, Gary N. Asher, Zachary O. Kadro, Susan Keen, Rania Ali, Emmanuel Coker-Schwimmer, Daniel E. Jonas
Journal: JAMA (2022)

<h3>Importance</h3> Atrial fibrillation (AF), the most common arrhythmia, increases the risk of stroke. <h3>Objective</h3> To review the evidence on screening for AF in adults without prior stroke to inform the US Preventive Services Task Force. <h3>Data Sources</h3> PubMed, Cochrane Library, and trial registries through October 5, 2020; references, experts, and literature surveillance through October 31, 2021. <h3>Study Selection</h3> Randomized clinical trials (RCTs) of screening among asymptomatic persons without known AF or prior stroke; test accuracy studies; RCTs of anticoagulation among persons with AF; systematic reviews; and observational studies reporting harms. <h3>Data Extraction and Synthesis</h3> Two reviewers assessed titles/abstracts, full-text articles, and study quality and extracted data; when at least 3 similar studies were available, meta-analyses were conducted. <h3>Main Outcomes and Measures</h3> Detection of undiagnosed AF, test accuracy, mortality, stroke, stroke-related morbidity, and harms. <h3>Results</h3> Twenty-six studies (N = 113 784) were included. In 1 RCT (n = 28 768) of twice-daily electrocardiography (ECG) screening for 2 weeks, the likelihood of a composite end point (ischemic stroke, hemorrhagic stroke, systemic embolism, all-cause mortality, and hospitalization for bleeding) was lower in the screened group over 6.9 years (hazard ratio, 0.96 [95% CI, 0.92-1.00];<i>P</i> = .045), but that study had numerous limitations. In 4 RCTs (n = 32 491), significantly more AF was detected with intermittent and continuous ECG screening compared with no screening (risk difference range, 1.0%-4.8%). Treatment with warfarin over a mean of 1.5 years in populations with clinical, mostly persistent AF was associated with fewer ischemic strokes (pooled risk ratio [RR], 0.32 [95% CI, 0.20-0.51]; 5 RCTs; n = 2415) and lower all-cause mortality (pooled RR, 0.68 [95% CI, 0.50-0.93]) compared with placebo. Treatment with direct oral anticoagulants was also associated with lower incidence of stroke (adjusted odds ratios range, 0.32-0.44) in indirect comparisons with placebo. The pooled RR for major bleeding for warfarin compared with placebo was 1.8 (95% CI, 0.85-3.7; 5 RCTs; n = 2415), and the adjusted odds ratio for major bleeding for direct oral anticoagulants compared with placebo or no treatment ranged from 1.38 to 2.21, but CIs did not exclude a null effect. <h3>Conclusions and Relevance</h3> Although screening can detect more cases of unknown AF, evidence regarding effects on health outcomes is limited. Anticoagulation was associated with lower risk of first stroke and mortality but with increased risk of major bleeding, although estimates for this harm are imprecise; no trials assessed benefits and harms of anticoagulation among screen-detected populations.
Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida
Authors: Jesús A Ballesteros, Carlos E Santibáñez-López, Caitlin M Baker, Ligia R Benavides, Tauana J Cunha, Guilherme Gainett, Andrew Z Ontano, Emily V W Setton, Claudia P Arango, Efrat Gavish-Regev, Mark S Harvey, Ward C Wheeler, Gustavo Hormiga, Gonzalo Giribet, Prashant P Sharma
Journal: Molecular Biology and Evolution (2022)

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification
Authors: Matthew Dapas, Andrea Dunaif
Journal: Endocrine Reviews (2022)

Polycystic ovary syndrome (PCOS) is among the most common disorders in women of reproductive age, affecting up to 15% worldwide, depending on the diagnostic criteria. PCOS is characterized by a constellation of interrelated reproductive abnormalities, including disordered gonadotropin secretion, increased androgen production, chronic anovulation, and polycystic ovarian morphology. It is frequently associated with insulin resistance and obesity. These reproductive and metabolic derangements cause major morbidities across the lifespan, including anovulatory infertility and type 2 diabetes (T2D). Despite decades of investigative effort, the etiology of PCOS remains unknown. Familial clustering of PCOS cases has indicated a genetic contribution to PCOS. There are rare Mendelian forms of PCOS associated with extreme phenotypes, but PCOS typically follows a non-Mendelian pattern of inheritance consistent with a complex genetic architecture, analogous to T2D and obesity, that reflects the interaction of susceptibility genes and environmental factors. Genomic studies of PCOS have provided important insights into disease pathways and have indicated that current diagnostic criteria do not capture underlying differences in biology associated with different forms of PCOS. We provide a state-of-the-science review of genetic analyses of PCOS, including an overview of genomic methodologies aimed at a general audience of non-geneticists and clinicians. Applications in PCOS will be discussed, including strengths and limitations of each study. The contributions of environmental factors, including developmental origins, will be reviewed. Insights into the pathogenesis and genetic architecture of PCOS will be summarized. Future directions for PCOS genetic studies will be outlined.
Ancient and historical DNA in conservation policy
Authors: Evelyn L. Jensen, David Díez-del-Molino, M. Thomas P. Gilbert, Laura D. Bertola, Filipa Borges, Vlatka Cubric-Curik, Miguel de Navascués, Peter Frandsen, Myriam Heuertz, Christina Hvilsom, Belén Jiménez-Mena, Antti Miettinen, Markus Moest, Patrícia Pečnerová, Ian Barnes, Cristiano Vernesi
Journal: Trends in Ecology & Evolution (2022)

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (Ne), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.
Ophthalmologic Findings in Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy
Authors: Susanna Roine, Mika Harju, Tero T. Kivelä, Minna Pöyhönen, Eeva Nikoskelainen, Seppo Tuisku, Hannu Kalimo, Matti Viitanen, Paula A. Summanen
Journal: Ophthalmology (2006)
Streptococci in Relation to Man in Health and Disease.
Authors: Anna Wessels Williams
Journal: JAMA (1933)

This work was referred for judgment to an expert bacteriologist, who happens to be a man of few words. His report was that it contained everything that was known on the streptococci, and that it covered a great deal of pathogenic bacteriology. That is a fair summary of the book. It covers in a well arranged order its entire field, including an extensive bibliography. It is a work that will be found valuable by all dermatologists.