tbuckley/cabot-search huggingface dataset:
CNN-based lung CT registration with multiple anatomical constraints
Authors: Alessa Hering, Stephanie Häger, Jan Moltz, Nikolas Lessmann, Stefan Heldmann, Bram van Ginneken
Journal: Medical Image Analysis (2021)

Deep-learning-based registration methods emerged as a fast alternative to conventional registration methods. However, these methods often still cannot achieve the same performance as conventional registration methods because they are either limited to small deformation or they fail to handle a superposition of large and small deformations without producing implausible deformation fields with foldings inside. In this paper, we identify important strategies of conventional registration methods for lung registration and successfully developed the deep-learning counterpart. We employ a Gaussian-pyramid-based multilevel framework that can solve the image registration optimization in a coarse-to-fine fashion. Furthermore, we prevent foldings of the deformation field and restrict the determinant of the Jacobian to physiologically meaningful values by combining a volume change penalty with a curvature regularizer in the loss function. Keypoint correspondences are integrated to focus on the alignment of smaller structures. We perform an extensive evaluation to assess the accuracy, the robustness, the plausibility of the estimated deformation fields, and the transferability of our registration approach. We show that it achieves state-of-the-art results on the COPDGene dataset compared to conventional registration method with much shorter execution time. In our experiments on the DIRLab exhale to inhale lung registration, we demonstrate substantial improvements (TRE below 1.2 mm) over other deep learning methods. Our algorithm is publicly available at https://grand-challenge.org/algorithms/deep-learning-based-ct-lung-registration/.
Silent Cerebral Infarct Pathophysiology Study in Sickle Cell Anemia Children By a Multimodal Approach
Authors: Valentine Brousse, David Grévent, Cecile Arnaud, Annie Kamden, Manoelle Kossorotoff, Mariane De Montalembert, Benedicte Boutonnat-Faucher, Slimane Allali, Keyne Charlot, Philippe Connes, Lydie Da Costa, Corinne Pondarré, Suzanne Verlhac
Journal: Blood (2017)
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals
Authors: Alison Tarke, John Sidney, Nils Methot, Esther Dawen Yu, Yun Zhang, Jennifer M. Dan, Benjamin Goodwin, Paul Rubiro, Aaron Sutherland, Eric Wang, April Frazier, Sydney I. Ramirez, Stephen A. Rawlings, Davey M. Smith, Ricardo da Silva Antunes, Bjoern Peters, Richard H. Scheuermann, Daniela Weiskopf, Shane Crotty, Alba Grifoni, Alessandro Sette
Journal: Cell Reports Medicine (2021)

The emergence of SARS-CoV-2 variants with evidence of antibody escape highlight the importance of addressing whether the total CD4
The role of osteoprotegerin (OPG) in fibrosis: its potential as a biomarker and/or biological target for the treatment of fibrotic diseases
Authors: Habibie Habibie, Adhyatmika Adhyatmika, Dedmer Schaafsma, Barbro N. Melgert
Journal: Pharmacology & Therapeutics (2021)

Fibrosis is defined by excessive formation and accumulation of extracellular matrix proteins, produced by myofibroblasts, that supersedes normal wound healing responses to injury and results in progressive architectural remodelling. Fibrosis is often detected in advanced disease stages when an organ is already severely damaged and can no longer function properly. Therefore, there is an urgent need for reliable and easily detectable markers to identify and monitor fibrosis onset and progression as early as possible; this will greatly facilitate the development of novel therapeutic strategies. Osteoprotegerin (OPG), a well-known regulator of bone extracellular matrix and most studied for its role in regulating bone mass, is expressed in various organs and functions as a decoy for receptor activator of nuclear factor kappa-B ligand (RANKL) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Recently, OPG has been linked to fibrosis and fibrogenesis, and has been included in a panel of markers to diagnose liver fibrosis. Multiple studies now suggest that OPG may be a general biomarker suitable for detection of fibrosis and/or monitoring the impact of fibrosis treatment. This review summarizes our current understanding of the role of OPG in fibrosis and will discuss its potential as a biomarker and/or novel therapeutic target for fibrosis.
Abstract 20: Novel Transfer of Low Viscosity Cyan Methacrylate on the Surfaces of the Sheep Heart Model and Paint Brush Technique
Authors: Mark Arokiaraj
Journal: Circulation Research (2016)

Aim: To develop a novel technique for the transfer of cyan methacrylate on the inner and outer surfaces of the sheep heart model. Methods: Low viscosity ultraviolet curable cyan methacrylate was mixed with commercially available dye to demonstrate the ability of transfer on the outer and inner surfaces of the in-vitro sheep heart model. 0.5 ml of cyan methacrylate was mixed with 0.2 ml of dye, and the material was injected over the surface of the heart in dry air, and it was allowed to fix for 2-3 seconds. Subsequently, the whole preparation was immersed in saline, and it was vigorously shaken to remove unbound compound. The similar experiment was performed without cyan methacrylate. By visual assessment, a significant quantity of the compound attaches to the surfaces of the heart compared to the dye alone, which was visualized after washing. After that, various techniques were investigated for efficient transfer of the compound on the heart surfaces soaked in saline. Of the various techniques paintbrush technique for the targeted transfer was effective (figure below). Also targeted areas like left atrial appendage, left ventricular inner surfaces at the origin of papillary muscle and left ventricular apex were some of the areas investigated successfully. The ultraviolet (UV) light source was a pen shaped device. It was observed that after ultraviolet treatment micro precipitates forms. The experiment was repeated in 3 different samples to observe the techniques. Conclusion: There is potential for transfer of low viscosity, UV curable cyan methacrylate on the surfaces of the heart. This could of potential to transfer growth factors or protein molecules attacked to cyan methacrylate.
Homeopathic Agents or Vitamins in Reducing Ecchymosis after Oculofacial Surgery
Authors: Jeremiah P. Tao, Vinay K. Aakalu, Suzanne K. Freitag, Rachel K. Sobel, Jill A. Foster, Edward J. Wladis, Timothy J. McCulley, Michael T. Yen
Journal: Ophthalmology (2021)
Mutational Signatures Associated with Intensity and Duration of Smoking in Myelodysplastic Syndromes (MDS)
Authors: Yazan F. Madanat, Tomas Radivoyevitch, Aziz Nazha, Yazeed Sawalha, Karam Al-Issa, Nour Abuhadra, Teodora Kuzmanovic, Bartlomiej Przychodzen, Cassandra M. Hirsch, Bhumika J. Patel, David Seastone, Yogenthiran Saunthararajah, Sudipto Mukherjee, Anjali S. Advani, Hetty E. Carraway, Aaron T. Gerds, Jaroslaw P. Maciejewski, Mikkael A. Sekeres
Journal: Blood (2017)
Therapist-Guided Internet-Based Treatments for Loneliness: A Randomized Controlled Three-Arm Trial Comparing Cognitive Behavioral Therapy and Interpersonal Psychotherapy
Authors: Anton Käll, Malin Bäck, Camilla Welin, Hanna Åman, Rasmus Bjerkander, Matilda Wänman, Tomas Lindegaard, Matilda Berg, Hajdi Moche, Roz Shafran, Gerhard Andersson
Journal: Psychotherapy and Psychosomatics (2021)

Introduction: Chronic loneliness has been linked to many adverse outcomes, including mental health problems. Psychological treatment of loneliness can be effective, but the evidence base is limited. Objective: To investigate the efficacy of 2 internet-based interventions based on cognitive behavioral therapy (ICBT) and interpersonal psychotherapy (IIPT) relative to a wait-list control group and each other. Methods: A total of 170 participants were recruited and randomized to either 9 weeks of ICBT (n = 68), IIPT (n = 68), or a wait-list condition (n = 34). The primary outcome was loneliness, measured using the UCLA Loneliness Scale before, during, and after treatment. Secondary measures of psychiatric disorders and quality of life were administered before and after treatment. Follow-up was conducted 4 months after the treatment had ended. Primary outcome data were analyzed using growth curve modeling. Secondary outcomes were analyzed using robust regression models. The trial was preregistered (ClinicalTrials.gov ID: NCT03807154). Results: The ICBT condition had a significantly greater impact on loneliness compared to the wait-list and IIPT conditions. Effect sizes were moderate to large (Cohen d = 0.71) compared to the wait-list and moderate (d = 0.53) compared to IIPT. The IIPT condition did not differ significantly from the wait-list. Both active treatments led to significant increases in quality of life. Only the ICBT group had significantly lower symptoms of depression and generalized anxiety compared to the wait-list group. Treatment gains were maintained but not improved at follow-up. Conclusions: ICBT can be an efficacious option for alleviating loneliness. The IIPT intervention was not as effective.
Neonatal Gonococcal Infection
Authors: H. Hunter Handsfield
Journal: JAMA (1973)

<i>Neisseria gonorrhoeae</i>was isolated from the orogastric aspirates (OGA) of 14 neonates in Seattle, including nine born at the University of Washington Hospital over a four-year period. Prematurity, prolonged rupture of the fetal membranes, associated maternal peripartum fever, histologic evidence of chorioamnionitis, OGA leukocytosis, and a clinical diagnosis of sepsis were more frequent among the infants whose OGA contained gonococci than among 153 infants whose OGA showed no pathogenic bacteria. Mothers whose peripartum endocervical, endometrial, or placental specimens contained<i>N gonorrhoeae</i>had an increased frequency of premature delivery and prolonged rupture of membranes. Gonococcal infection may have an adverse effect on the course of pregnancy, with resultant maternal and infant morbidity. Gonococcal amniotic-orogastric contamination is probably the most common form of neonatal colonization by<i>N gonorrhoeae</i>at the present time.
Quantification of US Food and Drug Administration Premarket Approval Statements for High-Risk Medical Devices With Pediatric Age Indications
Authors: Samuel J. Lee, Lauren Cho, Eyal Klang, James Wall, Stefano Rensi, Benjamin S. Glicksberg
Journal: JAMA Network Open (2021)

<h3>Importance</h3> Medical device companies submit premarket approval (PMA) statements to the US Food and Drug Administration (FDA) for approval of the highest-risk class of devices. Devices indicated for the pediatric population that use the PMA pathway have not been well characterized or analyzed. <h3>Objective</h3> To identify and characterize high-risk devices with pediatric age indications derived from PMA statements. <h3>Design, Setting, and Participants</h3> In this cross-sectional study of PMA statements, those statements containing the words<i>indicated</i>or<i>intended</i>for medical devices listed in the FDA PMA database as of February 2020 were retrieved. Age indications were manually annotated in these approval statements via PubAnnotation. Based on the PMA identification from the PMA statements, device metadata including product codes, regulation numbers, advisory panels, and approval dates were queried. <h3>Main Outcomes and Measures</h3> The main outcome was discernment of the distribution of devices indicated for the pediatric population (neonate, infant, child, and adolescent). Secondary measures included outlining the clinical specialties, device types, and lag time between the initial approval date and the first date of an approval statement with a pediatric indication for generic device categories. <h3>Results</h3> A total of 297 documents for 149 unique devices were analyzed. Based on the manual age annotations, 102 devices with a pediatric indication, 10 with a neonate age indication, 32 with an infant age indication, 60 with a child age indication, and 94 with an adolescent age indication were identified. For indications for patients from age 17 to 18 years, the number of devices available nearly doubled from 42 devices to 81 devices. Although more than half of the surveyed devices had a pediatric age indication, many were available only for a limited range of the pediatric population (age 18-21 years). For indications for patients from age 0 to 17 years, the mean (SD) number of clinical specialties at each age was 7.27 (1.4), and 12 clinical specialties were represented from ages 18 to 21 years. <h3>Conclusions and Relevance</h3> In this cross-sectional study on device PMA statements, a gap was identified in both quantity and diversity of high-risk devices indicated for the pediatric population. Because the current scarcity of pediatric devices may limit therapeutic possibilities for children, this study represents a step toward quantifying this scarcity and identifying clinical specialties with the greatest need for pediatric device innovation and may help inform future device development efforts.
三級ブチルヒドロキノンは,THP-1マクロファージ由来泡沫細胞における核内因子E2関連因子2/ヘムオキシゲナーゼ-1情報伝達を介して,ATP結合カセット輸送体AIの発現を上方調節する
Authors: Lu Qian, Tang Shi-lin, Liu Xiao-yan, Zhao Guo-jun, Ouyang Xin-ping, LV Yun-cheng, HE Ping-ping, Yao Feng, Chen Wu-jun, Tang Yan-yan, Zhang Min, Zhang Da-wei, Yin Kai, Tang Chao-ke
Journal: Circulation (2013)
Under Pressure: The Pulmonary Vasculature and Its Role in the Pediatric Cardiac ICU
Authors: Ryan D. Coleman, Raysa Morales-Demori, John Coulson, Lewis H. Romer
Journal: American Journal of Respiratory and Critical Care Medicine (2021)

Under Pressure: The Pulmonary Vasculature and Its Role in the Pediatric Cardiac ICU Pediatric patients with severe pulmonary hypertension (PH) represent one of the most challenging patient populations for clinicians to take care of, as their pulmonary vascular disease makes their propensity for rapid changes in hemodynamics quite high.In patients with underlying congenital or acquired heart disease who already have a myriad of anatomic and physiologic challenges, pulmonary vascular disease can be the "icing on the cake" when it comes to making their medical management particularly harrowing.To better characterize this particular cohort, in this issue of the Journal, Morell and colleagues (pp.454-461) provide a thoughtful and systematic analysis of risk of mortality in 1,709 neonates, children, and young adults (2,602 medical admissions) with PH who received care in 38 North American pediatric cardiac ICUs (PCICU) between 2014 and 2019 (1).Their findings lend granularity, a new venue, and eye-opening follow up to previous cautionary notes in the literature regarding the fragility of children with pulmonary vascular diseases of various etiologies (2, 3).The current work isolates some specific factors that help to organize thinking about risk assessment and reduction in this unique patient subset by drilling down into clinical scenarios involved and into constellations of interventions that may cause or be associated with increased mortality.One striking finding in this study is that the use of vasoactive infusions on the second day of the PCICU stay was the dominant factor for increased mortality.However, details of the specific vasoactive agents that were used in the cases under study are not listed in detail.Given this finding, some challenges in the use of these drugs in the setting of cardiac dysfunction with PH are worthy of note.a-adrenergic agents provide benefit by increasing systemic vascular resistance, diastolic pressure, and coronary perfusion, but a parallel increase in pulmonary vascular resistance may present an ailing right ventricle with increased afterload.b-adrenergic agents may increase cardiac output by increasing left ventricular contractility, but the effects of increased chronotropy on a hypertrophied and stiff right ventricle may be counterproductive, as filling time is cut short.Alternatively, avoidance of adrenergic receptor stimulation by using vasopressin infusions in the setting of cardiac dysfunction with PH in children has been shown to increase aortic pressure and improve systemic hemodynamics while avoiding increased pulmonary vascular resistance that challenges the right ventricle (4, 5).Milrinone is a particular pharmacologic agent that inspires heated debate in the PH population.Although some use it frequently in nearly all patients with PH, others tend to avoid it with equal veracity.In the current study, milrinone did not appear to add to mortality risk.
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Authors: Laura Schulz, Manuel Torres-Diz, Mariela Cortés-López, Katharina E. Hayer, Mukta Asnani, Sarah K. Tasian, Yoseph Barash, Elena Sotillo, Kathi Zarnack, Julian König, Andrei Thomas-Tikhonenko
Journal: Genome biology (2021)

Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
Abstract 97: Ca <sup>2+</sup> Influx Via <i> I <sub>CRAC</sub> </i> Channels is Involved in Increased Secretion/Deposition of Collagen by Human Failing Heart Ventricular Fibroblasts
Authors: Gracious R. Ross, Larisa Emelyanova, Farhan Rizvi, Yang Shi, Ekhson L. Holmuhamedov, Paul Werner, A. Jamil Tajik, Arshad Jahangir
Journal: Circulation Research (2016)

Introduction: Excessive cardiac fibrosis (CF) underlies mechanical and electrical dysfunction in heart failure (HF). However, the underlying mechanisms of increased CF are unclear. Recently, we reported increased Orai1 expression and I CRAC (calcium release-activated channels) -Ca 2+ influx in failing heart ventricular fibroblasts (hVF). Therefore, we studied the magnitude of collagen secretion/deposition by hVF from failing hearts and the involvement of Ca 2+ influx through I CRAC channels in this process. Hypothesis: We tested the hypothesis that collagen secretion/deposition by hVFs from failing hearts will be high and sensitive to inhibition of I CRAC channels, compared to normal hearts. Methods: Primary cultures of hVF obtained from HF patients undergoing LV assist device implantation (n=9) were compared to non-diseased hVF from trauma victims (n=4). The degree of fibrosis was analyzed by histology of LV tissue sections (5μm) with Masson’s trichrome staining. Collagen secretion/deposition after 48 h culture of hVFs from failing or normal hearts in the presence or absence of I CRAC inhibitor, YM-58483(10 μM), was assayed calorimetrically using Sircol™ kit. Data were analyzed by unpaired Student’s t-test. Results: Histology of the failing heart LV sections with Masson’s trichome staining showed severe fibrosis compared to control sections. The percentage of positive staining area to total area, measured using custom-developed ImageJ macro, was significantly (p&lt;0.05) higher in the failing heart (4.5±0.2%) compared to that of normal (0.1± 0.01%). The secretion/deposition of soluble collagen was significantly (p&lt;0.05) higher in failing heart hVF (86± 7.6 μg/10 6 cells) than normal heart hVF (58.4±8.8 μg/10 6 cells). Incubation of fibroblasts with the I CRAC inhibitor YM58486 (10 μM) for 48 h eliminated the increase in collagen secretion of HF fibroblasts (55.8± 7 μg/10 6 cells vs 66.8± 6 μg/10 6 cells, p=0.27). Conclusion: LV fibrosis is severe in HF patients. The magnitude of pro-fibrotic collagen secretion/deposition by hVF from HF patients is significantly high but sensitive to I CRAC inhibition. Selective targeting of fibroblast I CRAC may be a potential therapeutic tool to mitigate progression of CF and HF.
European Association of Urology Guidelines on Sexual and Reproductive Health—2021 Update: Male Sexual Dysfunction
Authors: Andrea Salonia, Carlo Bettocchi, Luca Boeri, Paolo Capogrosso, Joana Carvalho, Nusret Can Cilesiz, Andrea Cocci, Giovanni Corona, Kostantinos Dimitropoulos, Murat Gül, Georgios Hatzichristodoulou, T. Hugh Jones, Ates Kadioglu, Juan Ignatio Martínez Salamanca, Uros Milenkovic, Vaibhav Modgil, Giorgio Ivan Russo, Ege Can Serefoglu, Tharu Tharakan, Paolo Verze, Suks Minhas
Journal: European Urology (2021)
Identifying women at high-risk for breast cancer using data from the electronic health record compared to self-report.
Authors: Xinyi Li, Julia E. McGuinness, Alejandro Vanegas, Hilary Colbeth, Jennifer Vargas, Rossy Sandoval, Rita Kukafka, Katherine D Crew
Journal: Journal of Clinical Oncology (2017)

e13044 Background: One of the barriers to chemoprevention uptake among high-risk women is the lack of routine breast cancer risk assessment in the primary care setting. We calculated breast cancer risk using the Breast Cancer Surveillance Consortium (BCSC) model, which accounts for age, race/ethnicity, first-degree family history of breast cancer, benign breast disease, and mammographic density, using data collected from the electronic health record (EHR) compared to self-report. Methods: Among women undergoing screening mammography, we collected breast cancer risk information from the EHR and a self-administered survey. Eligibility criteria for calculating 5-year invasive breast cancer risk using the BCSC model included age 35-74, no prior history of breast cancer, mastectomy, or breast augmentation. We extracted data on demographics, structured first-degree family history, breast radiology and pathology reports from the EHR. We assessed agreement in breast cancer risk information between the EHR and self-report data. Results: Among 13,735 women with EHR data for BCSC risk calculation, 2708 women (20%) met high-risk criteria, based upon a 5-year breast cancer risk ≥1.67%. Among high-risk women, 2% were age 40-49, 23% age 50-59, 48% age 60-69, and 26% age 70-74. From the EHR, data was missing on 31% for race/ethnicity and 85% for family history. Among 2320 women with both EHR and self-report data, more complete information was available for race/ethnicity, family history, and breast biopsies in the surveys. More first-degree family history (14% vs. 3%) and prior breast biopsies (18% vs. 11%) were identified by self-report vs. EHR, respectively. However, more women with atypia and lobular carcinoma in situwere identified from the EHR. More high-risk women (20% vs. 16%) were identified with EHR vs. survey data, respectively, with correlation of 0.82. Conclusions: Among women undergoing screening mammography, we identified 20% who met high-risk criteria according to the BCSC model based upon EHR data, despite missing information on race/ethnicity, family history, and prior breast biopsies. This may serve as an initial screen for identifying women eligible for breast cancer chemoprevention.