tbuckley/cabot-search huggingface dataset:
SFPL: Sample-specific fine-grained prototype learning for imbalanced medical image classification
Authors: Yongbei Zhu, Shuo Wang, He Yu, Weimin Li, Jie Tian
Journal: Medical Image Analysis (2024)

Imbalanced classification is a common and difficult task in many medical image analysis applications. However, most existing approaches focus on balancing feature distribution and classifier weights between classes, while ignoring the inner-class heterogeneity and the individuality of each sample. In this paper, we proposed a sample-specific fine-grained prototype learning (SFPL) method to learn the fine-grained representation of the majority class and learn a cosine classifier specifically for each sample such that the classification model is highly tuned to the individual's characteristic. SFPL first builds multiple prototypes to represent the majority class, and then updates the prototypes through a mixture weighting strategy. Moreover, we proposed a uniform loss based on set representations to make the fine-grained prototypes distribute uniformly. To establish associations between fine-grained prototypes and cosine classifier, we propose a selective attention aggregation module to select the effective fine-grained prototypes for final classification. Extensive experiments on three different tasks demonstrate that SFPL outperforms the state-of-the-art (SOTA) methods. Importantly, as the imbalance ratio increases from 10 to 100, the improvement of SFPL over SOTA methods increases from 2.2% to 2.4%; as the training data decreases from 800 to 100, the improvement of SFPL over SOTA methods increases from 2.2% to 3.8%.
Revolutionizing Postoperative Free Flap Monitoring—The Promise of AI to Improve Health Outcomes
Authors: Zezhong Ye, Dan Sun, Sam E. Gary
Journal: JAMA Network Open (2024)

Jisu Kim, MD; Sang Mee Lee; Da Eun Kim; Sungjin Kim, MD; Myung Jin Chung, MD, PhD; Zero Kim, MD, PhD; Taeyoung Kim, PhD; Kyeong-Tae Lee, MD, PhD
A Phase II Placebo-Controlled Study of the Effect and Safety of Nanvuranlat in Patients with Advanced Biliary Tract Cancers Previously Treated by Systemic Chemotherapy
Authors: Junji Furuse, Masafumi Ikeda, Makoto Ueno, Masayuki Furukawa, Chigusa Morizane, Tetsuo Takehara, Tomohiro Nishina, Akiko Todaka, Naohiro Okano, Kazuo Hara, Yousuke Nakai, Kazuyoshi Ohkawa, Takashi Sasaki, Kazuya Sugimori, Naoyuki Yokoyama, Kouji Yamamoto
Journal: Clinical Cancer Research (2024)

To evaluate the efficacy and safety of nanvuranlat [an L-type amino acid transporter 1 inhibitor] monotherapy as a later-line treatment in advanced, metastatic, and refractory biliary tract cancers.
Development of an Automated Free Flap Monitoring System Based on Artificial Intelligence
Authors: Jisu Kim, Sang Mee Lee, Da Eun Kim, Sungjin Kim, Myung Jin Chung, Zero Kim, Taeyoung Kim, Kyeong-Tae Lee
Journal: JAMA Network Open (2024)

Meticulous postoperative flap monitoring is essential for preventing flap failure and achieving optimal results in free flap operations, for which physical examination has remained the criterion standard. Despite the high reliability of physical examination, the requirement of excessive use of clinician time has been considered a main drawback.
Convalescent plasma and predictors of mortality among hospitalized patients with COVID-19: a systematic review and meta-analysis
Authors: Massimo Franchini, Mario Cruciani, Carlo Mengoli, Arturo Casadevall, Claudia Glingani, Michael J. Joyner, Liise-anne Pirofski, Jonathon W. Senefeld, Shmuel Shoham, David J. Sullivan, Matteo Zani, Daniele Focosi
Journal: Clinical Microbiology and Infection (2024)
Posaconazole gastro-resistant tablets for preventing invasive fungal disease after haematopoietic stem cell transplantation: a propensity-matched cohort study
Authors: Jiaxin Cao, Pan Pan, Dan Feng, Mingyang Wang, Yawei Zheng, Nan Yang, Xin Chen, Weihua Zhai, Rongli Zhang, Qiaoling Ma, Jialin Wei, Donglin Yang, Yi He, Xiaodan Wang, Sizhou Feng, Mingzhe Han, Erlie Jiang, Aiming Pang
Journal: Clinical Microbiology and Infection (2024)
Which trial do we need? A pragmatic randomised trial of trimethoprim-sulfamethoxazole versus vancomycin for the treatment of methicillin-resistant Staphylococcus aureus bacteraemia in low-resource settings.
Authors: Judith Recht, Terry John Evans, Vilada Chansamouth, Koukeo Phommasone, Mayfong Mayxay, Elizabeth A. Ashley
Journal: Clinical Microbiology and Infection (2024)
Managing, surveying and assisting transgender people in prison: A comparative analysis of staff-members’ positioning toward transgender inmates among different correctional facilities in Italy
Authors: Alexander Hochdorn, Rafael Jefferson Oliveira, Paolo Cottone, Noemia de Morais Santos, Fabio Iglesias, Paolo Valerio, Roberto Vitelli
Journal: International Journal of Transgender Health (2024)

Background The present study intends to shed light on the (inter)subjective and professional modalities through which prison workers manage to cope with the presence of incarcerated transgender people in Italy.
Evaluation and management of hypertensive emergency
Authors: Joseph B Miller, Daniel Hrabec, Vijay Krishnamoorthy, Harish Kinni, Robert D Brook
Journal: BMJ (2024)

Abstract Hypertensive emergencies cause substantial morbidity and mortality, particularly when acute organ injury is present. Careful and effective strategies to reduce blood pressure and diminish the effects of pressure-mediated injury are essential. While the selection of specific antihypertensive medications varies little across different forms of hypertensive emergencies, the intensity of blood pressure reduction to the target pressure differs substantially. Treatment hinges on balancing the positive effects of lowering blood pressure with the potential for negative effects of organ hypoperfusion in patients with altered autoregulatory mechanisms. When patients do not have acute organ injury in addition to severe hypertension, they benefit from a conservative, outpatient approach to blood pressure management. In all cases, long term control of blood pressure is paramount to prevent recurrent hypertensive emergencies and improve overall prognosis. This review discusses the current evidence and guidelines on the evaluation and management of hypertensive emergency.
Preexisting Skin-Resident CD8 and γδ T-cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy
Authors: Zachary Z. Reinstein, Yue Zhang, Oscar E. Ospina, Matt D. Nichols, Victoria A. Chu, Alvaro de Mingo Pulido, Karol Prieto, Jonathan V. Nguyen, Rui Yin, Carlos Moran Segura, Ahmed Usman, Brittney Sell, Spencer Ng, Janis V. de la Iglesia, Sunandana Chandra, Jeffrey A. Sosman, Raymond J. Cho, Jeffrey B. Cheng, Ellie Ivanova, Sergei B. Koralov, Robbert J.C. Slebos, Christine H. Chung, Nikhil I. Khushalani, Jane L. Messina, Amod A. Sarnaik, Jonathan S. Zager, Vernon K. Sondak, Charles Vaske, Sungjune Kim, Andrew S. Brohl, Xinlei Mi, Brian G. Pierce, Xuefeng Wang, Brooke L. Fridley, Kenneth Y. Tsai, Jaehyuk Choi
Journal: Cancer Discovery (2024)

Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer with a ∼50% response rate to immune checkpoint blockade (ICB) therapy. To identify predictive biomarkers, we integrated bulk and single-cell RNA sequencing (RNA-seq) with spatial transcriptomics from a cohort of 186 samples from 116 patients, including bulk RNA-seq from 14 matched pairs pre- and post-ICB. In nonresponders, tumors show evidence of increased tumor proliferation, neuronal stem cell markers, and IL1. Responders have increased type I/II interferons and preexisting tissue resident (Trm) CD8 or Vδ1 γδ T cells that functionally converge with overlapping antigen-specific transcriptional programs and clonal expansion of public T-cell receptors. Spatial transcriptomics demonstrated colocalization of T cells with B and dendritic cells, which supply chemokines and costimulation. Lastly, ICB significantly increased clonal expansion or recruitment of Trm and Vδ1 cells in tumors specifically in responders, underscoring their therapeutic importance. These data identify potential clinically actionable biomarkers and therapeutic targets for MCC. Significance: MCC serves as a model of ICB response. We utilized the largest-to-date, multimodal MCC dataset (n = 116 patients) to uncover unique tumor-intrinsic properties and immune circuits that predict response. We identified CD8 Trm and Vδ1 T cells as clinically actionable mediators of ICB response in major histocompatibility complex-high and -low MCCs, respectively.
Changes in 6‐min walk test is an independent predictor of death in chronic heart failure with reduced ejection fraction
Authors: Peder L. Myhre, Øyunn Kleiven, Kristian Berge, Morten Grundtvig, Lars Gullestad, Stein Ørn
Journal: European Journal of Heart Failure (2024)

Functional capacity provides important clinical information in patients with heart failure (HF) and reduced ejection fraction (HFrEF). The 6-min walk test (6MWT) is a simple and inexpensive tool for assessing functional capacity and risk. Although change in 6MWT is frequently used as a surrogate outcome in HF trials, the association with mortality is unclear. We aimed to assess the prognostic importance of changes in 6MWT.
Non‐invasive prediction of pulmonary vascular disease‐related exercise intolerance and survival in non‐group 1 pulmonary hypertension
Authors: Yogesh N.V. Reddy, Hilary Dubrock, Paul M. Hassoun, Anna Hemnes, Evelyn Horn, Jane A. Leopold, Franz Rischard, Erika B. Rosenzweig, Nicholas S. Hill, Serpil C. Erzurum, Gerald J. Beck, Stephen C. Mathai, Monica Mukherjee, W.H. Wilson Tang, Barry A. Borlaug, Robert P. Frantz
Journal: European Journal of Heart Failure (2024)
MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Olaf Klingbeil, Damianos Skopelitis, Claudia Tonelli, Toyoki Yoshimoto, Aktan Alpsoy, Maria C. Panepinto, Francesca Minicozzi, Joseph R. Merrill, Amanda M. Cafiero, Disha Aggarwal, Suzanne Russo, Taehoon Ha, Osama E. Demerdash, Tse-Luen Wee, David L. Spector, Scott K. Lyons, David A. Tuveson, Paolo Cifani, Christopher R. Vakoc
Journal: Cancer Discovery (2024)

The Hippo signaling pathway is commonly dysregulated in human cancer, which leads to a powerful tumor dependency on the YAP/TAZ transcriptional coactivators. Here, we used paralog co-targeting CRISPR screens to identify the kinases MARK2/3 as absolute catalytic requirements for YAP/TAZ function in diverse carcinoma and sarcoma contexts. Underlying this observation is direct MARK2/3-dependent phosphorylation of NF2 and YAP/TAZ, which effectively reverses the tumor suppressive activity of the Hippo module kinases LATS1/2. To simulate targeting of MARK2/3, we adapted the CagA protein from H. pylori as a catalytic inhibitor of MARK2/3, which we show can regress established tumors in vivo. Together, these findings reveal MARK2/3 as powerful co-dependencies of YAP/TAZ in human cancer; targets that may allow for pharmacology that restores Hippo pathway-mediated tumor suppression.
Benralizumab for allergic asthma: a randomised, double-blind, placebo-controlled, trial
Authors: Gail M. Gauvreau, Roma Sehmi, J. Mark FitzGerald, Richard Leigh, Donald W. Cockcroft, Beth E. Davis, Irvin Mayers, Louis-Philippe Boulet, Dhuha Al-Sajee, Brittany M. Salter, Ruth P. Cusack, Terence Ho, Christiane E. Whetstone, Nadia Alsaji, Imran Satia, Kieran J. Killian, Patrick D. Mitchell, Iain P. Magee, Celine Bergeron, Mohit Bhutani, Viktoria Werkström, Tomasz Durżyński, Kathryn Shoemaker, Rohit K. Katial, Maria Jison, Paul Newbold, Christopher McCrae, Paul M. O'Byrne
Journal: European Respiratory Journal (2024)

Background Benralizumab induces rapid and near-complete depletion of eosinophils from blood and lung tissue. We investigated whether benralizumab could attenuate the allergen-induced late asthmatic response (LAR) in participants with allergic asthma. Methods Participants with allergic asthma who demonstrated increased sputum eosinophils and LAR at screening were randomised to benralizumab 30 mg or matched placebo given every 4 weeks for 8 weeks (3 doses). Allergen challenges were performed at weeks 9 and 12 when blood, sputum, bone marrow and bronchial tissue eosinophils and LAR were assessed. Results 46 participants (mean age 30.9 years) were randomised to benralizumab (n=23) or placebo (n=23). Eosinophils were significantly reduced in the benralizumab group compared with placebo in blood at 4 weeks and sputum and bone marrow at 9 weeks after treatment initiation. At 7 h after an allergen challenge at week 9, sputum eosinophilia was significantly attenuated in the benralizumab group compared to placebo (least squares mean difference −5.81%, 95% CI −10.69– −0.94%; p=0.021); however, the LAR was not significantly different (least squares mean difference 2.54%, 95% CI 3.05–8.12%; p=0.363). Adverse events were reported for seven (30.4%) and 14 (60.9%) participants in the benralizumab and placebo groups, respectively. Conclusion Benralizumab administration over 8 weeks resulted in a significant attenuation of blood, bone marrow and sputum eosinophilia in participants with mild allergic asthma; however, there was no change in the LAR, suggesting that eosinophils alone are not a key component of allergen-induced bronchoconstriction.
ERS Statement on Benign Pleural Effusions in Adults
Authors: Anand Sundaralingam, Elzbieta M Grabczak, Patrizia Burra, M.Inês Costa, Vineeth George, Eli Harriss, Ewa Jankowska, Julius P Janssen, Georgia Karpathiou, Christian B Laursen, Kornelija Maceviciute, Nick Maskell, Federico Mei, Blin Nagavci, Vasiliki Panou, Valentina Pinelli, José M Porcel, Sara Ricciardi, Samira Shojaee, Hugh Welch, Alberto Zanetto, Udaya Prabhakar Udayaraj, Giuseppe Cardillo, Najib M Rahman
Journal: European Respiratory Journal (2024)

The incidence of non-malignant pleural effusions (NMPE) far outweighs that of malignant pleural effusions (MPE) and is estimated to be at least 3-fold higher. These so called “benign” effusions do not follow a “benign course” in many cases, with mortality rates matching and sometimes exceeding that of MPEs. In addition to the impact on patients, healthcare systems are significantly affected, with recent US epidemiological data demonstrating that 75% of resource allocation for pleural effusion management is spent on NMPEs (excluding empyema). Despite this significant burden of disease, and by existing at the junction of multiple medical specialties, reflecting a heterogenous constellation of medical conditions, NMPEs are rarely the focus of research or the subject of management guidelines. With this ERS Taskforce, we assembled a multi-specialty collaborative across eleven countries and three continents to provide a Statement based on systematic searches of the medical literature to highlight evidence in the management of the following clinical areas: a diagnostic approach to transudative effusions, heart failure, hepatic hydrothorax, end stage renal failure, benign asbestos related pleural effusion, post-surgical effusion and non-specific pleuritis.
Long-term effect of obstructive sleep apnoea management on blood pressure in patients with resistant hypertension: the SARAH study
Authors: Gerard Torres, Manuel Sánchez-de-la-Torre, Esther Gracia-Lavedan, Ivan D. Benitez, Dolores Martinez, Mireia Dalmases, Lucía Pinilla, Olga Minguez, Rafaela Vaca, Lydia Pascual, Maria Aguilá, Anunciación Cortijo, Clara Gort, Miguel Ángel Martinez-Garcia, Olga Mediano, Sofía Romero Peralta, Ana Maria Fortuna-Gutierrez, Paola Ponte Marquez, Luciano F. Drager, Mayara Cabrini, Silvana de Barros, Juan Fernando Masa, Jaime Corral Peñafiel, Miguel Felez, Susana Vázquez, Jorge Abad, Francisco García-Rio, Raquel Casitas, Chi-Hang Lee, Ferran Barbé
Journal: European Respiratory Journal (2024)

Background There is a close relationship between obstructive sleep apnoea (OSA) and resistant hypertension (RH). However, studies assessing the long-term effect of diagnosing and treating OSA on blood pressure (BP) control in these patients are lacking. Methods To address this gap, we recruited 478 RH patients from hypertension units and followed them prospectively after they were screened for OSA through a sleep study. By performing 24-h ambulatory BP monitoring (ABPM) annually, the effect of OSA management was assessed. Results The patients had a median (interquartile range (IQR)) age of 64.0 (57.2–69.0) years, 67% were males and most were nonsleepy, with a median (IQR) apnoea–hypopnoea index (AHI) of 15.8 (7.9–30.7) events·h −1 . The median (IQR) follow-up time was 3.01 (2.93–3.12) years. At baseline, severe OSA was associated with uncontrolled BP, nocturnal hypertension and a nondipper circadian BP pattern. Moreover, these patients had higher BP values during follow-up than did patients in the other groups. However, among patients with moderate and severe OSA, the management of sleep disordered breathing, including the implementation of continuous positive airway pressure treatment, was associated with a reduction in 24-h ABPM parameters, especially night-time BP values, at the 1-year follow-up. These benefits were attenuated over time and only subjects with severe OSA maintained an ABPM night-time reduction at 3 years. Furthermore, clinical variables such as uncontrolled BP, sex and age showed a predictive value for the BP response at 1 year of follow-up. Conclusion A favourable long-term decrease in BP was detected by diagnosing and treating OSA in a cohort of RH patients from hypertension units, but over time this decrease was only partially maintained in severe OSA patients.
Telerehabilitation: a key player in reducing the travel emissions cost of respiratory healthcare?
Authors: Melissa Chong, Anne E. Holland, Angela T. Burge, Jaycie Perryman, Narelle S. Cox
Journal: European Respiratory Journal (2024)

<h3>Shareable abstract</h3> <b>Travel-related emissions are nearly 60% less for telerehabilitation (TR) than centre-based pulmonary rehabilitation (PR). TR may provide a reduced carbon option for PR delivery, but its use should be considered in the context of broader patient management.</b>https://bit.ly/3W5m3sw
Early respiratory system reactance predicts respiratory outcomes in preterm infants: a retrospective, multicentre study
Authors: Emanuela Zannin, Camilla Rigotti, Sven M. Schulzke, Richard Sindelar, Tobias Werther, Anna Lavizzari, Roland P. Neumann, Linda Wallström, Fabio Mosca, Maria Luisa Ventura, Raffaele L. Dellacà, Chiara Veneroni
Journal: European Respiratory Journal (2024)

Objective This multicenter, international, retrospective study aims to investigate whether respiratory system reactance (Xrs) assessed by respiratory oscillometry on the 7th day of life is associated with respiratory outcomes in preterm infants below 32 weeks’ gestation. Methods Sinusoidal pressure oscillations (2–5 cmH 2 O peak-to-peak, 10 Hz) were superimposed on the positive end-expiratory pressure (PEEP). We assessed the association of Xrs z-score with the duration of respiratory support using linear regression and with bronchopulmonary dysplasia (BPD, according to Jensen et al . 2019) using logistic regression. We used the likelihood ratio test to evaluate whether Xrs z-score adds significantly to clinical predictors, including gestational age (GA), birth weight (BW) and the National Institute of Child Health and Human Development (NICHD) BPD prediction model. Results One hundred and thirty-seven infants (median (Q1, Q3) GA=28.43 (26.11, 30.29) weeks) were included; 44 (32%) developed BPD. Xrs z-score was significantly associated with the duration of respiratory support (R 2 =0.35). Xrs z-score was significantly higher in infants who developed BPD (p&lt;0.001); the optimal cut-off value was 2.6, associated with 77% sensitivity and 80% specificity. In univariable analysis, per z-score increase in Xrs, the OR for BPD increased by 60% and the respiratory support by eight days. In multivariable analysis, Xrs z-score added significantly to the NICHD model and to GA and BW z-score to predict respiratory support duration (p=0.016 and p=0.014, respectively) and BPD development (p=0.003 and p&lt;0.001, respectively). Conclusion Xrs z-score on the 7th day after birth improves the prediction of respiratory outcome in preterm infants.
Chronic thromboembolic pulmonary hypertension is an uncommon complication of COVID-19: UK national surveillance and observational screening cohort studies
Authors: S. Ashwin Reddy, Joseph Newman, Olivia C. Leavy, Hakim Ghani, Joanna Pepke-Zaba, John E. Cannon, Karen K. Sheares, Dolores Taboada, Katherine Bunclark, Allan Lawrie, Cathie L. Sudlow, Colin Berry, James M. Wild, Jane A. Mitchell, Jennifer Quint, Jennifer Rossdale, Laura Price, Luke S. Howard, Martin Wilkins, Naveed Sattar, Philip Chowienczyk, Roger Thompson, Louise V. Wain, Alexander Horsley, Ling-Pei Ho, James D. Chalmers, Michael Marks, Krisnah Poinasamy, Betty Raman, Victoria C. Harris, Linzy Houchen-Wolloff, Christopher E. Brightling, Rachael A. Evans, Mark R. Toshner
Journal: European Respiratory Journal (2024)

Pulmonary embolism (PE) is a well-recognised complication of coronavirus disease 2019 (COVID-19) infection, and chronic thromboembolic pulmonary disease with and without pulmonary hypertension (CTEPD/CTEPH) are potential life-limiting consequences. At present the burden of CTEPD/CTEPH is unclear and optimal and cost-effective screening strategies yet to be established.
Characterization of omalizumab updosing patterns and predictive factors in chronic spontaneous urticaria: A prospective multicentric observational study
Authors: Guillaume Pierrard, Claire Bernier, Aurélie Du‐Thanh, Corina Bara, Angèle Soria, Florence Castelain, Isabelle Boccon‐Gibod, Florence Hacard, Juliette Delaunay, Laurence de Montjoye, Delphine Staumont‐Salle, Frédéric Dezoteux
Journal: Allergy (2024)

Limited information is available on the use of omalizumab (OMA) updosing since its introduction as a second-line therapy in chronic spontaneous urticaria (CSU) in 2014. Practical guidelines from health authorities are lacking, and the specific characteristics of patients requiring higher doses remain unknown. Our objectives were to characterize the patterns of OMA updosing (defined as changes in dose and/or injection intervals), to identify the predictive factors associated with updosing, and to improve CSU management. We conducted a prospective, multicentric, real-life observational study, including patients diagnosed with CSU and starting OMA. The data were collected at 0, 3, 6, and 9 months. The primary endpoint was the frequency of OMA updosing at 3 months. The secondary endpoints included an analysis of updosed patients' profile, and an assessment of OMA efficacy and safety. We included 153 patients. Twenty percent of patients were updosed at 3 months, and 27% in total during the 9-month follow-up. Practitioners mainly chose to increase the frequency of injections (66%). At baseline, the updosed patients were more likely to have more severe CSU (UCT < 4, p < 0.030), a lower lymphocyte count (<2000/mm3, p = 0.037), and low IgE levels (<70 UI/mL, p = 0.024). The side effects of OMA were not more frequent after updosing. One in five patient underwent updosing within just 3 months. OMA updosing is frequent in particular in cases of severe disease and low IgE blood levels.
Efficacy and safety of hypertonic saline therapy in ambulatory patients with heart failure: The <scp>SALT</scp>‐<scp>HF</scp> trial
Authors: Marta Cobo Marcos, Rafael de la Espriella, Josep Comín‐Colet, Isabel Zegrí‐Reiriz, Jorge Rubio Gracia, Jose Luis Morales‐Rull, Pau Llàcer, Pablo Díez‐Villanueva, Santiago Jiménez‐Marrero, Javier de Juan Bagudá, Carolina Ortiz Cortés, Maria Alejandra Restrepo‐Córdoba, Josebe Goirigolzarri‐Artaza, Jose Manuel García‐Pinilla, Elvira Barrios, Susana del Prado Díaz, Esther Montero Hernández, Marta Sanchez‐Marteles, Julio Núñez
Journal: European Journal of Heart Failure (2024)