tbuckley/cabot-search huggingface dataset:
GAN-based generation of realistic 3D volumetric data: A systematic review and taxonomy
Authors: André Ferreira, Jianning Li, Kelsey L. Pomykala, Jens Kleesiek, Victor Alves, Jan Egger
Journal: Medical Image Analysis (2024)

With the massive proliferation of data-driven algorithms, such as deep learning-based approaches, the availability of high-quality data is of great interest. Volumetric data is very important in medicine, as it ranges from disease diagnoses to therapy monitoring. When the dataset is sufficient, models can be trained to help doctors with these tasks. Unfortunately, there are scenarios where large amounts of data is unavailable. For example, rare diseases and privacy issues can lead to restricted data availability. In non-medical fields, the high cost of obtaining enough high-quality data can also be a concern. A solution to these problems can be the generation of realistic synthetic data using Generative Adversarial Networks (GANs). The existence of these mechanisms is a good asset, especially in healthcare, as the data must be of good quality, realistic, and without privacy issues. Therefore, most of the publications on volumetric GANs are within the medical domain. In this review, we provide a summary of works that generate realistic volumetric synthetic data using GANs. We therefore outline GAN-based methods in these areas with common architectures, loss functions and evaluation metrics, including their advantages and disadvantages. We present a novel taxonomy, evaluations, challenges, and research opportunities to provide a holistic overview of the current state of volumetric GANs.
Microbiome function and neurodevelopment in Black infants: vitamin B <sub>12</sub> emerges as a key factor
Authors: Kaitlyn Oliphant, Wilfredo Cruz Ayala, Rimma Ilyumzhinova, Kimberley Mbayiwa, Anna Sroka, Bingqing Xie, Bree Andrews, Kate Keenan, Erika C. Claud
Journal: Gut Microbes (2024)

The early life gut microbiome affects the developing brain, and therefore may serve as a target to support neurodevelopment of children living in stressful and under-resourced environments, such as Black youth living on the South Side of Chicago, for whom we observe racial disparities in health. Microbiome compositions/functions key to multiple neurodevelopmental facets have not been studied in Black children, a vulnerable population due to racial disparities in health; thus, a subsample of Black infants living in urban, low-income neighborhoods whose mothers participated in a prenatal nutrition study were recruited for testing associations between composition and function of the gut microbiome (16S rRNA gene sequencing, shotgun metagenomics, and targeted metabolomics of fecal samples) and neurodevelopment (developmental testing, maternal report of temperament, and observed stress regulation). Two microbiome community types, defined by high Lachnospiraceae or Enterobacteriaceae abundance, were discovered in this cohort from 16S rRNA gene sequencing analysis; the Enterobacteriaceae-dominant community type was significantly negatively associated with cognition and language scores, specifically in male children. Vitamin B12 biosynthesis emerged as a key microbiome function from shotgun metagenomics sequencing analysis, showing positive associations with all measured developmental skills (i.e., cognition, language, motor, surgency, effortful control, and observed stress regulation). Blautia spp. also were identified as substantial contributors of important microbiome functions, including vitamin B12 biosynthesis and related vitamin B12-dependent microbiome functions, anti-inflammatory microbial surface antigens, competitive mechanisms against pathobionts, and production of antioxidants. The results are promising with respect to the potential for exploring therapeutic candidates, such as vitamin B12 nutritional or Blautia spp. probiotic supplementation, to support the neurodevelopment of infants at risk for experiencing racial disparities in health.
In-hospital mortality of high-risk pulmonary embolism: a nationwide population-based cohort study in Portugal from 2010 to 2018
Authors: R. Calé, R. Ascenção, C. Bulhosa, H. Pereira, M. Borges, J. Costa, D. Caldeira
Journal: Pulmonology (2024)

The mortality associated with high-risk pulmonary embolism (PE) is remarkably high, and reperfusion to unload right ventricle should be a priority. However, several registries report reperfusion underuse. In Portugal, epidemiological data about the incidence, rate of reperfusion and mortality of high-risk PE are not known. Nationwide population-based temporal trend study in the incidence and outcome of high-risk PE, who were admitted to hospitals of the National Health Service in Portugal between 2010 and 2018. High-risk PE was defined as patients with PE who developed cardiogenic shock or cardiac arrest. International Classification of Diseases (ICD), 9th and 10th revision, Clinical Modification codes, were used for data from the period between 2010 and 2016 (ICD-9-CM) and 2017–2018 (ICD-10-CM), respectively. The assessment focused on trends in the use of reperfusion treatment, which was defined by application of thrombolysis or pulmonary embolectomy. A comparison was made between the use or non-use of reperfusion therapy in order to examine trends in in-hospital mortality among high-risk PE cases. From 2010 and 2018, there were 40.311 hospitalization episodes for PE in adult patients at hospitals of the National Health Service in mainland Portugal. There was a significant increase in the annual incidence of PE (41/100.000 inhabitants in 2010 to 46/100.000 in 2018; R2=0.582, p = 0.010). The average annual incidence was 45/100.000 inhabitants/year, with 2,7% of the PE episodes (1104) categorized as high-risk. The mortality rate associated with high-risk PE was high, although it has decreased over the years (74.2% in 2010 to 63.6% in 2018; R2=0.484; p = 0.022). Thrombolytic therapy was underused in high-risk PE, and its usage has not increased in recent years (17.3% in 2010 to 21.1% in 2018, R2=-0.127; p = 0.763). Surgical pulmonary embolectomy was used in 0.27% of cases, and there was no registry of catheter-directed thrombolysis. Patients with high-risk PE undergoing reperfusion therapy had lower in-hospital mortality compared to non-reperfused patients (OR=0.52; IC95% 0.38–0.70). In Portugal, between 2010 and 2018, very few patients with PE developed high-risk forms of the disease, but the mortality rate among those patients was high. The low reperfusion rate could be associated with high in-hospital mortality and highlights the need to implement advanced therapies, as an alternative to systemic thrombolysis.
Persistence of immune responses of a self-amplifying RNA COVID-19 vaccine (ARCT-154) versus BNT162b2
Authors: Yoshiaki Oda, Yuji Kumagai, Manabu Kanai, Yasuhiro Iwama, Iori Okura, Takeshi Minamida, Yukihiro Yagi, Toru Kurosawa, Pad Chivukula, Ye Zhang, Judd L Walson
Journal: The Lancet Infectious Diseases (2024)
PCSK9 inhibition with orally administered NNC0385-0434 in hypercholesterolaemia: a randomised, double-blind, placebo-controlled and active-controlled phase 2 trial
Authors: Michael J Koren, Olivier Descamps, Yoshiki Hata, Ellen Margo Hengeveld, G Kees Hovingh, Ignatios Ikonomidis, Maria D Radu Juul Jensen, Irene Hedelund Langbakke, Fabrice M A C Martens, Anette Luther Søndergaard, Adam Witkowski, Wolfgang Koenig
Journal: The Lancet Diabetes & Endocrinology (2024)
Invasive pneumococcal disease 3 years after introduction of a reduced 1 + 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a prospective national observational surveillance study
Authors: Marta Bertran, Joshua C D'Aeth, Fariyo Abdullahi, Seyi Eletu, Nick J Andrews, Mary E Ramsay, David J Litt, Shamez N Ladhani
Journal: The Lancet Infectious Diseases (2024)

BackgroundThe UK transition from a 2 + 1 to a 1 + 1 infant immunisation schedule with the 13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided with the start of the COVID-19 pandemic. We describe the epidemiology of invasive pneumococcal disease (IPD) in England over 6 financial years (April 1 to March 31) between 2017–18 and 2022–23.MethodsWe used prospective national surveillance data, including serotyping and whole-genome sequencing of invasive isolates, to analyse IPD trends in England by age and financial year. We compared breakthrough infections and vaccine failure rates in 2022–23 among children eligible for the 1 + 1 schedule with rates in cohorts of children eligible for the 2 + 1 schedule between 2017–18 and 2019–20. We assessed genomic changes over time by comparing Global Pneumococcal Sequencing Clusters and multilocus sequence types among PCV13 serotypes causing IPD.FindingsThere were 4598 laboratory-confirmed IPD cases in 2022–23, 3025 in 2021–22, 1240 in 2020–21, and 5316 in 2019–20. IPD incidence in 2022–23 was 14% lower than in 2019–20 (incidence rate ratio [IRR] 0·86, 95% CI 0·81–0·91; p<0·001). IPD incidence in 2022–23 compared with 2019–20 was 34% higher in children (aged <15 years) (378 cases vs 292 cases; IRR 1·34, 95% CI 1·08–1·68; p=0·009) and 17% lower in adults (aged 15 years and older; 4220 vs 5024; 0·83, 0·78–0·88; p<0·001). The proportion of PCV13-type IPD increased from 19·4% (95% CI 18·2–20·4; 957 of 4947) in 2019–20 to 29·7% (28·3–31·0; 1283 of 4326) in 2022–23, mainly due to serotype 3, but also serotypes 19F, 19A, and 4, alongside a decrease in non-PCV13 serotypes 8, 12F, and 9N. The increase in IPD incidence due to serotypes 3, 19A, and 19F was driven by clonal expansion of previously circulating strains, whereas serotype 4 expansion was driven by newer strains (ie, sequence types 801 and 15603). Breakthrough infections and vaccine failure rates were similar in children eligible for the 1 + 1 (1·07 per 100 000 person-years) and 2 + 1 (0·76 per 100 000 person-years; IRR 1·42, 95% CI 0·78–2·49; p=0·20) PCV13 schedules.InterpretationOverall, IPD incidence in England was lower in 2022–23, 2 years after removal of pandemic restrictions, than in 2019–20. Breakthrough and vaccine failure rates were not significantly different between children who received the 1 + 1 compared with the 2 + 1 PCV13 immunisation schedule. The post-pandemic increase in childhood IPD incidence and especially PCV13-type IPD will require close monitoring.FundingNone.
Estimating the effect of proximity to school on cyclist safety using a simultaneous-equations model with heterogeneity in covariance to address potential endogeneity
Authors: Shahram Heydari, Michael Forrest
Journal: Analytic Methods in Accident Research (2024)

Traffic safety around schools is a major concern for policy makers and as such safety interventions are often targeted near schools. This paper shows the importance of accounting for the potential endogeneity of proximity to school when attempting to estimate its impact on traffic safety. In this research, we use a Bayesian simultaneous econometric approach with heterogeneity in covariance to disentangle the true effect of proximity to school on cyclist injury frequencies at signalised intersections in an urban setting. We assess the robustness of the bivariate normal assumption, using a scale mixing approach. Notably, we found that proximity to school was associated with an increase in cyclist injuries and this association was stronger when endogeneity was accounted for in the model, confirming the importance of considering endogeneity in studies of traffic safety near schools. Our heterogeneity in covariance specification revealed systematic variations in the covariance structure, which would otherwise go unobserved, providing further insights into sources of heterogeneity with the same set of variables available in the data. A safety-in-numbers effect is also found for cyclists in the study area and period. This research offers policy implications based on the findings of the analysis including the need for safety interventions at intersections with high vehicle turning counts and those in proximity to public transport stops, and better informing decision-makers regarding the magnitude of the impact of proximity to school on cyclist safety at intersections.
Air pollution exposure and cardiometabolic risk
Authors: Sanjay Rajagopalan, Robert D Brook, Pedro R V O Salerno, Brendan Bourges-Sevenier, Philip Landrigan, Mark J Nieuwenhuijsen, Thomas Munzel, Salil V Deo, Sadeer Al-Kindi
Journal: The Lancet Diabetes & Endocrinology (2024)
The influence of safety warnings on the prescribing of JAK inhibitors
Authors: Mark D Russell, Zijing Yang, Ben Walter, Edward Alveyn, Katie Bechman, Aitana Miracle, Deepak Nagra, Maryam A Adas, Sam Norton, Andrew P Cope, Sinéad M Langan, James B Galloway
Journal: The Lancet Rheumatology (2024)
Nociceptive, neuropathic, or nociplastic low back pain? The low back pain phenotyping (BACPAP) consortium's international and multidisciplinary consensus recommendations
Authors: Jo Nijs, Eva Kosek, Alessandro Chiarotto, Chad Cook, Lieven A Danneels, César Fernández-de-las-Peñas, Paul W Hodges, Bart Koes, Adriaan Louw, Raymond Ostelo, Gwendolyne G M Scholten-Peeters, Michele Sterling, Othman Alkassabi, Hana Alsobayel, Darren Beales, Paraskevi Bilika, Jacqui R Clark, Liesbet De Baets, Christophe Demoulin, Rutger M J de Zoete, Ömer Elma, Annelie Gutke, Rikard Hanafi, Sabina Hotz Boendermaker, Eva Huysmans, Eleni Kapreli, Mari Lundberg, Anneleen Malfliet, Ney Meziat Filho, Felipe J J Reis, Lennard Voogt, Kory Zimney, Rob Smeets, Bart Morlion, Kurt de Vlam, Steven Z George
Journal: The Lancet Rheumatology (2024)
Assessment of Novel Therapeutics to Improve Access to Transplantation for Highly Sensitized Patients in a Shifting Clinical Landscape
Authors: James H. Lan
Journal: Journal of the American Society of Nephrology (2024)

British Columbia Provincial Immunology Laboratory, Vancouver Coastal Health, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; and Division of Nephrology, Kidney Transplant Program, University of British Columbia, Vancouver, British Columbia, Canada Correspondence: Dr. James H. Lan, Division of Nephrology, Immunology Laboratory, Department of Pathology and Laboratory Medicine, Kidney Transplant Program, Vancouver General Hospital, University of British Columbia, 910 West 10th Avenue, Room 1558 JPPN, Vancouver, British Columbia, Canada, V5Z 4E3. Email: [email protected] See related article, "Isatuximab Monotherapy for Desensitization in Highly Sensitized Patients Awaiting Kidney Transplant," on pages 347–360.
Farm animal exposure, respiratory illnesses, and nasal cell gene expression
Authors: Joshua Brownell, Kristine E. Lee, Deborah Chasman, Ronald Gangnon, Casper G. Bendixsen, Katherine Barnes, Kristine Grindle, Tressa Pappas, Yury A. Bochkov, Amy Dresen, Christine Hou, David B. Haslam, Christine M. Seroogy, Irene M. Ong, James E. Gern
Journal: Journal of Allergy and Clinical Immunology (2024)
The obesity-autophagy-cancer axis: Mechanistic insights and therapeutic perspectives
Authors: Amir Barzegar Behrooz, Marco Cordani, Alessandra Fiore, Massimo Donadelli, Joseph W. Gordon, Daniel J. Klionsky, Saeid Ghavami
Journal: Seminars in Cancer Biology (2024)

Autophagy, a self-degradative process vital for cellular homeostasis, plays a significant role in adipose tissue metabolism and tumorigenesis. This review aims to elucidate the complex interplay between autophagy, obesity, and cancer development, with a specific emphasis on how obesity-driven changes affect the regulation of autophagy and subsequent implications for cancer risk. The burgeoning epidemic of obesity underscores the relevance of this research, particularly given the established links between obesity, autophagy, and various cancers. Our exploration delves into hormonal influence, notably INS (insulin) and LEP (leptin), on obesity and autophagy interactions. Further, we draw attention to the latest findings on molecular factors linking obesity to cancer, including hormonal changes, altered metabolism, and secretory autophagy. We posit that targeting autophagy modulation may offer a potent therapeutic approach for obesity-associated cancer, pointing to promising advancements in nanocarrier-based targeted therapies for autophagy modulation. However, we also recognize the challenges inherent to these approaches, particularly concerning their precision, control, and the dual roles autophagy can play in cancer. Future research directions include identifying novel biomarkers, refining targeted therapies, and harmonizing these approaches with precision medicine principles, thereby contributing to a more personalized, effective treatment paradigm for obesity-mediated cancer.
Autophagy and the unfolded protein response shape the non-alcoholic fatty liver landscape: decoding the labyrinth
Authors: Zahra Dashti, Zeynab Yousefi, Pouria Kiani, Motahareh Taghizadeh, Mohammad Hasan Maleki, Mohammad Borji, Omid Vakili, Sayed Mohammad Shafiee
Journal: Metabolism (2024)
State-transition modeling of blood transcriptome predicts disease evolution and treatment response in chronic myeloid leukemia
Authors: David E. Frankhouser, Russell C. Rockne, Lisa Uechi, Dandan Zhao, Sergio Branciamore, Denis O’Meally, Jihyun Irizarry, Lucy Ghoda, Haris Ali, Jeffery M. Trent, Stephen Forman, Yu-Hsuan Fu, Ya-Huei Kuo, Bin Zhang, Guido Marcucci
Journal: Leukemia (2024)

Abstract Chronic myeloid leukemia (CML) is initiated and maintained by BCR::ABL which is clinically targeted using tyrosine kinase inhibitors (TKIs). TKIs can induce long-term remission but are also not curative. Thus, CML is an ideal system to test our hypothesis that transcriptome-based state-transition models accurately predict cancer evolution and treatment response. We collected time-sequential blood samples from tetracycline-off (Tet-Off) BCR::ABL-inducible transgenic mice and wild-type controls. From the transcriptome, we constructed a CML state-space and a three-well leukemogenic potential landscape. The potential’s stable critical points defined observable disease states. Early states were characterized by anti-CML genes opposing leukemia; late states were characterized by pro-CML genes. Genes with expression patterns shaped similarly to the potential landscape were identified as drivers of disease transition. Re-introduction of tetracycline to silence the BCR::ABL gene returned diseased mice transcriptomes to a near healthy state, without reaching it, suggesting parts of the transition are irreversible. TKI only reverted the transcriptome to an intermediate disease state, without approaching a state of health; disease relapse occurred soon after treatment. Using only the earliest time-point as initial conditions, our state-transition models accurately predicted both disease progression and treatment response, supporting this as a potentially valuable approach to time clinical intervention, before phenotypic changes become detectable.
Validated Clinical Score to Predict Gastroesophageal Reflux in Patients With Chronic Laryngeal Symptoms: COuGH RefluX
Authors: Amanda J. Krause, Alexander M. Kaizer, Dustin A. Carlson, Walter W. Chan, Chien-Lin Chen, C. Prakash Gyawali, Andrew Jenkins, John E. Pandolfino, Vinathi Polamraju, Ming-Wun Wong, Madeline Greytak, Rena Yadlapati
Journal: Clinical Gastroenterology and Hepatology (2024)

Discerning whether laryngeal symptoms result from gastroesophageal reflux is clinically challenging and a reliable tool to stratify patients is needed. We aimed to develop and validate a model to predict the likelihood of gastroesophageal reflux disease (GERD) among patients with chronic laryngeal symptoms.
Hierarchical Scaffold with Directional Microchannels Promotes Cell Ingrowth for Bone Regeneration
Authors: Yaling Cheng, Xing Li, Peiyang Gu, Ruiqi Mao, Yaping Zou, Lei Tong, Zhulian Li, Yujiang Fan, Xingdong Zhang, Jie Liang, Yong Sun
Journal: Advanced Healthcare Materials (2024)

Abstract Bone regenerative scaffolds with a bionic natural bone hierarchical porous structure provide a suitable microenvironment for cell migration and proliferation. Here, a bionic scaffold (DP‐PLGA/HAp) with directional microchannels is prepared by combining 3D printing and directional freezing technology. The 3D printed framework provides structural support for new bone tissue growth, while the directional pore embedded in the scaffolds provides an express lane for cell migration and nutrition transport, facilitating cell growth and differentiation. The hierarchical porous scaffolds achieve rapid infiltration and adhesion of bone marrow mesenchymal stem cells (BMSCs) and improve the expression of osteogenesis‐related genes. The rabbit cranial defect experiment presents significant new bone formation, demonstrating that DP‐PLGA/HAp offers an effective means to guide cranial bone regeneration. The combination of 3D printing and directional freezing technology might be a promising strategy for developing bone regenerative biomaterials.
An antigen-specific chimeric autoantibody receptor (CAAR) NK cell strategy for the elimination of anti-PLA2R1 and anti-THSD7A antibody-secreting cells
Authors: Larissa Seifert, Kristoffer Riecken, Gunther Zahner, Julia Hambach, Julia Hagenstein, Gudrun Dubberke, Tobias B. Huber, Friedrich Koch-Nolte, Boris Fehse, Nicola M. Tomas
Journal: Kidney International (2024)

Membranous nephropathy (MN) is an antibody-mediated disease of the kidney, typically resulting in nephrotic syndrome with urinary loss of high amounts of albumin and other plasma proteins. Phospholipase A2 receptor 1 (PLA2R1) and thrombospondin type-1 domain-containing protein 7A (THSD7A) were the first renal autoantigens identified in adult patients with MN.1,2 Importantly, we and others could demonstrate that autoantibodies in MN are not only excellent biomarkers to monitor immunological disease activity, but also cause the disease through the direct interaction with the autoantigen expressed on podocytes in the kidney.