tbuckley/cabot-search huggingface dataset:
After surgically induced remission, ileal and colonic mucosa-associated microbiota predicts Crohn’s disease recurrence
Authors: Cristian Hernández-Rocha, Williams Turpin, Krzysztof Borowski, Joanne M. Stempak, Ksenija Sabic, Kyle Gettler, Christopher Tastad, Colleen Chasteau, Ujunwa Korie, Mary Hanna, Abdul Khan, Emebet Mengesha, Alain Bitton, Marc B. Schwartz, Arthur Barrie, Lisa W. Datta, Mark Lazarev, Steven R. Brant, John D. Rioux, Dermot P.B. McGovern, Richard H. Duerr, L. Phil Schumm, Judy H. Cho, Mark S. Silverberg
Journal: Clinical Gastroenterology and Hepatology (2024)
Clinical trial designs to assess treatment effects on glomerular filtration rate decline
Authors: Hiddo J.L. Heerspink, Dustin J. Little, Lars Frison, Samvel B. Gasparyan, Christoph Wanner, Niels Jongs, Douwe Postmus
Journal: Kidney International (2024)

Glomerular filtration rate (GFR) decline is used as surrogate endpoint for kidney failure. Interventions that reduce chronic kidney disease (CKD) progression often exert acute GFR reductions which differ from their long-term benefits and complicate the estimation of long-term benefit. Here, we assessed the utility of two alternative trial designs (wash-out design and active run-in randomized withdrawal design) that attempt to exclude the impact of acute effects. Post-hoc analyses of two clinical trials that characterized the effect of an intervention with acute reductions in GFR were conducted. The two trials included a wash-out period (EMPA-REG Outcome testing empagliflozin vs placebo) or an active run-in period with a randomized withdrawal (SONAR testing atrasentan vs placebo). We compared the drug effect on GFR decline calculated from the first on-treatment visit to the end of treatment (chronic slope in a standard randomized trial design) with GFR change calculated from randomization to end of wash out, or GFR change from treatment-specific baseline GFR values (GFR at start-of-run-in for placebo and end-of-run-in for atrasentan) until end-of-treatment. The effect of empagliflozin versus placebo on chronic GFR slope was 1.72 (95% confidence interval 1.49-1.94) mL/min/1.73 m
Guided image generation for improved surgical image segmentation
Authors: Emanuele Colleoni, Ricardo Sanchez Matilla, Imanol Luengo, Danail Stoyanov
Journal: Medical Image Analysis (2024)

The lack of large datasets and high-quality annotated data often limits the development of accurate and robust machine-learning models within the medical and surgical domains. In the machine learning community, generative models have recently demonstrated that it is possible to produce novel and diverse synthetic images that closely resemble reality while controlling their content with various types of annotations. However, generative models have not been yet fully explored in the surgical domain, partially due to the lack of large datasets and due to specific challenges present in the surgical domain such as the large anatomical diversity. We propose Surgery-GAN, a novel generative model that produces synthetic images from segmentation maps. Our architecture produces surgical images with improved quality when compared to early generative models thanks to the combination of channel- and pixel-level normalization layers that boost image quality while granting adherence to the input segmentation map. While state-of-the-art generative models often generate overfitted images, lacking diversity, or containing unrealistic artefacts such as cartooning; experiments demonstrate that Surgery-GAN is able to generate novel, realistic, and diverse surgical images in three different surgical datasets: cholecystectomy, partial nephrectomy, and radical prostatectomy. In addition, we investigate whether the use of synthetic images together with real ones can be used to improve the performance of other machine-learning models. Specifically, we use Surgery-GAN to generate large synthetic datasets which we then use to train five different segmentation models. Results demonstrate that using our synthetic images always improves the mean segmentation performance with respect to only using real images. For example, when considering radical prostatectomy, we can boost the mean segmentation performance by up to 5.43%. More interestingly, experimental results indicate that the performance improvement is larger in the set of classes that are under-represented in the training sets, where the performance boost of specific classes reaches up to 61.6%.
Vibration-Controlled Transient Elastography–Based Parameters Predict Clinical Outcomes in Liver Transplant Recipients
Authors: Alok Baral, Shreya Garg, Madison Nguyen, Rehan Razzaq, Audrey Ang, Hiba Khan, Dylan Vainer, Vaishali Patel, Geneva Roache, Mark Muthiah, Idris Yakubu, Vinay Kumaran, Anh T. Bui, Mohammad Shadab Siddiqui
Journal: Clinical Gastroenterology and Hepatology (2024)
Endoscopic Glue Injection vs Glue Plus BRTO or TIPSS for Preventing Gastric Variceal Bleeding: A Randomized Controlled Trial
Authors: Sagnik Biswas, Manas Vaishnav, Shivanand Gamanagatti, Shekhar Swaroop, Umang Arora, Arnav Aggarwal, Anshuman Elhence, Deepak Gunjan, Saurabh Kedia, Soumya Jagannath Mahapatra, Ashwani Kumar Mishra, None Shalimar
Journal: Clinical Gastroenterology and Hepatology (2024)
Analysis of Circulating Tumor DNA Predicts Outcomes of Short-Course Consolidation Immunotherapy in Unresectable Stage III NSCLC
Authors: Soyeong Jun, Nikhil A Shukla, Greg Durm, Angela B Hui, Sha Cao, Apar Kishor Ganti, Salma K Jabbour, Christian Kunder, Ash A Alizadeh, Nasser H Hanna, Maximilian Diehn
Journal: Journal of Thoracic Oncology (2024)
Retraction notice to Tropheryma whipplei associated with diarrhoea in young children
Authors: F. Fenollar, P. Minodier, A. Boutin, R. Laporte, V. Brémond, G. Noël, S. Miramont, H. Richet, S. Benkouiten, J.-C. Lagier, J. Gaudart, J.-L. Jouve, D. Raoult
Journal: Clinical Microbiology and Infection (2024)
Hepatitis B virus DNA integration: Implications for diagnostics, therapy, and outcome
Authors: Fabien Zoulim, Pei-Jer Chen, Maura Dandri, Patrick T. Kennedy, Christoph Seeger
Journal: Journal of Hepatology (2024)

HBV DNA integration originally recognized as a non-functional byproduct of the HBV life cycle has now been accepted as a significant contributor to HBV pathogenesis and HDV persistence. Integrated HBV DNA is derived from linear genomic DNA present in virus particles or produced from aberrantly processed relaxed circular genomic DNA following an infection, and can drive expression of HBsAg and HBx. DNA integration events accumulate over the course of viral infection ranging from a few percent during early phases to nearly 100 percent of infected cells after prolonged chronic infection. HBV DNA integration events have primarily been investigated in the context of HCC development where they can activate known oncogenes and other growth promoting genes, cause chromosomal instability and presumably epigenetic alterations promoting tumor growth. More recent evidence suggests that HBsAg expression from integrated DNA might contribute to HBV pathogenesis by attenuating the immune response. Integrated DNA provides a source for envelope proteins required for HDV replication and hence represents a means for HDV persistence. Because integrated DNA is responsible for persistence of HBsAg in the absence of viral replication it impacts established criteria for the resolution of HBV infection which relies on HBsAg as a diagnostic marker. Integrated HBV DNA has been useful in assessing the turnover of infected hepatocytes which occurs during all phases of chronic hepatitis B including the initial phase of infection historically termed immune tolerant. HBV DNA integration was also shown to impact the development of novel therapies targeting viral RNAs.
Biological relapse in multiple myeloma: Outcome and treatment strategies in a Spanish real‐world setting
Authors: Adrián Alegre, Mercedes Gironella, Fernando Escalante, Juan M. Bergua, Carmen Martínez‐Chamorro, Aurelio López, Esther González, Abelardo Bárez, Nieves Somolinos, Ernesto P. Persona, Alexia S. Cabrera, Alfons Soler, Belén I. Rodríguez, Joaquín M. López, Yolanda González, Verónica C. Giménez, Antonia Sampol, Carolina Muñoz, David Vilanova, Marta Durán, Carlos Fernández de Larrea
Journal: HemaSphere (2024)

Abstract Recommendations regarding the best time to start treatment in patients with relapsed/refractory multiple myeloma (RRMM) after biological relapse/progression (BR) are unclear. This observational, prospective, multicenter registry aimed to evaluate the impact on time to progression (TTP) of treatment initiation at BR versus at symptomatic clinical relapse (ClinR) based on the Spanish routine practice in adult patients with RRMM. Patients had two or less previous treatment lines and at least one previous partial response. Baseline characteristics and treatment outcomes were recorded, and survival was analyzed. Of 225 patients, 110 were treated at BR (TxBR group) and 115 at ClinR (TxClinR group) according to the investigators' criteria. The proportion of patients with higher ECOG, previous noncomplete remission (CR), and second relapse were significantly higher in the TxBR group compared to the TxClinR group. TheTxClinR group showed improved outcomes, including TTP, compared to the TxBR group. Progression‐free survival increased in the TxClinR group (56.2 months) compared to the TxBR group (32.5 months) ( p = 0.0137), and median overall survival also increased ( p = 0.0897). Median TTP was significantly longer in patients relapsing from a CR (50.4 months) and in their first relapse (38.7 months) compared to those relapsing from a non‐CR response (32.9 months) and in their second relapse (25.2 months). Physicians seemed to start treatment earlier in RRMM patients with poor prognosis features. Previous responses to anti‐MM treatment and the number of prior treatment lines were identified as prognosis factors, whereby relapse from CR and first relapse were associated with a longer time to progression.
Positive and Negative Associations of Myopia with Ocular Diseases in Population-Based Studies
Authors: Jost B. Jonas, Mukharram M. Bikbov, Gyulli M. Kazakbaeva, Ya Xing Wang, Jie Xu, Vinay Nangia, Prabhat V. Nangia, Songhomitra Panda-Jonas
Journal: Ophthalmology (2024)
Excess Mortality and Loss of Life Expectancy After Myocardial Infarction: A Registry-Based Matched Cohort Study
Authors: Christian Reitan, Pontus Andell, Joakim Alfredsson, David Erlinge, Robin Hofmann, Bertil Lindahl, Moa Simonsson, Paul W. Dickman, Tomas Jernberg
Journal: Circulation (2024)

BACKGROUND: The effect of myocardial infarction (MI) on life expectancy is difficult to study because the prevalence of MI hinders direct comparison with the life expectancy of the general population. We sought to assess this in relation to age, sex, and left ventricular ejection fraction (LVEF) by comparing individuals with MI with matched comparators without previous MI. METHODS: We included patients with a first MI between 1991 and 2022 from the nationwide SWEDEHEART registry (Swedish Web-System for Enhancement and Development of Evidence-Based Care in Heart Disease Evaluated According to Recommended Therapies), each matched with up to 5 comparators on age, sex, and region of residence. Flexible parametric survival models were used to estimate excess mortality and mean loss of life expectancy (LOLE) depending on index year, age, sex, and LVEF, and adjusted for differences in characteristics. RESULTS: A total of 335 748 cases were matched to 1 625 396 comparators. A higher LOLE was observed in younger individuals, women, and those with reduced LVEF (&lt;50%). In 2022, the unadjusted and adjusted mean LOLE spanned from 11.1 and 9.5 years in 50-year-old women with reduced LVEF to 5 and 3.7 months in 80-year-old men with preserved LVEF. Between 1992 and 2022, the adjusted mean LOLE decreased by 36% to 55%: from 4.4 to 2.0 years and from 3.3 to 1.9 years in 50-year-old women and men, respectively, and from 1.7 to 1.0 years and from 1.4 to 0.9 years in 80-year-old women and men, respectively. CONCLUSIONS: LOLE is higher in younger individuals, women, and those with reduced LVEF, but is attenuated when adjusting for comorbidities and risk factors. Advances in MI treatment during the past 30 years have almost halved LOLE, with no clear sign of leveling off to a plateau.
Initial combination therapy with macitentan and tadalafil in patients with pulmonary arterial hypertension, with and without cardiac comorbidities
Authors: Vallerie V. McLaughlin, Olivier Sitbon, Kelly M. Chin, Nazzareno Galiè, Marius M. Hoeper, David G. Kiely, Gwen MacDonald, Nicolas Martin, Stephen C. Mathai, Andrew Peacock, Ahmed Tawakol, Adam Torbicki, Anton Vonk Noordegraaf, Stephan Rosenkranz
Journal: European Journal of Heart Failure (2024)

ABSTRACT Aims According to current guidelines, initial monotherapy should be considered for pulmonary arterial hypertension (PAH) patients with cardiopulmonary comorbidities. This analysis of combined data from the TRITON and REPAIR clinical trials, assesses efficacy and safety of initial double combination therapy in patients without vs. with 1–2 cardiac comorbidities. Methods and results Data were combined for patients from TRITON (NCT02558231) and REPAIR (NCT02310672) on initial macitentan and tadalafil double combination therapy (overall set, n = 148) and two subgroups defined as patients without cardiac comorbidities ( n = 62) and those with 1–2 cardiac comorbidities ( n = 78). Patients with ≥3 comorbidities were excluded from these studies. For the overall set, the median (Q1–Q3) duration of combined macitentan and tadalafil exposure was 513.0 (364.0–778.0) days, and was similar between subgroups. Change from baseline to Week 26 for pulmonary vascular resistance was −55% and −50% for patients without and with 1–2 cardiac comorbidities, respectively; marked improvements in other hemodynamic and functional parameters were also observed, although functional parameters improved to a lesser extent in patients with comorbidities. At Week 26, the majority of patients had improved PAH risk status, according to the non‐invasive four‐strata and REVEAL Lite 2.0 methods. The safety profile of initial macitentan plus tadalafil combination therapy was consistent with the known profiles of the two drugs, and similar between the subgroups. Conclusions Initial double combination therapy with macitentan plus tadalafil is efficacious in patients with PAH with 1–2 cardiac comorbidities and those without, with similar safety and tolerability profiles between the two groups.
Three Birds with One Stone: Copper Ions Assisted Synergistic Cuproptosis/Chemodynamic/Photothermal Therapy by a Three‐Pronged Approach
Authors: Mengyao Chen, Chang Xu, Chunhui Wang, Nan Huang, Zhixuan Bian, Yixuan Xiao, Juan Ruan, Fenyong Sun, Shuo Shi
Journal: Advanced Healthcare Materials (2024)

Copper is indispensable to organisms, while its homeostatic imbalance may interference normal cellular physiological processes and even induce cell death. Artificially regulating cellular copper content provides a viable strategy to activate antineoplastic effect. In light of this, a copper ions homeostasis perturbator (CuP-CL) with cinnamaldehyde (Cin) packaging and thermosensitive liposome coating is reported. Following laser exposure, the doping of Cu
Genomic instability in non–breast or ovarian malignancies of individuals with germline pathogenic variants in <i>BRCA1/2</i>
Authors: Lisa Elze, Rachel S van der Post, Janet R Vos, Arjen R Mensenkamp, Samhita Pamidimarri Naga, Juliet E Hampstead, Emma Vermeulen, Michiel Oorsprong, Tom Hofste, Michiel Simons, Iris D Nagtegaal, Nicoline Hoogerbrugge, Richarda M de Voer, Marjolijn J L Ligtenberg
Journal: JNCI Journal of the National Cancer Institute (2024)

Individuals with germline pathogenic variants in BRCA1 or BRCA2 are at a high risk of breast and ovarian carcinomas with BRCA1/2 deficiency and homologous recombination deficiency that can be detected by analysis of genome-wide genomic instability features such as large-scale state transitions, telomeric allelic imbalances, and genomic loss of heterozygosity. Malignancies with homologous recombination deficiency are more sensitive to platinum-based therapies and poly(ADP-ribose) polymerase inhibitors. We investigated the fraction of non-breast or ovarian malignancies that have BRCA1/2 deficiency and genomic instability features.
Association of inflammatory bowel disease incidence with isotretinoin usage: A meta-analysis and systematic review
Authors: Areeba Ahmed, Ayesha Liaquat, Saamia Raza, Eric Koza, Melissa Ma, Misha Haq, Victoria Shi, Ashhad Rabeegh, Michael D. Yi, Umer Nadir, Brian A. Cahn, Ross Pearlman, Daniel I. Schlessinger, Murad Alam
Journal: Journal of the American Academy of Dermatology (2024)
Impact of a point-of-care urine tenofovir assay on adherence to HIV pre-exposure prophylaxis among women in Kenya: a randomised pilot trial
Authors: Monica Gandhi, David V Glidden, Deepalika Chakravarty, Guohong Wang, Charlene Biwott, Peter Mogere, Gakuo Maina, Irene Njeru, Catherine Kiptinness, Phelix Okello, Matthew A Spinelli, Purba Chatterjee, Jennifer Velloza, Vallery Ogello, Andrew Medina-Marino, Hideaki Okochi, Nelly R Mugo, Kenneth Ngure
Journal: The Lancet HIV (2024)

Adherence challenges with oral tenofovir-based pre-exposure prophylaxis (PrEP) are common. We developed a point-of-care assay to objectively assess tenofovir in urine and conducted a pilot trial examining the impact of counselling informed by use of this urine assay on long-term PrEP adherence. This randomised trial enrolled women not in serodiscordant partnerships 3 months after PrEP initiation at the Kenya Medical Research Institute to compare standard-of-care adherence counselling versus counselling informed by the urine assay (urine-test counselling group) every 3 months for 12 months. In the standard of care group, urine samples were stored and tested at study end without participant feedback. Here we report the adherence primary outcome of hair concentrations of tenofovir at 12 months as a long-term metric (undetectable levels defined long-term non-adherence), as well as urine concentrations of tenofovir at each visit as a short-term adherence metric and acceptability of the assay assessed by quantitative surveys. Data were analysed by randomisation group. This completed trial was registered with ClinicalTrials.gov (NCT03935464). From March 17, 2021 to Jan 18, 2022 we enrolled 49 women in the urine-test counselling group and 51 in the standard of care group; retention was 86 (86%) of 100. Nine (21%) of 42 in the urine-test counselling group had hair samples at 12 months with tenofovir concentrations below the limit of quantification compared with 15 (37%) of 41 in the standard of care group. The relative odds of long-term non-adherence in the standard of care group compared with urine-test counselling were 3·53 (95% CI 1·03-12·03; p=0·044). Pre-intervention, urine tenofovir was detectable in 65% in the urine-test counselling group and 71% in the standard of care group (p=0·68). At 12 months, 31 (72%) of 43 in the intervention group had detectable urine tenofovir compared with 19 (45%) of 42 in the standard of care group (p=0·0015). 40 (93%) of 43 participants liked the test very much and only one disliked the test. One participant in the standard of care group was withdrawn at the 6-month visit due to HIV seroconversion. A low-cost urine tenofovir assay to inform PrEP counselling resulted in improvement in both short-term and long-term metrics of adherence. This urine tenofovir assay could help to improve long-term PrEP adherence. National Institute of Allergy and Infectious Diseases and National Institutes of Health.
Interpretable artificial intelligence to optimise use of imatinib after resection in patients with localised gastrointestinal stromal tumours: an observational cohort study
Authors: Dimitris Bertsimas, Georgios Antonios Margonis, Suleeporn Sujichantararat, Angelos Koulouras, Yu Ma, Cristina R Antonescu, Murray F Brennan, Javier Martín-Broto, Seehanah Tang, Piotr Rutkowski, Martin E Kreis, Katharina Beyer, Jane Wang, Elzbieta Bylina, Pawel Sobczuk, Antonio Gutierrez, Bhumika Jadeja, William D Tap, Ping Chi, Samuel Singer
Journal: The Lancet Oncology (2024)
Prevalence of all epilepsies in urban informal settlements in Nairobi, Kenya: a two-stage population-based study
Authors: Daniel M Mwanga, Damazo T Kadengye, Peter O Otieno, Frederick M Wekesah, Isaac C Kipchirchir, George O Muhua, Joan W Kinuthia, Thomas Kwasa, Abigael Machuka, Quincy Mongare, Samuel Iddi, Gabriel Davis Jones, Josemir W Sander, Symon M Kariuki, Arjune Sen, Charles R Newton, Gershim Asiki, Patrick Adjei, Albert Akpalu, Sabina Asiamah, Gershim Asiki, Mercy Atieno, Dan Bhwana, Mary Bitta, Neerja Chowdhary, Hellen Cross, Emmanuel K. Darkwa, Timothy Denison, Tarun Dua, Antony Godi, Simone Grassi, Samuel Iddi, Daniel Nana Yaw Abankwah, Symon M. Kariuki, Joan W. Kinuthia, Henrika Kimambo, Thomas Kwasa, Sloan Mahone, Gergana Manolova, William Matuja, David McDaid, Bruno Mmbando, Daniel Mtai Mwanga, Damazo T. Kadengye, Dorcas Muli, Frederick M Wekesah, Vivian Mushi, Charles R. Newton, Guillaume Pages, Peter O. Otieno, Josemir W. Sander, Arjune Sen, Cynthia Sottie, Isolide Massawe, Sonia Vallentin, Richard Walker, Stella Waruinge
Journal: The Lancet Global Health (2024)
Niobium carbide MXenzyme-Driven comprehensive cholesterol regulation for photoacoustic image-guided and anti-inflammatory photothermal ablation in atherosclerosis
Authors: Wenqi Pan, Jingyun Cheng, Xinyue Cao, Yi Zheng, Zhenyu Yang, Wei Feng, Yu Chen, Rong Wu
Journal: Bioactive Materials (2024)

Foam cells play a pivotal role in the progression of atherosclerosis progression by triggering inflammation within arterial walls. They release inflammatory molecules that attract additional immune cells, leading to further macrophage recruitment and plaque development. In this study, we develop an osteopontin (OPN) antibody-conjugated niobium carbide (Nb2C-aOPN) MXenzyme designed to selectively target and mildly ablate foam cells while reducing inflammation in the plaque microenvironment. This approach utilizes photonic hyperthermia to decrease plaque size by enhancing cholesterol regulation through both passive cholesterol outflow and positive cholesterol efflux. Nb2C-aOPN MXenzyme exhibits multiple enzyme-mimicking properties, including catalase, superoxide dismutase, peroxidase and glutathione peroxidase, and acts as a scavenger for reactive oxygen and nitrogen species. The inhibition of reactive oxygen and nitrogen species synergizes with photothermal ablation to promote positive cholesterol efflux, leading to reduced macrophage recruitment and a shift in macrophage phenotype from M1 to M2. This integrative strategy on cholesterol regulation and anti-inflammation highlights the potential of multifunctional 2D MXenzyme-based nanomedicine in advancing atherosclerotic regression.
68Ga-FAPI PET/CT Visualized Benign Metastasizing Leiomyoma With Bone Invasion
Authors: Tianxing Fang, Chongjiao Li, Yueli Tian, Zhiwei Xiao, Yong He
Journal: Clinical Nuclear Medicine (2024)

Benign metastasizing leiomyoma (BML) is a rare disease associated with pelvic leiomyoma. We report 18 F-FDG and 68 Ga-FAPI PET/CT findings in a 51-year-old woman with multiple BMLs. The mass in the abdominopelvic cavity and other metastatic lesions showed highly increased 68 Ga-FAPI uptake, whereas uptake of 18 F-FDG in those lesions was low. Our report demonstrates that 68 Ga-FAPI PET/CT showed a different result in detecting BML to 18 F-FDG PET/CT, and 68 Ga-FAPI PET/CT may be a promising method for whole-body evaluate metastases.