tbuckley/cabot-search huggingface dataset:
Clinical Factors Affecting Discrepancy Between Predicted and Long-term Actual Lung Function Following Surgery
Authors: Jae-Woo Ju, Minseok Suh, Hongyoon Choi, Kwon Jooong Na, Samina Park, Gi Jeong Cheon, Young Tae Kim
Journal: Clinical Nuclear Medicine (2024)

Purpose Lung cancer surgery outcomes depend heavily on preoperative pulmonary reserve, with forced expiratory volume in 1 second (FEV1) being a critical preoperative evaluation factor. Our study investigates the discrepancies between predicted and long-term actual postoperative lung function, focusing on clinical factors affecting these outcomes. Methods This retrospective observational study encompassed lung cancer patients who underwent preoperative lung perfusion SPECT/CT between 2015 and 2021. We evaluated preoperative and postoperative pulmonary function tests, considering factors such as surgery type, resected volume, and patient history including tuberculosis. Predicted postoperative lung function was calculated using SPECT/CT imaging. Results From 216 patients (men:women, 150:66; age, 67.9 ± 8.7 years), predicted postoperative FEV1% (ppoFEV1%) showed significant correlation with actual postoperative FEV1% ( r = 0.667; P &lt; 0.001). Paired t test revealed that ppoFEV1% was significantly lower compared with actual postoperative FEV1% ( P &lt; 0.001). The study identified video-assisted thoracic surgery (VATS) (odds ratio [OR], 3.90; 95% confidence interval [CI], 1.98–7.69; P &lt; 0.001) and higher percentage of resected volume (OR per 1% increase, 1.05; 95% CI, 1.01–1.09; P = 0.014) as significant predictors of postsurgical lung function improvement. Conversely, for the decline in lung function postsurgery, significant predictors included lower percentage of resected lung volume (OR per 1% increase, 0.92; 95% CI, 0.86–0.98; P = 0.011), higher preoperative FEV1% (OR, 1.03; 95% CI, 1.01–1.07; P = 0.009), and the presence of tuberculosis (OR, 5.19; 95% CI, 1.48–18.15; P = 0.010). Additionally, in a subgroup of patients with borderline lung function, VATS was related with improvement. Conclusions Our findings demonstrate that in more than half of the patients, actual postsurgical lung function exceeded predicted values, particularly following VATS and with higher volume of lung resection. It also identifies lower resected lung volume, higher preoperative FEV1%, and tuberculosis as factors associated with a postsurgical decline in lung function. The study underscores the need for precise preoperative lung function assessment and tailored postoperative management, with particular attention to patients with relevant clinical factors. Future research should focus on validation of clinical factors and exploring tailored approaches to lung cancer surgery and recovery.
A Peculiar Tau Accumulation Pattern Identified Via 18F-Florzolotau PET Imaging in a Patient With Frontotemporal Dementia Caused by a Mutation in the MAPT Gene
Authors: Qijun Li, Hang Li, Zhaoxia Huang, Yanfeng Li, Ruixue Cui
Journal: Clinical Nuclear Medicine (2024)

We reported imaging findings with a peculiar tau accumulation pattern in a 56 year-old woman with frontotemporal dementia caused by Q351R mutation in the microtubule-associated protein tau ( MAPT ) gene. She had a 10-year history of gradually worsening memory loss. 18 F-FDG PET demonstrated hypometabolism in medial temporal lobes, but 18 F-florbetapir PET manifested no abnormal amyloid beta deposition, which ruled out Alzheimer disease. 18 F-florzolotau PET showed tau proteins accumulated in medial temporal lobes, basal ganglia brainstem, and cerebellum. The pattern is different from other known MAPT gene mutation. Multitracer imaging can help differentiate between Alzheimer disease and frontotemporal dementia caused by MAPT mutation.
An integrated analysis of bile acid metabolism in humans with severe obesity
Authors: Ömrüm Aydin, Annika Wahlström, Patrick A. de Jonge, Abraham S. Meijnikman, Wilhelm Sjöland, Lisa Olsson, Marcus Henricsson, Marcus C. de Goffau, Stijn Oonk, Sjoerd C. Bruin, Yair I.Z. Acherman, Hanns-Ulrich Marschall, Victor E.A. Gerdes, Max Nieuwdorp, Fredrik Bäckhed, Albert K. Groen
Journal: Hepatology (2024)

Background and Aims: Bile acids (BA) are vital regulators of metabolism. BAs are AQ6 secreted in the small intestine, reabsorbed, and transported back to the liver, where they can modulate metabolic functions. There is a paucity of data regarding the portal BA composition in humans. This study aimed to address this knowledge gap by investigating portal BA composition and the relation with peripheral and fecal BA dynamics in conjunction with the gut microbiome. Approach and Results: Thirty-three individuals from the BARIA cohort were included. Portal plasma, peripheral plasma, and feces were collected. BA and C4 levels were measured employing mass spectrometry. FGF19 was measured using ELISA. Gut microbiota composition was determined through metagenomics analysis on stool samples. Considerable diversity in the portal BA composition was observed. The majority (n = 26) of individuals had a 9-fold higher portal than peripheral BA concentration. In contrast, 8 individuals showed lower portal BA concentration compared with peripheral and had higher levels of unconjugated and secondary BA in this compartment, suggesting more distal origin. The altered portal BA profile was associated with altered gut microbiota composition. In particular, taxa within Bacteroides were reduced in abundance in the feces of these individuals. Conclusions: Characterization of the portal BA composition in relation to peripheral and fecal BA increased insight into the dynamics of BA metabolism in individuals with obesity. Peripheral BA composition was much more diverse due to microbial metabolism. About 24% of the portal samples was surprisingly low in total BA; the underlying mechanism requires further exploration.
Burned-Out Testicular Carcinoma Presenting as Inferior Vena Cava Tumor Thrombus With Pulmonary Tumor Embolism on FDG PET/CT
Authors: Noa Shani Shrem, Daniel Levin, Keren Rouvinov, Gal Ben-Arie, Ilya Liberzon, Nir Hod
Journal: Clinical Nuclear Medicine (2024)

Abstract “Burned-out” testicular tumor is a very rare clinical phenomenon, which refers to the presence of a metastatic germ cell tumor with no clinical findings in the testicle due to spontaneous regression of the primary testicular lesion. We present an unusual case of burned-out testicular embryonal germ cell carcinoma presenting as an extensive inferior vena cava tumor thrombus with malignant pulmonary embolism in which FDG PET/CT played a pivotal role in detecting the extent and significance of the disease.
Elevated 68Ga-FAPI Activity in Benign Carotid Body Tumors
Authors: Yang Xie, Wenxin Tang, Xi Chen, Xue Bai, Yue Chen
Journal: Clinical Nuclear Medicine (2024)

Abstract We present 68 Ga-FAPI PET/CT findings of benign carotid body tumor in a 33-year-old woman. Benign carotid body tumor demonstrated intense tracer uptakes on 68 Ga-FAPI PET/CT. Our case suggests that benign carotid body tumors should be considered in the differential diagnosis of neck mass with elevated 68 Ga-FAPI activity.
Prospective genetic germline evaluation in a consecutive group of adult patients aged &lt;60 years with myelodysplastic syndromes
Authors: Enrico Attardi, Lucia Tiberi, Giorgio Mattiuz, Daniela Formicola, Elia Dirupo, Marco G. Raddi, Angela Consagra, Debora Vergani, Rosangela Artuso, Valeria Santini
Journal: HemaSphere (2024)

Relevance of germline (GL) predisposition in myelodysplastic syndromes (MDSs) was stressed in both 2022 WHO and International Consensus classifications, but its incidence is probably underestimated, especially in young adult patients. We selected a cohort of 31 consecutive de novo MDS patients with unusual young age (<60 years). We performed exome sequencing (ES) on DNA extracted from noninvasive sources (peripheral blood and saliva), filtering for a panel of 344 genes specifically tailored for detecting GL variants related to clonal and nonclonal cytopenia. We observed at least one high- or low-confidence GL MDS variant in 7/31 (22.6%) and 9/31 (29.0%) of cases, respectively. Four of 31 patients (12.9%) confirmed having established MDS/AML predisposing disorders. We found heterozygous variants in genes involved in DNA repair/cancer predisposition (
Realizing the clinical utility of saliva for monitoring oral diseases
Authors: Jeffrey L. Ebersole, Hatice Hasturk, Michaell Huber, Robert Gellibolian, Adam Markaryan, Xiaohua D. Zhang, Craig S. Miller
Journal: Periodontology 2000 (2024)

In the era of personalized/precision health care, additional effort is being expended to understand the biology and molecular mechanisms of disease processes. How these mechanisms are affected by individual genetics, environmental exposures, and behavioral choices will encompass an expanding role in the future of optimally preventing and treating diseases. Considering saliva as an important biological fluid for analysis to inform oral disease detection/description continues to expand. This review provides an overview of saliva as a diagnostic fluid and the features of various biomarkers that have been reported. We emphasize the use of salivary biomarkers in periodontitis and transport the reader through extant literature, gaps in knowledge, and a structured approach toward validating and determine the utility of biomarkers in periodontitis. A summation of the findings support the likelihood that a panel of biomarkers including both host molecules and specific microorganisms will be required to most effectively identify risk for early transition to disease, ongoing disease activity, progression, and likelihood of response to standard periodontal therapy. The goals would be to develop predictive algorithms that serve as adjunctive diagnostic tools which provide the clinician and patient important information for making informed clinical decisions.
Dynamics of Liver Stiffness Measurement and Clinical Course of Primary Biliary Cholangitis
Authors: Laurent Lam, Pierre-Antoine Soret, Sara Lemoinne, Bettina Hansen, Gideon Hirschfield, Aliya Gulamhusein, Aldo J. Montano-Loza, Ellina Lytvyak, Albert Parés, Ignasi Olivas, Maria-Carlota Londono, Sergio Rodríguez-Tajes, John E. Eaton, Karim T. Osman, Christoph Schramm, Marcial Sebode, Ansgar W. Lohse, George Dalekos, Nikolaos Gatselis, Frederik Nevens, Nora Cazzagon, Alessandra Zago, Francesco Paolo Russo, Annarosa Floreani, Nadir Abbas, Palak Trivedi, Douglas Thorburn, Francesca Saffioti, Laszlo Barkai, Davide Roccarina, Vicenza Calvaruso, Anna Fichera, Adèle Delamarre, Natalia Sobenko, Alejandra Maria Villamil, Esli Medina-Morales, Alan Bonder, Vilas Patwardhan, Cristina Rigamonti, Marco Carbone, Pietro Invernizzi, Laura Cristoferi, Adriaan van der Meer, Rozanne de Veer, Ehud Zigmond, Eyal Yehezkel, Andreas E. Kremer, Ansgar Deibel, Tony Bruns, Karsten Große, Aaron Wetten, Jessica Katharine Dyson, David Jones, Cynthia Levy, Atsushi Tanaka, Jérôme Dumortier, Georges-Philippe Pageaux, Victor de Lédinghen, Fabrice Carrat, Olivier Chazouillères, Christophe Corpechot
Journal: Clinical Gastroenterology and Hepatology (2024)

In primary biliary cholangitis (PBC), static liver stiffness measurement (LSM) has proven prognostic value. However, the added prognostic value of LSM time course in this disease remains uncertain.
Bioengineered Silk Protein‐Based 3D In Vitro Models for Tissue Engineering and Drug Development: From Silk Matrix Properties to Biomedical Applications
Authors: Yajun Shuai, Meidan Zheng, Subhas C. Kundu, Chuanbin Mao, Mingying Yang
Journal: Advanced Healthcare Materials (2024)

3D in vitro model has emerged as a valuable tool for studying tissue development, drug screening, and disease modeling. 3D systems can accurately replicate tissue microstructures and physiological features, mirroring the in vivo microenvironment departing from conventional 2D cell cultures. Various 3D in vitro models utilizing biomacromolecules like collagen and synthetic polymers have been developed to meet diverse research needs and address the complex challenges of contemporary research. Silk proteins, bearing structural and functional similarities to collagen, have been increasingly employed to construct advanced 3D in vitro systems, surpassing the limitations of 2D cultures. This review examines silk proteins' composition, structure, properties, and functions, elucidating their role in 3D in vitro models. Furthermore, recent advances in biomedical applications involving silk-based organoid models are discussed. In particular, the unique physiological attributes of silk matrix constituents in in vitro tissue constructs are highlighted, providing a meticulous evaluation of their importance. Additionally, it outlines the current research hurdles and complexities while contemplating future avenues, thereby paving the way for developing complex and biomimetic silk protein-based microtissues.
Impact of EML4-ALK Variants and Co-Occurring TP53 Mutations on Duration of First-Line ALK Tyrosine Kinase Inhibitor Treatment and Overall Survival in ALK Fusion-Positive NSCLC: Real-World Outcomes From the GuardantINFORM database
Authors: Kaushal Parikh, Anastasios Dimou, Konstantinos Leventakos, Aaron S Mansfield, Mohamed Shanshal, Yin Wan, Huamao M Lin, Sylvie Vincent, Jennifer Elliott, Ioana R Bonta
Journal: Journal of Thoracic Oncology (2024)
Sensitization against medical hyaluronidase in patients with confirmed hypersensitivity against hymenoptera species and its clinical implications
Authors: Mattis Bertlich, Daniela Hartmann, Saskia Freytag, Lars E French, Eva Oppel
Journal: British Journal of Dermatology (2024)

Abstract Background Hyaluronidase is an ubiquitous enzyme, present, among others, in hymenoptera venom and in medical formulations. The latter include use as an emergency treatment or to correct undesired outcomes of medical and aesthetic procedures using hyaluronic acid fillers. Objectives By performing detailed allergy work-ups including skin-prick tests (SPTs) we investigated whether patients with a history of allergic reaction to hymenoptera venom are also sensitized to medical grade hyaluronidase. Methods Ninety patients with a history of type-1 reaction to hymenoptera venom with and without a history of previous specific venom immunotherapy were included in the study. All underwent SPTs for medical hyaluronidase. All patients also underwent serological analysis for Api m2, the only commercially available IgE test for a hymenoptera hyaluronidase. Results Of the 90 patients with previous type-1 reactions to hymenoptera venom hyaluronidase included in the study, 60 had undergone previous venom immunotherapy; 30 did not. The majority (73 of 90) were allergic to wasps, followed by honeybees (14 of 90) and three were allergic to both. Neither patients having undergone previous immunotherapy nor those allergic to bees showed positive SPTs to medical hyaluronidase. Of those with a wasp allergy and naïve to immunotherapy, over 20% (5 of 23) showed positive SPTs to medical hyaluronidase. Healthy controls (0 of 30) without previous allergic reactions to hymenoptera did not show positive SPTs to medical hyaluronidase. Conclusions Sensitization to hyaluronidase is most common in wasp-allergic patients who have not had previous specific immunotherapy. As allergic reactions to medical hyaluronidase are reported to be scarce, this group is probably at the highest risk to develop anaphylaxis to medical hyaluronidase. While all patients with untreated anaphylaxis to hymenoptera venom should consult an allergy specialist, it is particularly important that those with untreated wasp allergies seek specialist advice before treatment with medical hyaluronidase is initiated.
Topical glyceryl trinitrate (GTN) and eccentric exercises in the treatment of mid-portion achilles tendinopathy (the NEAT trial): a randomised double-blind placebo-controlled trial
Authors: Paul D Kirwan, Trevor Duffy, Helen P French
Journal: British Journal of Sports Medicine (2024)

To investigate if daily treatment with glyceryl trinitrate (GTN) ointment, over 24 weeks combined with a 12-week eccentric exercise programme is more effective for chronic mid-portion Achilles tendinopathy than placebo ointment and eccentric exercise.
Where is the research on sport-related concussion in Olympic athletes? A descriptive report and assessment of the impact of access to multidisciplinary care on recovery
Authors: Thomas Romeas, Félix Croteau, Suzanne Leclerc
Journal: British Journal of Sports Medicine (2024)

Objectives This cohort study reported descriptive statistics in athletes engaged in Summer and Winter Olympic sports who sustained a sport-related concussion (SRC) and assessed the impact of access to multidisciplinary care and injury modifiers on recovery. Methods 133 athletes formed two subgroups treated in a Canadian sport institute medical clinic: earlier (≤7 days) and late (≥8 days) access. Descriptive sample characteristics were reported and unrestricted return to sport (RTS) was evaluated based on access groups as well as injury modifiers. Correlations were assessed between time to RTS, history of concussions, the number of specialist consults and initial symptoms. Results 160 SRC (median age 19.1 years; female=86 (54%); male=74 (46%)) were observed with a median (IQR) RTS duration of 34.0 (21.0–63.0) days. Median days to care access was different in the early (1; n SRC =77) and late (20; n SRC =83) groups, resulting in median (IQR) RTS duration of 26.0 (17.0–38.5) and 45.0 (27.5–84.5) days, respectively (p&lt;0.001). Initial symptoms displayed a meaningful correlation with prognosis in this study (p&lt;0.05), and female athletes (52 days (95% CI 42 to 101)) had longer recovery trajectories than male athletes (39 days (95% CI 31 to 65)) in the late access group (p&lt;0.05). Conclusions Olympic athletes in this cohort experienced an RTS time frame of about a month, partly due to limited access to multidisciplinary care and resources. Earlier access to care shortened the RTS delay. Greater initial symptoms and female sex in the late access group were meaningful modifiers of a longer RTS.
The effects of ciclosporin and methotrexate on kidney function in the treatment of severe atopic dermatitis in children – results from the TREAT trial
Authors: Gordon Bruce, Anna Rosala-Hallas, Ashley P Jones, Charles Turner, Neil Dalton, Eva Hilger, Susannah Baron, Paula Beattie, Fiona Browne, Sara J Brown, Joanna E Gach, Ross Hearn, Ben Esdaile, Mike J Cork, Emma Howard, Danielle Greenblatt, Suzannah August, Marie-Louise Lovgren, Farhiya Ashoor, Paula Williamson, Tess McPherson, Donal O'Kane, Jane Ravenscroft, Lindsay Shaw, Catherine Spowart, Bjorn R Thomas, Tracey Sach, Mandy Wan, Alan D Irvine, Manish D Sinha, Carsten Flohr
Journal: British Journal of Dermatology (2024)

Ciclosporin (CyA) and methotrexate (MTX) are frequently prescribed drugs for the treatment of atopic dermatitis in children and young people. Both can affect renal function and frequent blood monitoring is standard to monitor safety. We show that both CyA and MTX are not associated with decreased renal function and are safe and effective as a treatment for atopic dermatitis in children and young people.
Transcriptomic subtyping of gastrointestinal malignancies
Authors: Tim R. de Back, Sander R. van Hooff, Dirkje W. Sommeijer, Louis Vermeulen
Journal: Trends in cancer (2024)

Gastrointestinal (GI) cancers are highly heterogeneous at multiple levels. Tumor heterogeneity can be captured by molecular profiling, such as genetic, epigenetic, proteomic, and transcriptomic classification. Transcriptomic subtyping has the advantage of combining genetic and epigenetic information, cancer cell-intrinsic properties, and the tumor microenvironment (TME). Unsupervised transcriptomic subtyping systems of different GI malignancies have gained interest because they reveal shared biological features across cancers and bear prognostic and predictive value. Importantly, transcriptomic subtypes accurately reflect complex phenotypic states varying not only per tumor region, but also throughout disease progression, with consequences for clinical management. Here, we discuss methodologies of transcriptomic subtyping, proposed taxonomies for GI malignancies, and the challenges posed to clinical implementation, highlighting opportunities for future transcriptomic profiling efforts to optimize clinical impact.
<i>Bacteroides fragilis</i> alleviates necrotizing enterocolitis through restoring bile acid metabolism balance using bile salt hydrolase and inhibiting FXR-NLRP3 signaling pathway
Authors: Zhenhui Chen, Huijuan Chen, Wanwen Huang, Xiaotong Guo, Lu Yu, Jiamin Shan, Xiaoshi Deng, Jiaxin Liu, Wendan Li, Wei Shen, Hongying Fan
Journal: Gut Microbes (2024)

Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in premature infants with no specific treatments available. We aimed to identify the molecular mechanisms underlying NEC and investigate the therapeutic effects of Bacteroides fragilis on NEC. Clinical samples of infant feces, bile acid-targeted metabolomics, pathological staining, bioinformatics analysis, NEC rat model, and co-immunoprecipitation were used to explore the pathogenesis of NEC. Taxonomic characterization of the bile salt hydrolase (bsh) gene, enzyme activity assays, 16S rRNA sequencing, and organoids were used to explore the therapeutic effects of B. fragilis on NEC-related intestinal damage. Clinical samples, NEC rat models, and in vitro experiments revealed that total bile acid increased in the blood but decreased in feces. Moreover, the levels of FXR and other bile acid metabolism-related genes were abnormal, resulting in disordered bile acid metabolism in NEC. Taurochenodeoxycholic acid accelerated NEC pathogenesis and taurodeoxycholate alleviated NEC. B. fragilis displayed bsh genes and enzyme activity and alleviated intestinal damage by restoring gut microbiota dysbiosis and bile acid metabolism abnormalities by inhibiting the FXR-NLRP3 signaling pathway. Our results provide valuable insights into the therapeutic role of B. fragilis in NEC. Administering B. fragilis may substantially alleviate intestinal damage in NEC.
Surface‐Grafted Biocompatible Polymer Conductors for Stable and Compliant Electrodes for Brain Interfaces
Authors: Rachel Blau, Samantha M. Russman, Yi Qie, Wade Shipley, Allison Lim, Alexander X. Chen, Audithya Nyayachavadi, Louis Ah, Abdulhameed Abdal, Guillermo L. Esparza, Samuel J. Edmunds, Ritwik Vatsyayan, Sean P. Dunfield, Moumita Halder, Jesse V. Jokerst, David P. Fenning, Andrea R. Tao, Shadi A. Dayeh, Darren J. Lipomi
Journal: Advanced Healthcare Materials (2024)

Abstract Durable and conductive interfaces that enable chronic and high‐resolution recording of neural activity are essential for understanding and treating neurodegenerative disorders. These chronic implants require long‐term stability and small contact areas. Consequently, they are often coated with a blend of conductive polymers and are crosslinked to enhance durability despite the potentially deleterious effect of crosslinking on the mechanical and electrical properties. Here the grafting of the poly(3,4 ethylenedioxythiophene) scaffold, poly(styrenesulfonate)‐ b ‐poly(poly(ethylene glycol) methyl ether methacrylate block copolymer brush to gold, in a controlled and tunable manner, by surface‐initiated atom‐transfer radical polymerization (SI‐ATRP) is described. This “block‐brush” provides high volumetric capacitance (120 F cm ─3 ), strong adhesion to the metal (4 h ultrasonication), improved surface hydrophilicity, and stability against 10 000 charge–discharge voltage sweeps on a multiarray neural electrode. In addition, the block‐brush film showed 33% improved stability against current pulsing. This approach can open numerous avenues for exploring specialized polymer brushes for bioelectronics research and application.