tbuckley/cabot-search huggingface dataset:
Altered levels of phospholipases C, diacylglycerols, endocannabinoids, and <i>N</i>‐acylethanolamines in patients with hereditary angioedema due to <scp>FXII</scp> mutation
Authors: Anne Lise Ferrara, Francesco Palestra, Fabiana Piscitelli, Angelica Petraroli, Chiara Suffritti, Davide Firinu, Alberto López‐Lera, Teresa Caballero, Konrad Bork, Giuseppe Spadaro, Gianni Marone, Vincenzo Di Marzo, Maria Bova, Stefania Loffredo
Journal: Allergy (2024)

Hereditary angioedema (HAE) is a rare genetic disorder characterized by local, self-limiting edema due to temporary increase in vascular permeability. HAE with normal C1 esterase inhibitor (C1INH) activity includes the form with mutations in the F12 gene encoding for coagulation factor XII (FXII-HAE) causing an overproduction of bradykinin (BK) leading to angioedema attack. BK binding to B2 receptors (BK2R) leads to an activation of phospholipase C (PLC) and subsequent generation of second messengers: diacylglycerols (DAGs) and possibly the endocannabinoids (eCBs), 2-arachidonoylglycerol (2-AG) and anandamide (AEA), and eCB-related N-acylethanolamines [palmitoylethanolamide (PEA) and oleoylethanolamide (OEA)]. To date, there are no data on the role of these lipid mediators in FXII-HAE.
Metabolic phenotyping of patients with advanced chronic liver disease for better characterization of cirrhosis regression
Authors: Yuly P. Mendoza, Sofia Tsouka, Georg Semmler, Patcharamon Seubnooch, Katrin Freiburghaus, Mattias Mandorfer, Jaime Bosch, Mojgan Masoodi, Annalisa Berzigotti
Journal: Journal of Hepatology (2024)
Predictors of treatment outcome of psychological therapies for common mental health problems (CMHP) in older adults: A systematic literature review
Authors: Alexandra Schmidt, Nick Grey, Clara Strauss, Darya Gaysina
Journal: Clinical Psychology Review (2024)

Identifying factors that impact psychological treatment outcomes in older people with common mental health problems (CMHP) has important implications for supporting healthier and longer lives. The aim of the present study was to synthesise the evidence on predictors of psychological treatment outcomes in older people (aged 65+). PubMed, Scopus, Web of Science and PsycINFO were searched and 3929 articles were identified and screened, with 42 studies (N = 7978, M age = 68.9, SD age = 2.85) included: depression: k = 21, anxiety: k = 11, panic disorder: k = 3, mixed anxiety & depression: k = 3, PTSD: k = 2, various CMHP: k = 2, with CBT being the most common treatment (71%). The review identified 28 factors reported as significant predictors of treatment outcome in at least one study, across different domains: psychosocial (n = 9), clinical (n = 6), treatment-related (n = 6), socio-demographic (n = 4), neurobiological (n = 3). Homework completion was the most consistent predictor of positive treatment outcome. Baseline symptom severity was the most frequently studied significant predictor and across all conditions, with higher baseline symptom severity largely linked to worse treatment outcomes. No significant effects on treatment outcome were reported for gender, income and physical comorbidities. For a large majority of factors evidence was mixed or inconclusive. Further studies are required to identify factors affecting psychological treatment outcomes, which will be important for the development of personalised treatment approaches.
CO-DELIVERY of glutamic acid-extended peptide antigen and imidazoquinoline TLR7/8 agonist via ionizable lipid nanoparticles induces protective anti-tumor immunity
Authors: Tingting Ye, Zifu Zhong, Federica Cappellesso, Kim Deswarte, Yong Chen, Heleen Lauwers, Emily De Lombaerde, Mark Gontsarik, Stefan Lienenklaus, Dorien Van Lysebetten, Niek N. Sanders, Bart N. Lambrecht, Stefaan De Koker, Damya Laoui, Bruno G. De Geest
Journal: Biomaterials (2024)
Attention-Deficit/Hyperactivity Disorder Diagnoses in Finland During the COVID-19 Pandemic
Authors: Kirsi Auro, Ida Holopainen, Markus Perola, Aki S. Havulinna, Anu Raevuori
Journal: JAMA Network Open (2024)

Importance Several reports suggest an increase in attention-deficit/hyperactivity disorder (ADHD) symptoms during the COVID-19 pandemic. This nationwide study assessed new ADHD diagnoses and ADHD prevalence before and during the pandemic. Objective To investigate trends in new ADHD diagnoses, prevalence, and ADHD medication use from 2015 to 2022 in Finland. Design, Setting, and Participants This longitudinal cohort study comprised the entire Finnish population. ADHD diagnoses and medication use were obtained from nationwide registers and assessed at 3 time points: in 2015 and before (2020) and after (2022) the pandemic. Data were analyzed from January 2015 to June 2022. Main outcomes and Measures New ADHD diagnoses, ADHD lifetime prevalence, and ADHD medication use. Results The cohort comprised 5 572 420 individuals (2 819 645 women [50.6%]). Lifetime prevalence of ADHD increased by 2.7-fold during 2015 to 2022; prevalence was 1.02% in 2015 (95% CI, 1.01%-1.03%), 1.80% in 2020 (95% CI, 1.79%-1.81%), and 2.76% in 2022 (95% CI, 2.75%-2.77%). Young men aged 13 to 20 years had the highest lifetime prevalence of 11.68% (95% CI, 11.56%-11.81%) in 2022. New ADHD diagnoses doubled during the pandemic, from 238 per 100 000 in 2020 to 477 per 100 000 in 2022. The pandemic-associated incremental increase in new diagnoses was 18.60% (95% CI, 16.47%-20.49%; 9482 per 50 897 cases). Young women aged 13 to 20 years had a 2.6-fold increase in new diagnoses during the pandemic, from 577 per 100 000 in 2020 to 1488 per 100 000 in 2022, and women aged 21 to 30 years had a 3.0-fold increase, from 361 per 100 000 to 1100 per 100 000. New diagnoses increased by 2.9-fold among those older than 55 years (from 5 per 100 000 to 13 per 100 000 in women and from 5 per 100 000 to 14 per 100 000 in men). Boys younger than 13 years had the highest absolute rate of new ADHD diagnoses in 2022 (1745 per 100 000), but boys and young men younger than 21 years did not show a significant incremental increase in new diagnoses. Lifetime prevalence of ADHD medication purchases was 0.57% (95% CI, 0.56%-0.58%) in 2015 (31 771 [55.62%] of those with ADHD diagnosis), 1.15% (95% CI, 1.14%-1.16%) in 2020 (64 034 [63.83%]), and 1.69% (95% CI 1.68%-1.70%) in 2022 (92 557 [61.43%]), respectively. Conclusions and Relevance In this nationwide cohort study, new ADHD diagnoses and ADHD prevalence showed significant increase in Finland during the pandemic. ADHD medication use did not increase in relation to ADHD diagnoses. These results highlight potential adverse outcomes of pandemic-associated changes in living conditions.
Early Antibiotic Exposure and Bronchopulmonary Dysplasia in Very Preterm Infants at Low Risk of Early-Onset Sepsis
Authors: Wei Shi, Zheng Chen, Liping Shi, Siyuan Jiang, Jianguo Zhou, Xinyue Gu, Xiaoping Lei, Tiantian Xiao, Yanping Zhu, Aimin Qian, Wenhao Zhou, Shoo K. Lee, Lizhong Du, Jie Yang, Xiaolu Ma, Liyuan Hu, Chao Chen, Yun Cao, Xiuyong Chen, Huyan Zhang, Xiuying Tian, Jingyun Shi, Zhankui Li, Chuanzhong Yang, Ling Liu, Zuming Yang, Jianhua Fu, Yong Ji, Dongmei Chen, Changyi Yang, Rui Chen, Xiaoming Peng, Ruobing Shan, Shuping Han, Hui Wu, Lili Wang, Qiufen Wei, Mingxia Li, Yiheng Dai, Hong Jiang, Wenqing Kang, Xiaohui Gong, Xiaoyun Zhong, Yuan Shi, Shanyu Jiang, Bing Sun, Long Li, Zhenlang Lin, Jiangqin Liu, Jiahua Pan, Hongping Xia, Xiaoying Li, Falin Xu, Yinping Qiu, Li Ma, Ling Yang, Xiaori He, Yanhong Li, Deyi Zhuang, Qin Zhang, Wenbin Dong, Jianhua Sun, Kun Liang, Huaiyan Wang, Jinxing Feng, Liping Chen, Xinzhu Lin, Chunming Jiang, Chuan Nie, Linkong Zeng, Mingyan Hei, Hongdan Zhu, Hongying Mi, Zhaoqing Yin, Hongxia Song, Hongyun Wang, Dong Li, Yan Gao, Yajuan Wang, Liying Dai, Liyan Zhang, Yangfang Li, Qianshen Zhang, Guofang Ding, Jimei Wang, Xiaoxia Chen, Zhen Wang, Zheng Tang, Xiaomei Zhang, Xiaolan Zhang, Fang Wu, Yanxiang Chen, Ying Wu, Joseph Ting
Journal: JAMA Network Open (2024)

The overutilization of antibiotics in very preterm infants (VPIs) at low risk of early-onset sepsis (EOS) is associated with increased mortality and morbidities. Nevertheless, the association of early antibiotic exposure with bronchopulmonary dysplasia (BPD) remains equivocal.
Haematopoietic stem cell-derived immune cells have reduced X chromosome inactivation skewing in systemic lupus erythematosus
Authors: Amy L Roberts, Alessandro Morea, Ariella Amar, Magdalena West, Sarah Karrar, Rhiannon Lehane, Philip Tombleson, Deborah Cunningham Grahman, John A Reynolds, Chloe C Y Wong, David L Morris, Kerrin S Small, Timothy J Vyse
Journal: Annals of the Rheumatic Diseases (2024)

Systemic lupus erythematosus (SLE) shows a marked female bias in prevalence. X chromosome inactivation (XCI) is the mechanism which randomly silences one X chromosome to equalise gene expression between 46, XX females and 46, XY males. Though XCI is expected to result in a random pattern of mosaicism across tissues, some females display a significantly skewed ratio in immune cells, termed XCI-skew. We tested whether XCI was abnormal in females with SLE and hence contributes to sexual dimorphism.
A More Selective vs a Standard Risk-Stratified, Heparin-Based, Obstetric Thromboprophylaxis Protocol
Authors: Macie L. Champion, Christina T. Blanchard, Michelle Y. Lu, Ashley E. Shea, Anna I. Lively, J. Morgan Jenkins, Samantha E. Howell, Grace M. Lee, Brian M. Casey, Ashley N. Battarbee, Akila Subramaniam
Journal: JAMA (2024)

In 2016, our institution adopted a pregnancy-related venous thromboembolism (VTE) prophylaxis protocol based on American College of Obstetricians and Gynecologists guidelines that recommended postpartum heparin-based chemoprophylaxis (enoxaparin) based on a risk-stratified algorithm. In response to increased wound hematomas without significant reduction in VTE using this protocol, a more selective risk-stratified approach was adopted in 2021.
Varenicline and Nicotine Replacement Therapy for Smokers Admitted to Hospitals
Authors: Gregory R. Weeks, Rukshar K. Gobarani, Michael J. Abramson, Billie Bonevski, Ashley Webb, Dennis Thomas, Eldho Paul, Muhammad R. Sarwar, Brian J. Smith, Sharmilla Perinpanathan, Sue Kirsa, Jacqueline Parkinson, Darshana Meanger, Lisa Coward, Olivia Rofe, Paula Lee, Denise van den Bosch, Johnson George
Journal: JAMA Network Open (2024)

Varenicline is the most effective sole pharmacotherapy for smoking cessation. If used in combination with nicotine replacement therapy (NRT), cessation rates may be further improved, but the efficacy and safety of the combination need to be evaluated.
Endometrial Thickness as Diagnostic Triage for Endometrial Cancer Among Black Individuals
Authors: Kemi M. Doll, Mindy Pike, Julianna Alson, Patrice Williams, Erin Carey, Til Stürmer, Mollie Wood, Erica E. Marsh, Ronit Katz, Whitney R. Robinson
Journal: JAMA Oncology (2024)

Poor performance of the transvaginal ultrasonography triage strategy has been suggested as a contributor to racial disparity between Black individuals and White individuals in endometrial cancer (EC) stage at diagnosis in population-level simulation analyses.
Long-Term Prospective Outcomes of Intensity Modulated Radiotherapy for Locally Advanced Lung Cancer
Authors: Stephen G. Chun, Chen Hu, Ritsuko U. Komaki, Robert D. Timmerman, Steven E. Schild, Jeffrey A. Bogart, Michael C. Dobelbower, Walter Bosch, Vivek S. Kavadi, Samir Narayan, Puneeth Iyengar, Clifford Robinson, Jan Rothman, Adam Raben, Mark E. Augspurger, Robert M. MacRae, Rebecca Paulus, Jeffrey D. Bradley
Journal: JAMA Oncology (2024)

The optimal radiotherapy technique for unresectable locally advanced non-small cell lung cancer (NSCLC) is controversial, so evaluating long-term prospective outcomes of intensity-modulated radiotherapy (IMRT) is important.
Major Gaps in the Cascade of Care for Opioid Use Disorder
Authors: M. Allison Arwady, Miriam Delphin-Rittmon, Nora D. Volkow
Journal: JAMA (2024)

This Viewpoint examines a recent report that used data from the 2022 National Survey on Drug Use and Health to estimate the opioid cascade of care, a framework to characterize the adult US populations who needed and received opioid use disorder (OUD) treatment, as well as discusses ways in which clinicians can close gaps in care.
Increased Muc5AC and Decreased Ciliated Cells in Severe Asthma Partially Restored by Inhibition of IL-4Rα Receptor
Authors: Jonathan Boomer, Jiwoong Choi, Alexander Alsup, Mary Clare McGregor, Julia Lieu, Cooper Johnson, Chase Hall, Xiaosong Shi, Taewon Kim, Charles Goss, Daphne Lew, Stephanie Christenson, Prescott G. Woodruff, Annette Hastie, David Mauger, Sally E. Wenzel, Eric A. Hoffman, Ken B. Schechtman, Mario Castro
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

The role of IL-13 on the airway epithelium in severe asthma leading to airway remodeling remains poorly understood.
Misaligned Pharmacy Incentives in Value-Based Care
Authors: Nina Jain, Benjamin N. Rome, Mallika L. Mendu
Journal: JAMA (2024)

This Viewpoint explains some ways in which the alignment of incentives between payers and clinicians in value-based care (VBC) arrangements can be interrupted and proposes a multifaceted approach to realigning incentives for drug spending within VBC contracts to better provide value-based care and improve patient outcomes.
Circulating Metabolite Biomarkers of Glycemic Control in Youth-Onset Type 2 Diabetes
Authors: Zsu-Zsu Chen, Chang Lu, Jonathan M. Dreyfuss, Gaurav Tiwari, Xu Shi, Shuning Zheng, Danielle Wolfs, Laura Pyle, Petter Bjornstad, Laure El ghormli, Robert E. Gerszten, Elvira Isganaitis
Journal: Diabetes Care (2024)

We aimed to identify metabolites associated with loss of glycemic control in youth-onset type 2 diabetes.
Genome-Wide Allele Frequency Changes Reveal That Dynamic Metapopulations Evolve Differently
Authors: Pascal Angst, Christoph R Haag, Frida Ben-Ami, Peter D Fields, Dieter Ebert
Journal: Molecular Biology and Evolution (2024)

Abstract Two important characteristics of metapopulations are extinction–(re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in “classical” (large, stable, and panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation–selection–drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum. We followed changes in site frequency spectrum distribution in a natural metapopulation of the cyclically parthenogenetic pond-dwelling microcrustacean Daphnia magna using biannual pool-seq samples collected over a 5-yr period from 118 ponds occupied by subpopulations of known age. As expected under the propagule model, site frequency spectra in newly founded subpopulations trended toward intermediate allele frequencies and shifted toward right-skewed distributions as the populations aged. Immigration and subsequent hybrid vigor altered this dynamic. We show that the analysis of site frequency spectrum dynamics is a powerful approach to understand evolution in metapopulations. It allowed us to disentangle evolutionary processes occurring in a natural metapopulation, where many subpopulations evolve in parallel. Thereby, stochastic processes like founder and immigration events lead to a pattern of subpopulation divergence, while genetic drift leads to converging site frequency spectrum distributions in the persisting subpopulations. The observed processes are well explained by the propagule model and highlight that metapopulations evolve differently from classical populations.
Medical image registration via neural fields
Authors: Shanlin Sun, Kun Han, Chenyu You, Hao Tang, Deying Kong, Junayed Naushad, Xiangyi Yan, Haoyu Ma, Pooya Khosravi, James S. Duncan, Xiaohui Xie
Journal: Medical Image Analysis (2024)

Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to domain shift. Here we present a new neural network based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural networks to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic mini-batch gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. NIR is evaluated on two 3D MR brain scan datasets, demonstrating highly competitive performance in terms of both registration accuracy and regularity. Compared to traditional optimization-based methods, our approach achieves better results in shorter computation times. In addition, our methods exhibit performance on a cross-dataset registration task, compared to the pre-trained learning-based methods.
Age of Diabetes Diagnosis and Lifetime Risk of Dementia: The Atherosclerosis Risk in Communities (ARIC) Study
Authors: Jiaqi Hu, James R. Pike, Pamela L. Lutsey, A. Richey Sharrett, Lynne E. Wagenknecht, Timothy M. Hughes, Jesse C. Seegmiller, Rebecca F. Gottesman, Thomas H. Mosley, Elizabeth Selvin, Michael Fang, Josef Coresh
Journal: Diabetes Care (2024)

The impact of age of diabetes diagnosis on dementia risk across the life course is poorly characterized. We estimated the lifetime risk of dementia by age of diabetes diagnosis.
Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist
Authors: Yi-Ming Weng, David H Kavanaugh, Sean D Schoville
Journal: Molecular Biology and Evolution (2024)

Abstract The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype–environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
Comprehensive Risk Stratification to Guide an Optimal Preventive Strategy for Breast Radiation Dermatitis—Reply
Authors: Avidan Uriel Neumann, Kai Joachim Borm, Claudia Traidl-Hoffmann
Journal: JAMA Oncology (2024)

In Reply We thank Wong et al for their positive feedback and for highlighting questions about the effect of additional factors on our results showing skin microbiome as a biomarker for severe radiation dermatitis (RD).1
Clinical efficacy and autoantibody seroconversion with CD19-CAR T cell therapy in a patient with rheumatoid arthritis and coexisting myasthenia gravis
Authors: Aiden Haghikia, Tobias Hegelmaier, Denise Wolleschak, Martin Böttcher, Vaia Pappa, Jeremias Motte, Dominic Borie, Ralf Gold, Eugen Feist, Georg Schett, Dimitrios Mougiakakos
Journal: Annals of the Rheumatic Diseases (2024)
Prevalence of Gender-Affirming Surgical Procedures Among Minors and Adults in the US
Authors: Dannie Dai, Brittany M. Charlton, Elizabeth R. Boskey, Landon D. Hughes, Jaclyn M.W. Hughto, E. John Orav, Jose F. Figueroa
Journal: JAMA Network Open (2024)

This cross-sectional study uses a national dataset to examine the prevalence of gender-affirming surgical procedures among minors and adults in the US.
Comprehensive Risk Stratification to Guide an Optimal Preventive Strategy for Breast Radiation Dermatitis
Authors: Henry C. Y. Wong, Saverio Caini, Kimberly Corbin
Journal: JAMA Oncology (2024)

To the Editor In their observational study, Hülpüsch and colleagues1 concluded that the skin microbiome may be a useful biomarker for the personalized prevention of breast radiation dermatitis (RD). We applaud their efforts, but encourage further validation of the results in a larger patient sample.
Intranasal delivery of liposome encapsulated flavonoids ameliorates L-DOPA induced dyskinesia in hemiparkinsonian mice
Authors: Mohamed Rafiuddin Ahmed, Mohammed Inayathullah, Mithya Morton, Venkata Raveendra Pothineni, Kwangmin Kim, Mohamed Sohail Ahmed, Mustafeez Mujtaba Babar, Jayakumar Rajadas
Journal: Biomaterials (2024)
A Case of Gastric Thickening and a Large Ovarian Mass
Authors: Binbin Zheng-Lin, Katalin Kelemen, Allison Rosenthal
Journal: JAMA Oncology (2024)

A 35-year-old female patient with hypothyroidism and Ehler-Danlos syndrome presents with fatigue, abdominal distension, and dyspnea. What is your diagnosis?
Type 1 Invariant Natural Killer T Cells Drive Lung Fibrosis
Authors: Emily Calamita, Wing Han Liu, Patricia P Ogger, Leia Griffin, Christina Michalaki, Faye Murphy, Julie Worrell, Cormac McCarthy, Albert Agro, Marc Hertz, Toby M. Maher, Clare M. Lloyd, Philip Molyneaux, Vipin Kumar, Adam J Byrne
Journal: American Journal of Respiratory and Critical Care Medicine (2024)
A Dual-Armed Oncolytic Virus Shows Clinical Efficacy in Advanced Solid Cancers
Authors: Noelia Silva-Pilipich, Cristian Smerdou
Journal: Clinical Cancer Research (2024)

An oncolytic adenovirus armed with tumor necrosis factor-α and interleukin-2 was tested in patients with advanced solid tumors. Antitumor effects were observed in both treated and non-treated lesions, leading to long-term survival in some patients. This clinical trial shows the potential of oncolytic virotherapy for patients refractory to standard therapies. See related article by Pakola et al., p. 3715.
The Role of Biodiversity in the Development of Asthma and Allergic Sensitization: A State-of-the-Science Review
Authors: Inês Paciência, Needhi Sharma, Timo T. Hugg, Aino K. Rantala, Behzad Heibati, Wael K. Al-Delaimy, Maritta S. Jaakkola, Jouni J.K. Jaakkola
Journal: Environmental Health Perspectives (2024)

Changes in land use and climate change have been reported to reduce biodiversity of both the environment and human microbiota. These reductions in biodiversity may lead to inadequate and unbalanced stimulation of immunoregulatory circuits and, ultimately, to clinical diseases, such as asthma and allergies.