tbuckley/cabot-search huggingface dataset:
Cardiovascular Disease With Hormone Therapy and Ovarian Suppression in Premenopausal Breast Cancer Survivors
Authors: Elizabeth J Polter, Anna E Prizment, Rob F Walker, Zoe Ryan, Wendy Wang, Anne H Blaes, Pamela L Lutsey
Journal: JACC CardioOncology (2024)

Hormone therapies, including aromatase inhibitors and tamoxifen, are used with ovarian suppression to improve outcomes in premenopausal patients with breast cancer. Cardiovascular impacts of these treatments among premenopausal women are unknown. The aim of this study was to test the hypothesis that the use of aromatase inhibitors in combination with ovarian suppression, relative to tamoxifen, is associated with greater incident cardiovascular disease (CVD) risk in premenopausal breast cancer survivors. The MarketScan administrative claims databases (2013-2020) were used to identify enrollees younger than 55 years who had incident breast cancer and were treated with either an aromatase inhibitor and ovarian suppression or tamoxifen. Propensity score matching was used to balance treatment groups across confounding variables including age, breast cancer treatments, and comorbidities. The HR for CVD (including atrial fibrillation, myocardial infarction, stroke, heart failure hospitalization, angina, or coronary revascularization) was calculated by treatment group. In the matched cohort, over a median follow-up time of 1.55 years, the incidence rate was 2.3 per 100 person-years among users of aromatase inhibitors plus ovarian suppression (51 CVD events in 2,205 person-years) and 1.0 per 100 person-years for tamoxifen users (102 CVD events in 9,913 person-years). Users of aromatase inhibitors plus ovarian suppression had a 2.20-fold higher hazard of CVD than tamoxifen users (HR: 2.20; 95% CI: 1.57-3.09). In absolute terms, the incidence rate difference was 0.012 (95% CI: 0.006-0.019). Findings were robust to several sensitivity analyses. Premenopausal patients with breast cancer treated with aromatase inhibitors and ovarian suppression may be at elevated risk for CVD and should be monitored for cardiovascular risk.
Estimating the risk and spatial spread of measles in populations with high MMR uptake: Using school-household networks to understand the 2013 to 2014 outbreak in the Netherlands
Authors: James D. Munday, Katherine E. Atkins, Don Klinkenberg, Marc Meurs, Erik Fleur, Susan JM Hahné, Jacco Wallinga, Albert Jan van Hoek
Journal: PLoS Medicine (2024)

Background Measles outbreaks are still routine, even in countries where vaccination coverage exceeds the guideline of 95%. Therefore, achieving ambitions for measles eradication will require understanding of how unvaccinated children interact with others who are unvaccinated. It is well established that schools and homes are key settings for both clustering of unvaccinated children and for transmission of infection. In this study, we evaluate the potential for contacts between unvaccinated children in these contexts to facilitate measles outbreaks with a focus on the Netherlands, where large outbreaks have been observed periodically since the introduction of mumps, measles and rubella (MMR). Methods and findings We created a network of all primary and secondary schools in the Netherlands based on the total number of household pairs between each school. A household pair are siblings from the same household who attend a different school. We parameterised the network with individual level administrative school and household data provided by the Dutch Ministry for Education and estimates of school level uptake of the MMR vaccine. We analysed the network to establish the relative strength of contact between schools and found that schools associated with low vaccine uptake are highly connected, aided by a differentiated school system in the Netherlands (Coleman homophily index (CHI) = 0.63). We simulated measles outbreaks on the network and evaluated the model against empirical measles data per postcode area from a large outbreak in 2013 (2,766 cases). We found that the network-based model could reproduce the observed size and spatial distribution of the historic outbreak much more clearly than the alternative models, with a case weighted receiver operating characteristic (ROC) sensitivity of 0.94, compared to 0.17 and 0.26 for models that do not account for specific network structure or school-level vaccine uptake, respectively. The key limitation of our framework is that it neglects transmission routes outside of school and household contexts. Conclusions Our framework indicates that clustering of unvaccinated children in primary schools connected by unvaccinated children in related secondary schools lead to large, connected clusters of unvaccinated children. Using our approach, we could explain historical outbreaks on a spatial level. Our framework could be further developed to aid future outbreak response.
VIR-2218 (elebsiran) plus pegylated interferon-alfa-2a in participants with chronic hepatitis B virus infection: a phase 2 study
Authors: Man-Fung Yuen, Young-Suk Lim, Ki Tae Yoon, Tien-Huey Lim, Jeong Heo, Pisit Tangkijvanich, Won Young Tak, Vaidehi Thanawala, Daniel Cloutier, Shenghua Mao, Andre Arizpe, Andrea L Cathcart, Sneha V Gupta, Carey Hwang, Edward Gane
Journal: The Lancet. Gastroenterology & hepatology (2024)
Development of CARRA/PReS-endorsed consensus Core and Expanded Datasets in childhood-onset systemic lupus erythematosus for international registry-based research
Authors: Rebecca E Sadun, Jennifer C Cooper, Alexandre Belot, Tadej Avcin, Amita Aggarwal, Jenny Ainsworth, Alisha Akinsete, Stacy P Ardoin, Michael W Beresford, Lynette Bortey, Hermine I Brunner, Joyce C Chang, Coziana Ciurtin, Ashley Daftary, Barbara Eberhard, Candace H Feldman, Christian M Hedrich, Aimee O Hersh, Linda T Hiraki, David A Isenberg, Sylvia Kamphuis, Andrea M Knight, Lou Lambert, Deborah M Levy, Stephen D Marks, Naomi Maxwell, Angela Migowa, Katharine Moore, Seza Ozen, Rosalind Ramsey-Goldman, Angelo Ravelli, Bryce B Reeve, Tamar B Rubinstein, Claudia Saad-Magalhaes, Sujata Sawhney, Laura E Schanberg, Emily von Scheven, Christiaan Scott, Mary Beth Son, Gladys Tony, Elissa R Weitzman, Scott E Wenderfer, Alisha Woodside, Laura B Lewandowski, Eve Md Smith
Journal: Annals of the Rheumatic Diseases (2024)

Childhood-onset systemic lupus erythematosus (cSLE), representing 15%-20% of individuals with SLE, has been difficult to study globally due to differences between registries. This initiative, supported by Childhood Arthritis Rheumatology Research Alliance (CARRA) and Paediatric Rheumatology European Society (PReS), aims to create Core and Expanded cSLE Datasets to standardise and enhance research worldwide. 21 international cSLE experts and 4 patients participated in a Delphi process (questionnaires, 2 topic-specific focus groups and 3 virtual consensus meetings) to create 2 standardised cSLE datasets. The Core cSLE Dataset was designed to include data essential to meaningful clinical research across many settings. The Expanded cSLE Dataset was designed for centres able to consistently collect data to address broader research questions. Final data items for the Core and Expanded datasets were determined by consensus defined as >80% agreement) using an adapted nominal group technique and voting. The resulting Core cSLE Dataset contains 46 items, including demographics, clinical features, laboratory results, medications and significant adverse events. The Expanded cSLE Dataset adds 26 additional items and includes patient-reported outcomes. Consensus was also achieved regarding the frequency and time points for data collection: baseline, quarterly follow-up visits, annually and flare visits. Standardised Core and Expanded cSLE Datasets for registry-based international cSLE research were defined through the consensus of global experts and patient/caregiver representatives, endorsed by CARRA and PReS. These datasets incorporate disease-specific and patient-specific features, optimised for diverse settings to facilitate international collaborative research for children and adolescents with SLE worldwide.
Highly Pathogenic Avian Influenza A(H5N1) Virus infection in dairy cattle:threat of bird flu has expanded to open-air farmed livestock
Authors: Yitao Li, Zhihua Sun, Xuefeng Liu, Shuo Wei, Yan Zhang, Yining Fuxiang, Jun Qiao, Hui Zhang, Chencheng Xiao
Journal: Journal of Infection (2024)

Highlights•This is the first known case from dairy cattle infection with HPAI H5N1 viruses.•The bovine-origin HPAI H5N1 clade 2.3.4.4 b,B3.13 virus frequently spill out to other mammals and even humans.•Many of China 's dairy farms or pastoral areas are located along several global migratory bird lines,the threat of bird flu has expanded to open-air farmed livestock
Effects of Adopting Preventive Drug Lists on Medication Costs and Disparities by Income Over 2 Years: A Natural Experiment for Translation in Diabetes (NEXT-D) Study
Authors: Christine Y. Lu, Stephanie Argetsinger, Matthew Lakoma, Fang Zhang, J. Frank Wharam, Dennis Ross-Degnan
Journal: Diabetes Care (2024)

To examine the association between preventive drug lists (PDLs) and changes in medication costs among patients with diabetes insured in commercial health plans over 2 follow-up years. We conducted a quasiexperimental study using the Optum deidentified Clinformatics Data Mart Database (January 2003 to December 2017). The intervention group included 5,582 patients with diabetes age 12-64 years switched by employers to PDL coverage; the control group included 5,582 matched patients whose employers offered no PDL. Outcomes included out-of-pocket costs, standardized costs, and 30-day fills for all medications because PDL-associated savings could be used to pay for medicines in other classes and for five therapeutic classes covered by the PDLs (oral diabetes medications, insulins, test strips, antihypertensive drugs, and lipid-lowering drugs). Pre- to post-out-of-pocket spending for all medications declined by 29.7% in follow-up year 2 (95% CI -36.0, -23.4%) among PDL members relative to control individuals. Higher-income and lower-income PDL members experienced significant reductions in out-of-pocket spending for all medications in year 2 (30%) and for key therapeutic classes (range -23 to -67%). We found significant increases in use of key therapeutic classes in the overall population (range 8-15%) and in higher-income and lower-income PDL members (range 9-50%). PDLs offer an effective strategy for employers and insurers to lower member cost sharing and encourage increased use of important medications to prevent or manage chronic illnesses. For patients with diabetes, especially those with lower incomes, PDL coverage resulted in substantial and persistent reductions in out-of-pocket medication costs, medication use increases, and some increased use of more expensive products.
Association of Energy Intake and Dietary Glycemic Load in Different Time Periods With Cardiovascular Disease Mortality Among U.S. Adults With Type 2 Diabetes
Authors: Jin Dai, Roch Nianogo, Tannaz Moin, Nathan D. Wong, Qibin Qi, Daniela Sotres-Alvarez, Liwei Chen
Journal: Diabetes Care (2024)

To examine the associations of energy intake and glycemic load (GL) in different time periods during the day with cardiovascular disease (CVD) mortality risk in adults with type 2 diabetes.
Enhancing Variant Calling in Whole-Exome Sequencing Data Using Population-Matched Reference Genomes
Authors: Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu
Journal: Genomics Proteomics & Bioinformatics (2024)

Abstract Whole-exome sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), based on high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly published telomere-to-telomere (T2T) genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. Here we report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to ∼ 1% target regions in T2T-YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, T2T-YAO still outperforms GRCh38 genomes by obtaining 7.41% more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, T2T-YAO reduces half of variant calls of clinical significance which are mostly benign, while maintaining sensitivity in identifying pathogenic variants. T2T-YAO also outperforms T2T-CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic backgrounds of each ethnic group.
Gut microbiome therapy: fecal microbiota transplantation vs live biotherapeutic products
Authors: Do-Yeon Kim, So-Yeon Lee, Jae-Yun Lee, Tae Woong Whon, June-Young Lee, Che Ok Jeon, Jin-Woo Bae
Journal: Gut Microbes (2024)

The human intestine hosts a complex ecosystem of various microorganisms, collectively known as the gut microbiome, which significantly impacts human health. Disruptions in the gut microbiome are linked to various disorders, including gastrointestinal diseases, such as
Omalizumab is effective and safe in chronic inducible urticaria (CIndU): Real‐world data from a large multi‐national UCARE study
Authors: R. Soegiharto, M. Alizadeh Aghdam, J. A. Sørensen, E. van Lindonk, F. Bulut Demir, N. Mohammad Porras, Y. Matsuo, L. Kiefer, A. C. Knulst, M. Maurer, C. Ritchie, M. Rudenko, E. Kocatürk, R. F. J. Criado, S. Gregoriou, T. Bobylev, A. Kleinheinz, S. Takahagi, M. Hide, A. M. Giménez‐Arnau, A. Salman, R. Oztas Kara, B. S. Dikicier, M. B. A. van Doorn, S. F. Thomsen, J. M. P. A. van den Reek, H. Röckmann
Journal: Allergy (2024)

Abstract Background Long‐term data on the effectiveness and safety of omalizumab for chronic inducible urticaria (CIndU) in large populations are lacking. Objective To evaluate the effectiveness, safety, estimated omalizumab treatment duration and its predictors, as well as differences between CIndU subtypes, in a large long‐term CIndU cohort. Methods A multinational multicenter study was conducted at 14 specialized urticaria centres (UCAREs), including all CIndU patients ever treated with omalizumab from 2009 until July 2022. Kaplan–Meier survival and regression analyses were performed. Results Across 234 CIndU patients (55% female; mean age 37 years), 76% ( n = 178) had standalone CIndU and 24% ( n = 56) had predominant CIndU plus minor CSU, with an observation period up to 13 years. Most CIndU patients (73%, n = 145/200 with available data on response) had complete/good response to omalizumab treatment, without significant differences between CIndU subtypes. Sixty‐two (26%) patients discontinued omalizumab; due to well‐controlled disease (47%, n = 29), ineffectiveness (34%, n = 21), side effects (3%, n = 2), combination of ineffectiveness and side effects (3%, n = 2) and other reasons (13%, n = 8). The median estimated omalizumab treatment duration exceeded 5 years (54% drug survival at 5 years) and was mostly determined by well‐controlled disease. Higher age predicted a lower chance to discontinue omalizumab due to well‐controlled disease (HR 0.969, 95%CI 0.945–0.995). CIndU subtype and presence of minor CSU were not related to response and time until omalizumab discontinuation for any reason. Conclusion Omalizumab is highly effective and safe in CIndU patients, with long estimated treatment duration mainly reflecting long disease duration. Our data show omalizumab's high potential as treatment in any subtype of CIndU and support its clinical use for these patients.
Aerobic Physical Activity and Depression Among Patients With Cancer
Authors: Matthew Kulchycki, Henry Ratul Halder, Nicole Askin, Rasheda Rabbani, Fiona Schulte, Maya M. Jeyaraman, Lillian Sung, Deepak Louis, Lisa Lix, Allan Garland, Alyson L. Mahar, Ahmed Abou-Setta, Sapna Oberoi
Journal: JAMA Network Open (2024)

Importance Depression is prevalent among patients with cancer, affecting their quality of life and survival. Aerobic physical activity (APA) is an effective strategy for managing depression in the general population, but its effectiveness for reducing depressive symptoms among patients with cancer requires further study. Objective To evaluate whether APA decreases depression severity in patients with cancer by synthesizing data from published randomized clinical trials (RCTs). Data Sources Six databases (MEDLINE, Embase, Cochrane Central Register of Controlled Trials, CINAHL, PsycINFO, and Scopus) were systematically searched for relevant citations published between January 1, 1980, and July 5, 2023. Study Selection This systematic review and meta-analysis included RCTs comparing APA interventions with usual care, waitlist control, or attention control for managing depression in patients with cancer, irrespective of age and cancer type. Data Extraction and Synthesis Two reviewers independently conducted screening and data extraction. Risk of bias was evaluated using the Cochrane Risk of Bias Tool, version 2. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guideline was followed. Standardized mean differences (SMDs) were calculated using a random-effects model. Data collection and analyses were performed between June 2022 and March 2024. Main Outcomes and Measures The primary outcome was severity of self-reported depression reported within 1 month of the end of intervention (short term). Secondary outcomes were severity of self-reported depression between 1 and 6 months post intervention (medium term) and between 6 and 12 months post intervention (long term). Results This meta-analysis included 25 RCTs with a total of 1931 adults with cancer (age range, 18-80 years). Ten RCTs (40%) had low risk of bias. Aerobic physical activity was associated with decreased self-reported depression among adults with cancer across the 25 included trials (n = 1931 participants; SMD, −0.38 [95% CI, −0.59 to −0.18]; P &amp;amp;lt; .001; I 2 = 76%). This decrease in depression scores was also significant for the secondary outcomes of long-term depression across 3 trials (n = 299 participants; SMD, −0.32 [95% CI, −0.60 to −0.04]; P = .03; I 2 = 31%) but not for medium-term depression across 2 trials (n = 143 participants; SMD, −0.27 [95% CI, −0.60 to 0.06]; P = .10; I 2 = 0%). Conclusions and Relevance In this systematic review and meta-analysis, APA was associated with modest short-term and long-term reductions of depression among adults with cancer. Future studies should discern the effectiveness of APA in combination with other strategies for managing depression across various populations of patients with cancer.
Acetazolamide Therapy and Kidney Function in Persons with Non-albuminuric Diabetes Mellitus Type 1
Authors: Charles Ginsberg, Jesse C. Seegmiller, Volker Vallon, Sami SeungMi Jin, Robert L. Thomas, Schafer C. Boeder, Jeremy Pettus, Joachim H. Ix
Journal: Journal of the American Society of Nephrology (2024)

Key Points Low-dose acetazolamide reversibly lowered GFR in persons with type 1 diabetes mellitus, suggesting a possible role in relieving glomerular hyperfiltration. Low doses of acetazolamide were well tolerated in persons with type 1 diabetes. Background Sodium-glucose cotransporter-2 inhibitors (SGLT2is) lower the risk of kidney failure in persons with type 2 diabetes. The presumed mechanism of action is through greater delivery of sodium to the distal tubule and activation of tubuloglomerular feedback, which lowers GFR and intraglomerular pressure. SGLT2is are not approved for use in persons with type 1 diabetes because of the risk of diabetic ketoacidosis. Acetazolamide, a proximal tubule diuretic, delivers more sodium to the distal nephron and may activate tubuloglomerular feedback in a similar way to SGLT2is without a higher risk of diabetic ketoacidosis. The kidney effects and safety of acetazolamide in persons with type 1 diabetes have not been well studied. Methods We conducted a dose-escalation trial to determine the effects of three dosages of oral acetazolamide (62.5, 125, and 250 mg, all twice daily) in 12 persons with type 1 diabetes. Participants were treated for 2 weeks, followed by a 2-week washout period before exposure to the next dosage level. Blood and urine chemistries, as well as iohexol-measured GFR, were assessed before and after each treatment interval. We aimed to identify a dose that maximized measured GFR reductions while minimizing adverse effects. Results The mean age was 46±17 years, 100% were White, and 75% were female. The mean measured GFR was 89±18 ml/min per 1.73 m 2 at baseline. Acetazolamide reduced measured GFR by 15% (95% confidence interval [CI], 9 to 21), 14% (95% CI, 7 to 21), and 15% (95% CI, 10 to 21) after 2 weeks at the 62.5, 125, and 250 mg twice-daily dosage levels, respectively. The measured GFR reduction was fully reversed after each 2-week washout. Serum bicarbonate was reduced by 2.3, 4.2, and 4.4 mEq/L with escalating doses, and no episodes of hypokalemia (&lt;3.5 mEq/L) were observed. Conclusions Among persons with type 1 diabetes and preserved kidney function, acetazolamide caused an acute, reversible reduction in measured GFR without effects on glucose metabolism. Clinical Trial registry name and registration number: Acetazolamide in Persons with Type 1 Diabetes, NCT05473364.
GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis
Authors: Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye
Journal: Genomics Proteomics & Bioinformatics (2024)

Abstract Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.