tbuckley/cabot-search huggingface dataset:
LuLIPLEX: A Fast, Highly Sensitive, and Multiplexed Method for the Detection of IgE Against Major Allergens
Authors: Edouard Leveque, Cyprien Pecalvel, Natacha Casanovas, Sophie Goyard, Yves L. Janin, Thierry Rose, Benjamin Trouche‐Estival, Pol André Apoil, Marine Michelet, Laurent Guilleminault, Laurent L. Reber
Journal: Allergy (2024)

ABSTRACT Background Diagnosis of allergies is mostly based on the patient's clinical history and allergen provocation tests. Determination of specific IgE (sIgE) profiles can be performed to support allergy diagnosis. This is commonly done in vivo by the skin prick test or in vitro with automated systems. Several platforms exist to quantify sIgE levels, but all these methods require access to specific instruments, often delaying the test's results. The IgE luciferase‐linked immunosorbent assay (LuLISA) allows bioluminescent quantification of IgE against peanut in microliter samples, but this method awaits extension to other allergens. This study aimed to validate a new method, named LuLIPLEX, for multiplexed bioluminescent detection of sIgE against 20 major molecular allergens. Methods Quantification of sIgE against 12 recombinant or purified food allergens and eight aeroallergens was performed by LuLIPLEX versus standard IgE detection methods (ImmunoCAP, ISAC, ALEX, or NOVEOS). Multiplexed detection of IgE against these 20 allergens was performed within 45 min using 50 μL of serum, plasma, or whole blood samples. Results A head‐to‐head comparison between LuLIPLEX and standard IgE detection methods showed a high correlation among all allergens tested. sIgE profiles in polysensitized subjects could be determined within 45 min in serum and plasma samples, as well as using a single drop of capillary blood. Conclusions LuLIPLEX is a rapid and sensitive method to quantify sIgE levels against multiple allergens. Given that the test is very fast and can be performed on small and inexpensive luminometers, the IgE LuLIPLEX could allow point‐of‐care testing of sIgE profiles in allergic subjects.
Basophil Activation Test Positivity Decreases With Time in Immediate Allergic Reactions to Proton Pump Inhibitors
Authors: Rubén Fernandez‐Santamaria, Maria Salas, Adriana Ariza, Maria A. Jiménez, María R. González‐Mendiola, Maria L. Sanchez, Cosmin Boteanu, Cristobalina Mayorga, Tahia D. Fernandez, Maria J. Torres, Jose J. Laguna
Journal: Allergy (2024)
Human T cells engineered with an HLA-A2-restricted murine T-cell receptor targeting Glypican 3 effectively control human hepatocellular carcinoma in mice
Authors: Enric Vercher, Ángela Covo-Vergara, Enrique Conde, Mercedes Hernández-Rueda, Edurne Elizalde, Uxua Mancheño, Javier Glez-Vaz, Ibon Tamayo-Uria, Maritza R. García-García, Marta Ferrer-Roig, Javier Marañón-Lopez, David Repáraz, Marta Ruiz, Ascensión López-Díaz de Cerio, Susana Inogés, Mercedes Iñarrairaegui, Juan J. Lasarte, Bruno Sangro, Pablo Sarobe, Sandra Hervas-Stubbs
Journal: Hepatology (2024)

Glypican-3 (GPC3) is a promising target for T-cell therapy in hepatocellular carcinoma (HCC). While chimeric antigen receptor (CAR) T cells targeting GPC3 have demonstrated therapeutic efficacy, their effectiveness is limited by challenges such as low persistence and shedding of surface GPC3. Natural T-cell receptors (TCRs) may serve as an alternative, though identifying GPC3-specific TCRs within the endogenous repertoire is difficult.
Association of Postpartum Temperature Exposure with Postpartum Depression: A Retrospective Cohort Study in Southern California
Authors: Yi Sun, Kathryne S. Headon, Wajeeha Umer, Anqi Jiao, Jeff M. Slezak, Chantal C. Avila, Vicki Y. Chiu, David A. Sacks, Kelly T. Sanders, John Molitor, Tarik Benmarhnia, Jiu-Chiuan Chen, Darios Getahun, Jun Wu
Journal: Environmental Health Perspectives (2024)

Postpartum depression (PPD) has been associated with biological, emotional, social, and environmental factors. However, evidence regarding the effect of temperature on PPD is extremely limited.
<i>Notes from the Field:</i> Human Parvovirus B19 Infections Among Pregnant Persons — Minnesota, January–September 2024
Authors: Stephen Contag, Elizabeth M. Dufort, Sarah Lim, Tyler Winkelman, Jennifer Zipprich, Lindsey Erickson, Mel Anacker, Nayanjot Kaur Rai, Kristen Ojo, Danielle Kvasager, Henry D. Kunerth, R. Adams Dudley, Pamala Gahr, Kelly R. Bergmann, Alanna M. Chamberlain, Summer Martins, Stephen Waring, Bjorn Westgard, Kristin Sweet, Paul Drawz, Ruth Lynfield
Journal: MMWR Morbidity and Mortality Weekly Report (2024)
Environmental Exposures and Long COVID in a Prospective Population-Based Study in Catalonia (COVICAT Study)
Authors: Apolline Saucy, Ana Espinosa, Susana Iraola-Guzmán, Gemma Castaño-Vinyals, Barbara N. Harding, Marianna Karachaliou, Otavio Ranzani, Rafael De Cid, Judith Garcia-Aymerich, Manolis Kogevinas
Journal: Environmental Health Perspectives (2024)
Empowering Care Teams: Redefining Message Management to Enhance Care Delivery and Alleviate Oncologist Burnout
Authors: Brandon Anderson, Liisa Lyon, Michael Lee, Deepika Kumar, Elad Neeman, Ali Duffens, Dinesh Kotak, Hongxin Sun, Mary Reed, Raymond Liu
Journal: Journal of the National Comprehensive Cancer Network (2024)

Background: Widespread adoption of secure messaging (SM) provides patients with cancer with unprecedented access to medical providers at the expense of increased workload for oncologists. Herein, we analyze oncology SM clinical content and acuity and translate these to estimated cost savings from reduced appointments. Methods: This population-based retrospective cohort study examined the content of patient-initiated SM threads exchanged through the patient portal website or app over 1 year (June 1, 2021–May 31, 2022) at 21 Kaiser Permanente Northern California oncology practices, which typically do not have patient copayments associated with SM. A random sample of 500 SM threads were reviewed and categorized by message content, acuity, and appropriate level of service. Cost and time estimates were used to compare the cost of SM management by oncologists alone versus assisted by medical assistants and nurses. Results: During the study, 41,272 patients initiated 334,053 unique SM threads to 132 oncologists. Of the SM threads reviewed, only 26.8% required oncologist expertise. Based on thread content, the remaining 73.2% may have been better managed by a nurse (38.2%), medical assistant (28.4%), primary care physician (5.4%), or another subspecialty provider (1.2%). Emergency care was recommended in 2.4% of the threads reviewed. Significant medical care was provided to patients in 24.4% of the reviewed threads that would typically require an appointment. We estimate that the SM exchanges provided $11.2 million in care, including $3.6 million in avoided out-of-pocket copayment costs to patients and $7.6 million in missed billing codes. Conclusions: High utilization of SM generates additional workload for oncologists that could mostly be appropriately managed by alternate providers. The magnitude of unreimbursed medical care provided via SM and the use of SM for emergent medical situations creates an urgent need for new practice models. An alternative architecture for triaging, managing, and billing SM could reduce costs and oncologist burnout.
Progress Toward UNAIDS Global HIV Pre-Exposure Prophylaxis Targets: CDC-Supported Oral Pre-Exposure Prophylaxis — 37 Countries, 2017─2023
Authors: Megan E. Peck, Stephanie Davis, Elijah Odoyo-June, Jonathan Mwangi, Elvis Oyugi, Thai Hoang, Marcos Canda, Jessica Seleme, Maria Bock, Lylie Ndeikemona, Sibongile Dladla, Richard Machava, Nyagonde Nyagonde, Abdul Mashauri, Anna Colletar Awor, Stella Alamo, Omega Chituwo, Tina Chisenga, Rickie Malaba, Miriam Mutseta, Carrine Angumua, Kingsly Tse Nkwoh, Janique Ricketts, Kelly-Ann Gordon-Johnson, Victor Adamu, Scott Adamu-Oyegun, John Mondi Benson, Sudhir Bunga, Nasim Farach, Carlos Castaneda, Luis Bonilla, Sharmeen Premjee, Hanna B. Demeke, Gaston Djomand, Carlos Toledo, Ramona Bhatia
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Oral pre-exposure prophylaxis (PrEP) reduces HIV acquisition risk from sex by 99% and from injection drug use by ≥74% when used as recommended. The Joint United Nations Programme on HIV/AIDS (UNAIDS) has set a goal of 21.2 million persons using (initiating or continuing) PrEP globally in 2025. In 2016, CDC, with the U.S. President's Emergency Plan for AIDS Relief, joined ministries of health to implement PrEP globally. PrEP is beneficial for persons at substantial risk for acquiring HIV, including but not limited to key populations, which include female sex workers, men who have sex with men, persons in prisons and other enclosed settings, persons who inject drugs, and transgender persons. Annual country targets were used to guide scale-up. In 2023, CDC supported 856,816 PrEP initiations, which represents nearly one quarter of the 3.5 million persons globally who either initiated or continued PrEP that year. During 2017-2023, CDC supported PrEP initiations for 2,278,743 persons, 96.0% of whom were in sub-Saharan Africa. More than one half (64.0%) were female and 44.9% were aged 15-24 years. Overall, CDC achieved 118.7% of its PrEP initiation targets for the 7-year period. Among PrEP initiations for key populations, the majority in sub-Saharan Africa were female sex workers, whereas in Southeast Asia, Eurasia, and the Americas, the majority were men who have sex with men. Continued rapid scale-up is needed to meet the UNAIDS goal to end HIV as a public health threat.
Comparative Safety and Effectiveness of Bevacizumab Biosimilars to Originator for the Treatment of Metastatic Colorectal Cancer
Authors: Caroline Muñoz, Jaclyn M. Beca, Erind Dvorani, Rebecca E. Mercer, Jessica Arias, Andrea Adamic, Scott Gavura, Kelvin K.W. Chan
Journal: Journal of the National Comprehensive Cancer Network (2024)

Background: Ontario has publicly funded biosimilar bevacizumab for first-line metastatic colorectal cancer (mCRC) since 2019. Clinical trials demonstrate comparable efficacy and safety of bevacizumab biosimilars to originator bevacizumab. The objective of this study was to assess real-world safety and effectiveness of the implementation of bevacizumab biosimilars compared with originator bevacizumab in patients with mCRC. Methods: This was a population-based, retrospective study comparing Ontario patients starting treatment with bevacizumab biosimilars between August 12, 2019, and March 31, 2021, and starting treatment with originator bevacizumab between July 2, 2008, and August 11, 2019. Safety outcomes included death within 30 days of the last dose received, any hospitalization, direct hospitalization, and hospitalization resulting from bevacizumab-related toxicity, chemotherapy-related toxicity, and febrile neutropenia. Event rates were assessed using negative binomial and logistic regression. The effectiveness outcome was overall survival, calculated using Kaplan-Meier and Cox proportional hazards regression. A subgroup analysis compared safety and effectiveness outcomes between patients on bevacizumab biosimilar products and matched comparators. Results: We identified 8,996 patients who initiated first-line treatment of bevacizumab for mCRC. Accounting for duration of follow-up, no significant differences were observed in the rate of hospitalization between treatment groups. No differences in overall survival (log-rank P&gt;.05) or hazard ratios (propensity score–matched hazard ratio, 1.03; 95% CI, 0.92–1.16) were observed in the crude and propensity score–matched cohorts. Subgroup analysis demonstrated similar safety and effectiveness patterns. Conclusions: The demonstrated similarity in safety and effectiveness between bevacizumab biosimilars and originator bevacizumab provides further support for the use of and confidence in biosimilar products.
Detection of Increased Activity of Human Parvovirus B19 Using Commercial Laboratory Testing of Clinical Samples and Source Plasma Donor Pools — United States, 2024
Authors: David Alfego, Alfonso C. Hernandez-Romieu, Melissa Briggs-Hagen, Stephanie Dietz, Laura Gillim, Suzanne E. Dale, Ajay Grover, Jeffrey Albrecht, Deborah Sesok-Pizzini, Marcia Eisenberg, Cria O. Gregory, Brian Poirier
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

In most persons, human parvovirus B19 (B19) causes a mild respiratory illness, but infection can result in adverse health outcomes in persons who are pregnant, immunocompromised, or who have chronic hemolytic blood disorders. During the first quarter of 2024, several European countries reported increases in B19 activity. In the United States, there is no routine surveillance for B19. To assess increases in B19 activity in the United States, trends in testing and results from two independent populations were examined: 1) the presence of immunoglobulin (Ig) M antibodies, a marker of recent infection, in clinical specimens ordered by physicians and 2) B19 nucleic acid amplification testing (NAAT) in pooled donor source plasma from a large commercial laboratory during 2018-2024. The proportion of IgM-positive clinical specimens reached 9.9% in the second quarter (Q2) of 2024 after remaining <1.5% during 2020-2023 and was higher than Q2 peaks in 2018 (3.8%, p<0.001) and 2019 (5.1%, p<0.001). The prevalence of B19-NAAT-positive donor pools (512 donations per pool) reached 20% in June 2024 after remaining <2% during 2020-2023 and was higher than peaks in 2018 (6.7%, p<0.001) and 2019 (7.3%, p<0.001). Considering the B19 activity increase in the United States in 2024, promotion of measures to prevent respiratory viruses and monitor for adverse B19-related outcomes by health care providers and public health authorities might reduce adverse health outcomes in pregnant persons and others at increased risk.
Severe and Fatal Rocky Mountain Spotted Fever After Exposure in Tecate, Mexico — California, July 2023–January 2024
Authors: Anne M. Kjemtrup, Jill K. Hacker, Madeleine Monroe, Vicki Williams, Charles Lines, Karla Lopez, Christopher D. Paddock, Ann Carpenter, Johanna S. Salzer, Julian A. Villalba, Julu Bhatnagar, Seema Shah, Esmeralda Iniguez-Stevens, Theodore C. Efthemeou, Vannia Hernandez, Duc J. Vugia, Vicki L. Kramer
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Rocky Mountain spotted fever (RMSF) is a tickborne disease endemic in areas of the Americas. Persistent high incidence of the disease exists in northern Mexico, perpetuated by local populations of brown dog ticks (Rhipicephalus sanguineus sensu lato) and free-roaming dogs. Six cases of RMSF caused by Rickettsia rickettsii, including three deaths, were reported to the California Department of Public Health during July 2023-January 2024. All six patients were eventually determined to have had exposure to R. rickettsii in Tecate, Mexico, a municipality on the U.S. border that had not been previously described as a high-risk RMSF area. Identification and reporting of the cases were complicated by challenges in diagnosis. The serious nature of the disease and delays in initiating appropriate treatment can result in life-threatening consequences. Epidemiologic collaborations among local, state, federal, and international public health agencies were essential to identifying Tecate as the location of exposure. Further collaborations will be important for directing future prevention measures. Increased health care provider awareness of RMSF is critical on both sides of the border to facilitate earlier diagnosis and initiation of appropriate treatment.
Efficient and safe in vivo treatment of primary hyperoxaluria type 1 via LNP-CRISPR-Cas9-mediated glycolate oxidase disruption
Authors: Yanhong Jiang, Shuanghong Chen, Shenlin Hsiao, Haokun Zhang, Da Xie, Zi Jun Wang, Wendan Ren, Mingyao Liu, Jiaoyang Liao, Yuxuan Wu
Journal: Molecular Therapy (2024)
miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research
Authors: Lei Liu, Suqi Cao, Weili Lin, Zhigang Gao, Liu Yang, Lixin Zhu, Bin Yang, Guoqing Zhang, Ruixin Zhu, Dingfeng Wu
Journal: Gut Microbes (2024)

Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.
Unraveling the gut-skin axis in atopic dermatitis: exploiting insights for therapeutic strategies
Authors: Marcela Rios-Carlos, Daniel Cervantes-García, Laura E. Córdova-Dávalos, Luis G. Bermúdez-Humarán, Eva Salinas
Journal: Gut Microbes (2024)

Gut microbiota exert functions of high importance in the intestine. Furthermore, there is increasing evidence for its role in immune regulation and maintenance of homeostasis in many physiological processes taking place in distant tissues. In particular, in this review, we explore the impact of metabolites produced by the gut microbiota on the development of atopic dermatitis (AD). Probiotics and prebiotics balance the microbiota and promote the generation of bacterial metabolites, such as short-chain fatty acids and tryptophan derivates, which promote the regulation of the exacerbated AD immune response through regulatory T cells and IL-10 and TGF-β cytokines. Metabolites also have a direct action on keratinocytes once they reach the bloodstream. Besides, probiotics decrease the levels of metabolites associated with AD onset, such as phenols. Understanding all these crosstalk processes between the gut and the skin reveals a number of possibilities, mainly through the manipulation of the gut microbiome, which may represent therapeutic strategies that can contribute to the standard treatments of AD patients to improve their quality of life.
Transposable element 5mC methylation state of blood cells predicts age and disease
Authors: Francesco Morandini, Jinlong Y. Lu, Cheyenne Rechsteiner, Aladdin H. Shadyab, Ramon Casanova, Beverly M. Snively, Andrei Seluanov, Vera Gorbunova
Journal: Nature Aging (2024)

Transposable elements (TEs) are DNA sequences that expand selfishly in the genome, possibly causing severe cellular damage. While normally silenced, TEs have been shown to activate during aging. DNA 5-methylcytosine (5mC) is one of the main epigenetic modifications by which TEs are silenced and has been used to train highly accurate age predictors. Yet, one common criticism of such predictors is that they lack interpretability. In this study, we investigate the changes in TE 5mC methylation that occur during aging in human blood using published methylation array data. We find that evolutionarily young long interspersed nuclear elements 1 (L1s), the only known TEs capable of autonomous transposition in humans, undergo the fastest loss of 5mC methylation, suggesting an active mechanism of de-repression. The same young L1s also showed preferential gain in chromatin accessibility but not expression. The long terminal repeat retrotransposons THE1A and THE1C also showed very rapid 5mC loss. We then show that accurate age predictors can be trained on both 5mC methylation of individual TE copies and average methylation of TE families genome wide. Lastly, we show that while old L1s gradually lose 5mC during the entire lifespan, demethylation of young L1s only happens late in life and is associated with cancer. Transposable elements activate during aging with negative consequences. Morandini et al. show that transposons show rapid loss of methylation in peripheral blood mononuclear cells during aging and that models trained on transposon methylation accurately predict age.
Late-life protein or isoleucine restriction impacts physiological and molecular signatures of aging
Authors: Chung-Yang Yeh, Lucas C. S. Chini, Jessica W. Davidson, Gonzalo G. Garcia, Meredith S. Gallagher, Isaac T. Freichels, Mariah F. Calubag, Allison C. Rodgers, Cara L. Green, Reji Babygirija, Michelle M. Sonsalla, Heidi H. Pak, Michaela E. Trautman, Timothy A. Hacker, Richard A. Miller, Judith A. Simcox, Dudley W. Lamming
Journal: Nature Aging (2024)
Large language models surpass human experts in predicting neuroscience results
Authors: Xiaoliang Luo, Akilles Rechardt, Guangzhi Sun, Kevin K. Nejad, Felipe Yáñez, Bati Yilmaz, Kangjoo Lee, Alexandra O. Cohen, Valentina Borghesani, Anton Pashkov, Daniele Marinazzo, Jonathan Nicholas, Alessandro Salatiello, Ilia Sucholutsky, Pasquale Minervini, Sepehr Razavi, Roberta Rocca, Elkhan Yusifov, Tereza Okalova, Nianlong Gu, Martin Ferianc, Mikail Khona, Kaustubh R. Patil, Pui-Shee Lee, Rui Mata, Nicholas E. Myers, Jennifer K. Bizley, Sebastian Musslick, Isil Poyraz Bilgin, Guiomar Niso, Justin M. Ales, Michael Gaebler, N. Apurva Ratan Murty, Leyla Loued-Khenissi, Anna Behler, Chloe M. Hall, Jessica Dafflon, Sherry Dongqi Bao, Bradley C. Love
Journal: Nature Human Behaviour (2024)

Abstract Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. Here, to evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs indicated high confidence in their predictions, their responses were more likely to be correct, which presages a future where LLMs assist humans in making discoveries. Our approach is not neuroscience specific and is transferable to other knowledge-intensive endeavours.