tbuckley/cabot-search huggingface dataset:
Estrogens and breast cancer
Authors: J. Kim, P.N. Munster
Journal: Annals of Oncology (2024)

Estrogens have been associated with an increase in breast cancer risk. Yet emerging clinical and experimental evidence points to progestogens [endogenous progesterone or synthetic progesterone (progestin)] as the primary hormonal driver underlying seemingly estrogen-associated breast cancer risk. Estrogens may contribute to breast cancer risk indirectly by induction of the progesterone receptor and thus amplifying progesterone signaling. Large studies of hormonal contraceptives suggest that the small increase in breast cancer risk from hormonal contraceptives is mainly attributable to progestins, not estrogens. Estrogen-plus-progestin hormone replacement therapy (HRT) has consistently shown an increase in breast cancer risk among postmenopausal women, whereas estrogen-alone HRT has little impact on breast cancer risk in naturally or surgically menopausal women. In particular, the long-term follow-up of the Women's Health Initiative (WHI) randomized trials suggests a benefit of estrogen alone. Recent data further indicate that endogenously elevated estrogen during assisted reproductive technology (ART) exhibits little adverse effect on or potentially a reduction in breast cancer risk and recurrence. Also, accumulating evidence suggests that inhibition of progesterone signaling is a critical mechanism underlying the risk-reducing and therapeutic effects of antiestrogens. Estrogen HRT has shown an array of proven benefits, including ameliorating menopausal symptoms and improving bone health. Collective evidence thus suggests that estrogen HRT is likely to offer health benefits to perimenopausal or postmenopausal women, including breast cancer survivors, as well as young BRCA1/2 carriers with prophylactic oophorectomy for ovarian cancer prevention.
Targeting of TAMs: can we be more clever than cancer cells?
Authors: Julia Kzhyshkowska, Jiaxin Shen, Irina Larionova
Journal: Cellular and Molecular Immunology (2024)

АBSTRACT: With increasing incidence and geography, cancer is one of the leading causes of death, reduced quality of life and disability worldwide. Principal progress in the development of new anticancer therapies, in improving the efficiency of immunotherapeutic tools, and in the personification of conventional therapies needs to consider cancer-specific and patient-specific programming of innate immunity. Intratumoral TAMs and their precursors, resident macrophages and monocytes, are principal regulators of tumor progression and therapy resistance. Our review summarizes the accumulated evidence for the subpopulations of TAMs and their increasing number of biomarkers, indicating their predictive value for the clinical parameters of carcinogenesis and therapy resistance, with a focus on solid cancers of non-infectious etiology. We present the state-of-the-art knowledge about the tumor-supporting functions of TAMs at all stages of tumor progression and highlight biomarkers, recently identified by single-cell and spatial analytical methods, that discriminate between tumor-promoting and tumor-inhibiting TAMs, where both subtypes express a combination of prototype M1 and M2 genes. Our review focuses on novel mechanisms involved in the crosstalk among epigenetic, signaling, transcriptional and metabolic pathways in TAMs. Particular attention has been given to the recently identified link between cancer cell metabolism and the epigenetic programming of TAMs by histone lactylation, which can be responsible for the unlimited protumoral programming of TAMs. Finally, we explain how TAMs interfere with currently used anticancer therapeutics and summarize the most advanced data from clinical trials, which we divide into four categories: inhibition of TAM survival and differentiation, inhibition of monocyte/TAM recruitment into tumors, functional reprogramming of TAMs, and genetic enhancement of macrophages.
Rapid growth of acquired UBA1 mutations predisposes male patients to low-risk MDS
Authors: Peng Li, F. N. U. Alnoor, Wei Xie, Margaret Williams, Julie Feusier, Yi Ding, Xiangrong Zhao, Gang Zheng, Chen Zhao, Arthur W. Zieske, Youli Zu, Philipp W. Raess, Srinivas Tantravahi, Afaf Osman, Ami B. Patel, Tsewang Tashi, Jay L. Patel, Anna P. Matynia, Madhu P. Menon, Rodney R. Miles, Jeffrey R. Jacobsen, Tracy I. George, Douglas W. Sborov, Philippe Szankasi, Paul Rindler, Devin Close, Robert S. Ohgami
Journal: Leukemia (2024)
Examining the clinical role and educational preparation of heart failure nurses across <scp>Europe</scp>. A survey of the <scp>Heart Failure Association</scp> (<scp>HFA</scp>) of the European Society of Cardiology (<scp>ESC</scp>) and the <scp>Association</scp> of <scp>Cardiovascular Nursing</scp> and <scp>Allied Professions</scp> (<scp>ACNAP</scp>) of the <scp>ESC</scp>
Authors: Loreena Hill, Nicolas Girerd, Teresa Castiello, Tiny Jaarsma, Marco Metra, Guiseppe Rosano, Patrick Savage, Mark J. Schuuring, Maggie Simpson, Izabella Uchmanowicz, Maurizio Volterrani, Rhys Williams, Ekaterini Lambrinou, Camilla Hage
Journal: European Journal of Heart Failure (2024)

To describe the clinical practice and educational preparation of heart failure (HF) nurses across Europe and determine the key differences between countries.
Dysfunction of exhausted T cells is enforced by MCT11-mediated lactate metabolism
Authors: Ronal M. Peralta, Bingxian Xie, Konstantinos Lontos, Hector Nieves-Rosado, Kellie Spahr, Supriya Joshi, B. Rhodes Ford, Kevin Quann, Andrew T. Frisch, Victoria Dean, Mary Philbin, Anthony R. Cillo, Sebastian Gingras, Amanda C. Poholek, Lawrence P. Kane, Dayana B. Rivadeneira, Greg M. Delgoffe
Journal: Nature Immunology (2024)

Abstract CD8 + T cells are critical mediators of antitumor immunity but differentiate into a dysfunctional state, known as T cell exhaustion, after persistent T cell receptor stimulation in the tumor microenvironment (TME). Exhausted T (T ex ) cells are characterized by upregulation of coinhibitory molecules and reduced polyfunctionality. T cells in the TME experience an immunosuppressive metabolic environment via reduced levels of nutrients and oxygen and a buildup of lactic acid. Here we show that terminally T ex cells uniquely upregulate Slc16a11 , which encodes monocarboxylate transporter 11 (MCT11). Conditional deletion of MCT11 in T cells reduced lactic acid uptake by T ex cells and improved their effector function. Targeting MCT11 with an antibody reduced lactate uptake specifically in T ex cells, which, when used therapeutically in tumor-bearing mice, resulted in reduced tumor growth. These data support a model in which T ex cells upregulate MCT11, rendering them sensitive to lactic acid present at high levels in the TME.
Dynamics of the gut microbiome in individuals at risk of rheumatoid arthritis: a cross-sectional and longitudinal observational study
Authors: Christopher M Rooney, Ian B Jeffery, Kulveer Mankia, Mark H Wilcox, Paul Emery
Journal: Annals of the Rheumatic Diseases (2024)

This work aimed to resolve the conflicting reports on Prevotellaceae abundance in the development of rheumatoid arthritis (RA) and to observe structural, functional and temporal changes in the gut microbiome in RA progressors versus non-progressors.
Setting thresholds to determine COVID-19 activity levels using the mean standard deviation (MSD) method, England, 2022–2024
Authors: Mary A Sinnathamby, Tania Bourouphael, Jacob Boateng, Magali Collonnaz, Catherine Quinot, Nurin Abdul Aziz, Suzanne Elgohari, Rebecca E Green, Gavin Dabrera, Jamie Lopez-Bernal, Alex Allen
Journal: Eurosurveillance (2024)

We developed a new activity level setting threshold method, the mean standard deviation (MSD) method to quantify COVID-19 activity levels. This has been validated against the moving epidemic method (MEM), which has been used for influenza for many years, and we observed very similar results. The MSD method can prove to be a tool to use for respiratory viruses with limited historical data or seasonality to quantify activity levels when other respiratory viruses are also circulating.
Non-invasive Streptococcus pneumoniae infections are associated with different serotypes than invasive infections, Belgium, 2020 to 2023
Authors: Ioannis Passaris, Stéphanie Depickère, Toon Braeye, Marina Mukovnikova, Alexandra Vodolazkaia, Chloé Abels, Lize Cuypers, Stefanie Desmet, Pieter-Jan Ceyssens
Journal: Eurosurveillance (2024)

BackgroundDespite widely implemented pneumococcal vaccination programmes,
Post-disappearance scenarios: policy implications following the potential disappearance of B/Yamagata lineage influenza viruses
Authors: Marco Del Riccio, Marta C Nunes, Benjamin J Cowling, Bruno Lina, John W McCauley, Adam Meijer, Hanna Nohynek, Bronke Boudewijns, Saverio Caini
Journal: Eurosurveillance (2024)

The COVID-19 pandemic and related preventive measures reduced influenza virus circulation, notably causing the disappearance of the B/Yamagata lineage of influenza viruses. In this Perspective, we discuss the implications that this development may have for global influenza epidemiology, and the adjustments that may need to be implemented concerning surveillance strategies and practices, laboratory safety protocols, and influenza vaccine formulations. The disappearance of the B/Yamagata lineage might indeed alter the dynamics of the influenza disease burden (although in a way that is difficult to predict at the moment), and associated diagnostic practices, and may also necessitate updated biosafety levels and revised influenza surveillance strategies. Furthermore, the World Health Organization (WHO) recommended in September 2023 the exclusion of B/Yamagata antigens from future vaccines, with a shift towards trivalent vaccines or modified quadrivalent vaccines; this new scenario underscores the importance of robust global respiratory virus surveillance, effective communication with healthcare professionals and the population to maintain trust in vaccines, and a collaborative approach among health policymakers and vaccine manufacturers to navigate this epidemiological change.
Should all hospitalised patients colonised with Candida auris be considered for isolation?
Authors: Eelco FJ Meijer, Andreas Voss
Journal: Eurosurveillance (2024)

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Viral hepatitis knowledge and vaccination awareness among men who have sex with men (MSM) in 43 countries of the WHO European Region: results from the European MSM Internet Survey, EMIS-2017
Authors: Sofia Burdi, Michael Brandl, Ulrich Marcus, Erika Duffell, Ettore Severi, Antons Mozalevskis, Kristi Rüütel, Achim Dörre, Axel J Schmidt, Sandra Dudareva
Journal: Eurosurveillance (2024)

Background Recent hepatitis A virus outbreaks in Europe affecting men who have sex with men (MSM) and ongoing hepatitis B virus transmission among MSM underscore the ongoing need for viral hepatitis prevention in this population. Aim To describe viral hepatitis knowledge and associated factors among MSM in the WHO European Region to inform targeted prevention. Methods In the European MSM Internet Survey (EMIS-2017), basic knowledge was defined as correctly identifying at least 4 of 5 statements about viral hepatitis and vaccination. We described basic knowledge by country. In a multilevel logistic regression model, we estimated adjusted odds ratios (aOR) with 95% confidence intervals (CI) for having basic knowledge and explanatory variables: sociodemographic characteristics, history of hepatitis C and/or HIV diagnosis, sexual orientation disclosure at last sexually transmitted infections (STI) test and outness. Results Of 113,884 participants across 43 WHO European Region countries, 68% demonstrated basic knowledge, ranging from 50% in Israel to 80% in the Netherlands. Basic knowledge was significantly associated with older age (≥ 40 years vs &lt; 25 years, aOR: 2.9, 95% CI: 2.7–3.0), a history of hepatitis C and/or HIV diagnosis (aOR: 1.8, 95% CI: 1.7–1.9) and sexual orientation disclosure at last STI test (aOR: 1.3, 95% CI: 1.2–1.3), among other factors. Conclusions We found a knowledge disparity regarding viral hepatitis and hepatitis vaccination awareness among MSM across Europe, highlighting a need to address these gaps. A non-judgemental, accepting climate that allows individuals attending medical services to safely disclose their sexual orientation is fundamental to enable healthcare professionals to target information and preventative measures more effectively.
scDOT: optimal transport for mapping senescent cells in spatial transcriptomics
Authors: Nam D. Nguyen, Lorena Rosas, Timur Khaliullin, Peiran Jiang, Euxhen Hasanaj, Jose A. Ovando-Ricardez, Marta Bueno, Irfan Rahman, Gloria S. Pryhuber, Dongmei Li, Qin Ma, Toren Finkel, Melanie Königshoff, Oliver Eickelberg, Mauricio Rojas, Ana L. Mora, Jose Lugo-Martinez, Ziv Bar-Joseph
Journal: Genome biology (2024)

The low resolution of spatial transcriptomics data necessitates additional information for optimal use. We developed scDOT, which combines spatial transcriptomics and single cell RNA sequencing to improve the ability to reconstruct single cell resolved spatial maps and identify senescent cells. scDOT integrates optimal transport and expression deconvolution to learn non-linear couplings between cells and spots and to infer cell placements. Application of scDOT to lung spatial transcriptomics data improves on prior methods and allows the identification of the spatial organization of senescent cells, their neighboring cells and novel genes involved in cell-cell interactions that may be driving senescence.
Self-reported hepatitis A and B vaccination coverage among men who have sex with men (MSM), associated factors and vaccination recommendations in 43 countries of the WHO European Region: results from the European MSM Internet Survey, EMIS-2017
Authors: Michael Brandl, Axel J Schmidt, Ulrich Marcus, Erika Duffell, Ettore Severi, Antons Mozalevskis, Anda Kivite-Urtane, Matthias an der Heiden, Sandra Dudareva
Journal: Eurosurveillance (2024)

BackgroundHepatitis A and B vaccinations are recommended for men who have sex with men (MSM), given their increased risk of infection. However, data on vaccination programmes are scarce.AimTo use information on vaccination recommendations and vaccine uptake among MSM in the WHO European Region to guide prevention.MethodsFrom a large pan-European MSM Internet Survey (EMIS-2017), we analysed data on self-reported hepatitis A and B vaccination status by age, education, financial coping, settlement size, outness (disclosure of sexual behaviour), migration history and diagnosis with hepatitis C or HIV, using multivariable logistic regression. Additionally, we collected information on national hepatitis A and B vaccination recommendations.ResultsWe present data of 113,884 MSM, median age 36 years (IQR: 27-47). Vaccination for hepatitis A and B was recommended and free for MSM in 7 and 18 of 43 countries, respectively. Of all respondents, 48% (n = 50,966) reported ever being vaccinated against hepatitis A, and 53% (n = 56,889) against hepatitis B. Odds for being vaccinated against hepatitis A increased with outness ('out to (almost) all' aOR: 1.78, 95% CI: 1.72-1.85 vs 'out to none') and were higher in countries where vaccination was recommended and free for MSM (aOR: 2.22, 95% CI: 1.29-3.82 vs 'no recommendation'). Results for hepatitis B were similar (outness: aOR: 1.81, 95% CI: 1.75-1.88 and MSM-specific vaccination recommendation: aOR: 2.44, 95% CI: 1.54-3.85).ConclusionLarge proportions of MSM in Europe remain vulnerable to hepatitis A and B, despite available vaccination. Implementation of MSM-specific vaccination recommendations and greater efforts to improve the societal climate for MSM are needed to address gaps in vaccine coverage.
Candida auris fungaemia outbreak in a tertiary care academic hospital and emergence of a pan-echinocandin resistant isolate, Greece, 2021 to 2023
Authors: Joseph Meletiadis, Maria Siopi, Bram Spruijtenburg, Panagiota-Christina Georgiou, Maria Kostoula, Sophia Vourli, Frantzeska Frantzeskaki, Elisabeth Paramythiotou, Jacques F Meis, Iraklis Tsangaris, Spyros Pournaras
Journal: Eurosurveillance (2024)

After the start of the COVID-19 pandemic, a rapid rise in reported numbers and wide geographic spread of Candida auris -related invasive infections has been observed globally. However, the contemporary epidemiology of C. auris fungaemias in Greece remains unknown. An outbreak of C. auris bloodstream infections has been ongoing for almost 3 years in a Greek tertiary care academic hospital, with 89 C. auris -driven episodes appearing in five waves every 6–7 months following peaks in colonisation rates by 3–4 months. All isolates clustered in clade I and were genetically related, 84% were fluconazole-resistant and all were non-resistant to amphotericin B and echinocandins, except one pan-echinocandin-resistant isolate ( FKS1 S639F mutant) recovered from a patient on empiric therapy with anidulafungin. Notably, C. auris was in 2023 the most prevalent (34%) cause of candidaemia in our hospital. The accelerated and long-term transmission dynamics of C. auris fungaemia underscore the need for rigorous infection control measures, while antifungal stewardship is warranted to contain the selection of echinocandin-resistant isolates.
ANK Deficiency-Mediated Cytosolic Citrate Accumulation Promotes Aortic Aneurysm
Authors: Hao Wu, Zhiqing Li, Liu Yang, Lin He, Hao Liu, Shiyu Yang, Qinfeng Xu, Yanjie Li, Wenqiang Li, Yiran Li, Ze Gong, Yicong Shen, Xueyuan Yang, Jiaqi Huang, Fang Yu, Li, Junming Zhu, Luyang Sun, Yi Fu, Wei Kong
Journal: Circulation Research (2024)

Disturbed metabolism and transport of citrate play significant roles in various pathologies. However, vascular citrate regulation and its potential role in aortic aneurysm (AA) development remain poorly understood.
Traditional Chinese medicine in treating upper digestive tract cancers
Authors: Alexis Shiying Huang, Jiaying Wu, Aftab AMIN, Xiu-Qiong Fu, Zhi-Ling Yu
Journal: Molecular Cancer (2024)

Upper digestive tract cancers, such as oral cavity, laryngeal, esophageal, and gastric cancers, account for 10% of cancer cases and 14.5% of cancer-related deaths worldwide. Conventional treatments often provide limited survival benefits and are frequently associated with adverse effects and drug resistance. Chinese herbal drugs (CHDs) are widely used in the Far East for managing these cancers. In this narrative review, we summarize current clinical studies (published up to June 2024) on the use of 138 CHDs in the treatment of cancers and precancerous lesions of the upper digestive tract. For cancer treatment, 126 CHDs were tested, all in combination with conventional therapies. Each CHD increased the clinical efficacy and/or reduced the adverse effects of conventional therapies. The five-year survival rate is a critical metric for evaluating the clinical benefits of cancer treatments. Four of the CHDs were reported to increase five-year survival rates of patients receiving conventional therapies. The four CHDs are Sishen Jiedu Decoction, Pingxiao Tablet, Fuzheng Guben Granule, and Buyang Huanwu Tang. For managing precancerous lesions, 12 CHDs were tested: six used alone and six in combination with conventional therapies. Zengshengping is one of the CHDs used alone and is the only one that has been proven to prevent the development of esophageal cancer with convincing evidence. This review provides information about the clinical benefits of CHDs and offers a reference for their rational application in treating upper digestive tract cancers. The reviewed studies have limitations: most trials had small sample sizes and were not multi-center; only one study investigated the mechanisms of action of the studied CHD; and the active components of CHDs were not explored. To promote international recognition of CHDs, rigorously designed studies on clinical outcomes, mechanisms of action, and active components are warranted. Moreover, the studied CHDs should be standardized.
Contributors
Authors: Sunilkumar Sambhaji Ainwad, Ali Alazmani, Valerio Francesco Annese, E.V. Aslanyan, O.M. Bakhtin, Hossam Magdy Balaha, Paul Dominick E. Baniqued, Shailesh Vitthalrao Bhalerao, Sahbi Chaibi, Yupeng Chen, Woosang Cho, Iman Dehzangi, Prashant Desai, Usha Desai, César Javier Ortiz Echeverri, Jesús S. García-Salinas, A.S. Gerashchenko, James Giordano, Srinivas Rao Gorre, Christoph Guger, Srinivasa Rao Gundu, Asmaa El-Sayed Hassan, Tonatiuh Hernández-del-Toro, Gerardo Hernández-Nava, Raymond J. Holt, Keum-Shik Hong, Alexander E. Hramov, Ravichander Janapati, Aditi Jogdand, Abdennaceur Kachouri, Muhammad Jawad Khan, Sarika Khandelwal, Brandon J. King, V.N. Kiroy, E.M. Krivko, Shiu Kumar, Semen A. Kurkin, Chahira Mahjoub, Saeed Mian Qaisar, Mark Mon-Williams, J. Ryan Morehead, Seraphim S. Moumgiakmas, Faisal Mushtaq, Noman Naseer, Hammad Nazeer, Rupert Ortner, Ram Bilas Pachori, A.V. Paleev, Charan Arur Panem, George A. Papakostas, Dingyi Pei, Alexander N. Pisarchik, Ch. Rajendra Prasad, Archana Raut, Gemma J.M. Read, Carlos A. Reyes-García, Olivia Rice, A.I. Saevsky, Dimitrios Sakavalas, Nilima Salankar, Sebastián Salazar-Colores, Paul M. Salmon, Marc Sebastián-Romagosa, Tayyaba Shahwar, D.G. Shaposhnikov, Alok Sharma, Swakkhar Shatabda, I.G. Shevchenko, John R. Shook, Natali N. Shusharina, Sebastian Sieghartsleitner, Alejandro A. Torres-García, Ateeq Ur Rehman, Luis Villaseñor-Pineda, Ramana Vinjamuri, Akib Zaman
Journal: Brain-Computer Interfaces (2024)
Stimulus-independent noninvasive BCI based on EEG patterns of inner speech
Authors: V.N. Kiroy, E.V. Aslanyan, O.M. Bakhtin, E.M. Krivko, A.V. Paleev, A.S. Gerashchenko, I.G. Shevchenko, A.I. Saevsky, D.G. Shaposhnikov
Journal: Brain-Computer Interfaces (2024)
Results from the international collaborative systematic literature review informing the 2023 EULAR recommendations for the treatment of systemic sclerosis
Authors: Alain Lescoat, Eugenia Bertoldo, Jelena Čolić, Tania Santiago, Yossra A. Suliman, Jenny Emmel, Philip G. Conaghan, Yannick Allanore, Francesco del Galdo
Journal: Annals of the Rheumatic Diseases (2024)

<h3>Background</h3> The EULAR recommendations for the treatment of systemic sclerosis (SSc) were updated in 2017, informed by a systematic literature review (SLR) completed in 2014. <h3>Objectives</h3> The aim of this new SLR was to provide the most up-to-date literature to underpin contemporary EULAR recommendations for the management of SSc. <h3>Methods</h3> 30 searches for 30 interventions (including several outcomes/clinical questions), and 1 dedicated search (with several interventions) for calcinosis were prioritised by the task force. Three types of questions were defined: type I questions, unchanged as compared with the previous recommendations; type II questions exploring interventions already mentioned in the previous recommendations but with new outcomes; type III questions for new interventions. <h3>Results</h3> 14 490 abstracts were retrieved from the databases on 31 March 2022 and 2021 abstracts were retrieved on 11 October 2022. 483 new full texts were evaluated and 172 new articles were included for the first search and 9 for the second search. The majority of the questions covered by this SLR explored new interventions (40% of type III questions) or new outcomes (26% of type II questions). New interventions included targeted therapies such as abatacept, Janus kinase inhibitors or nintedanib, and updated questions incorporated the results from key game-changing randomised controlled trials including trials on tocilizumab, mycophenolate or rituximab in SSc-interstitial lung disease. <h3>Conclusions</h3> This SLR provides and summarises the highest level of evidence for the new EULAR recommendations for the treatment of SSc, providing an unprecedented comprehensive overview of recent knowledge on SSc treatments and participating in defining the future research agenda.