tbuckley/cabot-search huggingface dataset:
Modelling dataset bias in machine-learned theories of economic decision-making
Authors: Tobias Thomas, Dominik Straub, Fabian Tatai, Megan Shene, Tümer Tosik, Kristian Kersting, Constantin A. Rothkopf
Journal: Nature Human Behaviour (2024)

Abstract Normative and descriptive models have long vied to explain and predict human risky choices, such as those between goods or gambles. A recent study reported the discovery of a new, more accurate model of human decision-making by training neural networks on a new online large-scale dataset, choices13k. Here we systematically analyse the relationships between several models and datasets using machine-learning methods and find evidence for dataset bias. Because participants’ choices in stochastically dominated gambles were consistently skewed towards equipreference in the choices13k dataset, we hypothesized that this reflected increased decision noise. Indeed, a probabilistic generative model adding structured decision noise to a neural network trained on data from a laboratory study transferred best, that is, outperformed all models apart from those trained on choices13k. We conclude that a careful combination of theory and data analysis is still required to understand the complex interactions of machine-learning models and data of human risky choices.
RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9
Authors: Mengli Zhang, Judith Hyle, Xiaowen Chen, Ye Xin, Yingcai Jin, Jianxiang Zhang, Xue Yang, Xinfeng Chen, Shaela Wright, Zhenling Liu, Wojciech Rosikiewicz, Beisi Xu, Liusheng He, Hong Liu, Nana Ping, Depei Wu, Feiqiu Wen, Chunliang Li, Peng Xu
Journal: Genome biology (2024)

The oncogenic protein HOXA9 plays a critical role in leukemia transformation and maintenance, and its aberrant expression is a hallmark of most aggressive acute leukemia. Although inhibiting the upstream regulators of HOXA9 has been proven as a significant therapeutic intervention, the comprehensive regulation network controlling HOXA9 expression in leukemia has not been systematically investigated.
Analysing the accuracy of pressure measurements during exercise with pulmonary artery pressure sensors – Insights from the ACTION‐MEMS study
Authors: Evelyne Meekers, Thibault Petit, Jeroen Dauw, Henri Gruwez, Sebastiaan Dhont, Evert Luwel, Petra Nijst, Matthias Dupont, Philippe B. Bertrand, Pieter Martens, Wilfried Mullens
Journal: European Journal of Heart Failure (2024)
Genetic risk and likelihood of prostate cancer detection on first biopsy by ancestry
Authors: Kyung Min Lee, Tyler J Nelson, Alex Bryant, Craig C Teerlink, Roman Gulati, Meghana S Pagadala, Catherine Tcheandjieu, Kathryn M Pridgen, Scott L DuVall, Kosj Yamoah, Jason L Vassy, Tyler M Seibert, Richard L Hauger, Brent S Rose, Julie A Lynch
Journal: JNCI Journal of the National Cancer Institute (2024)

Abstract Despite differences in prostate cancer risk across ancestry groups, relative performance of prostate cancer genetic risks scores (GRS) for positive biopsy prediction in different ancestry groups is unknown. This cross-sectional retrospective analysis examines the association between a polygenic hazard score (PHS290) and risk of prostate cancer diagnosis upon first biopsy in male veterans using 2-sided tests. Our analysis included 36 717 veterans (10 297 of African ancestry). Unadjusted rates of positive first prostate biopsy increased with higher genetic risk (low risk: 34%, high risk: 58%; P &amp;lt; .001). Among men of African ancestry, higher genetic risk was associated with increased prostate cancer detection on first biopsy (odds ratio = 2.18, 95% confidence interval = 1.93 to 2.47), but the effect was stronger among men of European descent (odds ratio = 3.89, 95% confidence interval = 3.62 to 4.18). These findings suggest that incorporating genetic risk into prediction models could better personalize biopsy decisions, although further study is needed to achieve equitable genetic risk stratification among ancestry groups.
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Authors: Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q. Zhang, Ram S. Mani
Journal: Genome biology (2024)

The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac, and H3K27me3 but works well with just RAD21 signal. Integrative analysis reveals novel insights into the role of CTCF motif, its orientation, and CTCF binding on cohesin-mediated chromatin interactions.
Repeated peripheral infusions of anti-EGFRvIII CAR T cells in combination with pembrolizumab show no efficacy in glioblastoma: a phase 1 trial
Authors: Stephen J. Bagley, Zev A. Binder, Lamia Lamrani, Eliana Marinari, Arati S. Desai, MacLean P. Nasrallah, Eileen Maloney, Steven Brem, Robert A. Lustig, Goldie Kurtz, Michelle Alonso-Basanta, Pierre-Emmanuel Bonté, Christel Goudot, Wilfrid Richer, Eliane Piaggio, Shawn Kothari, Lea Guyonnet, Coralie L. Guerin, Joshua J. Waterfall, Suyash Mohan, Wei-Ting Hwang, Oliver Y. Tang, Meghan Logun, Meghna Bhattacharyya, Kelly Markowitz, Devora Delman, Amy Marshall, E. John Wherry, Sebastian Amigorena, Gregory L. Beatty, Jennifer L. Brogdon, Elizabeth Hexner, Denis Migliorini, Cecile Alanio, Donald M. O’Rourke
Journal: Nature Cancer (2024)
Efficacy and safety of JAK inhibitors in rheumatoid arthritis: update for the practising clinician
Authors: Zoltán Szekanecz, Maya H. Buch, Christina Charles-Schoeman, James Galloway, George A. Karpouzas, Lars Erik Kristensen, Steven R. Ytterberg, Attila Hamar, Roy Fleischmann
Journal: Nature Reviews Rheumatology (2024)
Adjuvant Chemotherapy and Outcomes in Older Adult Patients With Biliary Tract Cancer
Authors: Olumide B. Gbolahan, Xiaojie Zhi, Yuan Liu, Mihir M. Shah, David A. Kooby, Olatunji B. Alese
Journal: JAMA Network Open (2024)

Importance The association of adjuvant chemotherapy (AC) with survival in the general population of patients with resected biliary tract cancer (BTC) remains controversial. As such, the role of this treatment in the treatment of older adult patients (aged ≥70 years) needs to be evaluated. Objective To describe the patterns of use of AC and compare survival outcomes of AC and observation in older adult patients following resection of BTC. Design, Setting, and Participants This retrospective cohort study included 8091 older adult patients with resected BTC with data available in the National Cancer Database from January 1, 2004, to December 31, 2019. Patients were divided into 2 cohorts: AC and observation. The AC cohort was subdivided into single-agent and multiagent AC treatment. Exposures Adjuvant chemotherapy vs observation following BTC resection. Main Outcomes and Measures The primary outcome was overall survival (OS) of patients who received AC compared with observation following resection of BTC as evaluated using Kaplan-Meier estimates and multivariable Cox proportional hazards regression models. Inverse probability of treatment weighting and propensity score matching were performed to address indication bias. Results Between 2004 and 2019, of 8091 older adult patients with resected BTC identified (median [range] age, 77 [70-90] years; 5136 women [63.5%]; 2955 men [36.5%]), only one-third (2632 [32.5%]) received AC. There was an increase in the use of AC across the study period from 20.7% (n = 495) in 2004 to 2009 to 41.2% (n = 856) in 2016 to 2019. Age 80 years or older (odds ratio, 0.29; 95% CI, 0.25-0.33; P &amp;amp;lt; .001) and gallbladder primary site (odds ratio, 0.71; 95% CI, 0.61-0.83; P &amp;amp;lt; .001) were associated with a lower odds of AC. Following inverse probability of treatment weighting, as a composite, AC was not associated with improved survival (median OS, 20.5 months; 95% CI, 19.2-21.7 months) compared with observation (median OS, 19.0 months; 95% CI, 18.1-20.3 months). A longer median OS was associated with single-agent AC (21.5 months; 95% CI, 19.9-24.0 months) but not multiagent AC (19.1 months; 95% CI, 17.5-21.1 months) compared with observation (median OS, 17.3 months; 95% CI, 16.1-18.4 months). This improvement in OS with single-agent AC was not apparent on multivariable analysis (hazard ratio [HR], 0.97; 95% CI, 0.89-1.05; P = .44). However, age at diagnosis of 80 years or older (HR, 1.35; 95% CI, 1.28-1.42; P &amp;amp;lt; .001) and treatment at nonacademic centers (HR, 1.14; 95% CI, 1.07-1.20, P &amp;amp;lt; .001) were associated with worse OS. Conclusions and Relevance In this cohort study of older adult patients, AC was not associated with an improvement in survival compared with observation following BTC resection. These findings suggest the need for further study of AC for older adult patients who may benefit after curative intent surgery for BTC.
Seroprevalence of tick-borne encephalitis virus and vaccination coverage of tick-borne encephalitis, Sweden, 2018 to 2019
Authors: Bo Albinsson, Tove Hoffman, Linda Kolstad, Tomas Bergström, Gordana Bogdanovic, Anna Heydecke, Mirja Hägg, Torbjörn Kjerstadius, Ylva Lindroth, Annika Petersson, Marie Stenberg, Sirkka Vene, Patrik Ellström, Bengt Rönnberg, Åke Lundkvist
Journal: Eurosurveillance (2024)

Background In Sweden, information on seroprevalence of tick-borne encephalitis virus (TBEV) in the population, including vaccination coverage and infection, is scattered. This is largely due to the absence of a national tick-borne encephalitis (TBE) vaccination registry, scarcity of previous serological studies and use of serological methods not distinguishing between antibodies induced by vaccination and infection. Furthermore, the number of notified TBE cases in Sweden has continued to increase in recent years despite increased vaccination. Aim The aim was to estimate the TBEV seroprevalence in Sweden. Methods In 2018 and 2019, 2,700 serum samples from blood donors in nine Swedish regions were analysed using a serological method that can distinguish antibodies induced by vaccination from antibodies elicited by infection. The regions were chosen to reflect differences in notified TBE incidence. Results The overall seroprevalence varied from 9.7% (95% confidence interval (CI): 6.6–13.6%) to 64.0% (95% CI: 58.3–69.4%) between regions. The proportion of vaccinated individuals ranged from 8.7% (95% CI: 5.8–12.6) to 57.0% (95% CI: 51.2–62.6) and of infected from 1.0% (95% CI: 0.2–3.0) to 7.0% (95% CI: 4.5–10.7). Thus, more than 160,000 and 1,600,000 individuals could have been infected by TBEV and vaccinated against TBE, respectively. The mean manifestation index was 3.1%. Conclusion A difference was observed between low- and high-incidence TBE regions, on the overall TBEV seroprevalence and when separated into vaccinated and infected individuals. The estimated incidence and manifestation index argue that a large proportion of TBEV infections are not diagnosed.
Reappraisal of the conventional hemostasis tests as predictors of perioperative bleeding in the era of rebalanced hemostasis in cirrhosis
Authors: Armando Tripodi, Massimo Primignani, Roberta D’Ambrosio, Giulia Tosetti, Vincenzo La Mura, Pietro Lampertico, Flora Peyvandi
Journal: Hepatology (2024)

New global laboratory procedures mimicking the in vivo hemostasis process led to the changing paradigm of cirrhosis from the prototype of hemorrhagic diseases to a condition in which hemostasis is normal but fragile, thus justifying the hemorrhagic/thrombotic tendencies that affect these patients. The new paradigm was instrumental to change the management of cirrhosis. For example, international guidelines warn against the entrenched practice of testing patients with conventional hemostasis tests and infusing those with abnormalities with fresh-frozen plasma, coagulation factor concentrates, or platelets, prior to surgery/invasive procedures. These recommendations are, however, largely disattended. The practice of testing patients with the prothrombin time or viscoelastometry and using arbitrary cutoffs to make decisions on perioperative prophylaxis is still common and probably driven by medicolegal issues. There is no doubt that prothrombin time and congeners tests are unable to predict bleeding in cirrhosis. However, it cannot be excluded that some tests may be useful in patients who are severely decompensated. Large prospective collaborative studies are warranted. Enrolled patients should be randomized to receive perioperative prophylaxis based on laboratory testing (eg, viscoelastometry, thrombomodulin-modified thrombin generation) or to usual care. However, for these trials to be useful, a third group of patients who do not receive prophylaxis should be included. In conclusion, until results from these studies are available, physicians attending cirrhosis should refrain from using laboratory tests with arbitrary cutoffs to make decision on perioperative prophylaxis. Decision should be made by considering the clinical history of individual patients and the risk of hemorrhage of specific procedures.
Error in Affiliation
Authors: Giridhara Babu
Journal: JAMA Network Open (2024)

Hannah H. Leslie, PhD; Giridhara R. Babu, MBBS, PhD; Nolita Dolcy Saldanha, MPH; Anne-Marie Turcotte-Tremblay, PhD; Deepa Ravi, MS; Neena R. Kapoor, MSc; Suresh S. Shapeti, MBBS; Dorairaj Prabhakaran, MBBS, MD; Margaret E. Kruk, MD
Blood pressure levels and adverse cardiovascular outcomes in heart failure: A systematic review and meta‐analysis
Authors: Samuel Seidu, Claire A. Lawson, Setor K. Kunutsor, Kamlesh Khunti, Giuseppe M.C. Rosano
Journal: European Journal of Heart Failure (2024)

Existing data on the association between blood pressure levels and adverse cardiovascular outcomes in patients with heart failure (HF) are inconsistent. The optimal blood pressure targets for patients with HF remain uncertain. This study sought to assess the associations between blood pressure (systolic [SBP] and diastolic blood pressure [DBP]) levels and adverse cardiovascular disease (CVD) outcomes in patients with HF.
Increase of respiratory illnesses among children in Beijing, China, during the autumn and winter of 2023
Authors: Cheng Gong, Fang Huang, Luodan Suo, Xuejiao Guan, Lu Kang, Hui Xie, Geng Hu, Peng Yang, Quanyi Wang
Journal: Eurosurveillance (2024)

In 2023, through an ongoing respiratory pathogen surveillance system, we observed from mid-September onwards, an increase of respiratory illness among children aged ≤ 15 years presenting at hospital outpatient clinics in Beijing, China. Data indicated that illness was caused by multiple pathogens, predominantly
Mobilizing China and the Global Community to Confront the Treatment Desert for Pediatric Solid Tumors
Authors: Shuhang Wang, Yale Jiang, Rongshou Zheng, Yue Yu, Wenqiang Wei, Ning Li
Journal: Cancer Discovery (2024)

Summary: Pediatric solid tumors are distinct clinical entities that impose heavy socioeconomic burden and while their incidence has increased in recent years, treatment options are often limited, with only 27 drugs approved for pediatric solid tumors in the United States, and fewer still, 13, in China. The scale of the unmet medical need is immense and new efforts are urgently needed to develop efficient therapeutics and improve these children's lives.
Perilipin 1: a systematic review on its functions on lipid metabolism and atherosclerosis in mice and humans
Authors: Camille Desgrouas, Tabea Thalheim, Mathieu Cerino, Catherine Badens, Nathalie Bonello-Palot
Journal: Cardiovascular Research (2024)

The function of perilipin 1 in human metabolism was recently highlighted by the description of PLIN1 variants associated with various pathologies. These include severe familial partial lipodystrophy and early onset acute coronary syndrome. Additionally, certain variants have been reported to have a protective effect on cardiovascular diseases. The role of this protein remains controversial in mice and variant interpretation in humans is still conflicting. This literature review has two primary objectives (i) to clarify the function of the PLIN1 gene in lipid metabolism and atherosclerosis by examining functional studies performed in cells (adipocytes) and mice and (ii) to understand the impact of PLIN1 variants identified in humans based on the variant's location within the protein and the type of variant (missense or frameshift). To achieve these objectives, we conducted an extensive analysis of the relevant literature on perilipin 1, its function in cellular models and mice, and the consequences of its mutations in humans. We also utilized bioinformatics tools and consulted the Human Genetics Cardiovascular Disease Knowledge Portal to enhance the pathogenicity assessment of PLIN1 missense variants.
Microbiota and mucosal gene expression of fecal microbiota transplantation or placebo treated patients with chronic pouchitis
Authors: Anna K. Hartikainen, Imran Khan, Essi K. Karjalainen, Laura Renkonen-Sinisalo, Perttu Arkkila, Jonna Jalanka, Anna H. Lepistö, Reetta Satokari
Journal: Gut Microbes (2024)

Altered microbiota and impaired host immune function have been linked to the pathogenesis of pouchitis. We used 16S rRNA gene sequencing and RNA sequencing data from a previous randomized clinical trial (RCT) on fecal microbiota transplantation (FMT) therapy in 26 chronic pouchitis patients with one-year follow-up. We analyzed changes in both luminal and mucosal microbiota composition, as well as in host mucosal gene expression to gain insights into the host–microbiota interactions possibly underlying clinical outcomes of the patients. Antibiotic type and pattern of use were significant drivers of the luminal microbiota at baseline. Differential gene expression analysis indicated transition from ileal to colonic gene expression in the pouch, and upregulation in inflammation- and immune system-related pathways in the pouch. At 4 weeks, the non-relapsed FMT patients had a lower microbiota dissimilarity to the donor than the non-relapsed placebo patients (p = .02). While two FMT-treated patients showed a shift toward the donor's microbiota during the one-year follow-up, the overall FMT microbiota modulation effect was low. Patient's luminal and mucosal microbiota profiles were unstable in both FMT and placebo groups. Expression of the chemokine receptor CXCR4 was downregulated at 52 weeks compared to the baseline in the non-relapsed patients in both FMT and placebo groups. Microbiota modulation by FMT seems to be low in this patient group. The microbiota composition or alterations did not explain the relapse status of the patients. Some evidence for remission-related host gene expression pattern was found; specifically, CXCR4 expression may have a role in sustained remission.
Medical apprenticeships: what we know so far, and what happens next
Authors: Éabha Lynn
Journal: BMJ (2024)

Medical degree apprenticeships are coming to the UK this year. Supporters hope for increased accessibility to a medical career, while others raise concerns about equity and supervision. <b>Éabha Lynn</b> finds that much detail is still missing—but one medical school shares its plans with <i>The BMJ</i>
Humoral immune escape by current SARS-CoV-2 variants BA.2.86 and JN.1, December 2023
Authors: Lara M Jeworowski, Barbara Mühlemann, Felix Walper, Marie L Schmidt, Jenny Jansen, Andi Krumbholz, Etienne Simon-Lorière, Terry C Jones, Victor M Corman, Christian Drosten
Journal: Eurosurveillance (2024)

Variant BA.2.86 and its descendant, JN.1, of SARS-CoV-2 are rising in incidence across Europe and globally. We isolated recent JN.1, BA.2.86, EG.5, XBB.1.5 and earlier variants. We tested live virus neutralisation of sera taken in September 2023 from vaccinated and exposed healthy persons (n = 39). We found clear neutralisation escape against recent variants but no specific pronounced escape for BA.2.86 or JN.1. Neutralisation escape corresponds to recent variant predominance but may not be causative of the recent upsurge in JN.1 incidence.
Concerted synergy between viral-specific IgG and CD8+ T cells is critical for clearance of an HCV-related rodent hepacivirus
Authors: John Gridley, Brantley Holland, Eduardo Salinas, Sheetal Trivedi, Piyush Dravid, Elizabeth Elrod, Fengzhi Jin, Anuradha Kumari, Mariana N. Batista, Manoj Thapa, Charles M. Rice, Joseph Marcotrigiano, Amit Kapoor, Arash Grakoui
Journal: Hepatology (2024)

Evidence assessing the role of B cells and their antibodies, or lack thereof, in the spontaneous resolution of acute HCV infection is conflicting. Utilization of a strictly hepatotropic, HCV-related rodent hepacivirus (RHV) model circumvents many of the challenges facing the field in characterizing the immunological correlates of dichotomous infection outcomes. This study seeks to elucidate the importance of B cells in the clearance of acute RHV infection.
The social determinants of mental health and disorder: evidence, prevention and recommendations
Authors: James B. Kirkbride, Deidre M. Anglin, Ian Colman, Jennifer Dykxhoorn, Peter B. Jones, Praveetha Patalay, Alexandra Pitman, Emma Soneson, Thomas Steare, Talen Wright, Siân Lowri Griffiths
Journal: World Psychiatry (2024)

People exposed to more unfavourable social circumstances are more vulnerable to poor mental health over their life course, in ways that are often determined by structural factors which generate and perpetuate intergenerational cycles of disadvantage and poor health. Addressing these challenges is an imperative matter of social justice. In this paper we provide a roadmap to address the social determinants that cause mental ill health. Relying as far as possible on high-quality evidence, we first map out the literature that supports a causal link between social determinants and later mental health outcomes. Given the breadth of this topic, we focus on the most pervasive social determinants across the life course, and those that are common across major mental disorders. We draw primarily on the available evidence from the Global North, acknowledging that other global contexts will face both similar and unique sets of social determinants that will require equitable attention. Much of our evidence focuses on mental health in groups who are marginalized, and thus often exposed to a multitude of intersecting social risk factors. These groups include refugees, asylum seekers and displaced persons, as well as ethnoracial minoritized groups; lesbian, gay, bisexual, transgender and queer (LGBTQ+) groups; and those living in poverty. We then introduce a preventive framework for conceptualizing the link between social determinants and mental health and disorder, which can guide much needed primary prevention strategies capable of reducing inequalities and improving population mental health. Following this, we provide a review of the evidence concerning candidate preventive strategies to intervene on social determinants of mental health. These interventions fall broadly within the scope of universal, selected and indicated primary prevention strategies, but we also briefly review important secondary and tertiary strategies to promote recovery in those with existing mental disorders. Finally, we provide seven key recommendations, framed around social justice, which constitute a roadmap for action in research, policy and public health. Adoption of these recommendations would provide an opportunity to advance efforts to intervene on modifiable social determinants that affect population mental health.
Mycoplasma pneumoniae epidemic in Denmark, October to December, 2023
Authors: Anne Christine Nordholm, Bolette Søborg, Pikka Jokelainen, Karina Lauenborg Møller, Lotte Flink Sørensen, Tyra Grove Krause, Søren Anker Uldum, Hanne-Dorthe Emborg
Journal: Eurosurveillance (2024)

We report a surge of patients, especially children and adolescents, with respiratory disease caused by