tbuckley/cabot-search huggingface dataset:
Real-time PCR assay to detect the novel Clade Ib monkeypox virus, September 2023 to May 2024
Authors: Leonard Schuele, Leandre Murhula Masirika, Jean Claude Udahemuka, Freddy Belesi Siangoli, Justin Bengehya Mbiribindi, Pacifique Ndishimye, Frank M Aarestrup, Marion Koopmans, Bas B Oude Munnink, Richard Molenkamp
Journal: Eurosurveillance (2024)

Monkeypox virus (MPXV) is an emerging zoonotic pathogen with complex epidemiology necessitating rapid diagnosis and distinguishing between clades and subclades. The emerging Clade Ib lacks the genomic region used in the Clade I-specific assay from the Centers for Disease Control and Prevention. We report an MPXV real-time PCR to specifically detect Clade Ib. The assay demonstrated proficient sensitivity and specificity in 92 samples and can be included along other TaqMan-based assays to detect MPXV and distinguish between clades and subclades.
F18-FDG PET imaging as a diagnostic tool for immune checkpoint inhibitor–associated acute kidney injury
Authors: Shruti Gupta, Olivia Green-Lingren, Sudhir Bhimaniya, Aleksandra Krokhmal, Heather Jacene, Marlies Ostermann, Sugama Chicklore, Ben Sprangers, Christophe M Deroose, Sandra M Herrmann, Sophia L Wells, Sarah A Kaunfer, Jessica L Ortega, Clara García-Carro, Michael Bold, Kevin L Chen, Meghan E Sise, Pedram Heidari, Wai Lun Will Pak, Meghan D Lee, Pazit Beckerman, Yael Eshet, Raymond K Hsu, Miguel Hernandez Pampaloni, Arash Rashidi, Norbert Avril, Vicki Donley, Zain Mithani, Russ Kuker, Muhammad O Awiwi, Mindy X Wang, Sujal I Shah, Michael D Weintraub, Heiko Schoder, Raad B Chowdhury, Harish Seethapathy, Kerry L Reynolds, Maria Jose Soler, Ala Abudayyeh, Ilya Glezerman, David E Leaf
Journal: Journal of Clinical Investigation (2024)
Hospital surveillance of respiratory viruses during the COVID-19 pandemic and beyond: contribution to the WHO mosaic framework, Israel, 2020 to 2023
Authors: Lea Gur-Arie, Michal Stein, Hanna Sefty, Ilana S Fratty, Ital Nemet, Limor Kliker, Nofar Atari, Neta S Zuckerman, Alina Rosenberg, Heftziba Ivgi, Orit Golan-Shany, Nadav Sorek, Orna Schwartz-Harari, Michal Bromberg, Lital Keinan-Boker, Michal Mandelboim, Aharona Glatman-Freedman
Journal: Eurosurveillance (2024)

BackgroundA new respiratory virus surveillance platform, based on nationwide hospital laboratory data, was established in Israel during the COVID-19 pandemic.AimWe aimed to evaluate the performance of this platform with respect to the detection of influenza and respiratory syncytial virus (RSV) from week 36 in 2020 to week 15 in 2023, and how it fits with the World Health Organization (WHO) mosaic surveillance framework.MethodsData of respiratory samples from hospitalised patients sent for laboratory confirmation of influenza virus or RSV from 25 general hospital laboratories nationwide were collected. We analysed the weekly number and percentage of samples positive for influenza virus or RSV vis-à-vis SARS-CoV-2 activity and compared data from the new surveillance platform with existing surveillance platforms. Using data in the new surveillance platform, we analysed early stages of a 2021 out-of-season RSV outbreak and evaluated the capabilities of the new surveillance system with respect to objectives and domains of the WHO mosaic framework.ResultsThe new hospital-laboratory surveillance platform captured the activity of influenza virus and RSV, provided crucial data when outpatient sentinel surveillance was not operational and supported an out-of-season RSV outbreak investigation. The new surveillance platform fulfilled important objectives in all three domains of the mosaic framework and could serve for gathering additional information to fulfil more domain objectives.ConclusionThe new hospital laboratory surveillance platform provided essential data during the COVID-19 pandemic and beyond, fulfilled important domain objectives of the mosaic framework and could be adapted for the surveillance of other viruses.
Distinct Genes with Similar Functions Underlie Convergent Evolution in <i>Myotis</i> Bat Ecomorphs
Authors: Ariadna E Morales, Frank T Burbrink, Marion Segall, Maria Meza, Chetan Munegowda, Paul W Webala, Bruce D Patterson, Vu Dinh Thong, Manuel Ruedi, Michael Hiller, Nancy B Simmons
Journal: Molecular Biology and Evolution (2024)

Abstract Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies—gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features—have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.
Re: Iver Nordentoft, Sia Viborg Lindskrog, Karin Birkenkamp-Demtröder, et al. Whole-genome Mutational Analysis for Tumor-informed Detection of Circulating Tumor DNA in Patients with Urothelial Carcinoma. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2024.05.014
Authors: Xiaoliang Wu, Xiangyang Yao, Zhong Chen, Hua Xu
Journal: European Urology (2024)
TF-High-Evolutionary: <i>in vivo</i> mutagenesis of gene regulatory networks for the study of the genetics and evolution of the <i>Drosophila</i> regulatory genome
Authors: Xueying C Li, Vani Srinivasan, Ian Laiker, Natalia Misunou, Nicolás Frankel, Luisa F Pallares, Justin Crocker
Journal: Molecular Biology and Evolution (2024)

Abstract Understanding the evolutionary potential of mutations in gene regulatory networks is essential to furthering the study of evolution and development. However, in multicellular systems, genetic manipulation of regulatory networks in a targeted and high-throughput way remains challenging. In this study, we designed TF-High-Evolutionary (HighEvo), a transcription factor (TF) fused with a base editor (activation-induced deaminase), to continuously induce germline mutations at TF-binding sites across regulatory networks in Drosophila. Populations of flies expressing TF-HighEvo in their germlines accumulated mutations at rates an order of magnitude higher than natural populations. Importantly, these mutations accumulated around the targeted TF-binding sites across the genome, leading to distinct morphological phenotypes consistent with the developmental roles of the tagged TFs. As such, this TF-HighEvo method allows the interrogation of the mutational space of gene regulatory networks at scale and can serve as a powerful reagent for experimental evolution and genetic screens focused on the regulatory genome.
Modified montmorillonite armed probiotics with enhanced on-site mucus-depleted intestinal colonization and H2S scavenging for colitis treatment
Authors: Jiali Yang, Shengchan Ge, Shaochong Tan, Hua Liu, Mingzhu Yang, Wei Liu, Kaixiang Zhang, Zhenzhong Zhang, Junjie Liu, Jinjin Shi, Zhi-Hao Wang, Jitian Li
Journal: Journal of Controlled Release (2024)
Epidemiological and environmental investigation of the ‘big four’ Vibrio species, 1994 to 2021: a Baltic Sea retrospective study
Authors: Greta Gyraitė, Marija Kataržytė, Martynas Bučas, Greta Kalvaitienė, Sandra Kube, Daniel PR Herlemann, Christian Pansch, Anders F Andersson, Tarja Pitkanen, Anna-Maria Hokajärvi, Aune Annus-Urmet, Gerhard Hauk, Martin Hippelein, Eglė Lastauskienė, Matthias Labrenz
Journal: Eurosurveillance (2024)

Background The Vibrio genus comprises several bacterial species present in the Baltic Sea region (BSR), which are known to cause human infections. Aim To provide a comprehensive retrospective analysis of Vibrio -induced infections in the BSR from 1994 to 2021, focusing on the ‘big four’ Vibrio species – V. alginolyticus , V. cholerae non-O1/O139, V. parahaemolyticus and V. vulnificus – in eight European countries (Denmark, Estonia, Finland, Germany, Latvia, Lithuania, Poland and Sweden) bordering the Baltic Sea. Methods Our analysis includes data on infections, Vibrio species distribution in coastal waters and environmental data received from national health agencies or extracted from scientific literature and online databases. A redundancy analysis was performed to determine the potential impact of several independent variables, such as sea surface temperature, salinity, the number of designated coastal beaches and year, on the Vibrio infection rate. Results For BSR countries conducting surveillance, we observed an exponential increase in total Vibrio infections (n = 1,553) across the region over time. In Sweden and Germany, total numbers of Vibrio spp. and infections caused by V. alginolyticus and V. parahaemolyticus positively correlate with increasing sea surface temperature. Salinity emerged as a critical driver of Vibrio spp. distribution and abundance. Furthermore, our proposed statistical model reveals 12 to 20 unreported cases in Lithuania and Poland, respectively, countries with no surveillance. Conclusions There are discrepancies in Vibrio surveillance and monitoring among countries, emphasising the need for comprehensive monitoring programmes of these pathogens to protect human health, particularly in the context of climate change.
Persistent elevation in incidence of pneumonia in children in England, 2023/24
Authors: Daniel Todkill, Theresa Lamagni, Richard Pebody, Mary Ramsay, Daisy Woolham, Alicia Demirjian, Antoine Salzmann, Meera Chand, Helen E Hughes, Christopher Bennett, Russell Hope, Conall H Watson, Colin S Brown, Alex J Elliot
Journal: Eurosurveillance (2024)

Since November 2023, the absolute number of attendances at emergency departments for pneumonia among children aged 5-14 years in England have been above expected levels for the time of year. This increased signal peaked during March 2024 but then persisted into early summer 2024 despite decreases in prevalence of seasonal respiratory pathogens. Record linkage between emergency department and laboratory databases points to this unusual activity being driven largely by
Perianal fistulising Crohn’s disease: utilising the TOpClass classification in clinical practice to provide targeted individualised care
Authors: Luke N. Hanna, Sulak Anandabaskaran, Nusrat Iqbal, Jeroen Geldof, Jean-Frédéric LeBlanc, Anders Dige, Lilli Lundby, Séverine Vermeire, André D’Hoore, Bram Verstockt, Gabriele Bislenghi, Danny De Looze, Triana Lobaton, Dirk Van de Putte, Antonino Spinelli, Michele Carvello, Silvio Danese, Christianne J. Buskens, Krisztina Gecse, Roel Hompes, Marte Becker, Jarmila van der Bilt, Wilhelmus Bemelman, Shaji Sebastian, Gordan Moran, Amy L. Lightner, Serre-Yu Wong, Jean-Frédéric Colombel, Benjamin L. Cohen, Stefan Holubar, Nik S. Ding, Cori Behrenbruch, Kapil Sahnan, Ravi Misra, Phillip Lung, Ailsa Hart, Phil Tozer
Journal: Clinical Gastroenterology and Hepatology (2024)

Perianal fistulation is a challenging phenotype of Crohn's disease, with significant impact on quality of life. Historically, fistulae have been classified anatomically in relation to the sphincter complex, and management guidelines have been generalized, with lack of attention to the clinical heterogenicity seen. The recent 'TOpClass classification system' for perianal fistulizing Crohn's disease (PFCD) addresses this issue, and classifies patients into defined groups, which provide a focus for fistula management that aligns with disease characteristics and patient goals. In this article, we discuss the clinical applicability of the TOpClass model and provide direction on its use in clinical practice.
GPR17 modulates anxiety-like behaviors via basolateral amygdala to ventral hippocampal CA1 glutamatergic projection
Authors: Ruizhe Nie, Xinting Zhou, Jiaru Fu, Shanshan Hu, Qilu Zhang, Weikai Jiang, Yizi Yan, Xian Cao, Danhua Yuan, Yan Long, Hao Hong, Susu Tang
Journal: Acta Pharmaceutica Sinica B (2024)

Anxiety disorders are one of the most epidemic and chronic psychiatric disorders. An incomplete understanding of anxiety pathophysiology has limited the development of highly effective drugs against these disorders. GPR17 has been shown to be involved in multiple sclerosis and some acute brain injury disorders. However, no study has investigated the role of GPR17 in psychiatric disorders. In a well-established chronic restraint stress (CRS) mouse model, using a combination of pharmacological and molecular biology techniques, viral tracing,
Proactive integrated consultation-liaison psychiatry and time spent in hospital by older medical inpatients in England (The HOME Study): a multicentre, parallel-group, randomised controlled trial
Authors: Michael Sharpe, Jane Walker, Maike van Niekerk, Mark Toynbee, Nicholas Magill, Chris Frost, Ian R White, Simon Walker, Ana Duarte, Colm Owens, Chris Dickens, Annabel Price, Michael Sharpe, Jane Walker, Maike van Niekerk, Mark Toynbee, Nicholas Magill, Chris Frost, Ian R White, Simon Walker, Ana Duarte, Colm Owens, Chris Dickens, Annabel Price, Peter Aitken, Tomasz Bajorek, Gunes Berk, Rhian Bold, Katy Burke, Jonathan Burns, Shelley Campbell, Hannah Chaitow, Felix Clay, Michael Daly, Tobit Emmens, Elliot Hampsey, Naomi Hannaway, Jessica Harris, Rowan Harwood, Laura Hill, Harriet Hobbs, Laura Hollands, Sophie Howitt, Rhian Kant, Sarah E Lamb, Daniel Lasserson, Hochang Benjamin Lee, Eleanor Macey, Aelfrida Palmer, Julie Philps, Louise Pollard, Isabelle Rocroi, Anna Scholz, Sasha Shepperd, Gabrielle Sirois-Giguere, Luke Solomons, Ben Steward, Will Turner, Michael Yousif
Journal: The Lancet Psychiatry (2024)

Older people admitted to hospital in an emergency often have prolonged inpatient stays that worsen their outcomes, increase health-care costs, and reduce bed availability. Growing evidence suggests that the biopsychosocial complexity of their problems, which include cognitive impairment, depression, anxiety, multiple medical illnesses, and care needs resulting from functional dependency, prolongs hospital stays by making medical treatment less efficient and the planning of post-discharge care more difficult. We aimed to assess the effects of enhancing older inpatients' care with Proactive Integrated Consultation-Liaison Psychiatry (PICLP) in The HOME Study. We have previously described the benefits of PICLP reported by patients and clinicians. In this Article, we report the effectiveness and cost-effectiveness of PICLP-enhanced care, compared with usual care alone, in reducing time in hospital.
Small extracellular vesicles carrying reovirus, tumor antigens, interferon-β, and damage-associated molecular patterns for efficient tumor treatment
Authors: Naomi Shuwari, Chieko Inoue, Ikuho Ishigami, Kentaro Jingushi, Mariko Kamiya, Shigeru Kawakami, Kazutake Tsujikawa, Masashi Tachibana, Hiroyuki Mizuguchi, Fuminori Sakurai
Journal: Journal of Controlled Release (2024)

Small extracellular vesicles (SEV) have attracted much attention both as mediators of intercellular communication and as drug delivery systems. In addition, recent studies have shown that SEV containing virus components and virus particles are released from virus-infected cells. Oncolytic viruses, which efficiently kill tumor cells by tumor cell-specific replication, have been actively studied as novel anticancer agents in clinical and preclinical studies. However, it remains to be fully elucidated whether SEV released from oncolytic virus-infected cells are involved in the antitumor effects of oncolytic viruses. In this study, we examined the tumor cell killing efficiencies and innate immune responses following treatment with SEV released from oncolytic reovirus-infected tumor cells in vitro and in vivo. Reovirus-infected B16 cells secreted SEV associated with or containing reovirus particles (Reo-SEV) with a diameter of approximately 130 nm and a zeta potential of -17 mV, although death of reovirus-infected B16 cells was not observed. The secreted Reo-SEV also contained interferon (IFN)-β, tumor antigens, and damage-associated molecular patterns (DAMPs), including heat shock proteins (HSPs). Reo-SEV were secreted from the tumor tissues of reovirus-injected mice. Inhibition of the SEV secretion pathway using GW4869, which is a neutral sphingomyelinase inhibitor, resulted in significant reduction in the infectious titers of reovirus in the culture supernatants, suggesting that the cells released progeny virus via the SEV secretion pathway. Reo-SEV more efficiently killed mouse tumor cells and induced innate immune responses in mouse bone marrow-derived dendritic cells than reovirus. Reovirus and Reo-SEV mediated efficient and comparable levels of growth suppression of B16 subcutaneous tumors and induction of tumor infiltration of CD8+ T cells following intravenous administration. These results indicate that Reo-SEV are a promising oncolytic agent and that SEV are an effective delivery vehicle for oncolytic virus.
Targeting PI3K family with small-molecule inhibitors in cancer therapy: current clinical status and future directions
Authors: Hongyao Li, Xiang Wen, Yueting Ren, Zhichao Fan, Jin Zhang, Gu He, Leilei Fu
Journal: Molecular Cancer (2024)

The Phosphatidylinositol-3-kinase (PI3K) family is well-known to comprise three classes of intracellular enzymes. Class I PI3Ks primarily function in signaling by responding to cell surface receptor stimulation, while class II and III are more involved in membrane transport. Under normal physiological conditions, the PI3K signaling network orchestrates cell growth, division, migration and survival. Aberrant activation of the PI3K signaling pathway disrupts cellular activity and metabolism, often marking the onset of cancer. Currently, the Food and Drug Administration (FDA) has approved the clinical use of five class I PI3K inhibitors. These small-molecule inhibitors, which exhibit varying selectivity for different class I PI3K family members, are primarily used in the treatment of breast cancer and hematologic malignancies. Therefore, the development of novel class I PI3K inhibitors has been a prominent research focus in the field of oncology, aiming to enhance potential therapeutic selectivity and effectiveness. In this review, we summarize the specific structures of PI3Ks and their functional roles in cancer progression. Additionally, we critically evaluate small molecule inhibitors that target class I PI3K, with a particular focus on their clinical applications in cancer treatment. Moreover, we aim to analyze therapeutic approaches for different types of cancers marked by aberrant PI3K activation and to identify potential molecular targets amenable to intervention with small-molecule inhibitors. Ultimately, we propose future directions for the development of therapeutic strategies that optimize cancer treatment outcomes by modulating the PI3K family.
Metadata-enhanced contrastive learning from retinal optical coherence tomography images
Authors: Robbie Holland, Oliver Leingang, Hrvoje Bogunović, Sophie Riedl, Lars Fritsche, Toby Prevost, Hendrik P.N. Scholl, Ursula Schmidt-Erfurth, Sobha Sivaprasad, Andrew J. Lotery, Daniel Rueckert, Martin J. Menten
Journal: Medical Image Analysis (2024)

Deep learning has potential to automate screening, monitoring and grading of disease in medical images. Pretraining with contrastive learning enables models to extract robust and generalisable features from natural image datasets, facilitating label-efficient downstream image analysis. However, the direct application of conventional contrastive methods to medical datasets introduces two domain-specific issues. Firstly, several image transformations which have been shown to be crucial for effective contrastive learning do not translate from the natural image to the medical image domain. Secondly, the assumption made by conventional methods, that any two images are dissimilar, is systematically misleading in medical datasets depicting the same anatomy and disease. This is exacerbated in longitudinal image datasets that repeatedly image the same patient cohort to monitor their disease progression over time. In this paper we tackle these issues by extending conventional contrastive frameworks with a novel metadata-enhanced strategy. Our approach employs widely available patient metadata to approximate the true set of inter-image contrastive relationships. To this end we employ records for patient identity, eye position (i.e. left or right) and time series information. In experiments using two large longitudinal datasets containing 170,427 retinal optical coherence tomography (OCT) images of 7912 patients with age-related macular degeneration (AMD), we evaluate the utility of using metadata to incorporate the temporal dynamics of disease progression into pretraining. Our metadata-enhanced approach outperforms both standard contrastive methods and a retinal image foundation model in five out of six image-level downstream tasks related to AMD. We find benefits in both a low-data and high-data regime across tasks ranging from AMD stage and type classification to prediction of visual acuity. Due to its modularity, our method can be quickly and cost-effectively tested to establish the potential benefits of including available metadata in contrastive pretraining.
Trends in invasive Haemophilus influenzae serotype b (Hib) disease in England; 2012/13 to 2022/23
Authors: Erjola Hani, Fariyo Abdullahi, Marta Bertran, Seyi Eletu, Joshua D’Aeth, David J. Litt, Norman K. Fry, Shamez N. Ladhani
Journal: Journal of Infection (2024)

Haemophilus influenzae serotype b (Hib) conjugate vaccines have been highly successful in reducing the Hib disease worldwide. Recently, several European countries have reported an increase in invasive Hib disease. We aimed to describe the epidemiology, clinical characteristics, genomic trends, and outcomes of invasive Hib disease over the past 11 years in England.
A Sticky Mess- Are moisturizers over-utilized in dermatitis care?
Authors: Susan Nedorost
Journal: Journal of the American Academy of Dermatology (2024)

Microbial dysbiosis is increasingly understood to influence allergic sensitization and skin barrier defects in dermatitis. Occlusion, such as from moisturizers, fosters microbial dysbiosis, and increases itch in many patients with dermatitis. Nevertheless, use of moisturizers in dermatitis remains part of dermatologic guidelines. This is a review of the evidence of benefits and adverse effects of moisturizers in dermatitis and a proposal for moderation in their clinical use.