tbuckley/cabot-search huggingface dataset:
Dietary Polycyclic Aromatic Hydrocarbon (PAH) Consumption and Risk of Adverse Birth Outcomes: A Systematic Review and Meta-Analysis
Authors: Christian Sewor, Sebastian Eliason, Jouni J.K. Jaakkola, A. Kofi Amegah
Journal: Environmental Health Perspectives (2024)

There is suggestive epidemiological evidence that maternal dietary polycyclic aromatic hydrocarbons (PAH) may increase the risk of adverse birth outcomes. We sought to summarize the available evidence on the effect of dietary PAH exposure on birth outcomes.
Electronic Alerts in Acute Kidney Injury—More Questions Than Answers
Authors: Shabnam Hamidi, S. Joseph Kim, Bourne L. Auguste
Journal: JAMA Network Open (2024)

Ting Li, MD, PhD; Buyun Wu, MD, PhD; Li Li, MD; Ao Bian, MD, PhD; Juan Ni, MD; Kang Liu, MD; Zhongke Qin, MD; Yudie Peng, MD; Yining Shen, MD; Mengru Lv, MD; Xinyi Lu, MD; Changying Xing, MD, PhD; Huijuan Mao, MD, PhD
Erosive hand osteoarthritis and sarcopenia: data from Osteoarthritis Initiative cohort
Authors: Kamyar Moradi, Robert M Kwee, Bahram Mohajer, Ali Guermazi, Frank W Roemer, Hamza Ahmed Ibad, Ida K Haugen, Francis Berenbaum, Shadpour Demehri
Journal: Annals of the Rheumatic Diseases (2024)

There is no evidence linking specific osteoarthritis (OA) types, such as erosive hand OA (EHOA), with distant generalised changes in muscle composition (sarcopenia), which can potentially be modified. This study pioneers the exploration of the association between EHOA and sarcopenia, both of which are predominantly observed in the older adults.
The IDEAL framework for surgical robotics: development, comparative evaluation and long-term monitoring
Authors: Hani J. Marcus, Pedro T. Ramirez, Danyal Z. Khan, Hugo Layard Horsfall, John G. Hanrahan, Simon C. Williams, David J. Beard, Rani Bhat, Ken Catchpole, Andrew Cook, Katrina Hutchison, Janet Martin, Tom Melvin, Danail Stoyanov, Maroeska Rovers, Nicholas Raison, Prokar Dasgupta, David Noonan, Deborah Stocken, Georgia Sturt, Anne Vanhoestenberghe, Baptiste Vasey, Peter McCulloch, Aswin Chari, Fanny Ficuciello, Effy Vayena, Christopher Baber, Marco Zenati, Alan Kuntz, Karen Kerr, Nigel Horwood, Katherine Anderon, Ka-Wai Kwok, Rich Mahoney, Bill Peine, Ferdinando Rodriquez Y. Baena, Pietro Valdastri, Richard Leparmentier, Len Evans, Rebecca Langley, Garnette Sutherland, Sanju Lama, Naeem Soomro, Justin Collins, Mario M. Leitao, James Kinross, Alvin Goh, Bernard Park, Matthias Weigl, Rebecca Randell, Steven Yule, Duncan McPherson, Laura Pickup, Richard Skipworth, Jennifer Anger, Denny Yu, Lora Cavuoto, Ann Bisantz, Tara Cohen, Mirre Scholte, Guy Maddern, Laura Sampietro-Colom, Alane Clark, Tammy J. Clifford, Belen Corbacho, Cynthia Iglesias, Janneke Grutters, Katrina Hutchinson, Lesley Booth, Heather Draper, Len Evans, Sarah Goering, Alexander A. Kon, Rebecca Langley, Rob Sparrow, Kamran Ahmed, Deena Harji, Teodor Grantcharov, Lars Konge, Art Sedrakyan, Joel Horowitz, Arsenio Paez
Journal: Nature Medicine (2024)
Mental health changes in partners of transgender and gender nonconforming individuals as a result of partner gender transition: What about me?
Authors: Kyle M. Ockerman, Sabrina H. Han, Rachel H. Safeek, Markos Mardourian, Nhan S. Trieu, Bauback Safa, Alexes Hazen, Sarah Sorice-Virk
Journal: International Journal of Transgender Health (2024)

Purpose Research on the psychosocial impact of gender transitioning on partners of transgender and gender nonconforming (TGNC) individuals is scarce in the literature. Here, we assessed mental health in partners of TGNC individuals.
Principlism and contemporary ethical considerations for providers of transgender health care
Authors: Luke R. Allen, Noah Adams, Florence Ashley, Cody Dodd, Diane Ehrensaft, Lin Fraser, Maurice Garcia, Simona Giordano, Jamison Green, Thomas Johnson, Justin Penny, Katherine Rachlin, Jaimie Veale
Journal: International Journal of Transgender Health (2024)

Background: Transgender health care is a subject of much debate among clinicians, political commentators, and policy-makers. While the World Professional Association of Transgender Health (WPATH) Standards of Care (SOC) establish clinical standards, these standards contain implied ethics but lack explicit focused discussion of ethical considerations in providing care. An ethics chapter in the SOC would enhance clinical guidelines.
Gut microbiome for predicting immune checkpoint blockade-associated adverse events
Authors: Muni Hu, Xiaolin Lin, Tiantian Sun, Xiaoyan Shao, Xiaowen Huang, Weiwei Du, Mengzhe Guo, Xiaoqiang Zhu, Yilu Zhou, Tianying Tong, Fangfang Guo, Ting Han, Xiuqi Wu, Yi Shi, Xiuying Xiao, Youwei Zhang, Jie Hong, Haoyan Chen
Journal: Genome Medicine (2024)

Abstract Background The impact of the gut microbiome on the initiation and intensity of immune-related adverse events (irAEs) prompted by immune checkpoint inhibitors (ICIs) is widely acknowledged. Nevertheless, there is inconsistency in the gut microbial associations with irAEs reported across various studies. Methods We performed a comprehensive analysis leveraging a dataset that included published microbiome data ( n = 317) and in-house generated data from 16S rRNA and shotgun metagenome samples of irAEs ( n = 115). We utilized a machine learning-based approach, specifically the Random Forest (RF) algorithm, to construct a microbiome-based classifier capable of distinguishing between non-irAEs and irAEs. Additionally, we conducted a comprehensive analysis, integrating transcriptome and metagenome profiling, to explore potential underlying mechanisms. Results We identified specific microbial species capable of distinguishing between patients experiencing irAEs and non-irAEs. The RF classifier, developed using 14 microbial features, demonstrated robust discriminatory power between non-irAEs and irAEs (AUC = 0.88). Moreover, the predictive score from our classifier exhibited significant discriminative capability for identifying non-irAEs in two independent cohorts. Our functional analysis revealed that the altered microbiome in non-irAEs was characterized by an increased menaquinone biosynthesis, accompanied by elevated expression of rate-limiting enzymes menH and menC . Targeted metabolomics analysis further highlighted a notably higher abundance of menaquinone in the serum of patients who did not develop irAEs compared to the irAEs group. Conclusions Our study underscores the potential of microbial biomarkers for predicting the onset of irAEs and highlights menaquinone, a metabolite derived from the microbiome community, as a possible selective therapeutic agent for modulating the occurrence of irAEs.
Recurrent lymphoid and myeloid relapses due to treatment cessations reveal natural history of Ph‐positive B‐ALL and pose a diagnostic challenge
Authors: Shimin Hu, Elias J. Jabbour, Collin Y. Hu, Guilin Tang, Wei Wang, L. Jeffrey Medeiros, Carlos Bueso‐Ramos
Journal: American Journal of Hematology (2024)

Ph+ B-ALL or Lymphoid blast phase of CML. The authors declare no conflict of interest with regard to content of this study. The data supporting this study's findings are available from the corresponding author upon reasonable request.
Author Correction: Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial
Authors: Matthew D. Galsky, Siamak Daneshmand, Sudeh Izadmehr, Edgar Gonzalez-Kozlova, Kevin G. Chan, Sara Lewis, Bassam El Achkar, Tanya B. Dorff, Jeremy Paul Cetnar, Brock O. Neil, Anishka D’Souza, Ronac Mamtani, Christos Kyriakopoulos, Tomi Jun, Mahalya Gogerly-Moragoda, Rachel Brody, Hui Xie, Kai Nie, Geoffrey Kelly, Amir Horowitz, Yayoi Kinoshita, Ethan Ellis, Yohei Nose, Giorgio Ioannou, Rafael Cabal, Diane M. Del Valle, G. Kenneth Haines, Li Wang, Kent W. Mouw, Robert M. Samstein, Reza Mehrazin, Nina Bhardwaj, Menggang Yu, Qianqian Zhao, Seunghee Kim-Schulze, Robert Sebra, Jun Zhu, Sacha Gnjatic, John Sfakianos, Sumanta K. Pal
Journal: Nature Medicine (2024)
Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses
Authors: Lu Lu, Feifei Zhang, Liam Brierley, Gail Robertson, Margo Chase-Topping, Samantha Lycett, Mark Woolhouse
Journal: Molecular Biology and Evolution (2024)

Abstract Transmissibility, the ability to spread within host populations, is a prerequisite for a pathogen to have epidemic or pandemic potential. Here, we estimate the phylogenies of human infectivity and transmissibility using 1,408 genome sequences from 743 distinct RNA virus species/types in 59 genera. By repeating this analysis using data sets censored by virus discovery date, we explore how temporal changes in the known diversity of RNA viruses—especially recent increases in recognized nonhuman viruses—have altered these phylogenies. Over time, we find significant increases in the proportion of RNA virus genera estimated to have a nonhuman-infective ancestral state, in the fraction of distinct human virus lineages that are purely human-transmissible or strictly zoonotic (compared to mixed lineages), and in the number of human viruses with nearest relatives known not to infect humans. Our results are consistent with viruses that are capable of spreading in human populations commonly emerging from a nonhuman reservoir. This is more likely in lineages that already contain human-transmissible viruses but is rare in lineages that contain only strictly zoonotic viruses.
Compact CRISPR genetic screens enabled by improved guide RNA library cloning
Authors: Seok-Jin Heo, Lauren D. Enriquez, Scot Federman, Amy Y. Chang, Rachel Mace, Kaivalya Shevade, Phuong Nguyen, Adam J. Litterman, Shawn Shafer, Laralynne Przybyla, Eric D. Chow
Journal: Genome biology (2024)

Abstract CRISPR genome editing approaches theoretically enable researchers to define the function of each human gene in specific cell types, but challenges remain to efficiently perform genetic perturbations in relevant models. In this work, we develop a library cloning protocol that increases sgRNA uniformity and greatly reduces bias in existing genome-wide libraries. We demonstrate that our libraries can achieve equivalent or better statistical power compared to previously reported screens using an order of magnitude fewer cells. This improved cloning protocol enables genome-scale CRISPR screens in technically challenging cell models and screen formats.
Non-canonical antigens are the largest fraction of peptides presented by MHC class I in mismatch repair deficient murine colorectal cancer
Authors: Giuseppe Rospo, Rosaria Chilà, Vittoria Matafora, Veronica Basso, Simona Lamba, Alice Bartolini, Angela Bachi, Federica Di Nicolantonio, Anna Mondino, Giovanni Germano, Alberto Bardelli
Journal: Genome Medicine (2024)

Abstract Background Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate into a wide array of neoepitopes; however, a systematic classification of the neoantigen repertoire in MMRd CRC is lacking. Mass spectrometry peptidomics has demonstrated the existence of MHC class I associated peptides (MAPs) originating from non-coding DNA regions. Based on these premises we investigated DNA genomic regions responsible for generating MMRd-induced peptides. Methods We exploited mouse CRC models in which the MMR gene Mlh1 was genetically inactivated. Isogenic cell lines CT26 Mlh1 +/+ and Mlh1 -/- were inoculated in immunocompromised and immunocompetent mice. Whole genome and RNA sequencing data were generated from samples obtained before and after injection in murine hosts. First, peptide databases were built from transcriptomes of isogenic cell lines. We then compiled a database of peptides lost after tumor cells injection in immunocompetent mice, likely due to immune editing. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matched next-generation sequencing databases were employed to identify the DNA regions from which the immune-targeted MAPs originated. Finally, we adopted in vitro T cell assays to verify whether MAP-specific T cells were part of the in vivo immune response against Mlh1 -/- cells. Results Whole genome sequencing analyses revealed an unbalanced distribution of immune edited alterations across the genome in Mlh1 -/- cells grown in immunocompetent mice. Specifically, untranslated (UTR) and coding regions exhibited the largest fraction of mutations leading to highly immunogenic peptides. Moreover, the integrated computational and LC-MS/MS analyses revealed that MAPs originate mainly from atypical translational events in both Mlh1 +/+ and Mlh1 -/- tumor cells. In addition, mutated MAPs—derived from UTRs and out-of-frame translation of coding regions—were highly enriched in Mlh1 -/- cells. The MAPs trigger T-cell activation in mice primed with Mlh1 -/- cells. Conclusions Our results suggest that—in comparison to MMR proficient CRC—MMRd tumors generate a significantly higher number of non-canonical mutated peptides able to elicit T cell responses. These results reveal the importance of evaluating the diversity of neoepitope repertoire in MMRd tumors.
Author Correction: Neuronal types in the mouse amygdala and their transcriptional response to fear conditioning
Authors: Hannah Hochgerner, Shelly Singh, Muhammad Tibi, Zhige Lin, Niv Skarbianskis, Inbal Admati, Osnat Ophir, Nuphar Reinhardt, Shai Netser, Shlomo Wagner, Amit Zeisel
Journal: Nature Neuroscience (2024)
Dynamic and selective engrams emerge with memory consolidation
Authors: Douglas Feitosa Tomé, Ying Zhang, Tomomi Aida, Olivia Mosto, Yifeng Lu, Mandy Chen, Sadra Sadeh, Dheeraj S. Roy, Claudia Clopath
Journal: Nature Neuroscience (2024)

Episodic memories are encoded by experience-activated neuronal ensembles that remain necessary and sufficient for recall. However, the temporal evolution of memory engrams after initial encoding is unclear. In this study, we employed computational and experimental approaches to examine how the neural composition and selectivity of engrams change with memory consolidation. Our spiking neural network model yielded testable predictions: memories transition from unselective to selective as neurons drop out of and drop into engrams; inhibitory activity during recall is essential for memory selectivity; and inhibitory synaptic plasticity during memory consolidation is critical for engrams to become selective. Using activity-dependent labeling, longitudinal calcium imaging and a combination of optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted contextual fear conditioning experiments that supported our model's predictions. Our results reveal that memory engrams are dynamic and that changes in engram composition mediated by inhibitory plasticity are crucial for the emergence of memory selectivity.
Adjuvant sintilimab in resected high-risk hepatocellular carcinoma: a randomized, controlled, phase 2 trial
Authors: Kang Wang, Yan-Jun Xiang, Hong-Ming Yu, Yu-Qiang Cheng, Zong-Han Liu, Ying-Yi Qin, Jie Shi, Wei-Xing Guo, Chong-De Lu, Ya-Xin Zheng, Fei-Guo Zhou, Mao-Lin Yan, Hong-Kun Zhou, Chao Liang, Fan Zhang, Wen-Jing Wei, Wan Yee Lau, Jing-Jing Li, Yan-Fang Liu, Shu-Qun Cheng
Journal: Nature Medicine (2024)
Causality-enriched epigenetic age uncouples damage and adaptation
Authors: Kejun Ying, Hanna Liu, Andrei E. Tarkhov, Marie C. Sadler, Ake T. Lu, Mahdi Moqri, Steve Horvath, Zoltán Kutalik, Xia Shen, Vadim N. Gladyshev
Journal: Nature Aging (2024)
A generative model of memory construction and consolidation
Authors: Eleanor Spens, Neil Burgess
Journal: Nature Human Behaviour (2024)

Abstract Episodic memories are (re)constructed, share neural substrates with imagination, combine unique features with schema-based predictions and show schema-based distortions that increase with consolidation. Here we present a computational model in which hippocampal replay (from an autoassociative network) trains generative models (variational autoencoders) to (re)create sensory experiences from latent variable representations in entorhinal, medial prefrontal and anterolateral temporal cortices via the hippocampal formation. Simulations show effects of memory age and hippocampal lesions in agreement with previous models, but also provide mechanisms for semantic memory, imagination, episodic future thinking, relational inference and schema-based distortions including boundary extension. The model explains how unique sensory and predictable conceptual elements of memories are stored and reconstructed by efficiently combining both hippocampal and neocortical systems, optimizing the use of limited hippocampal storage for new and unusual information. Overall, we believe hippocampal replay training generative models provides a comprehensive account of memory construction, imagination and consolidation.
An ETFDH-driven metabolon supports OXPHOS efficiency in skeletal muscle by regulating coenzyme Q homeostasis
Authors: Juan Cruz Herrero Martín, Beñat Salegi Ansa, Gerardo Álvarez-Rivera, Sonia Domínguez-Zorita, Pilar Rodríguez-Pombo, Belén Pérez, Enrique Calvo, Alberto Paradela, David G. Miguez, Alejandro Cifuentes, José M. Cuezva, Laura Formentini
Journal: Nature Metabolism (2024)

Abstract Coenzyme Q (Q) is a key lipid electron transporter, but several aspects of its biosynthesis and redox homeostasis remain undefined. Various flavoproteins reduce ubiquinone (oxidized form of Q) to ubiquinol (QH 2 ); however, in eukaryotes, only oxidative phosphorylation (OXPHOS) complex III (CIII) oxidizes QH 2 to Q. The mechanism of action of CIII is still debated. Herein, we show that the Q reductase electron-transfer flavoprotein dehydrogenase (ETFDH) is essential for CIII activity in skeletal muscle. We identify a complex (comprising ETFDH, CIII and the Q-biosynthesis regulator COQ2) that directs electrons from lipid substrates to the respiratory chain, thereby reducing electron leaks and reactive oxygen species production. This metabolon maintains total Q levels, minimizes QH 2 -reductive stress and improves OXPHOS efficiency. Muscle-specific Etfdh −/− mice develop myopathy due to CIII dysfunction, indicating that ETFDH is a required OXPHOS component and a potential therapeutic target for mitochondrial redox medicine.
Ralstonia pickettii bloodstream infections with potential genomic link to internationally distributed contaminated saline solution, Germany, October 2023
Authors: Manuel Krone, Vera Rauschenberger, Vera Blaschke, Heike Claus, Oliver Kurzai, Stefanie Kampmeier
Journal: Eurosurveillance (2024)

Ralstonia pickettii is a Gram-negative rod which may cause invasive infections when they contaminate liquid medical products. After R. pickettii was detected in blood cultures and a stem cell product from three patients in a tertiary care hospital in Germany, whole genome sequencing of these three isolates and two water isolates from the environment was performed. Core genome multilocus sequence typing analysis showed that the three patient isolates were closely related and there was a large distance to the environmental isolates. In a genomic comparison, the patients’ isolates were distantly related to an R. pickettii strain from a cluster in Australia suspected to be caused by contaminated saline produced in India, while all liquid medical products with a link to all patients were produced in Europe or the United States. Our data point towards an ongoing risk by an unknown common source that could be traced back to medical products contaminated with R. pickettii and potentially distributed worldwide. Investigating invasive R. pickettii infections, identifying and testing medical products administered to the patients and timely whole genome sequencing may help identify the exact source of this potentially global outbreak.
A case of swine influenza A(H1N2)v in England, November 2023
Authors: Jade Cogdale, Beatrix Kele, Richard Myers, Ruth Harvey, Abi Lofts, Tanya Mikaiel, Katja Hoschler, Ashley C Banyard, Joe James, Benjamin C Mollett, Alexander MP Byrne, Jamie Lopez-Bernal, Conall H Watson, Meera Chand, William Welfare, Deborah A Williamson, Isabel Oliver, Simon Padfield, Andrew Lee, Suzanne Calvert, Martin A Bewley, Louise Wallace, Simon deLusignan, Nicola S Lewis, Ian H Brown, Maria Zambon
Journal: Eurosurveillance (2024)

Under International Health Regulations from 2005, a human infection caused by a novel influenza A virus variant is considered an event that has potential for high public health impact and is immediately notifiable to the World Health Organisation. We here describe the clinical, epidemiological and virological features of a confirmed human case of swine influenza A(H1N2)v in England detected through community respiratory virus surveillance. Swabbing and contact tracing helped refine public health risk assessment, following this unusual and unexpected finding.
Time trends and modifiable factors of COVID-19 contact tracing coverage, Geneva, Switzerland, June 2020 to February 2022
Authors: Denis Mongin, Nils Bürgisser, Delphine Sophie Courvoisier
Journal: Eurosurveillance (2024)

Background Contact tracing was one of the central non-pharmaceutical interventions implemented worldwide to control the spread of SARS-CoV-2, but its effectiveness depends on its ability to detect contacts. Aim Evaluate the proportion of secondary infections captured by the contact tracing system in Geneva. Methods We analysed 166,892 concomitant infections occurring at the same given address from June 2020 until February 2022 using an extensive operational database of SARS-CoV-2 tests in Geneva. We used permutation to compare the total number of secondary infections occurring at the same address with that reported through manual contact tracing. Results Contact tracing captured on average 41% of secondary infections, varying from 23% during epidemic peaks to 60% during low epidemic activity. People living in wealthy neighbourhoods were less likely to report contacts (odds ratio (OR): 1.6). People living in apartment buildings were also less likely to report contacts than those living in a house (OR: 1.1–3.1) depending on the SARS-CoV-2 variant, the building size and the presence of shops. This under-reporting of contacts in apartment buildings decreased during periods of mandatory wearing of face masks and restrictions on private gatherings. Conclusion Contact tracing alone did not detect sufficient secondary infections to reduce the spread of SARS-CoV-2. Campaigns targeting specific populations, such as those in wealthy areas or apartment buildings, could enhance coverage. Additionally, measures like wearing face masks, improving ventilation and implementing restrictions on gatherings should also be considered to reduce infections resulting from interactions that may not be perceived as high risk.
Early-onset group B streptococcal infections in five Nordic countries with different prevention policies, 1995 to 2019
Authors: Verna Björklund, Harri Saxén, Olof Hertting, Emma Louise Malchau Carlsen, Steen Hoffmann, Stellan Håkansson, Valtýr Stefánsson Thors, Ásgeir Haraldsson, Anne Karin Brigtsen, Henrik Döllner, Heikki Huhtamäki, Tytti Pokka, Terhi Susanna Ruuska
Journal: Eurosurveillance (2024)

BackgroundNeonatal early-onset disease caused by group B