tbuckley/cabot-search huggingface dataset:
Exploring the origins and evolution of oxygenic and anoxygenic photosynthesis in deeply branched <i>Cyanobacteriota</i>
Authors: Sha Tan, Lan Liu, Jian-Yu Jiao, Meng-Meng Li, Chao-Jian Hu, Ai-Ping Lv, Yan-Ling Qi, Yu-Xian Li, Yang-Zhi Rao, Yan-Ni Qu, Hong-Chen Jiang, Rochelle M Soo, Paul N Evans, Zheng-Shuang Hua, Wen-Jun Li
Journal: Molecular Biology and Evolution (2024)

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.
Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish
Authors: Li Ren, Mengxue Luo, Jialin Cui, Xin Gao, Hong Zhang, Ping Wu, Zehong Wei, Yakui Tai, Mengdan Li, Kaikun Luo, Shaojun Liu
Journal: Genomics Proteomics & Bioinformatics (2024)

Abstract Intergeneric hybridization greatly reshapes regulatory interactions among allelic and non-allelic genes. However, their effects on growth diversity remain poorly understood in animals. In this study, we conducted whole-genome sequencing and RNA sequencing (RNA-seq) analyses in diverse hybrid varieties resulting from the intergeneric hybridization of goldfish (Carassius auratus red var.) and common carp (Cyprinus carpio). These hybrid individuals were characterized by distinct mitochondrial genomes and copy number variations. Through a weighted gene correlation network analysis, we identified 3693 genes as candidate growth-regulated genes. Among them, the expression of 3672 genes in subgenome R (originating from goldfish) displayed negative correlations with growth rate, whereas 20 genes in subgenome C (originating from common carp) exhibited positive correlations. Notably, we observed intriguing patterns in the expression of slc2a12 in subgenome C, showing opposite correlations with body weight that changed with water temperatures, suggesting differential interactions between feeding activity and weight gain in response to seasonal changes for hybrid animals. In 40.31% of alleles, we observed dominant trans-regulatory effects in the regulatory interaction between distinct alleles from subgenomes R and C. Integrating analyses of allelic-specific expression and DNA methylation data revealed that the influence of DNA methylation on both subgenomes shapes the relative contribution of allelic expression to the growth rate. These findings provide novel insights into the interaction of distinct subgenomes that underlie heterosis in growth traits and contribute to a better understanding of multiple allele traits in animals.
PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era
Authors: Yu-Hao Huang, Yi-Fei Sun, Hao Li, Hao-Sen Li, Hong Pang
Journal: Molecular Biology and Evolution (2024)

The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.
Nano-mupirocin as tumor-targeted antibiotic: Physicochemical, immunotoxicological and pharmacokinetic characterization, and effect on gut microbiome
Authors: Ahuva Cern, Sarah L. Skoczen, Kelsie S. Snapp, Atara Hod, Daniel Zilbersheid, Yaelle Bavli, Tamar Alon-Maimon, Gilad Bachrach, Xiaohui Wei, Bella Berman, Moran Yassour, Edward Cedrone, Barry W. Neun, Marina A. Dobrovolskaia, Jeffrey D. Clogston, Stephan T. Stern, Yechezkel Barenholz
Journal: Journal of Controlled Release (2024)
Understanding the role of swirling flow in dry powder inhalers implications for design considerations and pulmonary delivery
Authors: Jiale Chen, Yuqing Ye, Qingliang Yang, Ziyi Fan, Yuanyuan Shao, Xiaoyang Wei, Kaiqi Shi, Jie Dong, Ying Ma, Jesse Zhu
Journal: Journal of Controlled Release (2024)

Dry powder inhalers (DPIs) are widely employed to treat respiratory diseases, offering numerous advantages such as high dose capacity and stable formulations. However, they usually face challenges in achieving sufficient pulmonary drug delivery and minimizing excessive oropharyngeal deposition. This review provides a new viewpoint to address these challenges by focusing on the role of swirling flow, a crucial yet under-researched aspect that induces strong turbulence. In the review, we comprehensively discuss both key classic designs (tangential inlet, swirling chamber, grid mesh, and mouthpiece) and innovative designs in inhalers, exploring how the induced swirling flow initiates powder dispersion and promotes delivery efficiency. Valuable design considerations to effectively coordinate inhalers with formulations and patients are also provided. It is highlighted that the delicate manipulation of swirling flow is essential to maximize benefits. By emphasizing the role of swirling flow and its potential application, this review offers promising insights for advancing DPI technology and optimizing therapeutic outcomes in inhaled therapy.
Improving the accuracy of bulk fitness assays by correcting barcode processing biases
Authors: Ryan Seamus McGee, Grant Kinsler, Dmitri Petrov, Mikhail Tikhonov
Journal: Molecular Biology and Evolution (2024)

Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.
Feasibility of wearable sensor signals and self-reported symptoms to prompt at-home testing for acute respiratory viruses in the USA (DETECT-AHEAD): a decentralised, randomised controlled trial
Authors: Giorgio Quer, Erin Coughlin, Jorge Villacian, Felipe Delgado, Katherine Harris, John Verrant, Matteo Gadaleta, Ting-Yang Hung, Janna Ter Meer, Jennifer M Radin, Edward Ramos, Monique Adams, Lomi Kim, Jason W Chien, Katie Baca-Motes, Jay A Pandit, Dmitri Talantov, Steven R Steinhubl
Journal: The Lancet Digital Health (2024)
Effectiveness of pneumococcal vaccination in adults with common immune-mediated inflammatory diseases in the UK: a case–control study
Authors: Georgina Nakafero, Matthew J Grainge, Tim Card, Christian D Mallen, Jonathan S Nguyen Van-Tam, Abhishek Abhishek
Journal: The Lancet Rheumatology (2024)

People with immune-mediated inflammatory disease are at increased risk of pneumococcal pneumonia. The effectiveness of pneumococcal vaccination in people with immune-mediated inflammatory diseases has not been evaluated. We investigated the effectiveness of pneumococcal vaccination in preventing morbidity and mortality associated with pneumonia in patients with immune-mediated inflammatory diseases.
3-Dimensional Echocardiographic Prediction of Left Ventricular Outflow Tract Area Prior to Transcatheter Mitral Valve Replacement
Authors: Joanna Bartkowiak, Chrisoula Dernektsi, Vratika Agarwal, Mark A Lebehn, Treena A Williams, Russel A Brandwein, Nicolas Brugger, Christoph Gräni, Stephan Windecker, Torsten P Vahl, Tamim M Nazif, Isaac George, Susheel K Kodali, Fabien Praz, Rebecca T Hahn
Journal: JACC. Cardiovascular imaging (2024)
Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system
Authors: Vini Tiwari, Bharat Prajapati, Yaw Asare, Alkmini Damkou, Hao Ji, Lu Liu, Nawraa Naser, Garyfallia Gouna, Katarzyna B. Leszczyńska, Jakub Mieczkowski, Martin Dichgans, Qing Wang, Riki Kawaguchi, Zechuan Shi, Vivek Swarup, Daniel H. Geschwind, Marco Prinz, Ozgun Gokce, Mikael Simons
Journal: Immunity (2024)

The reduced ability of the central nervous system to regenerate with increasing age limits functional recovery following demyelinating injury. Previous work has shown that myelin debris can overwhelm the metabolic capacity of microglia, thereby impeding tissue regeneration in aging, but the underlying mechanisms are unknown. In a model of demyelination, we found that a substantial number of genes that were not effectively activated in aged myeloid cells displayed epigenetic modifications associated with restricted chromatin accessibility. Ablation of two class I histone deacetylases in microglia was sufficient to restore the capacity of aged mice to remyelinate lesioned tissue. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune reprogramming.
An NIR-propelled janus nanomotor with enhanced ROS-scavenging, immunomodulating and biofilm-eradicating capacity for periodontitis treatment
Authors: Xuan Bai, Wenan Peng, Ying Tang, Ziming Wang, Jingmei Guo, Fangfang Song, Hongye Yang, Cui Huang
Journal: Bioactive Materials (2024)

Periodontitis is an inflammatory disease caused by bacterial biofilms, which leads to the destruction of periodontal tissue. Current treatments, such as mechanical cleaning and antibiotics, struggle to effectively address the persistent biofilms, inflammation, and tissue damage. A new approach involves developing a Janus nanomotor (J-CeM@Au) by coating cerium dioxide-doped mesoporous silica (CeM) with gold nanoparticles (AuNPs). This nanomotor exhibits thermophoretic motion when exposed to near-infrared (NIR) laser light due to the temperature gradient produced by the photothermal effects of asymmetrically distributed AuNPs. The NIR laser provides the energy for propulsion and activates the nanomotor's antibacterial properties, allowing it to penetrate biofilms and kill bacteria. Additionally, the nanomotor's ability to scavenge reactive oxygen species (ROS) can modulate the immune response and create a regenerative environment, promoting the healing of periodontal tissue. Overall, this multifunctional nanomotor offers a promising new approach for treating periodontitis by simultaneously addressing biofilm management and immune modulation with autonomous movement.
Limitations for Assessing Optimism and Physical Functioning in Women
Authors: Chung-Chun Cheng, Peng-Ju Huang, Chia-Hao Hsu
Journal: JAMA Psychiatry (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Psychiatry HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Psychiatry journal
Does a Patient’s Ability to Pay For Health Care Make Their Life Worth Saving?
Authors: Zara Cooper
Journal: JAMA Network Open (2024)

Graeme Hoit, MD; Duminda N. Wijeysundera, MD, PhD; Doulia M. Hamad, MD; Aaron Nauth, MD, MSc; Amit Atrey, MD, MSc; Mansur Halai, MD; Eric Walser, MD, MSc; Anton Nikouline, MD; Avery B. Nathens, MD, PhD, MPH; Amir Khoshbin, MD, MSc
Area Deprivation and Disease Severity in Adult Patients With Discoid Lupus Erythematosus
Authors: Daniella Forman Faden, Lillian Xie, Caroline Stone, Lais Lopes Almeida Gomes, Todd Le, Nnenna Ezeh, William R. Buckingham, Amy Kind, Ruth Ann Vleugels, Victoria P. Werth, Lisa Arkin, Katharina S. Shaw
Journal: JAMA Dermatology (2024)

Importance The association of area deprivation with outcomes in discoid lupus erythematosus (DLE) remains poorly understood. Objective To determine the association between US Census block measures of deprivation and disease severity in adult patients with DLE. Design, Setting, and Participants This cross-sectional study included 154 patients with DLE seen between January 1, 2007, and January 1, 2024, at a single-center referral-based specialty rheumatologic-dermatology clinic in Philadelphia, Pennsylvania. Patients were aged 18 to 73 years and were enrolled in the University of Pennsylvania’s Cutaneous Lupus Erythematosus Database study. Data were analyzed between January 1, 2024, and May 8, 2024. Exposures Residence in a highly disadvantaged area as geocoded by a state area deprivation index (ADI). Main Outcomes and Measures The main outcome was DLE disease severity as codified by the validated Cutaneous Lupus Erythematosus Disease Area and Severity Index (CLASI) damage and activity scores. Results A total of 154 adult patients with DLE (128 women [83%] and 26 men [17%]; mean [SD] age, 43 [13] years; 6 [4%] Asian individuals, 98 [64%] Black individuals, 2 [1%] Hispanic individuals, 46 [30%] White individuals, and 2 individuals [1%] with other race or ethnicity; 78 [51%] with an ADI &amp;amp;gt;5; 43 who currently smoked [28%];and 56 [36%] with concurrent systemic lupus erythematosus) were included in the analysis. By multivariable logistic regression, residence within communities with an ADI greater than 5 was associated with nearly 4-fold greater odds of moderate to severe damage (odds ratio [OR], 3.90; 95% CI, 1.27-12.69] and activity (OR, 3.31; 95% CI, 1.27-9.44). Concurrent cigarette smoking was similarly associated with greater odds of moderate to severe damage (OR, 3.15; 95% CI, 1.09-10.29). After controlling for ADI and other confounders, race was not significantly associated with DLE disease severity. Conclusions and Relevance The results of this cross-sectional study suggest that geospatial disadvantage is associated with DLE disease severity independent of race. This invites a paradigm shift that considers the social context within which racial disparities are observed, highlighting the potential for geographically targeted interventions and policy changes to improve patient outcomes in DLE.
Addressing Undertreatment of Atrial Fibrillation With Community Pharmacists
Authors: Arthur L. Allen, Geoffrey D. Barnes
Journal: JAMA Network Open (2024)

Roopinder K. Sandhu, MD, MPH; Miriam Fradette, BSc, Pharm; Meng Lin, MSc; Erik Youngson, MMath; Darren Lau, MD; Tammy J. Bungard, BSP, PharmD; Ross T. Tsuyuki, PharmD, MSc; Lisa Dolovich, PharmD, MSc; Jeff S. Healey, MD, MSc; Finlay A. McAlister, MD, MSc
Isatuximab plus carfilzomib–dexamethasone versus carfilzomib–dexamethasone in patients with relapsed multiple myeloma (IKEMA): overall survival analysis of a phase 3, randomised, controlled trial
Authors: Kwee Yong, Thomas Martin, Meletios-Athanasios Dimopoulos, Joseph Mikhael, Marcelo Capra, Thierry Facon, Roman Hajek, Ivan Špička, Ross Baker, Kihyun Kim, Gracia Martinez, Chang-Ki Min, Ludek Pour, Xavier Leleu, Albert Oriol, Youngil Koh, Kenshi Suzuki, France Casca, Sandrine Macé, Marie-Laure Risse, Philippe Moreau
Journal: The Lancet Haematology (2024)
Brentuximab vedotin plus cyclophosphamide, doxorubicin, etoposide, and prednisone followed by brentuximab vedotin consolidation in CD30-positive peripheral T-cell lymphomas: a multicentre, single-arm, phase 2 study
Authors: Alex F Herrera, Jasmine Zain, Kerry J Savage, Tatyana Feldman, Jonathan E Brammer, Lu Chen, Sandrine Puverel, Leslie Popplewell, Lihua Elizabeth Budde, Matthew Mei, Chitra Hosing, Ranjit Nair, Lori Leslie, Shari Daniels, Lacolle Peters, Stephen Forman, Steven Rosen, Larry Kwak, Swaminathan P Iyer
Journal: The Lancet Haematology (2024)
Human mobility patterns in Brazil to inform sampling sites for early pathogen detection and routes of spread: a network modelling and validation study
Authors: Juliane F Oliveira, Andrêza L Alencar, Maria Célia L S Cunha, Adriano O Vasconcelos, Gerson G Cunha, Ray B Miranda, Fábio M H S Filho, Corbiniano Silva, Emanuele Gustani-Buss, Ricardo Khouri, Thiago Cerqueira-Silva, Luiz Landau, Manoel Barral-Netto, Pablo Ivan P Ramos
Journal: The Lancet Digital Health (2024)

Detecting and foreseeing pathogen dispersion is crucial in preventing widespread disease transmission. Human mobility is a fundamental issue in human transmission of infectious agents. Through a mobility data-driven approach, we aimed to identify municipalities in Brazil that could comprise an advanced sentinel network, allowing for early detection of circulating pathogens and their associated transmission routes.
Realigning the physical activity research agenda for population health, equity, and wellbeing
Authors: Ding Ding, Sebastien Chastin, Deborah Salvo, Tracy Nau, Klaus Gebel, Miguel Adriano Sanchez-Lastra, Mengyun Luo, Inacio Crochemore-Silva, Ulf Ekelund, Adrian Bauman
Journal: The Lancet (2024)
Many crises, one call to action: advancing gender equality in health in response to polycrises
Authors: Rajat Khosla, Gita Sen, Tedros Adhanom Ghebreyesus, Winnie Byanyima, Sima Bahous, Debora Diniz, Sara Hossain, Natalia Kanem, Ulrika Karlsson, Laura Laski, Dina Mired, Catherine Russell, Tlaleng Mofokeng, Achim Steiner, Volker Türk, Johanna Riha
Journal: The Lancet (2024)
Nemolizumab with concomitant topical therapy in adolescents and adults with moderate-to-severe atopic dermatitis (ARCADIA 1 and ARCADIA 2): results from two replicate, double-blind, randomised controlled phase 3 trials
Authors: Jonathan I Silverberg, Andreas Wollenberg, Adam Reich, Diamant Thaçi, Franz J Legat, Kim A Papp, Linda Stein Gold, Jean-David Bouaziz, Andrew E Pink, José Manuel Carrascosa, Barbara Rewerska, Jacek C Szepietowski, Dorota Krasowska, Blanka Havlíčková, Monika Kalowska, Nina Magnolo, Sylvia Pauser, Navid Nami, Maxwell B Sauder, Vipul Jain, Kamila Padlewska, Soo Yeon Cheong, Patricia Fleuranceau Morel, Liliana Ulianov, Christophe Piketty
Journal: The Lancet (2024)
Insight the long-term biodegradable Mg-RE-Sr alloy for orthopaedics implant via friction stir processing
Authors: Yixing Zhu, Mengran Zhou, Weikang Zhao, Yingxin Geng, Yujie Chen, Han Tian, Yifan Zhou, Gaoqiang Chen, Ruizhi Wu, Yufeng Zheng, Qingyu Shi
Journal: Bioactive Materials (2024)

Magnesium alloys, noted for their substantial mechanical strength and exceptional biocompatibility, are increasingly being considered for use in biodegradable implants. However, their rapid degradation and significant hydrogen release have limited their applications in orthopaedics. In this study, a novel Mg-RE-Sr alloy was created by friction stir processing to modify its microstructure and enhance its degradation performance. Through microstructural characterization, the friction stir processing effectively refined the grains, accelerated the re-dissolution of precipitates, and ensured a uniform distribution of these phases. The processed alloy demonstrated improved comprehensive properties, with an
Iron scavenging and myeloid cell polarization
Authors: Natalie Ludwig, Stefania Cucinelli, Simon Hametner, Martina U. Muckenthaler, Lucas Schirmer
Journal: Trends in Immunology (2024)

Myeloid cells that populate all human organs and blood are a versatile class of innate immune cells. They are crucial for sensing and regulating processes as diverse as tissue homeostasis and inflammation and are frequently characterized by their roles in either regulating or promoting inflammation. Recent studies in cultured cells and mouse models highlight the role of iron in skewing the functional properties of myeloid cells in tissue damage and repair. Here, we review certain emerging concepts on how iron influences and determines myeloid cell polarization in the context of its uptake, storage, and metabolism, including in conditions such as multiple sclerosis (MS), sickle cell disease, and tumors.