tbuckley/cabot-search huggingface dataset:
A retrospective review of isotretinoin treatment-related mental health and sexual function outcomes in a tertiary acne clinic
Authors: Kyriaki Stefania Mitsaki, Sumir Chawla, Eirini E Merika
Journal: British Journal of Dermatology (2024)

Isotretinoin is the gold standard treatment for severe acne, but it has been controversially linked to psychiatric and sexual disorders. Using the well-validated PHQ-9 and CADI scoring systems, we demonstrated significantly improved mental health outcomes following completion of isotretinoin treatment for acne in our patient cohort over a 3-year period. We report no cases of suicidal ideation, suicide or erectile dysfunction.
Imaging-Guided Cardiac Resynchronization Therapy Lead Placement in Patients with Congenitally Corrected Transposition of the Great Arteries
Authors: Luuk H G A Hopman, Frebus J van Slochteren, Thelma C Konings, Emanuele Rondanina, Cornelis P Allaart, Marco J W Götte, Vokko P van Halm
Journal:  (2024)
Annelid Comparative Genomics and the Evolution of Massive Lineage-specific Genome Rearrangement in Bilaterians
Authors: Thomas D Lewin, Isabel Jiah-Yih Liao, Yi-Jyun Luo
Journal: Molecular Biology and Evolution (2024)

Abstract The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.
The role of helper lipids in optimising nanoparticle formulations of self-amplifying RNA
Authors: Beatriz D Barbieri, David J Peeler, Karnyart Samnuan, Suzanne Day, Kai Hu, Hadijatou J Sallah, John S Tregoning, Paul F McKay, Robin J Shattock
Journal: Journal of Controlled Release (2024)

Lipid nanoparticle (LNP) formulation plays a vital role in RNA vaccine delivery. However, further optimisation of self-amplifying RNA (saRNA) vaccine formulation could help enhance seroconversion rates in humans and improve storage stability. Altering either the ionisable or helper lipid can alter the characteristics and performance of formulated saRNA through the interplay of the phospholipid's packing parameter and the geometrical shape within the LNP membrane. In this study, we compared the impact of three helper lipids (DSPC, DOPC, or DOPE) used with two different ionisable lipids (MC3 and C12-200) on stability, transfection efficiency and the inflammation and immunogenicity of saRNA. While helper lipid identity altered saRNA expression across four cell lines in vitro, this was not predictive of an ex vivo or in vivo response. The helper lipid used influenced LNP storage where DSPC provided the best stability profile over four weeks at 2-8 °C. Importantly, helper lipid impact on LNP storage stability was the best predictor of expression in human skin explants, where C12-200 in combination with DSPC provided the most durable expression. C12-200 LNPs also improved protein expression (firefly luciferase) and humoral responses to a SARS-CoV-2 spike saRNA vaccine compared to MC3 LNPs, where the effect of helper lipids was less apparent. Nevertheless, the performance of C12-200 in combination with DSPC appears optimal for saRNA when balancing preferred storage stability requirements against in vivo and ex vivo potency. These data suggest that helper lipid influences the stability and functionality of ionisable lipid nanoparticle-formulated saRNA.
A path forward for <i>Staphylococcus aureus</i> vaccine development
Authors: Stephanie A. Fritz, Juliane Bubeck Wardenburg
Journal: The Journal of Experimental Medicine (2024)

The pursuit of a vaccine to quell Staphylococcus aureus disease has been unfruitful. In this Viewpoint, we explore the biological linkage between microbial niche acquisition and host immunity as a basis to guide future vaccine efforts.
Functional overlap of inborn errors of immunity and metabolism genes defines T cell metabolic vulnerabilities
Authors: Andrew R. Patterson, Gabriel A. Needle, Ayaka Sugiura, Erin Q. Jennings, Channing Chi, KayLee K. Steiner, Emilie L. Fisher, Gabriella L. Robertson, Caroline Bodnya, Janet G. Markle, Ryan D. Sheldon, Russell G. Jones, Vivian Gama, Jeffrey C. Rathmell
Journal: Science Immunology (2024)

Inborn errors of metabolism (IEMs) and immunity (IEIs) are Mendelian diseases in which complex phenotypes and patient rarity have limited clinical understanding. Whereas few genes have been annotated as contributing to both IEMs and IEIs, immunometabolic demands suggested greater functional overlap. Here, CRISPR screens tested IEM genes for immunologic roles and IEI genes for metabolic effects and found considerable previously unappreciated crossover. Analysis of IEMs showed that N-linked glycosylation and the hexosamine pathway enzyme Gfpt1 are critical for T cell expansion and function. Further, T helper (T H 1) cells synthesized uridine diphosphate N -acetylglucosamine more rapidly and were more impaired by Gfpt1 deficiency than T H 17 cells. Screening IEI genes found that Bcl11b promotes the CD4 T cell mitochondrial activity and Mcl1 expression necessary to prevent metabolic stress. Thus, a high degree of functional overlap exists between IEM and IEI genes, and immunometabolic mechanisms may underlie a previously underappreciated intersection of these disorders.
A biodegradable microgrooved and tissue mechanocompatible citrate-based scaffold improves bladder tissue regeneration
Authors: Madeleine Goedegebuure, Matthew I. Bury, Xinlong Wang, Pasquale Sanfelice, Federico Cammarata, Larry Wang, Tiffany T. Sharma, Nachiket Rajinikanth, Vikram Karra, Vidhika Siddha, Arun K. Sharma, Guillermo A. Ameer
Journal: Bioactive Materials (2024)

Chronic bladder dysfunction due to bladder disease or trauma is detrimental to affected patients as it can lead to increased risk of upper urinary tract dysfunction. Current treatment options include surgical interventions that enlarge the bladder with autologous bowel tissue to alleviate pressure on the upper urinary tract. This highly invasive procedure, termed bladder augmentation enterocystoplasty (BAE), significantly increases the risk of patient morbidity and mortality due to the incompatibility between bowel and bladder tissue. Therefore, patients would significantly benefit from an alternative treatment strategy that can regenerate healthy tissue and restore overall bladder function. Previous research has demonstrated the potential of citrate-based scaffolds co-seeded with bone marrow-derived stem/progenitor cells as an alternative graft for bladder augmentation. Recognizing that contact guidance can potentially influence tissue regeneration, we hypothesized that microtopographically patterned scaffolds would modulate cell responses and improve overall quality of the regenerated bladder tissue. We fabricated microgrooved (MG) scaffolds using the citrate-based biomaterial poly (1,8-octamethylene-citrate- co- octanol) (POCO) and co-seeded them with human bone marrow-derived mesenchymal stromal cells (MSCs) and CD34 + hematopoietic stem/progenitor cells (HSPCs). MG POCO scaffolds supported MSC and HSPC attachment, and MSC alignment within the microgrooves. All scaffolds were characterized and assessed for bladder tissue regeneration in an established nude rat bladder augmentation model. In all cases, normal physiological function was maintained post-augmentation, even without the presence of stem/progenitor cells. Urodynamic testing at 4-weeks post-augmentation for all experimental groups demonstrated that bladder capacity increased and bladder compliance was normal. Histological evaluation of the regenerated tissue revealed that cell-seeded scaffolds restored normal bladder smooth muscle content and resulted in increased revascularization and peripheral nerve regeneration. The presence of microgrooves on the cell-seeded scaffolds increased microvasculature formation by 20 % and urothelial layer thickness by 25 % in the regenerating tissue. Thus, this work demonstrates that microtopography engineering can influence bladder tissue regeneration to improve overall anatomical structure and re-establish bladder physiology.
Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling
Authors: Gregory Holste, Mingquan Lin, Ruiwen Zhou, Fei Wang, Lei Liu, Qi Yan, Sarah H. Van Tassel, Kyle Kovacs, Emily Y. Chew, Zhiyong Lu, Zhangyang Wang, Yifan Peng
Journal: npj Digital Medicine (2024)

Deep learning has enabled breakthroughs in automated diagnosis from medical imaging, with many successful applications in ophthalmology. However, standard medical image classification approaches only assess disease presence at the time of acquisition, neglecting the common clinical setting of longitudinal imaging. For slow, progressive eye diseases like age-related macular degeneration (AMD) and primary open-angle glaucoma (POAG), patients undergo repeated imaging over time to track disease progression and forecasting the future risk of developing a disease is critical to properly plan treatment. Our proposed Longitudinal Transformer for Survival Analysis (LTSA) enables dynamic disease prognosis from longitudinal medical imaging, modeling the time to disease from sequences of fundus photography images captured over long, irregular time periods. Using longitudinal imaging data from the Age-Related Eye Disease Study (AREDS) and Ocular Hypertension Treatment Study (OHTS), LTSA significantly outperformed a single-image baseline in 19/20 head-to-head comparisons on late AMD prognosis and 18/20 comparisons on POAG prognosis. A temporal attention analysis also suggested that, while the most recent image is typically the most influential, prior imaging still provides additional prognostic value.
A rare case of primary esophageal Paget’s disease with underlying invasive adenocarcinoma
Authors: Xue Chen, Heng Zhang, Aihua Qian, Xi Chen
Journal: Endoscopy (2024)

A 53-year-old man presented to Ruijin Hospital, having been followed up for 9 months with an esophageal lesion that had initially been detected during a routine esophagogastroduodenoscopy (EGD) and had been diagnosed histopathologically as a high grade intraepithelial neoplasia (HGIN).
Unraveling the secrets: Evolution of resistance mediated by membrane proteins
Authors: Xue Yang, Min Li, Zi-Chang Jia, Yan Liu, Shun-Fan Wu, Mo-Xian Chen, Ge-Fei Hao, Qing Yang
Journal: Drug Resistance Updates (2024)

Membrane protein-mediated resistance is a multidisciplinary challenge that spans fields such as medicine, agriculture, and environmental science. Understanding its complexity and devising innovative strategies are crucial for treating diseases like cancer and managing resistant pests in agriculture. This paper explores the dual nature of resistance mechanisms across different organisms: On one hand, animals, bacteria, fungi, plants, and insects exhibit convergent evolution, leading to the development of similar resistance mechanisms. On the other hand, influenced by diverse environmental pressures and structural differences among organisms, they also demonstrate divergent resistance characteristics. Membrane protein-mediated resistance mechanisms are prevalent across animals, bacteria, fungi, plants, and insects, reflecting their shared survival strategies evolved through convergent evolution to address similar survival challenges. However, variations in ecological environments and biological characteristics result in differing responses to resistance. Therefore, examining these differences not only enhances our understanding of adaptive resistance mechanisms but also provides crucial theoretical support and insights for addressing drug resistance and advancing pharmaceutical development.
Material-driven immunomodulation and ECM remodeling reverse pulmonary fibrosis by local delivery of stem cell-laden microcapsules
Authors: Yujie Zhang, Yuan Zhao, Chuanfeng An, Yiyang Guo, Yubin Ma, Fei Shao, Yonggang Zhang, Kai Sun, Fang Cheng, Changle Ren, Lijun Zhang, Bingbing Sun, Yang Zhang, Huanan Wang
Journal: Biomaterials (2024)
Folylpolyglutamate synthetase inactivation in relapsed ALL induces a druggable folate metabolic vulnerability
Authors: Hui Li, Yao Chen, Ming Ding, Jingjing Liu, Huiying Sun, Houshun Fang, Samuel W Brady, Yan Xu, Fabian Glaser, Xiaotu Ma, Yabin Tang, Liang Du, Xiaoyu Wu, Shuxuan Wang, Liang Zhu, Benshang Li, Shuhong Shen, Jinghui Zhang, Liang Zheng, Jiyang Yu, Yehuda G Assaraf, Bin-Bing S Zhou
Journal: Drug Resistance Updates (2024)
Ultrastructural, metabolic and genetic characteristics of determinants facilitating the acquisition of macrolide resistance by Streptococcus pneumoniae
Authors: Xueqing Wu, Babek Alibayov, Xi Xiang, Santiago M Lattar, Fuminori Sakai, Austin A Medders, Brenda S Antezana, Lance E Keller, Ana G J Vidal, Yih-Ling Tzeng, D Ashley Robinson, David S Stephens, Yunsong Yu, Jorge E Vidal
Journal: Drug Resistance Updates (2024)

To investigate the molecular events associated with acquiring macrolide resistance genes [ mefE / mel (Mega) or ermB ] in Streptococcus pneumoniae ( Spn ) during nasopharyngeal colonization. Genomic analysis of 128 macrolide-resistant Spn isolates revealed recombination events in genes of the conjugation apparatus, or the competence system, in strains carrying Tn 916 -related elements. Studies using confocal and electron microscopy demonstrated that during the transfer of Tn 916 -related elements in nasopharyngeal cell biofilms, pneumococcal strains formed clusters facilitating their acquisition of resistance determinants at a high recombination frequency (rF). Remarkably, these aggregates comprise both encapsulated and nonencapsulated pneumococci that span extracellular and intracellular compartments. rF assessments showed similar rates regardless Mega was associated with large integrative and conjugative elements (ICEs) (>23 kb) or not (∼5.4 kb). The rF for Mega Class IV(c) insertion region (∼53 kb) was three orders of magnitude higher than the transformation of the capsule locus. Metabolomics studies of the microenvironment created by colonization of human nasopharyngeal cells revealed a link between the acquisition of ICEs and the pathways involving nicotinic acid and sucrose. Pneumococcal clusters, both extracellular and intracellular, facilitate macrolide resistance acquisition, and ICEs were acquired at a higher frequency than the capsule locus. Metabolic changes could serve as intervention targets. • Recombination hotspots were identified within the Tn 2010 conjugation machinery of Spn CC271 strains. • Extracellular and intracellular clusters of pneumococci facilitate macrolide resistance acquisition. • Macrolide resistance acquisition via recombination is more frequent than classic capsule locus transformation events. • Pneumococci and nasopharyngeal create a microenvironment altering host metabolites, linked to increased macrolide resistance acquisition.
Cholangioscope-assisted evaluation and endoscopic incision of stricture caused by thick mucosal bridge in Crohn’s disease
Authors: Xianzong Ma, Lang Yang, Yan Jia, Zilin Kang, Mingjie Zhang, Dongliang Yu, Peng Jin
Journal: Endoscopy (2024)

A 32-year-old man with an 8-year history of Crohn's disease (Montreal classification A2, L3, B2p) presented with recurrent abdominal pain. After regular treatment with ustekinumab for 3 years, recent computed tomography revealed severe stricture in the ascending colon ([Fig. 1]), and colonoscopy showed colorectal mucosal healing. However, two tiny holes were observed and could not be passed by the colonoscope ([Fig. 2]).
Correction: Prospective feasibility study of a novel rigidizing stabilizing overtube in the resection of complex gastrointestinal polyps
Authors: Salmaan Jawaid, Ahmed F. Aboelezz, Gehad Daba, Mai Khalaf, Fares Ayoub, Noor Zabad, Michael Mercado, Tara Keihanian, Mohamed Othman
Journal: Endoscopy (2024)

Correction to: Prospective feasibility study of a novel rigidizing stabilizing overtube in the resection of complex gastrointestinal polypsEndoscopy eFirstDOI: 10.1055/a-2350-4059
Endoscopic glue injection therapy with N-butyl-2-cyanoacrylate for bleeding from isolated large rectal varices
Authors: Shigenaga Matsui, Hiroshi Kashida, Masahiro Takita, Masatoshi Kudo
Journal: Endoscopy (2024)

A 64-year-old woman with history of hepatitis C cirrhosis (Child-Pugh class C) was admitted to our institution with hematochezia. Her esophagogastric varices had been treated at our hospital 6 and 3 years previously by balloon-occluded retrograde transvenous obliteration (B-RTO) and endoscopic injection sclerotherapy (EIS), respectively, and she was being treated for refractory ascites with concentrated ascites reinfusion therapy (CART). She was found to be anemic (hemoglobin 6.0 g/dL) and renal dysfunction was also noted, with a blood urea nitrogen level of 117 mg/dL and creatinine level of 2.87 mg/dL. Plain abdominal computed tomography (CT) revealed liver cirrhosis with massive ascites ([Fig. 1]).
Public health interventions to address digital determinants of children's health and wellbeing
Authors: Louise Holly, Sandro Demaio, Ilona Kickbusch
Journal: The Lancet Public Health (2024)

The increasing use of digital media and devices by children has led to growing concerns that spending time online without sufficient guarding is having negative effects on their health and wellbeing. In this Viewpoint, we argue that children's use of digital technologies and engagement in digital environments should be recognised as important determinants of their health and that a public health approach is required to protect children from digital harms. Drawing on lessons from well-established approaches to address other public health challenges, we summarise three groups of public health interventions that can help delay media use among very young children, reduce digital media use among children of all ages, and mitigate any harmful consequences of children's digital media use. To build healthy digital environments for children now and future generations, we recommend a precautionary approach to governance that prioritises children's health and wellbeing, recognises their desire to enjoy the benefits of the digital world, and allows children to have a role in shaping their digital futures.
Efficacy and safety of immune checkpoint inhibitors for individuals with advanced EGFR-mutated non-small-cell lung cancer who progressed on EGFR tyrosine-kinase inhibitors: a systematic review, meta-analysis, and network meta-analysis
Authors: Yi Zhao, Ying He, Wei Wang, Qi Cai, Fan Ge, Zisheng Chen, Jianqi Zheng, Yuan Zhang, Hongsheng Deng, Ying Chen, Shen Lao, Hengrui Liang, Wenhua Liang, Jianxing He
Journal: The Lancet Oncology (2024)
Comparison of clinical selection-based genetic testing with phenotype-agnostic extensive germline sequencing to diagnose genetic predisposition in children with cancer: a prospective diagnostic study
Authors: Jette J Bakhuizen, Freerk van Dijk, Marco J Koudijs, Reno S Bladergroen, Sebastian B B Bon, Saskia M J Hopman, Lennart A Kester, Mariëtte E G Kranendonk, Jan L C Loeffen, Stephanie E Smetsers, Edwin Sonneveld, Melissa Tachdjian, Evelien de Vos-Kerkhof, Catherine Goudie, Johannes H M Merks, Roland P Kuiper, Marjolijn C J Jongmans
Journal: The Lancet Child & Adolescent Health (2024)
Alternating gemcitabine plus nab-paclitaxel and gemcitabine alone versus continuous gemcitabine plus nab-paclitaxel after induction treatment of metastatic pancreatic cancer (ALPACA): a multicentre, randomised, open-label, phase 2 trial
Authors: Klara Dorman, Stefan Boeck, Karel Caca, Maximilian Reichert, Thomas J Ettrich, Helmut Oettle, Oliver Waidmann, Dominik P Modest, Lothar Müller, Patrick Michl, Stephan Kanzler, Daniel Pink, Anke Reinacher-Schick, Michael Geißler, Henning Pelz, Volker Kunzmann, Swantje Held, Thomas Schichtl, Volker Heinemann, Frank Kullmann
Journal: The Lancet. Gastroenterology & hepatology (2024)
Comparison of platinum combination chemotherapy plus pembrolizumab versus platinum combination chemotherapy plus nivolumab–ipilimumab for treatment-naive advanced non-small-cell lung cancer in Japan (JCOG2007): an open-label, multicentre, randomised, phase 3 trial
Authors: Yoshimasa Shiraishi, Shogo Nomura, Shunichi Sugawara, Hidehito Horinouchi, Yasuto Yoneshima, Hidetoshi Hayashi, Koichi Azuma, Satoshi Hara, Seiji Niho, Ryo Morita, Masafumi Yamaguchi, Toshihide Yokoyama, Kiyotaka Yoh, Takayasu Kurata, Hiroaki Okamoto, Masaki Okamoto, Takashi Kijima, Kazuo Kasahara, Yutaka Fujiwara, Shuji Murakami, Shintaro Kanda, Hiroaki Akamatsu, Shinnosuke Takemoto, Hiroyasu Kaneda, Toshiyuki Kozuki, Masahiko Ando, Yuta Sekino, Haruhiko Fukuda, Yuichiro Ohe, Isamu Okamoto
Journal: The Lancet Respiratory Medicine (2024)
The long wait for long-acting HIV prevention and treatment formulations
Authors: Willem Daniel Francois Venter, Monica Gandhi, Simiso Sokhela, Kenly Sikwese, Helen Bygrave, Louis Da Gama, Ndiviwe Mphothulo, Lise Jamieson, Mark J Siedner, Anton L Pozniak, Pablo Rojo, Solange L Baptiste, Jacque Wambui, Gesine Meyer-Rath, Brian Honermann, Mitchell Warren, Linda-Gail Bekker, Phumla Sinxadi, Simon Collins, Jessica Burry, Karlien Möller, Polly Clayden, Andrew Owen, Andrew Hill
Journal: The Lancet HIV (2024)
Projected health and economic effects of a pan-tuberculosis treatment regimen: a modelling study
Authors: Theresa S Ryckman, C Finn McQuaid, Ted Cohen, Nicolas A Menzies, Emily A Kendall
Journal: The Lancet Global Health (2024)

A pan-tuberculosis regimen that could be initiated without knowledge of drug susceptibility has been proposed as an objective of tuberculosis regimen development. We modelled the health and economic benefits of such a regimen and analysed which of its features contribute most to impact and savings.
Endoscopic ultrasound-guided hepaticogastrostomy for patients with frequent respiratory fluctuations using a novel hybrid guidewire to prevent guidewire shearing
Authors: Takeshi Ogura, Yuki Uba, Nobuhiro Hattori, Jun Matsuno, Hiroki Nishikawa
Journal: Endoscopy (2024)

Endoscopic ultrasound-guided hepaticogastrostomy (EUS-HGS) is widely attempted in patients after failed endoscopic retrograde cholangiopancreatography (ERCP) [1] [2]. EUS-HGS requires several procedural steps, including bile duct puncture, guidewire insertion, tract dilation, and stent deployment. Among these procedural steps, guidewire insertion may be most challenging, especially in nonexpert hands [3]. A liver impaction technique may be useful for improving the technical success rate of guidewire insertion [4] [5]; however, this technique often cannot be performed, especially in patients with nondilated bile ducts or frequent respiratory fluctuations, because guidewire visualization on EUS images can be difficult.