tbuckley/cabot-search huggingface dataset:
Graph Signal Processing, Graph Neural Network and Graph Learning on Biological Data: A Systematic Review
Authors: Rui Li, Xin Yuan, Mohsen Radfar, Peter Marendy, Wei Ni, Terrence J. O'Brien, Pablo Casillas-Espinosa
Journal: IEEE Reviews in Biomedical Engineering (2021)

Graph networks can model data observed across different levels of biological systems that span from population graphs (with patients as network nodes) to molecular graphs that involve omics data. Graph-based approaches have shed light on decoding biological processes modulated by complex interactions. This paper systematically reviews graph-based analysis methods of Graph Signal Processing (GSP), Graph Neural Networks (GNNs) and graph topology inference, and their applications to biological data. This work focuses on the algorithms of graph-based approaches and the constructions of graph-based frameworks that are adapted to a broad range of biological data. We cover the Graph Fourier Transform and the graph filter developed in GSP, which provides tools to investigate biological signals in the graph domain that can potentially benefit from the underlying graph structures. We also review the node, graph, and interaction oriented applications of GNNs with inductive and transductive learning manners for various biological targets. As a key component of graph analysis, we provide a review of graph topology inference methods that incorporate assumptions for specific biological objectives. Finally, we discuss the biological application of graph analysis methods within this exhaustive literature collection, potentially providing insights for future research in biological sciences.
Smoking and the Heart
Authors: Sharon Parmet, Cassio Lynm, Richard M. Glass
Journal: JAMA (2003)

Smoking and the Heart Most people know that smoking is bad for your lungs and can cause cancer.However, fewer may be aware of the effects of smoking on the heart and the circulatory system-the arteries and veins that carry the blood throughout the body.The July 2, 2003, issue of JAMA includes an article about the beneficial effects of quitting smoking on the heart and circulatory system.
Transmural intestinal fibrosis in men and mice
Authors: Clemens Neufert
Journal: Gut (2021)

Transmural intestinal fibrosis involving the mesenteric fat is a prominent feature of Crohn’s disease (CD) eliciting painful complications such as stenosis and fistulas of the intestine which are well-known since the pathological and clinical entity of CD was characterised by Burrill Bernard Crohn.1

However, although the armamentarium of inflammatory bowel disease (IBD) therapies has substantially expanded—for example, by the introduction of antibodies and small molecules targeting immune cells and inflammatory pathways—there are still no anti-fibrotic medical therapeutics available in clinical practice of patient with IBD care. In fact, key elements of transmural intestinal fibrosis directed therapy are still limited to endoscopic balloon dilatation or surgical resection. Although the major clinical need is evident, some issues make studies addressing transmural intestinal fibrosis particularly difficult, for example, tissue analysis for cellular and molecular characterisations usually needs prior surgery. Moreover, clinical studies of intestinal fibrosis have remained challenging, for example, because the symptoms and individual disease burden associated with fibrosis can be highly variable, and methods to monitor reliably the degree of fibrosis in serial analyses are still restricted. Recent efforts to define standardised treatment targets and to establish a consented histopathological scoring system are important steps which could aid more successful clinical trials and drug development within this field of exceptional relevance.2 3 In addition to the challenges of fibrosis research in humans, preclinical studies are confined by the limitations of the model systems at hand. There are several in vivo systems currently available such as sporadic, chemically-induced or microbial-based models of intestinal fibrosis which all have specific pros and cons related to the triggers of fibrosis induction. However, a major constraint of all of the …
Impaired skin barrier and allergic sensitization in early infancy
Authors: Sabina Wärnberg Gerdin, Anine Lie, Anna Asarnoj, Magnus P. Borres, Karin C. Lødrup Carlsen, Martin Färdig, Jon R. Konradsen, Christine Monceyron Jonassen, Caroline‐Aleksi Olsson Mägi, Eva Maria Rehbinder, Knut Rudi, Håvard Ove Skjerven, Anne Cathrine Staff, Cilla Söderhäll, Sandra G. Tedner, Marianne van Hage, Riyas Vettukattil, Björn Nordlund
Journal: Allergy (2021)

Factors predicting allergic sensitization in the first 6 months of life are poorly understood. We aimed to determine whether eczema, dry skin, and high transepidermal water loss (TEWL) at 3 months were associated with allergic sensitization at 6 months of age and, secondarily, to establish whether these characteristics predicted sensitization from 3 to 6 months of age.At 3 months of age, 1,994 infants from the population-based PreventADALL birth cohort in Norway and Sweden were assessed for eczema and dry skin on the cheeks and/or extensors; impaired skin barrier function, defined as TEWL in the upper quartile (>9.4 g/m2 /h), and allergen-specific IgE levels <0.1 kUA /L, available in 830. At 6 months, we assessed allergic sensitization to any food (egg, cow's milk, peanut, wheat, soy) or inhalant (birch, timothy grass, dog, and cat) allergen by a skin prick test wheal diameter ≥2 mm larger than negative control.Any sensitization was found in 198 of the 1,994 infants (9.9%), the majority to food allergens (n = 177, 8.9%). Eczema, dry skin, and high TEWL at 3 months increased the risk of sensitization at 6 months; adjusted odds ratios 4.20 (95% CI 2.93-6.04), 2.09 (95% CI 1.51-2.90) and 3.67 (95% CI 2.58-5.22), respectively. Eczema predicted sensitization with 55.6% sensitivity and 68.1% specificity; dry skin with 65.3% sensitivity and 57.3% specificity; and high TEWL with 61.7% sensitivity and 78.1% specificity.Eczema, dry skin, and high TEWL at 3 months predicted allergic sensitization at 6 months of age.
Nigel Hawkes: medical journalist and director of Straight Statistics
Authors: Annabel Ferriman
Journal: BMJ (2021)

In June 2010 the medical journalist Nigel Hawkes, who has died from a heart attack at the age of 78, ran into one of Health Secretary Andrew Lansley’s advisers whom he knew well and whom he greeted warmly since they were old friends. “You’re a troublemaker,” she hissed, “always writing those ghastly articles in The BMJ .” And she turned away.

This story, recounted in one of Hawkes’s columns, demonstrates one of his great strengths as a journalist. He was well known for being politically right of centre in his private life, but he never allowed party preferences, personal prejudice, or pettiness to cloud his judgment when it came to writing.

He was also unique in being able to take an impenetrable statistical conundrum and not only explain it to you clearly but delight you with his explanation. He made statistics fun and sweetened even the most labyrinthine complexities of NHS organisation.

Fiona Godlee, editor in chief of The BMJ , described him thus: “He was such a pillar of strength and wisdom and wit. We relied …
TCT-378 Functional Mitral Regurgitation Staging and Its Relationship to Outcomes in the COAPT Trial
Authors: Joao Cavalcante, Federico Asch, Santiago Garcia, Neil Weissman, Paul Sorajja, Diego Medvedofsky, Zhipeng Zhou, Maria Alu, Rebecca Hahn, JoAnn Lindenfeld, William Abraham, Bjorn Redfors, Michael Mack, Gregg Stone
Journal: Journal of the American College of Cardiology (2021)
Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing
Authors: Zhengmao Zhang, Hanwen Bai, Jon Blumenfeld, Andrew B. Ramnauth, Irina Barash, Martin Prince, Adrian Y. Tan, Alber Michaeel, Genyan Liu, Ines Chicos, Lior Rennert, Stavros Giannakopoulos, Karen Larbi, Stuart Hughes, Steven P. Salvatore, Brian D. Robinson, Sandip Kapur, Hanna Rennert
Journal: Journal of the American Society of Nephrology (2021)

Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by the development of multiple cysts in the kidneys. It is often caused by pathogenic mutations in PKD1 and PKD2 genes that encode polycystin proteins. Although the molecular mechanisms for cystogenesis are not established, concurrent inactivating germline and somatic mutations in PKD1 and PKD2 have been previously observed in renal tubular epithelium (RTE).To further investigate the cellular recessive mechanism of cystogenesis in RTE, we conducted whole-genome DNA sequencing analysis to identify germline variants and somatic alterations in RTE of 90 unique kidney cysts obtained during nephrectomy from 24 unrelated participants.Kidney cysts were overall genomically stable, with low burdens of somatic short mutations or large-scale structural alterations. Pathogenic somatic "second hit" alterations disrupting PKD1 or PKD2 were identified in 93% of the cysts. Of these, 77% of cysts acquired short mutations in PKD1 or PKD2 ; specifically, 60% resulted in protein truncations (nonsense, frameshift, or splice site) and 17% caused non-truncating mutations (missense, in-frame insertions, or deletions). Another 18% of cysts acquired somatic chromosomal loss of heterozygosity (LOH) events encompassing PKD1 or PKD2 ranging from 2.6 to 81.3 Mb. 14% of these cysts harbored copy number neutral LOH events, while the other 3% had hemizygous chromosomal deletions. LOH events frequently occurred at chromosomal fragile sites, or in regions comprising chromosome microdeletion diseases/syndromes. Almost all somatic "second hit" alterations occurred at the same germline mutated PKD1/2 gene.These findings further support a cellular recessive mechanism for cystogenesis in ADPKD primarily caused by inactivating germline and somatic variants of PKD1 or PKD2 genes in kidney cyst epithelium.
Transcriptome‐based identification of novel endotypes in adult atopic dermatitis
Authors: Alain Lefèvre‐Utile, Melissa Saichi, Péter Oláh, Marc Delord, Bernhard Homey, Vassili Soumelis
Journal: Allergy (2021)

Atopic dermatitis (AD) is a frequent and heterogeneous inflammatory skin disease, for which personalized medicine remains a challenge. High-throughput approaches have improved understanding of the complex pathophysiology of AD. However, a purely data-driven AD classification is still lacking.To address this question, we applied an original unsupervised approach on the largest available transcriptome dataset of AD lesional (n = 82) and healthy (n = 213) skin biopsies.Taking into account pathological and physiological state, a variance-based filtering revealed 222 AD-specific hyper-variable genes that efficiently classified the AD samples into 4 clusters that turned out to be clinically and biologically distinct. Comparison of gene expressions between clusters identified 3 sets of upregulated genes used to derive metagenes (MGs): MG-I (19 genes) was associated with IL-1 family signaling (including IL-36A and 36G) and skin remodeling, MG-II (23 genes) with negative immune regulation (including IL-34 and 37) and skin architecture, and MG-III (17 genes) with B lymphocyte immunity. Sample clusters differed in terms of disease severity (p = .02) and S. aureus (SA) colonization (p = .02). Cluster 1 contained the most severe AD, highest SA colonization, and overexpressed MG-I. Cluster 2 was characterized by less severe AD, low SA colonization, and high MG-II expression. Cluster 3 included mild AD, mild SA colonization, and mild expression of all MGs. Cluster 4 had the same clinical features as cluster 3 but had hyper-expression of MG-III. Last, we successfully validated our method and results in an independent cohort.Our study revealed unrecognized AD endotypes with specific underlying biological pathways, highlighting novel pathophysiological mechanisms. These data could provide new insights into personalized treatment strategies.
Single-Cell Multi-Omics Reveals the Genetic, Cellular and Molecular Landscape of <i>TP53</i> Mutated Leukemic Transformation in MPN
Authors: Alba Rodriguez-Meira, Haseeb Rahman, Ruggiero Norfo, Wei Wen, Agathe Chédeville, Jennifer O'Sullivan, Guanlin Wang, Aimee Paterson, Eleni Louka, Charlotte K Brierley, Warren W Kretzschmar, Francois Girodon, Zemin Ren, Matthew Bashton, Amir Enshaei, Mark W. Drummond, Florence Pasquier, Christophe Marzac, Claire N. Harrison, Isabelle Plo, Sten Eirik W Jacobsen, Supat Thongjuea, Bethan Psaila, Ileana Antony-Debre, Adam J. Mead
Journal: Blood (2021)
Clinical trial challenges, design considerations, and outcome measures in rare CNS tumors
Authors: Terri S Armstrong, Mark R Gilbert
Journal: Neuro-Oncology (2021)

Clinical research for patients with rare cancers has been very challenging. First and foremost, patient accrual to clinical trials typically requires a network, cooperative group, or even international collaboration in order to achieve the necessary numbers of patients to adequately evaluate a new treatment or intervention. Similar limitations in preclinical models and in the understanding the natural history of the disease or pertinent prognostic factors further impede the development of hypothesis-based, appropriately powered clinical trials. However, despite these challenges, several studies in rare cancers, including ependymoma and subependymal giant cell astrocytoma, have helped to establish new treatment regimens. Importantly, in these seminal trials, patient outcomes measures were critical in describing the clinical benefit derived from the therapy, underscoring the need to incorporate these measures in future trials. While obstacles still remain, novel and creative approaches to clinical trial designs have been developed that can be used to study new treatments for patients with rare cancers, thereby addressing a significant unmet need.
BNT162b2 vaccination induces durable SARS-CoV-2–specific T cells with a stem cell memory phenotype
Authors: Gisella Guerrera, Mario Picozza, Silvia D’Orso, Roberta Placido, Marta Pirronello, Alice Verdiani, Andrea Termine, Carlo Fabrizio, Flavia Giannessi, Manolo Sambucci, Maria Pia Balice, Carlo Caltagirone, Antonino Salvia, Angelo Rossini, Luca Battistini, Giovanna Borsellino
Journal: Science Immunology (2021)

SARS-CoV-2 mRNA vaccination induces stem cell memory T cells specific for the virus that persist up to 6 months.
Eleanor Kay Ashton
Authors: Scott Frazer
Journal: BMJ (2021)

Eleanor Kay Ashton was born to Robert and Mamie Scott, the owners of a boarding house on the Isle of Man. She excelled at Park Road Girls High School—for science lessons she and five other girls had to go to the boys’ high school. Although she had the grades and desire, she only went to university after pressure from determined aunts. She was successful at university too: in her final year at Liverpool Medical School, she was awarded the Henry Briggs memorial medal for obstetrics and gynaecology as well as the Dean’s medal …
Extensive frontal focused ultrasound mediated blood–brain barrier opening for the treatment of Alzheimer’s disease: a proof-of-concept study
Authors: So Hee Park, Kyoungwon Baik, Seun Jeon, Won Seok Chang, Byoung Seok Ye, Jin Woo Chang
Journal: Translational Neurodegeneration (2021)

Abstract Background Focused ultrasound (FUS)-mediated blood–brain barrier (BBB) opening has shown efficacy in removal of amyloid plaque and improvement of cognitive functions in preclinical studies, but this is rarely reported in clinical studies. This study was conducted to evaluate the safety, feasibility and potential benefits of repeated extensive BBB opening. Methods In this open-label, prospective study, six patients with Alzheimer’s disease (AD) were enrolled at Severance Hospital in Korea between August 2020 and September 2020. Five of them completed the study. FUS-mediated BBB opening, targeting the bilateral frontal lobe regions over 20 cm 3 , was performed twice at three-month intervals. Magnetic resonance imaging, 18 F-Florbetaben (FBB) positron emission tomography, Caregiver-Administered Neuropsychiatric Inventory (CGA-NPI) and comprehensive neuropsychological tests were performed before and after the procedures. Results FUS targeted a mean volume of 21.1 ± 2.7 cm 3 and BBB opening was confirmed at 95.7% ± 9.4% of the targeted volume. The frontal-to-other cortical region FBB standardized uptake value ratio at 3 months after the procedure showed a slight decrease, which was statistically significant, compared to the pre-procedure value (− 1.6%, 0.986 vs 1.002, P = 0.043). The CGA-NPI score at 2 weeks after the second procedure significantly decreased compared to baseline (2.2 ± 3.0 vs 8.6 ± 6.0, P = 0.042), but recovered after 3 months (5.2 ± 5.8 vs 8.6 ± 6.0, P = 0.89). No adverse effects were observed. Conclusions The repeated and extensive BBB opening in the frontal lobe is safe and feasible for patients with AD. In addition, the BBB opening is potentially beneficial for amyloid removal in AD patients.
Strengthening the reporting of observational studies in epidemiology using mendelian randomisation (STROBE-MR): explanation and elaboration
Authors: Veronika W Skrivankova, Rebecca C Richmond, Benjamin A R Woolf, Neil M Davies, Sonja A Swanson, Tyler J VanderWeele, Nicholas J Timpson, Julian P T Higgins, Niki Dimou, Claudia Langenberg, Elizabeth W Loder, Robert M Golub, Matthias Egger, George Davey Smith, J Brent Richards
Journal: BMJ (2021)

Mendelian randomisation (MR) studies allow a better understanding of the causal effects of modifiable exposures on health outcomes, but the published evidence is often hampered by inadequate reporting. Reporting guidelines help authors effectively communicate all critical information about what was done and what was found. STROBE-MR (strengthening the reporting of observational studies in epidemiology using mendelian randomisation) assists authors in reporting their MR research clearly and transparently. Adopting STROBE-MR should help readers, reviewers, and journal editors evaluate the quality of published MR studies. This article explains the 20 items of the STROBE-MR checklist, along with their meaning and rationale, using terms defined in a glossary. Examples of transparent reporting are used for each item to illustrate best practices.
포스터전시 : 고주파 열치료 후 발생한 3도 피부화상
Authors: 빅의주, 장재영, 학지영, 정승원, 김상균, 천영국, 김영석, 문종호, 조영덕, 김홍수, 이준성, 이문성, 심찬섭, 김부성
Journal: Clinical and Molecular Hepatology (2008)
Stem cell-derived neuronal relay strategies and functional electrical stimulation for treatment of spinal cord injury
Authors: Bi-Qin Lai, Xiang Zeng, Wei-Tao Han, Ming-Tian Che, Ying Ding, Ge Li, Yuan-Shan Zeng
Journal: Biomaterials (2021)

The inability of adult mammals to recover function lost after severe spinal cord injury (SCI) has been known for millennia and is mainly attributed to a failure of brain-derived nerve fiber regeneration across the lesion. Potential approaches to re-establishing locomotor function rely on neuronal relays to reconnect the segregated neural networks of the spinal cord. Intense research over the past 30 years has focused on endogenous and exogenous neuronal relays, but progress has been slow and the results often controversial. Treatments with stem cell-derived neuronal relays alone or together with functional electrical stimulation offer the possibility of improved repair of neuronal networks. In this review, we focus on approaches to recovery of motor function in paralyzed patients after severe SCI based on novel therapies such as implantation of stem cell-derived neuronal relays and functional electrical stimulation. Recent research progress offers hope that SCI patients will one day be able to recover motor function and sensory perception.
Gut non-bacterial microbiota contributing to alcohol-associated liver disease
Authors: Wenkang Gao, Yixin Zhu, Jin Ye, Huikuan Chu
Journal: Gut Microbes (2021)

Intestinal microbiota, dominated by bacteria, plays an important role in the occurrence and the development of alcohol-associated liver disease (ALD), which is one of the most common liver diseases around the world. With sufficient studies focusing on the gut bacterial community, chronic alcohol consumption is now known as a key factor that alters the composition of gut bacterial community, increases intestinal permeability, causes intestinal dysfunction, induces bacterial translocation, and exacerbates the process of ALD via gut-liver axis. However, gut non-bacterial communities including fungi, viruses, and archaea, which may also participate in the disease, has received little attention relative to the gut bacterial community. This paper will systematically collect the latest literatures reporting non-bacterial communities in mammalian health and disease, and review their mechanisms in promoting the development of ALD including CLEC7A pathway, Candidalysin (a peptide toxin secreted by Candida albicans), metabolites, and other chemical substances secreted or regulated by gut commensal mycobiome, virome, and archaeome, hoping to bring novel insights on our current knowledge of ALD.
TCT-140 A Novel Device for TR Reduction With a Feature of “3D Leaflet” Hanging in the Center of the Tricuspid Valve With an Atraumatic Anchoring Mechanism: The Pivot-TR System
Authors: Lee Seung-Whan, Pil Hyung Lee, Dae-Hee Kim, Tae Oh Kim, Dong Hyun Yang, Huunjung Koo, Min-Ku Chon, Yong-Hyun Park, Markus Reinthaler, Jai-Wun Park, Fabian Barbieri, June Hong Kim
Journal: Journal of the American College of Cardiology (2021)
Nidogen1-enriched extracellular vesicles accelerate angiogenesis and bone regeneration by targeting Myosin-10 to regulate endothelial cell adhesion
Authors: Pengzhen Cheng, Tianqing Cao, Xueyi Zhao, Weiguang Lu, Sheng Miao, Fenru Ning, Dong Wang, Yi Gao, Long Wang, Guoxian Pei, Liu Yang
Journal: Bioactive Materials (2021)

The technique bottleneck of repairing large bone defects with tissue engineered bone is the vascularization of tissue engineered grafts. Although some studies have shown that extracellular vesicles (EVs) derived from bone marrow mesenchymal stem cells (BMSCs) promote bone healing and repair by accelerating angiogenesis, the effector molecules and the mechanism remain unclear, which fail to provide ideas for the future research and development of cell-free interventions. Here, we found that Nidogen1-enriched EV (EV-NID1) derived from BMSCs interferes with the formation and assembly of focal adhesions (FAs) by targeting myosin-10, thereby reducing the adhesion strength of rat arterial endothelial cells (RAECs) to the extracellular matrix (ECM), and enhancing the migration and angiogenesis potential of RAECs. Moreover, by delivery with composite hydrogel, EV-NID1 is demonstrated to promote angiogenesis and bone regeneration in rat femoral defects. This study identifies the intracellular binding target of EV-NID1 and further elucidates a novel approach and mechanism, thereby providing a cell-free construction strategy with precise targets for the development of vascularized tissue engineering products.