tbuckley/cabot-search huggingface dataset:
Inference of host-pathogen interaction matrices from genome-wide polymorphism data
Authors: Hanna Märkle, Sona John, Lukas Metzger, Eleanor Barnes, Emma Hudson, Paul Klenerman, Peter Simmonds, Chris Holmes, Graham Cooke, Geoffrey Dusheiko, John McLauchlan, Mark Harris, William Irving, Philip Troke, Diana Brainard, John McHutchinson, Charles Gore, Rachel Halford, Graham R Foster, Cham Herath, M Azim Ansari, Vincent Pedergnana, Aurélien Tellier
Journal: Molecular Biology and Evolution (2024)

Abstract Host–pathogen coevolution is defined as the reciprocal evolutionary changes in both species due to genotype × genotype (G×G) interactions at the genetic level determining the outcome and severity of infection. While co-analyses of hosts and pathogen genomes (co-genome-wide association studies) allow us to pinpoint the interacting genes, these do not reveal which host genotype(s) is/are resistant to which pathogen genotype(s). The knowledge of this so-called infection matrix is important for agriculture and medicine. Building on established theories of host–pathogen interactions, we here derive four novel indices capturing the characteristics of the infection matrix. These indices can be computed from full genome polymorphism data of randomly sampled uninfected hosts, as well as infected hosts and their pathogen strains. We use these indices in an approximate Bayesian computation method to pinpoint loci with relevant G×G interactions and to infer their underlying interaction matrix. In a combined single nucleotide polymorphism dataset of 451 European humans and their infecting hepatitis C virus (HCV) strains and 503 uninfected individuals, we reveal a new human candidate gene for resistance to HCV and new virus mutations matching human genes. For two groups of significant human–HCV (G×G) associations, we infer a gene-for-gene infection matrix, which is commonly assumed to be typical of plant–pathogen interactions. Our model-based inference framework bridges theoretical models of G×G interactions with host and pathogen genomic data. It, therefore, paves the way for understanding the evolution of key G×G interactions underpinning HCV adaptation to the European human population after a recent expansion.
Allergen immunotherapy adverse events in adults with respiratory allergies‐data from ADER: An EAACI task force report
Authors: Julijana Asllani, Dimitrios Mitsias, George Konstantinou, Etleva Qirko, Mirela Hitaj, Sybi Musollari, George Christoff, Silviya Novakova, Michael Makris, Mira Radulovic Pevec, Branko Pevec, Adriana Muntean, Vesna Tomic‐Spiric, Rajica Stosovic, Mitja Kosnik, Dilsad Mungan, Todor A. Popov, Moises Calderon, Nikolaos G. Papadopoulos
Journal: Allergy (2024)

Registries can yield important insights on allergen immunotherapy (AIT) outcomes in daily clinical practice. However, systematic recordings of adverse events (AE) due to AIT in real-life are lacking.
Recent advances in spatio-temporally controllable systems for management of glioma
Authors: Huiwen Zhang, Wanqi Zhu, Wei Pan, Xiuyan Wan, Na Li, Bo Tang
Journal: Asian Journal of Pharmaceutical Sciences (2024)

Malignant glioma remains one of the most aggressive intracranial tumors with devastating clinical outcomes despite the great advances in conventional treatment approaches, including surgery and chemotherapy. Spatio-temporally controllable approaches to glioma are now being actively investigated due to the preponderance, including spatio-temporal adjustability, minimally invasive, repetitive properties, etc. External stimuli can be readily controlled by adjusting the site and density of stimuli to exert the cytotoxic on glioma tissue and avoid undesired injury to normal tissues. It is worth noting that the removability of external stimuli allows for on-demand treatment, which effectively reduces the occurrence of side effects. In this review, we highlight recent advancements in drug delivery systems for spatio-temporally controllable treatments of glioma, focusing on the mechanisms and design principles of sensitizers utilized in these controllable therapies. Moreover, the potential challenges regarding spatio-temporally controllable therapy for glioma are also described, aiming to provide insights into future advancements in this field and their potential clinical applications.
Beyond the PROSPECT Trial
Authors: Alexis Puvrez, Oana Mirea, Stella Marchetta, Bert Vandenberk, Gábor Vörös, Erwan Donal, Nicholas Cauwenberghs, Lennert Minten, Laurine Wouters, Ward Heggermont, Martin Penicka, Ahmed S. Youssef, Jürgen Duchenne, Jens-Uwe Voigt
Journal: JACC. Cardiovascular imaging (2024)
Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids
Authors: Yu-Hang Zhang, Ran Xie, Chen-Shu Dai, Hong-Wei Gao, Gan Zhou, Tian-Tian Qi, Wen-Yu Wang, Hua Wang, Yi-Min Cui
Journal: Journal of Hepatology (2024)
Targeting <scp>CD13</scp>/aminopeptidase N as a novel therapeutic approach for scleroderma fibrosis
Authors: Sei Muraoka, William D. Brodie, Megan N. Mattichak, Mikel Gurrea‐Rubio, Yuzo Ikari, Caroline Foster, M. Asif Amin, Neha Khanna, Hafsa Amin, Phillip L. Campbell, Sirapa Vichaikul, Ellen N. Model, Morgan M. Omara, Steven Petrovski, Karly Kozicki, Camilia Amarista, Anna Webber, Mustafa Ali, Pamela J. Palisoc, Jonatan Hervoso, Jeffrey H. Ruth, Lam C. Tsoi, John Varga, Johann E. Gudjonsson, Dinesh Khanna, David A. Fox, Pei‐Suen Tsou
Journal: Arthritis & Rheumatology (2024)

Objective Systemic sclerosis (SSc) is an autoimmune multisystem disease with poorly understood pathogenesis and ineffective treatment options. Soluble CD13 (sCD13), generated by the cleavage of cell surface CD13 via matrix metalloproteinase 14 (MMP14), signals through the bradykinin receptor B1 (B1R) to elicit pro‐inflammatory, pro‐arthritic, and pro‐angiogenic responses. In this study, we explored the antifibrotic potential of targeting the sCD13‐B1R axis in SSc. Methods The expression of CD13, B1R, and MMP14 was examined in SSc skin and explanted dermal fibroblasts. The efficacy of B1R antagonists in the inhibition on fibrosis was determined in vitro and in vivo. Results Expression of the genes for CD13, B1R, and MMP14 was elevated in skin biopsies from patients with diffuse cutaneous (dc) SSc. Notably, single‐cell analysis of SSc skin biopsies revealed the highest BDKRB1 expression in COL8A1 ‐positive myofibroblasts, a population exclusively seen in SSc. Transforming growth factor beta (TGFβ) induced the expression of BDKRB1 and production of sCD13 by dcSSc skin fibroblasts. Treatment of dcSSc fibroblasts with sCD13 promoted fibrotic gene expression, signaling, cell proliferation, migration, and gel contraction. The pro‐fibrotic responses of sCD13 or TGFβ were prevented by a B1R antagonist. Mice lacking Cd13 or Bdkrb1 were resistant to bleomycin‐induced skin fibrosis and inflammation. Pharmacological B1R inhibition had a comparable antifibrotic effect. Conclusion These results are the first to demonstrate a key role for sCD13 in SSc skin fibrosis and suggest that targeting the sCD13‐B1R signaling axis is a promising novel therapeutic approach for SSc. image
ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH
Authors: Yasmine J Liu, Masaki Kimura, Xiaoxu Li, Jonathan Sulc, Qi Wang, Sandra Rodríguez-López, Angelique M L Scantlebery, Keno Strotjohann, Hector Gallart-Ayala, Archana Vijayakumar, Robert P Myers, Julijana Ivanisevic, Riekelt H Houtkooper, G Mani Subramanian, Takanori Takebe, Johan Auwerx
Journal: Journal of Hepatology (2024)

Recent findings reveal the importance of tryptophan-initiated de novo nicotinamide adenine dinucleotide (NAD
The safety and efficacy of neoadjuvant PD-1 inhibitor plus chemotherapy for patients with locally advanced gastric cancer: A systematic review and meta-analysis
Authors: Zhiyuan Yu, Chen Liang, Qixuan Xu, Zhen Yuan, Miao Chen, Rui Li, Sixin Zhou, Peiyu Li, Bo Wei, Xudong Zhao
Journal: International Journal of Surgery (2024)

Background: The extensive utilization of immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) has achieved significant advancements in the treatment of diverse solid tumors. The present meta-analysis aims to evaluate the safety and efficacy of neoadjuvant chemotherapy (NCT) plus PD-1 inhibitor for patients with locally advanced gastric cancer (LAGC). Methods: An electronic search of PubMed, EmBase, and the Cochrane Library was performed to identify the clinical trials of NCT + PD-1 inhibitor vs. NCT in patients with LAGC. The retrieval period extended from the establishment of the corresponding database until April 2024, and meta-analysis was conducted using Stata (version 15) software. Subsequently, direct comparative analysis was used to compare pooled results of neoadjuvant immunochemotherapy (NICT) with NCT. Results: After screening, 6 phase II/III randomized controlled trials (RCTs) and 9 retrospective studies with 2,953 patients were included. In meta-analysis, NICT group demonstrated a significantly higher rate of pathological complete response (pCR) ( P &lt;0.001) and R0 resection ( P =0.001), and a lower 2-year recurrence rate ( P =0.001) compared to the NCT group. The NICT group, however, exhibited a higher incidence of severe treatment-related adverse events (TRAEs) ( P =0.044). Additionally, the NICT and NCT groups exhibited no statistical differences in terms of the number of harvested lymph nodes, the occurrence of total TRAEs and postoperative complications, as well as the duration of postoperative hospitalization. Conclusions: The combination of PD-1 inhibitor + NCT in LAGC patients enhances the likelihood of achieving radical surgery and improves prognosis, albeit to some extent increasing the risk of severe TRAEs. NICT is anticipated to emerge as the preferred neoadjuvant therapy option for patients diagnosed with LAGC.
Identifying the optimal measurement timing and hemodynamic targets of portal pressure gradient after TIPS in patients with cirrhosis and variceal bleeding: a prospective cohort study
Authors: Yong Lv, Qiuhe Wang, Bohan Luo, Wei Bai, Menghao Li, Kai Li, Zhengyu Wang, Dongdong Xia, Wengang Guo, Xiaomei Li, Jie Yuan, Na Zhang, Xing Wang, Huahong Xie, Yanglin Pan, Yongzhan Nie, Zhanxin Yin, Daiming Fan, Guohong Han
Journal: Journal of Hepatology (2024)
Early outcomes of minimally invasive surgery versus thoracotomy for non-small cell lung cancer patients with neoadjuvant immunochemotherapy: a multi-center real-world study
Authors: Hanbo Pan, Hang Chen, Zhen Ge, Yu Tian, Junwei Ning, Ningyuan Zou, Hongda Zhu, Jiaqi Zhang, Yixing Tao, Zenan Gu, Long Jiang, Zongxiang Duan, Zhichao Pang, Min Zheng, Chengwei Zhou, Guomo Ruan, Ziming Li, Yingjie Hu, Hui Yin, Weicheng Kong, Jia Huang, Guodong Xu, Qingquan Luo
Journal: International Journal of Surgery (2024)

Pan, Hanbo Ph.D; Chen, Hang MD; Ge, Zhen MD; Tian, Yu Ph.D; Ning, Junwei MD; Zou, Ningyuan MD; Zhu, Hongda MD; Zhang, Jiaqi MD; Tao, Yixing MD; Gu, Zenan Ph.D; Jiang, Long Ph.D, MD; Duan, Zongxiang MD; Pang, Zhichao MD; Zheng, Min MD; Zhou, Chengwei MD; Ruan, Guomo MD; Li, Ziming MD; Hu, Yingjie MD; Yin, Hui; Kong, Weicheng MD; Huang, Jia MD; Xu, Guodong MD; Luo, Qingquan MD, FACS, FRCS Author Information
Impact of sleep deprivation on surgical performance on a robotic surgery simulator
Authors: Laura I. Hanke, Nadja Apelt, Samaneh Hasari, Inka Tuin, Jochem König, Tobias Huber, Oliver Muensterer, Jan Goedeke
Journal: International Journal of Surgery (2024)

Hanke, Laura Isabel MD; Apelt, Nadja MD; Hasari, Samaneh MD; Tuin, Inka MD; König, Jochem MD, PhD; Huber, Tobias MD, PhD; Muensterer, Oliver MD, PhD; Goedeke, Jan Author Information
Predicting all-cause mortality and postoperative pneumonia after geriatric hip fracture surgery: a retrospective multicenter cohort study
Authors: Xiping Shen, Jian Li, Wei Lv, Bo Huang, Ji Wu, Zhigang Zheng
Journal: International Journal of Surgery (2024)

aDepartment of General surgery, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province, China bDepartment of Radiology, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province, China cDepartment of Clinical Research Center for Surgery, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province, China dDepartment of Orthopedics, Changshu No.2 People's Hospital, The Affiliated Changshu Hospital of Nantong University, Changshu, Jiangsu, China eDepartment of Orthopedics, Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu Province, China fDepartment of Radiology, Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu Province, China gDepartment of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China Running title: predicting all-cause mortality Xiping Shen and Jian Li: First author and Co-first author These authors contributed equally to this work. Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. *Corresponding authors. Address: Department of Clinical Research Center for Surgery and Radiology, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou, Jiangsu Province, China, No. 2666, Ludang Road, Wujiang District, Suzhou, Jiangsu Province, China. Tel.: +860 512 828 812 48. E-mail: [email protected] (J. Wu); Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. Pudong new District, Shanghai, China. Tel.: +860 218 266 451 2. E-mail: [email protected] (Z. Zheng). Supplemental Digital Content is available for this article. Direct URL citations are provided in the HTML and PDF versions of this article on the journal's website, www.lww.com/international-journal-of-surgery. Published online ■ ■ This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/
Efficacy and safety of phototherapies for upper lip scars in cleft lip patients: A systematic review and meta-analysis
Authors: Siqi Wei, Guang Zhang, Qian Wu, Tao Song, Ningbei Yin, Yongqian Wang
Journal: International Journal of Surgery (2024)

Cleft lip is a prevalent congenital developmental defect, and its surgical repair often results in scarring that adversely impacts facial aesthetics, function, and mental health. Numerous studies have examined the efficacy and safety of phototherapy for scar treatment. However, definitive evidence is lacking. This study aims to evaluate the effectiveness and safety of phototherapies for treating upper lip scars in cleft lip patients.
Laparoscopic versus open pancreatoduodenectomy for periampullary tumors: A randomized clinical trial
Authors: Yoo-Seok Yoon, Woohyung Lee, Chang Moo Kang, Taeho Hong, Sang Hyun Shin, Jung Woo Lee, Dae Wook Hwang, Ki Byung Song, Jae Woo Kwon, Min Kyu Sung, In Kyong Shim, Jung Bok Lee, Song Cheol Kim
Journal: International Journal of Surgery (2024)

There is a lack of robust evidence on the efficacy of laparoscopic pancreatoduodenectomy compared to open surgery. This study was aimed to compare time to functional recovery (FR) between laparoscopic and open pancreatoduodenectomy.
What is the effect of bariatric surgery on health-related quality of life in people with obesity? observational cohort analysis of the United Kingdom national bariatric surgery registry
Authors: John Buckell, Peter K. Small, Susan A. Jebb, Paul Aveyard, Omar Khan, Emma Rose McGlone
Journal: International Journal of Surgery (2024)

Previous small studies investigating health-related quality of life (HRQoL) following bariatric surgery have demonstrated heterogenous effects. This study aimed to use National Bariatric Surgery Registry (NBSR) records to investigate the relationship between weight and HRQoL in people undergoing bariatric surgery in the UK.
Chlorhexidine gluconate versus povidone-iodine for nasal bacteria decolonization before transsphenoidal surgery in patients with pituitary neuroendocrine tumors: A prospective, randomized, double-blind, non-inferiority trial
Authors: Jinyu Qian, Jie Lin, Jin Liu, Yali Gong, Shufang Zheng, Lu Mei, Xin Tang, Lina Xie, Hong Li, Chao Zhang, Feilong Wang, Xue Yang, Rong Hu, Hua Feng, Jishu Xian, Binbin Tan, Yujie Chen
Journal: International Journal of Surgery (2024)

This study aimed to compare the nasal decolonization efficacy and comfort between chlorhexidine gluconate (CHG) and povidone-iodine (PVP) to provide an evidence basis for clinical guidance.
The feasibility of targeted axillary dissection for breast cancer axillary surgery de-escalation after neoadjuvant therapy: A prospective cohort study
Authors: Qing-Da Fan, Zhao Bi, Li-Guo Gong, Peng Chen, Bin-Bin Cong, Peng-Fei Qiu, Bao-wei Duan, Yu-Guang Chen, Yong-Sheng Wang
Journal: International Journal of Surgery (2024)

Targeted axillary dissection (TAD) after neoadjuvant therapy (NAT) includes removing of marked and sentinel lymph nodes (SLNs). The aim was to investigate the optimization of TAD localization techniques after NAT among breast cancer patients.
Effects of supplementing extracorporeal shockwave therapy (ESWT) to hyaluronic acid (HA) injection among patients with rotator cuff lesions without complete tear: A prospective double-blinded randomized study
Authors: Jih-Yang Ko, Chung-Cheng Huang, Po-Hua Huang, Jeng-Wei Chen, Chin-Yi Liao, Shu-Jui Kuo
Journal: International Journal of Surgery (2024)

The study investigates the combined efficacy of subacromial hyaluronic acid (HA) injections and extracorporeal shockwave therapy (ESWT) in managing rotator cuff lesions without complete tears.
Esketamine vs. placebo combined with erector spinae plane block vs. intercostal nerve block on quality of recovery following thoracoscopic lung resection: A randomized controlled factorial trial
Authors: Jing-hui Hu, Zhang-zhen Zhong, Hai-jing Shi, Jie Wang, Shaomu Chen, Xi-sheng Shan, Hua-yue Liu, Hong Liu, Lingzhong Meng, Fu-hai Ji, Ke Peng
Journal: International Journal of Surgery (2024)

Background: Multimodal analgesic strategy is pivotal for enhanced recovery after surgery. The objective of this trial was to assess the effect of subanesthetic esketamine vs. placebo combined with erector spinae plane block (ESPB) vs. intercostal nerve block (ICNB) on postoperative recovery following thoracoscopic lung resection. Materials and methods: This randomized, controlled, 2×2 factorial trial was conducted at a university hospital in Suzhou, China. One hundred adult patients undergoing thoracoscopic lung surgery were randomized to one of four groups (esketamine-ESPB, esketamine-ICNB, placebo-ESPB, and placebo-ICNB) to receive i.v. esketamine 0.3 mg/kg or normal saline placebo combined with ESPB or ICNB using 0.375% ropivacaine 20 mL. All patients received flurbiprofen axetil and patient-controlled fentanyl. The primary outcome was quality of recovery (QoR) at 24 h postoperatively, assessed using the QoR-15 scale, with a minimal clinically important difference of 6.0. Results: The median age was 57 years and 52% were female. No significant interaction effect was found between esketamine and regional blocks on QoR ( P =0.215). The QoR-15 score at 24 h was 111.5±5.8 in the esketamine group vs. 105.4±4.5 in the placebo group (difference=6.1, 95% CI, 4.0–8.1; P &lt;0.001); 109.7±6.2 in the ESPB group vs. 107.2±5.6 in the ICNB group (difference=2.5, 95% CI, 0.2–4.9; P =0.033; not statistically significant after Bonferroni correction). Additionally, esketamine resulted in higher QoR-15 scores at 48 h (difference=4.6) and hospital discharge (difference=1.6), while ESPB led to a higher QoR-15 score at 48 h (difference=3.0). Conclusions: For patients undergoing thoracoscopic lung resection, subanesthetic esketamine improved QoR after surgery, while ICNB can be used interchangeably with ESPB as a component of multimodal analgesia.
Endovascular treatment for large ischemic core stroke: challenges and opportunities
Authors: Chenglin Tong, Lingjia Xu
Journal: International Journal of Surgery (2024)

aDepartment of Emergency Internal Medicine, Shaoxing Second Hospital, Shaoxing, Zhejiang, 312000, China bDepartment of Neurology, Shaoxing Second Hospital, Shaoxing, Zhejiang, 312000, China Chenglin Tong and Lingjia Xu: The authors contributed equally to this work. Assistance with the study: none. Financial support and sponsorship: This study was supported by the Medical and Health Science and Technology Project of Zhejiang Province (Grant No. 2024KY492). Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ *Corresponding author. Address: Department of Emergency Internal Medicine, Shaoxing Second Hospital, Shaoxing, Zhejiang, 312000, China. E-mail: [email protected] (C. Tong). This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms. http://creativecommons.org/licenses/by-nc-sa/4.0/
Effects of individualized positive end-expiratory pressure on intraoperative oxygenation and postoperative pulmonary complications in patients requiring pneumoperitoneum with Trendelenburg position: A systematic review and meta-analysis
Authors: Lingqi Gao, Bingyan Zhang, Jiazheng Qi, Xu Zhao, Xiaojie Yan, Bing Li, Jingjing Shen, Tingting Gu, Qiong Yu, Mengqiang Luo, Yingwei Wang
Journal: International Journal of Surgery (2024)

Whether individualized positive end-expiratory pressure (PEEP) improves intraoperative oxygenation and reduces postoperative pulmonary complications (PPCs) remains unclear. This systematic review and meta-analysis examined whether individualized PEEP is associated with improved intraoperative oxygenation and reduce PPCs for patients needing pneumoperitoneum with the Trendelenburg position during surgery.