tbuckley/cabot-search huggingface dataset:
Bispecific antibodies and CAR-T cells: dueling immunotherapies for large B-cell lymphomas
Authors: Asaad Trabolsi, Artavazd Arumov, Jonathan H. Schatz
Journal: Blood Cancer Journal (2024)

Despite recent advances in frontline therapy for diffuse large B-cell lymphoma (DLBCL), at least a third of those diagnosed still will require second or further lines for relapsed or refractory (rel/ref) disease. A small minority of these can be cured with standard chemoimmunotherapy/stem-cell transplant salvage approaches. CD19-directed chimeric antigen receptor T-cell (CAR-19) therapies are increasingly altering the prognostic landscape for rel/ref patients with DLBCL and related aggressive B-cell non-Hodgkin lymphomas. Long-term follow up data show ongoing disease-free outcomes consistent with cure in 30-40% after CAR-19, including high-risk patients primary refractory to or relapsing within 1 year of frontline treatment. This has made CAR-19 a preferred option for these difficult-to-treat populations. Widespread adoption, however, remains challenged by logistical and patient-related hurdles, including a requirement for certified tertiary care centers concentrated in urban centers, production times of at least 3-4 weeks, and high per-patients costs similar to allogeneic bone-marrow transplantation. Bispecific antibodies (BsAbs) are molecular biotherapies designed to bind and activate effector T-cells and drive them to B-cell antigens, leading to a similar cellular-dependent cytotoxicity as CAR-19. May and June of 2023 saw initial approvals of next-generation BsAbs glofitamab and epcoritamab in DLBCL as third or higher-line therapy, or for patients ineligible for CAR-19. BsAbs have similar spectrum but generally reduced severity of immune related side effects as CAR-19 and can be administered in community settings without need to manufacture patient-specific cellular products. To date and in contrast to CAR-19, however, there is no convincing evidence of cure after BsAbs monotherapy, though follow up is limited. The role of BsAbs in DLBCL treatment is rapidly evolving with trials investigating use in both relapsed and frontline curative-intent combinations. The future of DLBCL treatment is bound increasingly to include effector cell mediated immunotherapies, but further optimization of both cellular and BsAb approaches is needed.
Learning continuous shape priors from sparse data with neural implicit functions
Authors: Tamaz Amiranashvili, David Lüdke, Hongwei Bran Li, Stefan Zachow, Bjoern H. Menze
Journal: Medical Image Analysis (2024)

Statistical shape models are an essential tool for various tasks in medical image analysis, including shape generation, reconstruction and classification. Shape models are learned from a population of example shapes, which are typically obtained through segmentation of volumetric medical images. In clinical practice, highly anisotropic volumetric scans with large slice distances are prevalent, e.g., to reduce radiation exposure in CT or image acquisition time in MR imaging. For existing shape modeling approaches, the resolution of the emerging model is limited to the resolution of the training shapes. Therefore, any missing information between slices prohibits existing methods from learning a high-resolution shape prior. We propose a novel shape modeling approach that can be trained on sparse, binary segmentation masks with large slice distances. This is achieved through employing continuous shape representations based on neural implicit functions. After training, our model can reconstruct shapes from various sparse inputs at high target resolutions beyond the resolution of individual training examples. We successfully reconstruct high-resolution shapes from as few as three orthogonal slices. Furthermore, our shape model allows us to embed various sparse segmentation masks into a common, low-dimensional latent space – independent of the acquisition direction, resolution, spacing, and field of view. We show that the emerging latent representation discriminates between healthy and pathological shapes, even when provided with sparse segmentation masks. Lastly, we qualitatively demonstrate that the emerging latent space is smooth and captures characteristic modes of shape variation. We evaluate our shape model on two anatomical structures: the lumbar vertebra and the distal femur, both from publicly available datasets.
Prevalence of SARS-CoV-2 infections among Swedish healthcare workers on duty in December 2023
Authors: Katherina Aguilera, Oscar Bladh, Ulrika Marking, Nina Greilert Norin, Ali Rihani, Dorina Ujvari, Frank Chenfei Ning, Jonas Klingström, Sebastian Havervall, Mikael Åberg, Kim Blom, Jessica J. Alm, Charlotte Thålin
Journal: The Lancet Regional Health - Europe (2024)

C 1: Prevalence, viral load, and viral variants among Swedish healthcare workers on duty in December 2023.A) Percentage positive per day during December 4-15, 2023.Bars show total number of tested participants per day; grey = negative; black = positive.Numbers above bar depict percent positive.B) Individual Ct-values (SARS CoV-2 N-gene) for each positive sample as an indication of viral load.C) Viral variant identification by whole genome sequencing in each positive sample December 4-15, 2023.Bars show total number of diagnosed infections per day, and their individual variants JN.1, JN.2, JN.3, JN.8, BA.2.86.1 and XBB.1.Ct; Cyclic threshold, NA; Not available.
Sex-determining region Y gene promotes liver fibrosis and accounts for sexual dimorphism in its pathophysiology
Authors: Xiao-Ning Wu, Meng-Zhou Wang, Nan Zhang, Wei Zhang, Jian Dong, Meng-Yun Ke, Jun-Xi Xiang, Feng Ma, Feng Xue, Jing-Jing Hou, Zhi-Jie Ma, Fu-Min Wang, Xue-Min Liu, Rongqian Wu, Timothy M. Pawlik, Kai Ye, Jun Yu, Xu-Feng Zhang, Yi Lyu
Journal: Journal of Hepatology (2024)
One - or more - blind spot(s) unveiled in the new definition of decompensated cirrhosis
Authors: Florent Artru, Thomas Reiberger
Journal: Journal of Hepatology (2024)

It is generally accepted that the development of variceal bleeding, hepatic encephalopathy (HE), jaundice, and ascites denotes the transition from compensated to decompensated cirrhosis.1,2 Decompensation usually occurs in patients with clinically significant portal hypertension, as defined by a hepatic venous pressure gradient ≥10 mmHg. The critical place of decompensation in the natural history of cirrhosis has recently been emphasized by analyses considering death as a competing event of decompensation, thereby, acknowledging that decompensation usually precedes death in patients with compensated cirrhosis.
Chimeric antigen receptor-modified macrophages ameliorate liver fibrosis in preclinical models
Authors: Hanren Dai, Cheng Zhu, Qian Huai, Wentao Xu, Jiejie Zhu, Xu Zhang, Xianzheng Zhang, Beicheng Sun, Honghai Xu, Minghua Zheng, Xiaolei Li, Hua Wang
Journal: Journal of Hepatology (2024)
Immunotherapeutic effects of specific and nonspecific mRNA‐lipid nanoparticles in a mouse model of HDM‐induced airway inflammation
Authors: Chanatip Thanasarnthungcharoen, Supapich Chanasit, Laurence Fievez, Theerayuth Kaewamatawong, Piyachat Patniboon, Paulo J. C. Lin, Fabrice Bureau, Alain Jacquet
Journal: Allergy (2024)

The data that support the findings of this study are available from the corresponding author upon reasonable request. Data S1. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Indwelling pleural catheters or chest drains for managing malignant pleural effusions: a distinction without a difference?
Authors: Udit Chaddha, José M. Porcel, Septimiu D. Murgu
Journal: European Respiratory Journal (2024)

<h3>Extract</h3> In patients with symptomatic malignant pleural effusion (MPE), definitive effusion management is traditionally achieved by either indwelling pleural catheter (IPC) placement or by attempting chemical pleurodesis (instilling graded talc slurry through a chest drain or insufflating talc during a thoracoscopy) [1]. The goal of these interventions has been symptom palliation (usually dyspnoea and, less commonly, chest pain), and both IPCs and talc pleurodesis have been shown to be comparably effective in achieving this purpose (as assessed by patient-reported visual analogue scale) [2]. However, both have their pros and cons.
Phosphorylation-Regulated Dynamic Phase Separation of HIP-55 Protects Against Heart Failure
Authors: Yunqi Jiang, Jinge Gu, Xiaodou Niu, Jiaojiao Hu, Yongzhen Zhang, Dan Li, Yida Tang, Cong Liu, Zijian Li
Journal: Circulation (2024)

Heart failure (HF), which is the terminal stage of many cardiovascular diseases, is associated with low survival rates and a severe financial burden. The mechanisms, especially the molecular mechanism combined with new theories, underlying the pathogenesis of HF remain elusive. We demonstrate that phosphorylation-regulated dynamic liquid-liquid phase separation of HIP-55 (hematopoietic progenitor kinase 1-interacting protein of 55 kDa) protects against HF. Fluorescence recovery after photobleaching assay, differential interference contrast analysis, pull-down assay, immunofluorescence, and immunohistochemical analysis were used to investigate the liquid-liquid phase separation capacity of HIP-55 and its dynamic regulation in vivo and in vitro. Mice with genetic deletion of HIP-55 and mice with cardiac-specific overexpression of HIP-55 were used to examine the role of HIP-55 on β-adrenergic receptor hyperactivation-induced HF. Mutation analysis and mice with specific phospho-resistant site mutagenesis were used to identify the role of phosphorylation-regulated dynamic liquid-liquid phase separation of HIP-55 in HF. Genetic deletion of HIP-55 aggravated HF, whereas cardiac-specific overexpression of HIP-55 significantly alleviated HF in vivo. HIP-55 possesses a strong capacity for phase separation. Phase separation of HIP-55 is dynamically regulated by AKT-mediated phosphorylation at S269 and T291 sites, failure of which leads to impairment of HIP-55 dynamic phase separation by formation of abnormal aggregation. Prolonged sympathetic hyperactivation stress induced decreased phosphorylation of HIP-55 S269 and T291, dysregulated phase separation, and subsequent aggregate formation of HIP55. Moreover, we demonstrated the important role of dynamic phase separation of HIP-55 in inhibiting hyperactivation of the β-adrenergic receptor-mediated P38/MAPK (mitogen-activated protein kinase) signaling pathway. A phosphorylation-deficient HIP-55 mutation, which undergoes massive phase separation and forms insoluble aggregates, loses the protective activity against HF. Our work reveals that the phosphorylation-regulated dynamic phase separation of HIP-55 protects against sympathetic/adrenergic system-mediated heart failure.
Rotator cuff tears
Authors: Asheesh Bedi, Julie Bishop, Jay Keener, Drew A. Lansdown, Ofer Levy, Peter MacDonald, Nicola Maffulli, Joo Han Oh, Vani J. Sabesan, Joaquin Sanchez-Sotelo, Riley J. Williams, Brian T. Feeley
Journal: Nature Reviews Disease Primers (2024)
Optimizing skin disease diagnosis: harnessing online community data with contrastive learning and clustering techniques
Authors: Yue Shen, Huanyu Li, Can Sun, Hongtao Ji, Daojun Zhang, Kun Hu, Yiqi Tang, Yu Chen, Zikun Wei, Junwei Lv
Journal: npj Digital Medicine (2024)

Skin diseases pose significant challenges in China. Internet health forums offer a platform for millions of users to discuss skin diseases and share images for early intervention, leaving large amount of valuable dermatology images. However, data quality and annotation challenges limit the potential of these resources for developing diagnostic models. In this study, we proposed a deep-learning model that utilized unannotated dermatology images from diverse online sources. We adopted a contrastive learning approach to learn general representations from unlabeled images and fine-tuned the model on coarsely annotated images from Internet forums. Our model classified 22 common skin diseases. To improve annotation quality, we used a clustering method with a small set of standardized validation images. We tested the model on images collected by 33 experienced dermatologists from 15 tertiary hospitals and achieved a 45.05% top-1 accuracy, outperforming the published baseline model by 3%. Accuracy increased with additional validation images, reaching 49.64% with 50 images per category. Our model also demonstrated transferability to new tasks, such as detecting monkeypox, with a 61.76% top-1 accuracy using only 50 additional images in the training process. We also tested our model on benchmark datasets to show the generalization ability. Our findings highlight the potential of unannotated images from online forums for future dermatology applications and demonstrate the effectiveness of our model for early diagnosis and potential outbreak mitigation.
Advancing diagnosis and research for rare genetic diseases in Indigenous peoples
Authors: Gareth Baynam, Daria Julkowska, Sarah Bowdin, Azure Hermes, Christopher R. McMaster, Elissa Prichep, Étienne Richer, Francois H. van der Westhuizen, Gabriela M. Repetto, Helen Malherbe, Juergen K. V. Reichardt, Laura Arbour, Maui Hudson, Kelly du Plessis, Melissa Haendel, Phillip Wilcox, Sally Ann Lynch, Shamir Rind, Simon Easteal, Xavier Estivill, Nadine Caron, Meck Chongo, Yarlalu Thomas, Mary Catherine V. Letinturier, Barend Christiaan Vorster
Journal: Nature Genetics (2024)
Publisher Correction: p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity
Authors: Carmen Adriaens, Laura Standaert, Jasmine Barra, Mathilde Latil, Annelien Verfaillie, Peter Kalev, Bram Boeckx, Paul. W. G Wijnhoven, Enrico Radaelli, William Vermi, Eleonora Leucci, Gaëlle Lapouge, Benjamin Beck, Joost van den Oord, Shinichi Nakagawa, Tetsuro Hirose, Anna. A Sablina, Diether Lambrechts, Stein Aerts, Cédric Blanpain, Jean-Christophe Marine
Journal: Nature Medicine (2024)

In the version of this article initially published, three of the four FACS plots shown in Fig. 5c were incorrect duplicates of the control plot at left; a correct Fig.
Prescription opioids induced microbial dysbiosis worsens severity of chronic pancreatitis and drives pain hypersensitivity
Authors: Kousik Kesh, Junyi Tao, Nillu Ghosh, Richa Jalodia, Salma Singh, Rajinder Dawra, Sabita Roy
Journal: Gut Microbes (2024)

Opioids, such as morphine and oxycodone, are widely used for pain management associated with chronic pancreatitis (CP); however, their impact on the progression and pain sensitivity of CP has never been evaluated. This report investigates the impact of opioid use on the severity of CP, pain sensitivity, and the gut microbiome. C57BL/6 mice were divided into control, CP, CP with morphine/oxycodone, and either morphine or oxycodone alone groups. CP was induced by administration of caerulein (50ug/kg/h, i.p. hourly x7, twice a week for 10 weeks). The mouse-to-pancreas weight ratio, histology, and Sirius red staining were performed to measure CP severity. Tail flick and paw pressure assays were used to measure thermal and mechanical pain. DNA was extracted from the fecal samples and subjected to whole-genome shotgun sequencing. Germ-free mice were used to validate the role of gut microbiome in sensitizing acute pancreatic inflammation. Opioid treatment exacerbates CP by increasing pancreatic necrosis, fibrosis, and immune-cell infiltration. Opioid-treated CP mice exhibited enhanced pain hypersensitivity and showed distinct clustering of the gut microbiome compared to untreated CP mice, with severely compromised gut barrier integrity. Fecal microbiota transplantation (FMT) from opioid-treated CP mice into germ-free mice resulted in pancreatic inflammation in response to a suboptimal caerulein dose. Together, these analyses revealed that opioids worsen the severity of CP and induce significant alterations in pain sensitivity and the gut microbiome in a caerulein CP mouse model. Microbial dysbiosis plays an important role in sensitizing the host to pancreatic inflammation.
Pregnancy outcomes and risk factors of serious cardiovascular adverse events in pregnant women with pulmonary hypertension
Authors: Yanming Kang, Xiaoqin Jiang
Journal: International Journal of Surgery (2024)

Department of Anesthesiology, West China Second University Hospital, Sichuan University, Chengdu 610041, China bKey Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article. Published online ■ ■ *Corresponding author. Address: West China Women's and Children's Hospital: Sichuan University West China Second University Hospital CHINA. E-mail address: [email protected] (X. Jiang). This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/
Remote programming in stage I sacral neuromodulation: a Multi-Center prospective feasibility study
Authors: Jibo Jing, Lingfeng Meng, Yaoguang Zhang, Xinhao Wang, Wen Zhu, Qingwei Wang, Li Lu, Wei Song, Yifei Zhang, Yan Li, Jiaxing Ning, Haoran Wang
Journal: International Journal of Surgery (2024)

Objective: Sacral neuromodulation (SNM) has emerged as an effective therapy for refractory lower urinary tract dysfunction (LUTD). Remote programming holds promise in addressing the time and economic burdens associated with outpatient programming, especially for patients in the observation period following Stage I implant surgery (where the lead is implanted first without the pulse generator). The study aimed to explore the effectiveness and patient satisfaction of remote programming for Stage I SNM patients, and analyze the benefits patients gain from remote programming. Methods: This prospective study was conducted at multiple high-level clinical SNM centers in China. Patients requiring SNM implantation were enrolled and divided into two groups based on patient preference: remote programming (RP) group and outpatient control (OC) group. Patient attitudes toward RP were assessed through questionnaires, and the degree of symptom improvement was compared between the two groups to explore the usability of RP. Results: A total of 63 participants from 6 centers were included in the study, with 32 belonging to the RP group. The remote programming system presents a high level of usability (98%) and willingness (satisfaction rate: 96.83%) in result of questionnaire. RP showed a significant advantage in improving patients’ score of ICSI/ICPI (medianΔICSI/ICPI RP vs OC= -13.50 vs -2, P =0.015). And slightly ameliorate urinary symptoms such as pain (medianΔVAS RP vs OC= -1 vs 0, P = 0.164 ) and urgency ( medianΔOBASS -2.5 vs -1, P = 0,229), but the difference was not statistically significant. RP did not significantly impact the quality of life of patients ( P =0.113), so do the rate of phase-two conversion ( P = 0.926) or programming parameters. Conclusion: To the best of our knowledge, the presented study is the first multicenter research focusing on the remote programming of Stage I SNM patients. Through the clinical implementation and patient feedback, we demonstrate that remote programming is not inferior to in-person programming in terms of success rate, effectiveness, safety, and patient satisfaction.
Prognosis of uterine and extrauterine low-grade endometrial stromal sarcoma：an observational cohort study
Authors: Qianwen Dai, Baolin Xu, Huanwen Wu, Yan You, Lei Li
Journal: International Journal of Surgery (2024)

Objective: Little is known about the survival differences between uterine and extrauterine low-grade endometrial stromal sarcoma (LGESS). Survival outcomes, consisting of disease-free survivals and overall survivals, were compared in these two entities. Methods: From February 2012 to June 2019, all primary LGESS cases and LGESS cases with first recurrence in the study center were reviewed. The clinicopathological characteristics and survival outcomes of extrauterine and uterine LGESS patients were compared for both primary and recurrent diseases. Results: During the study period, 143 patients with primary LGESS and 56 patients with recurrent LGESS were included and followed up to June 1, 2020, among whom 8 (5.6%) and 10 (17.8%) patients were identified as having extrauterine LGESS. Patients with primary and recurrent extrauterine LGESS had similar clinicopathological characteristics to those of patients with uterine LGESS. In primary or in recurrent LGESS cases, in univariate analysis, patients with uterine and extrauterine LGESS had similar disease-free intervals after the last treatment, and they also had similar overall survivals after the diagnosis. Ovarian preservation led to significantly increased recurrence for primary LGESS (hazard ratio [HR] 4.9, 95% confidence interval [95% CI] 2.3-10.1, P &lt;0.001) and repeated recurrence for recurrent LGESS (HR 3.1, 95% CI 1.3-7.3, P =0.009). Surgical treatment for recurrent LGESS decreased repeated recurrence after the first recurrence (HR 0.2, 95% CI 0.1-0.7, P =0.006). No factors were found to be associated with the overall survival of primary or recurrent LGESS. Conclusion: The clinical characteristics and survival outcomes of extrauterine LGESS are similar to those of uterine LGESS. Surgery is the treatment of choice for recurrent LGESS. Ovarian preservation is detrimental to disease-free survival but not to overall survival in both uterine and extrauterine LGESS.
Application of ChatGPT in Pediatric surgery: Opportunities and challenges
Authors: Changkun Mao, Yuanyuan Bao, Yuanyuan Yang, Yongsheng Cao
Journal: International Journal of Surgery (2024)

aDepartment of Urology, Anhui Provincial Children's Hospital, Hefei,Anhui, 230041, China bDepartment of Electrocardiogram, Anhui Maternal and Child Health Hospital, Hefei Anhui, 230001, China Changkun Mao and Yuanyuan Bao: These authors have contributed equally to this work. Running title:Application of ChatGPT in Pediatric Surgery Sponsorships or competing interests that may be relevant to content are disclosed at the end of this article Published online ■ ■ *Corresponding author. Address: Anhui Provincial Children's Hospital, CHINA. E-mail address: [email protected] (Y. Cao). This is an open access article distributed under the Creative Commons Attribution-ShareAlike License 4.0, which allows others to remix, tweak, and build upon the work, even for commercial purposes, as long as the author is credited and the new creations are licensed under the identical terms. http://creativecommons.org/licenses/by-sa/4.0/