CLIP

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  • 文章类型: Journal Article
    近年来,人工智能领域见证了合成图像生成的显着激增,由深度学习技术的进步驱动。这些合成图像,通常是通过复杂的算法创建的,紧密模仿真实的照片,模糊现实和人为之间的界限。合成视觉效果的激增提出了一个紧迫的挑战:如何准确可靠地区分真实图像和生成图像。这篇文章,特别是,探索了检测由文本到图像扩散模型生成的图像的任务,强调这一领域的挑战和特点。为了评估这一点,我们使用两个最先进的模型来考虑从MSCOCO和Wikimedia数据集中的标题生成的图像:稳定扩散和GLIDE。我们的实验表明,可以使用简单的多层感知器(MLP)检测生成的图像,从CLIP或RoBERTA提取的特征开始,或使用传统的卷积神经网络(CNN)。这些模型实现了显着的性能,特别是当在大型数据集预训练。我们还观察到,在稳定扩散生成的图像上训练的模型偶尔可以检测到GLIDE生成的图像,但仅限于MSCOCO数据集。然而,相反的情况并非如此。最后,我们发现,在某些情况下,将相关的文本信息与图像结合起来可以带来更好的泛化能力,特别是如果文本特征与视觉特征密切相关。我们还发现,图像中描绘的主题类型可以显着影响性能。这项工作提供了对检测生成图像的可行性的见解,并对现实应用中的安全和隐私问题产生了影响。重现我们结果的代码可在以下网址获得:https://github.com/davide-coccomini/Detecting-Images-Generated-by-Differs。
    In recent years, the field of artificial intelligence has witnessed a remarkable surge in the generation of synthetic images, driven by advancements in deep learning techniques. These synthetic images, often created through complex algorithms, closely mimic real photographs, blurring the lines between reality and artificiality. This proliferation of synthetic visuals presents a pressing challenge: how to accurately and reliably distinguish between genuine and generated images. This article, in particular, explores the task of detecting images generated by text-to-image diffusion models, highlighting the challenges and peculiarities of this field. To evaluate this, we consider images generated from captions in the MSCOCO and Wikimedia datasets using two state-of-the-art models: Stable Diffusion and GLIDE. Our experiments show that it is possible to detect the generated images using simple multi-layer perceptrons (MLPs), starting from features extracted by CLIP or RoBERTa, or using traditional convolutional neural networks (CNNs). These latter models achieve remarkable performances in particular when pretrained on large datasets. We also observe that models trained on images generated by Stable Diffusion can occasionally detect images generated by GLIDE, but only on the MSCOCO dataset. However, the reverse is not true. Lastly, we find that incorporating the associated textual information with the images in some cases can lead to a better generalization capability, especially if textual features are closely related to visual ones. We also discovered that the type of subject depicted in the image can significantly impact performance. This work provides insights into the feasibility of detecting generated images and has implications for security and privacy concerns in real-world applications. The code to reproduce our results is available at: https://github.com/davide-coccomini/Detecting-Images-Generated-by-Diffusers.
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  • 文章类型: Journal Article
    背景:胃内镜黏膜下剥离术(ESD)用于位于胃的上中部(U/M)三分之一的较大曲率上的病变仍然具有挑战性,即使是经验丰富的内窥镜医师。因此,我们开发了一种新颖的牵引技术,称为外病变夹线法(O-CTM)。在这种方法中,一根夹线连接到圆周切口线外部的健康粘膜,并应用牵引使范围和病变接近ESD。这里,与不使用O-CTM的ESD相比,我们评估了使用O-CTM的ESD的疗效.
    方法:我们回顾性分析了2015年9月至2024年4月期间63例接受胃ESD的连续患者的数据,这些患者的63例病变位于胃U/M三分之一的较大曲率处。主要结果是手术时间,次要结果是切除速度,整块切除,O-CTM和无O-CTMESD组的R0切除和并发症。
    结果:在63个包括的病变中,在2015年9月至2022年6月期间,37例切除无O-CTM(无O-CTM组),2022年7月至2024年4月期间,使用O-CTM切除了26个病灶(O-CTM组).O-CTM组手术时间明显缩短(40分钟vs.77分钟,p=0.01)比无O-CTM组。切除速度也明显更快(20.1mm2/minvs.11.3mm2/min,p=0.02)。整块切除率无显著差异,R0切除率,观察并发症。
    结论:与不使用O-CTM的ESD相比,使用O-CTM的胃ESD在减少手术时间和提高切除速度方面是有益的,用于治疗位于U/M区域较大曲率的病变。
    BACKGROUND: Gastric endoscopic submucosal dissection (ESD) for lesions located on the greater curvature of the upper and middle (U/M) third of the stomach remains challenging, even for experienced endoscopists. Accordingly, we have developed a novel traction technique, termed the outside-lesion clip-thread method (O-CTM). In this method, a clip thread is attached to the healthy mucosa outside the circumferential incision line, and traction is applied to bring the scope and lesion into proximity for ESD. Here, we assessed the efficacy of ESD using the O-CTM compared to ESD without the O-CTM.
    METHODS: We retrospectively reviewed data from 63 consecutive patients who underwent gastric ESD for 63 lesions located on the greater curvature of the U/M third of the stomach between September 2015 and April 2024. The primary outcome was the operation time, and secondary outcomes were resection speed, en bloc resection, R0 resection and complications in the O-CTM and without O-CTM ESD groups.
    RESULTS: Of the 63 included lesions, 37 were resected without the O-CTM between September 2015 and June 2022 (without O-CTM group), and 26 lesions were resected using the O-CTM between July 2022 and April 2024 (O-CTM group). The O-CTM group had significantly shorter operation times (40 min vs. 77 min, p = 0.01) than the without O-CTM group. The resection speed was also significantly faster (20.1 mm2/min vs. 11.3 mm2/min, p = 0.02). No significant differences in en bloc resection rate, R0 resection rate, and complications were observed.
    CONCLUSIONS: Gastric ESD using O-CTM is beneficial when compared with the ESD without O-CTM in reducing operation time and improving resection speeds for treating lesions located on the greater curvature of the U/M region.
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  • 文章类型: Journal Article
    大型和巨大的颅内动脉瘤(LGIA)已成为血管内技术无法提供令人满意的结果的范例。然而,显微外科手术之后是不可忽略的死亡率。自从引入分流装置以来,这种情况可能已经改变。
    关于显微外科手术和血管内结果的当代和标准化修订,重点是前循环LGIA。
    在两个数据库(PubMed和Embase)中对前循环LGIA的治疗结果进行了系统的文献检索,在引入分流器2008/01/01之后,直到2023/05/20。小案例系列(<5例),系列包括>15%的后循环动脉瘤,未报告临床和/或血管造影结果的研究被排除.
    确定了44项相关研究(观察性队列),包括2923名主要来自前循环的LGIA。平均随访22(±20)个月。1494(51%)LGIA进行了血管内治疗,1427(49%)进行了显微外科治疗。根据随机效应模型,有利临床结局的汇总率为85.8%(CI95%82.6-88.4),完全闭塞69.4%(CI95%63.7-7.46),并发症19.6%(CI95%16-23.9)和死亡率5.6%(CI95%4.4-7.1).专注于治疗类型,显微手术的闭塞率较高(842/993,85%vs874/1,299,67%),尽管良好的结局在血管内的发生率略高(1045/1,135,92%vs1120/1,294,87%).
    根据有关闭塞率的当代数据,功能结果,和并发症,前循环LGIAs的主要或次要治疗似乎是合理的。LGIA的显微手术闭塞率较高。关于报告并发症和管理策略的专家共识是必要的。
    UNASSIGNED: Large and Giant intracranial aneurysms (LGIAs) have become the paradigm for which endovascular techniques do not provide satisfactory results. Yet, microsurgery is followed by non-negligible rates of morbimortality. This scenario may have changed since the introduction of flow-diversion devices.
    UNASSIGNED: Contemporary and standardised revision on microsurgical and endovascular results, with emphasis on anterior circulation LGIAs.
    UNASSIGNED: A systematic literature search was conducted in two databases (PubMed and Embase) on treatment outcomes of LGIAs of the anterior circulation, after the introduction of flow-diverters 2008/01/01, till 2023/05/20. Small case series (<5 cases), series including >15% of posterior circulation aneurysms, and studies not reporting clinical and/or angiographic outcomes were excluded.
    UNASSIGNED: 44 relevant studies (observational cohorts) were identified, including 2923 LGIAs predominantly from anterior circulation. Mean follow-up 22 (±20) months. 1494 (51%) LGIAs were treated endovascularly and 1427 (49%) microsurgically. According to the random effects model, pooled rates of favourable clinical outcomes were 85.8% (CI 95% 82.6-88.4), complete occlusion 69.4% (CI 95% 63.7-7.46), complications 19.6% (CI 95%16-23.9) and mortality 5.6% (CI 95% 4.4-7.1). Focusing on type of treatment, occlusion rates are higher with microsurgical (842/993, 85% vs 874/1,299, 67%), although good outcomes are slightly more frequent with endovascular (1045/1,135, 92% vs 1120/1,294, 87%).
    UNASSIGNED: According to contemporary data about occlusion rates, functional outcomes, and complications, primary or secondary treatment of LGIAs of the anterior circulation seems justified. Microsurgical occlusion rates are higher in LGIAs. An expert consensus on reporting complications and management strategies is warranted.
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  • 文章类型: Journal Article
    真核细胞具有高度组织化的结构。尽管新生RNA上剪接体的时空排列驱动剪接,直接支持这一进程的核架构仍不清楚。这里,我们表明,组装在RNA上的RNA结合蛋白(RBPs)在人和小鼠细胞中形成网状物。RNA剪接中的核心和辅助RBPs使两个不同的网状物相邻但明显地分布在整个细胞核中。这是通过RBP的带电和不带电的固有无序区域(IDR)之间的互斥动力学实现的。这两种类型的网状物竞争pre-mRNA上的空间占据以调节剪接。此外,RBP网的光遗传学增强导致异常剪接,特别是涉及神经变性的基因。与神经退行性疾病相关的基因突变通常在RBPs的IDR中发现,携带这些突变的细胞表现出受损的网状物形成。我们的结果揭示了RBP网络驱动RNA剪接的空间组织。
    The eukaryotic nucleus has a highly organized structure. Although the spatiotemporal arrangement of spliceosomes on nascent RNA drives splicing, the nuclear architecture that directly supports this process remains unclear. Here, we show that RNA-binding proteins (RBPs) assembled on RNA form meshworks in human and mouse cells. Core and accessory RBPs in RNA splicing make two distinct meshworks adjacently but distinctly distributed throughout the nucleus. This is achieved by mutual exclusion dynamics between the charged and uncharged intrinsically disordered regions (IDRs) of RBPs. These two types of meshworks compete for spatial occupancy on pre-mRNA to regulate splicing. Furthermore, the optogenetic enhancement of the RBP meshwork causes aberrant splicing, particularly of genes involved in neurodegeneration. Genetic mutations associated with neurodegenerative diseases are often found in the IDRs of RBPs, and cells harboring these mutations exhibit impaired meshwork formation. Our results uncovered the spatial organization of RBP networks to drive RNA splicing.
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  • 文章类型: Journal Article
    目的:术中破裂(IOR)是颅内动脉瘤破裂的手术夹闭过程中最常见的不良事件。除了增加外科医生的经验和早期的近端控制,没有降低IOR风险的方法。因此,我们的目的是评估在夹闭前部分血管内弹簧圈栓塞保护动脉瘤是否降低了IOR.
    方法:我们对在两个三级学术中心接受手术夹闭治疗的颅内动脉瘤破裂患者进行了回顾性分析。我们比较了接受部分血管内弹簧圈栓塞术以在夹闭之前保护动脉瘤的患者的患者特征和结果。主要结果是IOR。次要结果是住院死亡率和出院目的地。
    结果:我们分析了100例患者。27例患者进行了部分血管内动脉瘤保护。年龄,性别,蛛网膜下腔出血的严重程度,部分栓塞组和非栓塞组之间的动脉瘤位置相似.部分栓塞动脉瘤的中位尺寸较大(7.0mm[四分位距5.95-8.7]vs.4.6mm[3.3-6.0];P<0.001)。在手术夹钳期间,与未栓塞的动脉瘤相比,部分栓塞的动脉瘤发生IOR的频率较低(2/27,7.4%,vs.30/73,41%;P=0.001)。部分栓塞动脉瘤患者的住院死亡率为14.8%(4/27),未栓塞患者的住院死亡率为28.8%(21/73)(P=0.20)。部分栓塞动脉瘤患者出院回家或住院康复率为74.0%,未栓塞患者为56.2%(P=0.11)。2/27(7.4%)患者发生部分栓塞并发症。
    结论:术前部分血管内弹簧圈栓塞治疗破裂动脉瘤与手术夹闭治疗期间IOR频率降低有关。这些结果以及术前部分血管内弹簧圈栓塞对功能结局的影响应通过随机试验得到证实。
    OBJECTIVE: Intraoperative rupture (IOR) is the most common adverse event encountered during surgical clip obliteration of ruptured intracranial aneurysms. Besides increasing surgeon experience and early proximal control, no methods exist to decrease IOR risk. Thus, our objective was to assess if partial endovascular coil embolization to protect the aneurysm before clipping decreases IOR.
    METHODS: We conducted a retrospective analysis of patients with ruptured intracranial aneurysms that were treated with surgical clipping at two tertiary academic centers. We compared patient characteristics and outcomes of those who underwent partial endovascular coil embolization to protect the aneurysm before clipping to those who did not. The primary outcome was IOR. Secondary outcomes were inpatient mortality and discharge destination.
    RESULTS: We analyzed 100 patients. Partial endovascular aneurysm protection was performed in 27 patients. Age, sex, subarachnoid hemorrhage severity, and aneurysm location were similar between the partially-embolized and non-embolized groups. The median size of the partially-embolized aneurysms was larger (7.0 mm [interquartile range 5.95-8.7] vs. 4.6 mm [3.3-6.0]; P < 0.001). During surgical clipping, IOR occurred less frequently in the partially-embolized aneurysms than non-embolized aneurysms (2/27, 7.4%, vs. 30/73, 41%; P = 0.001). Inpatient mortality was 14.8% (4/27) in patients with partially-embolized aneurysms and 28.8% (21/73) in patients without embolization (P = 0.20). Discharge to home or inpatient rehabilitation was 74.0% in patients with partially-embolized aneurysms and 56.2% in patients without embolization (P = 0.11). A complication from partial embolization occurred in 2/27 (7.4%) patients.
    CONCLUSIONS: Preoperative partial endovascular coil embolization of ruptured aneurysms is associated with a reduced frequency of IOR during definitive treatment with surgical clip obliteration. These results and the impact of preoperative partial endovascular coil embolization on functional outcomes should be confirmed with a randomized trial.
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  • 文章类型: Journal Article
    蛋白质-RNA相互作用的发现可以更深入地了解RNA加工。最近的多重交联和免疫沉淀(CLIP)技术,例如抗体条形码化的eCLIP(ABC)显着增加了映射RNA结合蛋白(RBP)结合位点的通量。然而,多路复用CLIP数据集是多变量的,并且每个RBP遭受非均匀信噪比。为了解决这个问题,我们开发了Mudskipper,一个多功能的计算套件,包括两个组件:一个Dirichlet多项混合模型,用于解释ABC数据集的多变量性质,一个软掩蔽方法,用于识别和消除低信噪比的RBP中的非特异性蛋白质-RNA相互作用。Mudskipper在多重数据集上显示出比现有工具更高的精确度和召回率,并支持重复元件和小型非编码RNA的分析。我们的发现揭示了剪接结果和变异相关的破坏,能够对RBPs介导的疾病和调节进行更高通量的研究。
    The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.
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  • 文章类型: Journal Article
    物种识别是了解各种生物的丰度和分布的关键部分,对于生物多样性的保护和管理至关重要。传统的基于视觉的深度学习驱动的物种识别需要大量的标记良好,高质量的图像数据,对稀有和濒危物种的收集具有挑战性。此外,基于特定物种设计的识别方法泛化能力差,难以适应新的物种识别场景。为了解决这些问题,基于对比语言-图像预训练(CLIP)的零镜头物种识别已成为研究热点。然而,以前的研究主要利用物种的视觉描述信息和分类学信息来提高零射识别性能,利用物种的地理分布特征来提高零射识别性能尚未得到探索。为了填补这个空白,我们提出了一种CLIP驱动的零射物种识别方法,该方法结合了物种地理分布的知识。首先,我们根据物种地理分布统计数据设计了三个提示。然后,附加到物种数据集中的每个图像的纬度和经度坐标信息被转换为地址,它们被整合在一起,形成每个物种的地理分布知识。最后,通过训练后的CLIP图像编码器和文本编码器获取特征后,通过计算相似度得出物种识别结果。我们对iNaturalist2021数据集中的多个物种数据集进行了广泛的实验,哺乳动物的零射识别精度,软体动物,爬行动物,两栖动物,鸟,昆虫占44.96%,15.27%,17.51%,9.47%,28.35%,和7.03%,改善了2.07%,0.48%,0.35%,1.12%,1.64%,和0.61%,分别,与默认提示的CLIP相比。实验结果表明,融合地理分布统计数据可以有效提高零拍物种识别的性能,为物种领域知识的利用提供了新的途径。
    Species recognition is a crucial part of understanding the abundance and distribution of various organisms and is important for biodiversity conservation and management. Traditional vision-based deep learning-driven species recognition requires large amounts of well-labeled, high-quality image data, the collection of which is challenging for rare and endangered species. In addition, recognition methods designed based on specific species have poor generalization ability and are difficult to adapt to new species recognition scenarios. To address these issues, zero-shot species recognition based on Contrastive Language-Image Pre-training (CLIP) has become a research hotspot. However, previous studies have primarily utilized visual descriptive information and taxonomic information of species to improve zero-shot recognition performance, and the use of geographic distribution characteristics of species to improve zero-shot recognition performance has not been explored. To fill this gap, we proposed a CLIP-driven zero-shot species recognition method that incorporates knowledge of the geographic distribution of species. First, we designed three prompts based on the species geographic distribution statistical data. Then, the latitude and longitude coordinate information attached to each image in the species dataset was converted into addresses, and they were integrated together to form the geographical distribution knowledge of each species. Finally, species recognition results were derived by calculating the similarity after acquiring features by the trained CLIP image encoder and text encoder. We conducted extensive experiments on multiple species datasets from the iNaturalist 2021 dataset, where the zero-shot recognition accuracies of mammals, mollusks, reptiles, amphibians, birds, and insects were 44.96%, 15.27%, 17.51%, 9.47%, 28.35%, and 7.03%, an improvement of 2.07%, 0.48%, 0.35%, 1.12%, 1.64%, and 0.61%, respectively, as compared to CLIP with default prompt. The experimental results show that the fusion of geographic distribution statistical data can effectively improve the performance of zero-shot species recognition, which provides a new way to utilize species domain knowledge.
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  • 文章类型: Journal Article
    在过去的几十年里,先天性心脏病(CHD)的研究得益于各种模型系统和分子生物学技术的发展,从而可以分析单基因以及全球效应。在这一章中,我们首先描述不同的模型,包括冠心病患者及其家属,从无脊椎动物到哺乳动物的动物模型,和各种细胞培养系统。此外,讨论了实验操作这些模型的技术。第二,我们介绍了心脏表型分析技术,包括小鼠和细胞培养模型的分析,心脏发生的实时成像,和固定心脏的组织学方法。最后,描述了最重要和最新的分子生物学技术。这些包括基因分型技术,下一代测序的不同应用,和转录组的分析,表观基因组,蛋白质组,和代谢组。总之,本章介绍的模型和技术对于研究心脏的功能和发育以及了解CHD的分子通路至关重要.
    Over the last few decades, the study of congenital heart disease (CHD) has benefited from various model systems and the development of molecular biological techniques enabling the analysis of single gene as well as global effects. In this chapter, we first describe different models including CHD patients and their families, animal models ranging from invertebrates to mammals, and various cell culture systems. Moreover, techniques to experimentally manipulate these models are discussed. Second, we introduce cardiac phenotyping technologies comprising the analysis of mouse and cell culture models, live imaging of cardiogenesis, and histological methods for fixed hearts. Finally, the most important and latest molecular biotechniques are described. These include genotyping technologies, different applications of next-generation sequencing, and the analysis of transcriptome, epigenome, proteome, and metabolome. In summary, the models and technologies presented in this chapter are essential to study the function and development of the heart and to understand the molecular pathways underlying CHD.
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  • 文章类型: Journal Article
    RNA结合蛋白(RBP)调节RNA加工的关键方面,包括可变剪接,通过物理结合RNA分子的mRNA降解和定位。当前映射这些相互作用的方法,如CLIP,依赖于一次纯化单个蛋白质。我们的新方法,ePRINT,在全球范围内绘制RBP-RNA相互作用网络,而无需纯化单个RBP。ePRINT使用外切核糖核酸酶XRN1精确定位RBP结合位点的5'端,并揭示感兴趣的RBP的直接和间接靶标。重要的是,ePRINT还可以发现在细胞命运转变之间差异激活的RBP,包括神经祖细胞分化为神经元。
    RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new method, ePRINT, maps RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT uses exoribonuclease XRN1 to precisely map the 5\' end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons.
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  • 文章类型: Review
    上消化道(GI)出血提出了实质性的临床挑战。初始管理通常包括24小时内的复苏和内窥镜检查,尽管早期内镜检查(<12h)对高危患者的益处仍存在争议。治疗目标包括停止急性出血,防止再出血,使用包括内窥镜在内的多模式方法,药理学,血管造影,和手术方法。药物如血管加压素,前列腺素,质子泵抑制剂是有效的,但是抗血栓使用的增加增加了消化道出血的发病率.内镜止血,尤其是非静脉曲张出血,采用电凝法和加热器探针等技术,关注单极电凝对组织的损伤。新的方法如Hemosproke和Endoclot在制造机械填塞方面显示出希望,但有局限性。目前,一线治疗包括热探针和血液夹,超范围夹出现较大的溃疡出血。金探针,双极电凝和注射相结合,提供有针对性的凝血,但面临与设备相关的问题。未来的进步涉及结合技术和改进内窥镜成像,探索组合方法的研究显示出了希望。持续的研究对于制定标准化和有效的出血管理策略至关重要。
    Upper gastrointestinal (GI) hemorrhage presents a substantial clinical challenge. Initial management typically involves resuscitation and endoscopy within 24 h, although the benefit of very early endoscopy (< 12 h) for high-risk patients is debated. Treatment goals include stopping acute bleeding, preventing rebleeding, and using a multimodal approach encompassing endoscopic, pharmacological, angiographic, and surgical methods. Pharmacological agents such as vasopressin, prostaglandins, and proton pump inhibitors are effective, but the increase in antithrombotic use has increased GI bleeding morbidity. Endoscopic hemostasis, particularly for nonvariceal bleeding, employs techniques such as electrocoagulation and heater probes, with concerns over tissue injury from monopolar electrocoagulation. Novel methods such as Hemospray and Endoclot show promise in creating mechanical tamponades but have limitations. Currently, the first-line therapy includes thermal probes and hemoclips, with over-the-scope clips emerging for larger ulcer bleeding. The gold probe, combining bipolar electrocoagulation and injection, offers targeted coagulation but has faced device-related issues. Future advancements involve combining techniques and improving endoscopic imaging, with studies exploring combined approaches showing promise. Ongoing research is crucial for developing standardized and effective hemorrhage management strategies.
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