Pub Date : 2024-12-01Epub Date: 2024-03-18DOI: 10.1080/01652176.2024.2326007
Keon Kim, Hee-Hong Kim, Jae-Beom Joo, Ock-Kyu Kim, Sin-Wook Park, Guk-Hyun Suh, Woong-Bin Ro, Chang-Min Lee
Pancreatic alpha amylase (P-AMY) is used as a biomarker of acute pancreatitis (AP) in human medicine. To our knowledge, there are no studies evaluating the usefulness of P-AMY in dogs with AP. In this study, we evaluated the diagnostic value of P-AMY, currently not verified in veterinary medicine. The AP group (n = 40) consisted of dogs with AP diagnosed using clinical signs and laboratory examinations, including abnormal canine pancreatic lipase (cPL) concentration, and compatible abdominal ultrasound examination at first presentation. Evaluation of the canine AP severity (CAPS) score was performed. The control group (n = 38) was composed of normal dogs without any abnormalities in clinical findings, blood exams or diagnostic imaging. The correlation of P-AMY with cPL was confirmed by Pearson's correlation analysis (r = 0.564, p < .001). The sensitivity and specificity for the most appropriate cut-off values of P-AMY were recorded similar to the values of DGGR. The dogs with AP and CAPS ≥11 had significantly higher serum P-AMY (p = .016) contrary to DGGR lipase and cPL. Furthermore, there was a significant difference in the median P-AMY dependent on the presence of systemic inflammatory response syndrome (p = .001). P-AMY showed similar level of diagnostic accuracy along with sensitivity and specificity compared to DGGR lipase. In addition, P-AMY showed a significant association with CAPS score, contrary to cPL and DGGR lipase. Along with other biomarkers associated with AP, P-AMY has the potential of usefulness as a supportive diagnostic and prognostic biomarker of AP in dogs.
在人类医学中,胰腺α-淀粉酶(P-AMY)被用作急性胰腺炎(AP)的生物标志物。据我们所知,目前还没有研究评估 P-AMY 在犬急性胰腺炎患者中的作用。在这项研究中,我们评估了 P-AMY 的诊断价值,目前在兽医学中尚未得到验证。AP 组(n = 40)由首次发病时通过临床症状和实验室检查(包括犬胰脂肪酶(cPL)浓度异常)以及腹部超声波检查确诊为 AP 的犬组成。对犬 AP 严重程度(CAPS)进行了评估。对照组(n = 38)由临床表现、血液检查或诊断成像均无异常的正常犬组成。Pearson 相关性分析(r = 0.564,p p = .016)证实了 P-AMY 与 cPL 的相关性,与 DGGR 脂肪酶和 cPL 的相关性相反。此外,P-AMY 的中位数与全身炎症反应综合征的存在有显著差异(p = .001)。与 DGGR 脂肪酶相比,P-AMY 显示出相似的诊断准确性、灵敏度和特异性。此外,与 cPL 和 DGGR 脂肪酶相比,P-AMY 与 CAPS 评分有显著关联。与其他与 AP 相关的生物标记物一起,P-AMY 有可能成为狗 AP 的辅助诊断和预后生物标记物。
{"title":"Evaluation of the clinical usefulness of pancreatic alpha amylase as a novel biomarker in dogs with acute pancreatitis: a pilot study.","authors":"Keon Kim, Hee-Hong Kim, Jae-Beom Joo, Ock-Kyu Kim, Sin-Wook Park, Guk-Hyun Suh, Woong-Bin Ro, Chang-Min Lee","doi":"10.1080/01652176.2024.2326007","DOIUrl":"10.1080/01652176.2024.2326007","url":null,"abstract":"<p><p>Pancreatic alpha amylase (P-AMY) is used as a biomarker of acute pancreatitis (AP) in human medicine. To our knowledge, there are no studies evaluating the usefulness of P-AMY in dogs with AP. In this study, we evaluated the diagnostic value of P-AMY, currently not verified in veterinary medicine. The AP group (<i>n</i> = 40) consisted of dogs with AP diagnosed using clinical signs and laboratory examinations, including abnormal canine pancreatic lipase (cPL) concentration, and compatible abdominal ultrasound examination at first presentation. Evaluation of the canine AP severity (CAPS) score was performed. The control group (<i>n</i> = 38) was composed of normal dogs without any abnormalities in clinical findings, blood exams or diagnostic imaging. The correlation of P-AMY with cPL was confirmed by Pearson's correlation analysis (<i>r</i> = 0.564, <i>p</i> < .001). The sensitivity and specificity for the most appropriate cut-off values of P-AMY were recorded similar to the values of DGGR. The dogs with AP and CAPS ≥11 had significantly higher serum P-AMY (<i>p</i> = .016) contrary to DGGR lipase and cPL. Furthermore, there was a significant difference in the median P-AMY dependent on the presence of systemic inflammatory response syndrome (<i>p</i> = .001). P-AMY showed similar level of diagnostic accuracy along with sensitivity and specificity compared to DGGR lipase. In addition, P-AMY showed a significant association with CAPS score, contrary to cPL and DGGR lipase. Along with other biomarkers associated with AP, P-AMY has the potential of usefulness as a supportive diagnostic and prognostic biomarker of AP in dogs.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"44 1","pages":"1-7"},"PeriodicalIF":6.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10949834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-07-09DOI: 10.1007/s10555-024-10198-3
Yunxiu Qiu, Tong Gao, Bryan Ronain Smith
The circulation of tumor cells through the bloodstream is a significant step in tumor metastasis. To better understand the metastatic process, circulating tumor cell (CTC) survival in the circulation must be explored. While immune interactions with CTCs in recent decades have been examined, research has yet to sufficiently explain some CTC behaviors in blood flow. Studies related to CTC mechanical responses in the bloodstream have recently been conducted to further study conditions under which CTCs might die. While experimental methods can assess the mechanical properties and death of CTCs, increasingly sophisticated computational models are being built to simulate the blood flow and CTC mechanical deformation under fluid shear stresses (FSS) in the bloodstream.Several factors contribute to the mechanical deformation and death of CTCs as they circulate. While FSS can damage CTC structure, diverse interactions between CTCs and blood components may either promote or hinder the next metastatic step-extravasation at a remote site. Overall understanding of how these factors influence the deformation and death of CTCs could serve as a basis for future experiments and simulations, enabling researchers to predict CTC death more accurately. Ultimately, these efforts can lead to improved metastasis-specific therapeutics and diagnostics specific in the future.
{"title":"Mechanical deformation and death of circulating tumor cells in the bloodstream.","authors":"Yunxiu Qiu, Tong Gao, Bryan Ronain Smith","doi":"10.1007/s10555-024-10198-3","DOIUrl":"10.1007/s10555-024-10198-3","url":null,"abstract":"<p><p>The circulation of tumor cells through the bloodstream is a significant step in tumor metastasis. To better understand the metastatic process, circulating tumor cell (CTC) survival in the circulation must be explored. While immune interactions with CTCs in recent decades have been examined, research has yet to sufficiently explain some CTC behaviors in blood flow. Studies related to CTC mechanical responses in the bloodstream have recently been conducted to further study conditions under which CTCs might die. While experimental methods can assess the mechanical properties and death of CTCs, increasingly sophisticated computational models are being built to simulate the blood flow and CTC mechanical deformation under fluid shear stresses (FSS) in the bloodstream.Several factors contribute to the mechanical deformation and death of CTCs as they circulate. While FSS can damage CTC structure, diverse interactions between CTCs and blood components may either promote or hinder the next metastatic step-extravasation at a remote site. Overall understanding of how these factors influence the deformation and death of CTCs could serve as a basis for future experiments and simulations, enabling researchers to predict CTC death more accurately. Ultimately, these efforts can lead to improved metastasis-specific therapeutics and diagnostics specific in the future.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":" ","pages":"1489-1510"},"PeriodicalIF":7.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-07-17DOI: 10.1097/SLA.0000000000006445
Julia Adriana Kasmirski, Jason R Frank, Brenessa Lindeman
{"title":"Competency-Based Assessment in North American Surgical Training: A Tale of 2 Countries.","authors":"Julia Adriana Kasmirski, Jason R Frank, Brenessa Lindeman","doi":"10.1097/SLA.0000000000006445","DOIUrl":"10.1097/SLA.0000000000006445","url":null,"abstract":"","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":" ","pages":"925-927"},"PeriodicalIF":7.5,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-07-19DOI: 10.1080/01652176.2024.2379327
Chien-Hui Chen, Chao-Chin Chang, Wei-Che Chen, Ya-Jane Lee
Hair cortisol concentration (HCC) and a questionnaire were used as indicators of chronic stress status and quality of life (QoL), respectively, in cats. To date, there has been limited research on the simultaneous application of both indicators in unwell cats. Our aim was to evaluate HCC and questionnaire data obtained from a healthy cat cohort (n = 61) and cat cohorts with either chronic kidney disease (CKD) (n = 78) or suspected feline infectious peritonitis (FIP) (n = 24). Furthermore, we also investigated the correlation between HCC and clinical pathological data. For this study, hair from the abdomen of cats was collected and analyzed for HCC using a commercial ELISA kit. Owners also completed a questionnaire, from which average-item-weighted-impact-scores (AWISs) were calculated. Cats with late-stage-CKD (median, HCC = 330.15 pg/mg, AWIS = -0.43) presented with a significantly higher HCC (p < 0.01) and a significantly lower AWIS (p < 0.01) than cats with early-stage-CKD (HCC = 183.56 pg/mg, AWIS = 1.08). Similarly, there were significant differences in both HCC (p < 0.001) and AWIS (p < 0.001) between cats with suspected FIP (HCC = 896.27 pg/mg, AWIS = -1.97) and healthy cats (HCC = 181.24 pg/mg, AWIS = 1.24). The degree of consistency between the HCC results and the questionnaire results reminds us that the severity of a chronic disease or the presence of a life-threatening disease can significantly increase stress and thus can affect the QoL of cats.
毛发皮质醇浓度(HCC)和问卷调查分别被用作猫咪慢性压力状态和生活质量(QoL)的指标。迄今为止,将这两个指标同时应用于不健康猫咪的研究还很有限。我们的目的是评估从健康猫群组(61 只)和患有慢性肾病 (CKD) (78 只)或疑似猫传染性腹膜炎 (FIP) (24 只)的猫群组中获得的 HCC 和问卷调查数据。此外,我们还调查了 HCC 与临床病理数据之间的相关性。在这项研究中,我们收集了猫腹部的毛发,并使用商业 ELISA 试剂盒对毛发进行了 HCC 分析。猫主人还填写了一份调查问卷,并从中计算出平均项目加权影响分数(AWIS)。晚期 CKD 猫(中位数,HCC = 330.15 pg/mg,AWIS = -0.43)的 HCC 明显更高(p p p p
{"title":"Evaluation of chronic stress status and quality of life in cats suffering from chronic kidney disease and suspected feline infectious peritonitis based on hair cortisol concentration analysis and a questionnaire.","authors":"Chien-Hui Chen, Chao-Chin Chang, Wei-Che Chen, Ya-Jane Lee","doi":"10.1080/01652176.2024.2379327","DOIUrl":"10.1080/01652176.2024.2379327","url":null,"abstract":"<p><p>Hair cortisol concentration (HCC) and a questionnaire were used as indicators of chronic stress status and quality of life (QoL), respectively, in cats. To date, there has been limited research on the simultaneous application of both indicators in unwell cats. Our aim was to evaluate HCC and questionnaire data obtained from a healthy cat cohort (<i>n</i> = 61) and cat cohorts with either chronic kidney disease (CKD) (<i>n</i> = 78) or suspected feline infectious peritonitis (FIP) (<i>n</i> = 24). Furthermore, we also investigated the correlation between HCC and clinical pathological data. For this study, hair from the abdomen of cats was collected and analyzed for HCC using a commercial ELISA kit. Owners also completed a questionnaire, from which average-item-weighted-impact-scores (AWISs) were calculated. Cats with late-stage-CKD (median, HCC = 330.15 pg/mg, AWIS = -0.43) presented with a significantly higher HCC (<i>p</i> < 0.01) and a significantly lower AWIS (<i>p</i> < 0.01) than cats with early-stage-CKD (HCC = 183.56 pg/mg, AWIS = 1.08). Similarly, there were significant differences in both HCC (<i>p</i> < 0.001) and AWIS (<i>p</i> < 0.001) between cats with suspected FIP (HCC = 896.27 pg/mg, AWIS = -1.97) and healthy cats (HCC = 181.24 pg/mg, AWIS = 1.24). The degree of consistency between the HCC results and the questionnaire results reminds us that the severity of a chronic disease or the presence of a life-threatening disease can significantly increase stress and thus can affect the QoL of cats.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"44 1","pages":"1-9"},"PeriodicalIF":7.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11262211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141724983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Malnutrition poses a significant threat to global health, resulting from an inadequate intake of essential nutrients that adversely impacts vital organs and overall bodily functioning. Periodic examinations and mass screenings, incorporating both conventional and non-invasive techniques, have been employed to combat this challenge. However, these approaches suffer from critical limitations, such as the need for additional equipment, lack of comprehensive feature representation, absence of suitable health indicators, and the unavailability of smartphone implementations for precise estimations of Body Fat Percentage (BFP), Basal Metabolic Rate (BMR), and Body Mass Index (BMI) to enable efficient smart-malnutrition monitoring. To address these constraints, this study presents a groundbreaking, scalable, and robust smart malnutrition-monitoring system that leverages a single full-body image of an individual to estimate height, weight, and other crucial health parameters within a multi-modal learning framework. Our proposed methodology involves the reconstruction of a highly precise 3D point cloud, from which 512-dimensional feature embeddings are extracted using a headless-3D classification network. Concurrently, facial and body embeddings are also extracted, and through the application of learnable parameters, these features are then utilized to estimate weight accurately. Furthermore, essential health metrics, including BMR, BFP, and BMI, are computed to comprehensively analyze the subject's health, subsequently facilitating the provision of personalized nutrition plans. While being robust to a wide range of lighting conditions across multiple devices, our model achieves a low Mean Absolute Error (MAE) of ± 4.7 cm and ± 5.3 kg in estimating height and weight.
{"title":"Integrating multimodal learning for improved vital health parameter estimation.","authors":"Ashish Marisetty, Prathistith Raj Medi, Praneeth Nemani, Venkanna Udutalapally, Debanjan Das","doi":"10.1016/j.compbiomed.2024.109104","DOIUrl":"10.1016/j.compbiomed.2024.109104","url":null,"abstract":"<p><p>Malnutrition poses a significant threat to global health, resulting from an inadequate intake of essential nutrients that adversely impacts vital organs and overall bodily functioning. Periodic examinations and mass screenings, incorporating both conventional and non-invasive techniques, have been employed to combat this challenge. However, these approaches suffer from critical limitations, such as the need for additional equipment, lack of comprehensive feature representation, absence of suitable health indicators, and the unavailability of smartphone implementations for precise estimations of Body Fat Percentage (BFP), Basal Metabolic Rate (BMR), and Body Mass Index (BMI) to enable efficient smart-malnutrition monitoring. To address these constraints, this study presents a groundbreaking, scalable, and robust smart malnutrition-monitoring system that leverages a single full-body image of an individual to estimate height, weight, and other crucial health parameters within a multi-modal learning framework. Our proposed methodology involves the reconstruction of a highly precise 3D point cloud, from which 512-dimensional feature embeddings are extracted using a headless-3D classification network. Concurrently, facial and body embeddings are also extracted, and through the application of learnable parameters, these features are then utilized to estimate weight accurately. Furthermore, essential health metrics, including BMR, BFP, and BMI, are computed to comprehensively analyze the subject's health, subsequently facilitating the provision of personalized nutrition plans. While being robust to a wide range of lighting conditions across multiple devices, our model achieves a low Mean Absolute Error (MAE) of ± 4.7 cm and ± 5.3 kg in estimating height and weight.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"183 ","pages":"109104"},"PeriodicalIF":4.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Continuous Glucose Monitoring (CGM) provides a detailed representation of glucose fluctuations in individuals, offering a rich dataset for understanding glycemic control in diabetes management. This study explores the potential of Riemannian manifold-based geometric clustering to analyze and interpret CGM data for individuals with Type 1 Diabetes (T1D) and healthy controls (HC), aiming to enhance diabetes management and treatment personalization.
Methods: We utilized CGM data from publicly accessible datasets, covering both T1D individuals on insulin and HC. Data were segmented into daily intervals, from which 27 distinct glycemic features were extracted. Uniform Manifold Approximation and Projection (UMAP) was then applied to reduce dimensionality and visualize the data, with model performance validated through correlation analysis between Silhouette Score (SS) against HC cluster and HbA1c levels.
Results: UMAP effectively distinguished between T1D on daily insulin and HC groups, with data points clustering according to glycemic profiles. Moderate inverse correlations were observed between SS against HC cluster and HbA1c levels, supporting the clinical relevance of the UMAP-derived metric.
Conclusions: This study demonstrates the utility of UMAP in enhancing the analysis of CGM data for diabetes management. We revealed distinct clustering of glycemic profiles between healthy individuals and diabetics on daily insulin indicating that in most instances insulin does not restore a normal glycemic phenotype. In addition, the SS quantifies day by day the degree of this continued dysglycemia and therefore potentially offers a novel approach for personalized diabetes care.
{"title":"Riemannian manifold-based geometric clustering of continuous glucose monitoring to improve personalized diabetes management.","authors":"Jiafeng Song, Jocelyn McNeany, Yifei Wang, Tanicia Daley, Arlene Stecenko, Rishikesan Kamaleswaran","doi":"10.1016/j.compbiomed.2024.109255","DOIUrl":"10.1016/j.compbiomed.2024.109255","url":null,"abstract":"<p><strong>Background: </strong>Continuous Glucose Monitoring (CGM) provides a detailed representation of glucose fluctuations in individuals, offering a rich dataset for understanding glycemic control in diabetes management. This study explores the potential of Riemannian manifold-based geometric clustering to analyze and interpret CGM data for individuals with Type 1 Diabetes (T1D) and healthy controls (HC), aiming to enhance diabetes management and treatment personalization.</p><p><strong>Methods: </strong>We utilized CGM data from publicly accessible datasets, covering both T1D individuals on insulin and HC. Data were segmented into daily intervals, from which 27 distinct glycemic features were extracted. Uniform Manifold Approximation and Projection (UMAP) was then applied to reduce dimensionality and visualize the data, with model performance validated through correlation analysis between Silhouette Score (SS) against HC cluster and HbA1c levels.</p><p><strong>Results: </strong>UMAP effectively distinguished between T1D on daily insulin and HC groups, with data points clustering according to glycemic profiles. Moderate inverse correlations were observed between SS against HC cluster and HbA1c levels, supporting the clinical relevance of the UMAP-derived metric.</p><p><strong>Conclusions: </strong>This study demonstrates the utility of UMAP in enhancing the analysis of CGM data for diabetes management. We revealed distinct clustering of glycemic profiles between healthy individuals and diabetics on daily insulin indicating that in most instances insulin does not restore a normal glycemic phenotype. In addition, the SS quantifies day by day the degree of this continued dysglycemia and therefore potentially offers a novel approach for personalized diabetes care.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"183 ","pages":"109255"},"PeriodicalIF":4.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-11-04DOI: 10.1016/j.compbiomed.2024.109302
Muhammad Tahir, Mahboobeh Norouzi, Shehroz S Khan, James R Davie, Soichiro Yamanaka, Ahmed Ashraf
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA methylation, histone modifications, chromatin conformation, and non-coding RNA. The changes in gene regulation and expression can manifest in the form of various diseases and disorders such as cancer and congenital deformities. Over the last few decades, high-throughput experimental approaches have been used to identify and understand epigenetic changes, but these laboratory experimental approaches and biochemical processes are time-consuming and expensive. To overcome these challenges, machine learning and artificial intelligence (AI) approaches have been extensively used for mapping epigenetic modifications to their phenotypic manifestations. In this paper we provide a narrative review of published research on AI models trained on epigenomic data to address a variety of problems such as prediction of disease markers, gene expression, enhancer-promoter interaction, and chromatin states. The purpose of this review is twofold as it is addressed to both AI experts and epigeneticists. For AI researchers, we provided a taxonomy of epigenetics research problems that can benefit from an AI-based approach. For epigeneticists, given each of the above problems we provide a list of candidate AI solutions in the literature. We have also identified several gaps in the literature, research challenges, and recommendations to address these challenges.
表观遗传学包括在不改变基本基因序列的情况下改变基因表达的机制。基因表达的表观遗传调控是由 DNA 甲基化、组蛋白修饰、染色质构象和非编码 RNA 等几种机制启动和维持的。基因调控和表达的变化可表现为各种疾病和失调,如癌症和先天性畸形。在过去的几十年里,高通量实验方法已被用于识别和了解表观遗传变化,但这些实验室实验方法和生化过程耗时且昂贵。为了克服这些挑战,机器学习和人工智能(AI)方法已被广泛用于映射表观遗传修饰及其表型表现。在本文中,我们对已发表的有关人工智能模型的研究进行了叙述性综述,这些模型是在表观基因组数据的基础上训练而成的,用于解决疾病标志物预测、基因表达、增强子-启动子相互作用和染色质状态等各种问题。本综述具有双重目的,既面向人工智能专家,也面向表观遗传学家。对于人工智能研究人员,我们提供了可从基于人工智能的方法中获益的表观遗传学研究问题分类法。对于表观遗传学家,我们针对上述每个问题提供了一份候选人工智能解决方案的文献列表。我们还指出了文献中的几个空白点、研究挑战以及应对这些挑战的建议。
{"title":"Artificial intelligence and deep learning algorithms for epigenetic sequence analysis: A review for epigeneticists and AI experts.","authors":"Muhammad Tahir, Mahboobeh Norouzi, Shehroz S Khan, James R Davie, Soichiro Yamanaka, Ahmed Ashraf","doi":"10.1016/j.compbiomed.2024.109302","DOIUrl":"10.1016/j.compbiomed.2024.109302","url":null,"abstract":"<p><p>Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA methylation, histone modifications, chromatin conformation, and non-coding RNA. The changes in gene regulation and expression can manifest in the form of various diseases and disorders such as cancer and congenital deformities. Over the last few decades, high-throughput experimental approaches have been used to identify and understand epigenetic changes, but these laboratory experimental approaches and biochemical processes are time-consuming and expensive. To overcome these challenges, machine learning and artificial intelligence (AI) approaches have been extensively used for mapping epigenetic modifications to their phenotypic manifestations. In this paper we provide a narrative review of published research on AI models trained on epigenomic data to address a variety of problems such as prediction of disease markers, gene expression, enhancer-promoter interaction, and chromatin states. The purpose of this review is twofold as it is addressed to both AI experts and epigeneticists. For AI researchers, we provided a taxonomy of epigenetics research problems that can benefit from an AI-based approach. For epigeneticists, given each of the above problems we provide a list of candidate AI solutions in the literature. We have also identified several gaps in the literature, research challenges, and recommendations to address these challenges.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"183 ","pages":"109302"},"PeriodicalIF":4.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-09-27DOI: 10.1016/j.envpol.2024.125040
Wei-Li Jia, Fang-Zhou Gao, Chao Song, Chang-Er Chen, Chuan-Xin Ma, Jason C White, Guang-Guo Ying
The widespread utilization of antibiotics in livestock has promoted the accumulation and diffusion of antibiotics and antibiotic resistance in agricultural soils and crops. Here we investigated the mechanisms of antibiotic uptake and accumulation in swine wastewater (SW)-treated radish (Raphanus sativus L.) and subsequent impacts on endophyte antibiotic resistance. Under SW treatments, exposure to 500 μg/L sulfamethazine (SMZ) and enrofloxacin (EFX) significantly affected radish biomass, with SMZ causing 63.0% increases and EFX causing 36.3% decreases relative to the untreated control. EFX uptake by radish were from 5 to 100-folds over SMZ. Passive diffusion through anion channel proteins on cell membranes was an important route for SMZ uptake, while both passive diffusion and energy-dependent processes contributed to the uptake of EFX. Bacterial community was time-dependent as a function of both antibiotics and SW, the bacterial alpha diversity in liquid solution co-treated with antibiotics and SW increased over time. The abundance of antibiotic resistance genes (ARGs) in the roots was positively correlated with ARGs in the Hoagland's solution under antibiotic-alone treatments. EFX co-exposure with SW enhanced the dissemination of ARGs from swine wastewater into plant roots, and significant correlations existed between ARGs and integrons in both Hoagland's solution and roots. These findings increased our understanding of the fate of antibiotics in crops and their subsequent impacts on antibiotic resistance of endophytic bacteria.
{"title":"Swine wastewater co-exposed with veterinary antibiotics enhanced the antibiotic resistance of endophytes in radish (Raphanus sativus L.).","authors":"Wei-Li Jia, Fang-Zhou Gao, Chao Song, Chang-Er Chen, Chuan-Xin Ma, Jason C White, Guang-Guo Ying","doi":"10.1016/j.envpol.2024.125040","DOIUrl":"10.1016/j.envpol.2024.125040","url":null,"abstract":"<p><p>The widespread utilization of antibiotics in livestock has promoted the accumulation and diffusion of antibiotics and antibiotic resistance in agricultural soils and crops. Here we investigated the mechanisms of antibiotic uptake and accumulation in swine wastewater (SW)-treated radish (Raphanus sativus L.) and subsequent impacts on endophyte antibiotic resistance. Under SW treatments, exposure to 500 μg/L sulfamethazine (SMZ) and enrofloxacin (EFX) significantly affected radish biomass, with SMZ causing 63.0% increases and EFX causing 36.3% decreases relative to the untreated control. EFX uptake by radish were from 5 to 100-folds over SMZ. Passive diffusion through anion channel proteins on cell membranes was an important route for SMZ uptake, while both passive diffusion and energy-dependent processes contributed to the uptake of EFX. Bacterial community was time-dependent as a function of both antibiotics and SW, the bacterial alpha diversity in liquid solution co-treated with antibiotics and SW increased over time. The abundance of antibiotic resistance genes (ARGs) in the roots was positively correlated with ARGs in the Hoagland's solution under antibiotic-alone treatments. EFX co-exposure with SW enhanced the dissemination of ARGs from swine wastewater into plant roots, and significant correlations existed between ARGs and integrons in both Hoagland's solution and roots. These findings increased our understanding of the fate of antibiotics in crops and their subsequent impacts on antibiotic resistance of endophytic bacteria.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":" ","pages":"125040"},"PeriodicalIF":7.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-10-04DOI: 10.1007/s10555-024-10206-6
Obada Ababneh, Daisuke Nishizaki, Shumei Kato, Razelle Kurzrock
Immune checkpoint inhibitors have shaped the landscape of cancer treatment. However, many patients either do not respond or suffer from later progression. Numerous proteins can control immune system activity, including multiple tumor necrosis factor (TNF) superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) members; these proteins play a complex role in regulating cell survival and death, cellular differentiation, and immune system activity. Notably, TNFSF/TNFRSF molecules may display either pro-tumoral or anti-tumoral activity, or even both, depending on tumor type. Therefore, TNF is a prototype of an enigmatic two-faced mediator in oncogenesis. To date, multiple anti-TNF agents have been approved and/or included in guidelines for treating autoimmune disorders and immune-related toxicities after immune checkpoint blockade for cancer. A confirmed role for the TNFSF/TNFRSF members in treating cancer has proven more elusive. In this review, we highlight the cancer-relevant TNFSF/TNFRSF family members, focusing on the death domain-containing and co-stimulation members and their signaling pathways, as well as their complicated role in the life and death of cancer cells.
{"title":"Tumor necrosis factor superfamily signaling: life and death in cancer.","authors":"Obada Ababneh, Daisuke Nishizaki, Shumei Kato, Razelle Kurzrock","doi":"10.1007/s10555-024-10206-6","DOIUrl":"10.1007/s10555-024-10206-6","url":null,"abstract":"<p><p>Immune checkpoint inhibitors have shaped the landscape of cancer treatment. However, many patients either do not respond or suffer from later progression. Numerous proteins can control immune system activity, including multiple tumor necrosis factor (TNF) superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) members; these proteins play a complex role in regulating cell survival and death, cellular differentiation, and immune system activity. Notably, TNFSF/TNFRSF molecules may display either pro-tumoral or anti-tumoral activity, or even both, depending on tumor type. Therefore, TNF is a prototype of an enigmatic two-faced mediator in oncogenesis. To date, multiple anti-TNF agents have been approved and/or included in guidelines for treating autoimmune disorders and immune-related toxicities after immune checkpoint blockade for cancer. A confirmed role for the TNFSF/TNFRSF members in treating cancer has proven more elusive. In this review, we highlight the cancer-relevant TNFSF/TNFRSF family members, focusing on the death domain-containing and co-stimulation members and their signaling pathways, as well as their complicated role in the life and death of cancer cells.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":" ","pages":"1137-1163"},"PeriodicalIF":4.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-01Epub Date: 2024-10-12DOI: 10.1080/01652176.2024.2412297
Xi He, Xue-Mei Fang, Yu-Tong Qiao, Jia-Li Su, Sheng-Qiu Tang, Ya-Biao Weng, Rui-Qing Lin
Pigeon coccidiosis caused by Eimeria spp. is an important veterinary disease with a significant economic impact on the pigeon industry. Preventive measures for Eimeria columbarum in pigeons have been hampered by the lack of extensive genetic, morphological, and biological data on the oocysts. In this study, we examined the prevalence and identity of Eimeria spp. in domestic pigeons from seven cities in Guangdong Province, China. Data show that coccidiosis was prevalent in domestic pigeons in Guangdong Province, with an overall Eimeria spp. detection rate of 73.4%. Five Eimeria species were identified, including E. columbarum (73.4%), Eimeria kapotei (25.6%), Eimeria labbeana (19.6%), Eimeria duculai (19.6%), and Eimeria tropicalis (6.7%). We obtained single oocyst-derived lines of the dominant E. columbarum from fecal specimens. E. columbarum oocysts measured 20.06 ± 0.69 μm × 18.63 ± 1.03 μm, and sporocysts measured 10.29 ± 0.82 μm × 85.38 ± 0.46 μm. In infection experiment using obtained E. columbarum isolates, 60-day-old coccidia-free pigeons exhibited a prepatent period of 105 h and patent period of 9-10 days followed by severe diarrhea, depression, anorexia, and emaciation. Endogenous development of the parasite was observed mainly in the cytoplasm of epithelial cells in the duodenum, jejunum, ileum, and rectum. Two generations of meronts developed on days 3 and 4 after infection, respectively, while gamont and gamete developed on day 5 after infection. The morphological, genetic, and biological data are expected to be useful in elucidating the biological characterization of pigeon coccidiosis to develop measures against the treatment and containment of this disease.
{"title":"Molecular identification and biological characterization of <i>Eimeria columbarum</i> from domestic pigeons (<i>Columba livia domestica</i>) in Guangdong, China.","authors":"Xi He, Xue-Mei Fang, Yu-Tong Qiao, Jia-Li Su, Sheng-Qiu Tang, Ya-Biao Weng, Rui-Qing Lin","doi":"10.1080/01652176.2024.2412297","DOIUrl":"https://doi.org/10.1080/01652176.2024.2412297","url":null,"abstract":"<p><p>Pigeon coccidiosis caused by <i>Eimeria</i> spp. is an important veterinary disease with a significant economic impact on the pigeon industry. Preventive measures for <i>Eimeria columbarum</i> in pigeons have been hampered by the lack of extensive genetic, morphological, and biological data on the oocysts. In this study, we examined the prevalence and identity of <i>Eimeria</i> spp. in domestic pigeons from seven cities in Guangdong Province, China. Data show that coccidiosis was prevalent in domestic pigeons in Guangdong Province, with an overall <i>Eimeria</i> spp. detection rate of 73.4%. Five <i>Eimeria</i> species were identified, including <i>E. columbarum</i> (73.4%), <i>Eimeria kapotei</i> (25.6%), <i>Eimeria labbeana</i> (19.6%), <i>Eimeria duculai</i> (19.6%), and <i>Eimeria tropicalis</i> (6.7%). We obtained single oocyst-derived lines of the dominant <i>E. columbarum</i> from fecal specimens. <i>E. columbarum</i> oocysts measured 20.06 ± 0.69 μm × 18.63 ± 1.03 μm, and sporocysts measured 10.29 ± 0.82 μm × 85.38 ± 0.46 μm. In infection experiment using obtained <i>E. columbarum</i> isolates, 60-day-old coccidia-free pigeons exhibited a prepatent period of 105 h and patent period of 9-10 days followed by severe diarrhea, depression, anorexia, and emaciation. Endogenous development of the parasite was observed mainly in the cytoplasm of epithelial cells in the duodenum, jejunum, ileum, and rectum. Two generations of meronts developed on days 3 and 4 after infection, respectively, while gamont and gamete developed on day 5 after infection. The morphological, genetic, and biological data are expected to be useful in elucidating the biological characterization of pigeon coccidiosis to develop measures against the treatment and containment of this disease.</p>","PeriodicalId":7,"journal":{"name":"ACS Applied Polymer Materials","volume":"44 1","pages":"1-11"},"PeriodicalIF":7.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11486315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}