Studies to examine the impact of end-of-life (EOL) discussions on the utilization of life-sustaining treatments near death are limited and have inconsistent findings. This nationwide population-based cohort study determined the impact of EOL discussions on the utilization of life-sustaining treatments in the last three months of life in Taiwanese cancer patients. From 2012 to 2018, this cohort study included adult cancer patients, which were confirmed by pathohistological reports. Life-sustaining treatments during the last three months of life included cardiopulmonary resuscitation, intubation, and defibrillation. EOL discussions in cancer patients were confirmed by their medical records. Association of EOL discussions with utilization of life-sustaining treatments were assessed using multiple logistic regression. Of 381,207 patients, the mean age was 70.5 years and 19.4% of the subjects received life-sustaining treatments during the last three months of life. After adjusting for other covariates, those who underwent EOL discussions were less likely to receive life-sustaining treatments during the last three months of life compared to those who did not . Considering the type of treatments, EOL discussions correlated with a lower likelihood of receiving cardiopulmonary resuscitation , endotracheal intubation , and defibrillation . Since EOL discussions are associated with less aggressive care, our study supports the importance of providing these discussions to cancer patients during the EOL treatment. Patients often experience pain, dyspnea, and distress during the end-of-life (EOL) care. Aggressive EOL treatment has predicted lower quality of life3 and greater regret about treatment decisions4.Cancer is the second leading cause of death worldwide, and was responsible for an estimated 10 million deaths in 20205. It is considered a means for helping patients die in their preferred treatment and is emphasised as an end-of-life care strategy5. A previous report showed that patients engaging in ACP have more stable EOL preferences compared to those who do not6.Advance care planning (ACP) is the process of discussing patient preferences regarding life-sustaining treatments and place of death during EOL care, and involves healthcare professionals, patients, and their family7. Although cancer patients may avoid discussing their preference of life-sustaining treatments during EOL discussions9, healthcare providers are allowed—or morally obligated—to decide whether life-sustaining treatments are viable for terminal cancer patients10.Comprehensive EOL discussions with physicians during the ACP consultation could allow cancer patients to confront the limitations of medical treatments and consider their preferences regarding life-sustaining treatments through the EOL treatment. A meta-analysis review showed that these discussions predicted an increased use of hospice care and better quality of death8. In another observational study in the US involving 145 patients with advanced cancer, EOL discussions lowered the rates of ventilation and resuscitations during the EOL treatment2. Previous studies on the association between EOL discussions and the use of life-sustaining treatment, however, have used small sample sizes (n = 145)2 and inadequately controlled for potential confounders such as dementia8.Although EOL discussions offer patients the opportunity to define their expectations for life-sustaining treatments that they want to receive during the EOL treatment, the impact of EOL discussions on the use of life-sustaining treatments near death has not been extensively studied. A US cohort study followed up 332 patients with advanced cancer and found that patients who participated in EOL discussions were less likely to receive ventilation  and resuscitation  during the EOL treatment compared to those who did notEOL discussions serve to maximize patients’ quality of life while considering their goals and expectations regarding EOL treatment. It is important to understand the impact of these discussions on the administration of life-sustaining treatments among terminally ill patients. We therefore conducted a nationwide population-based cohort study to determine the impact of EOL discussions on the utilization of life-sustaining treatments during the last three months of life among Taiwanese cancer patients, from 2012 to 2018.11. While patients were admitted to the hospital, healthcare providers offered EOL discussions to those with life-limiting diseases11. During the discussions, healthcare providers discuss patients’ goals and preferences concerning medical care and life-sustaining treatments towards the end of their lives11. Each EOL discussion with a patient awards the healthcare provider with the equivalent of US$7511. There should be a record of all discussion content in the patient’s medical chart and each session must be at least an hour long11.The Taiwan National Health Insurance Administration, since 2012, has initiated an EOL discussions program that encourages healthcare providers to provide these discussions to terminally ill patients12. It is a large-scale database derived from the national health insurance system, which consists of registration files and original claims data. The database de-identified and scrambled the patients’ identification codes before releasing the data for research purposes13.This nationwide cohort study used the Taiwan National Health Insurance Research Database (NHIRD), which contains healthcare data from more than 99% of the population in Taiwan14. This registry was also linked to Taiwan’s death certificate database to confirm the demise of cancer patients15. The Institutional Review Board of Taipei City Hospital (no. TCHIRB-10709107-W) approved this study. The informed consents for study participants were waived by the Institutional Review Board of Taipei City Hospital. All methods in this study were performed in accordance with relevant guidelines and regulations. This study is also in accordance with the Declaration of Helsinki.This cohort study selected subjects aged 18 years or older who had received a cancer diagnosis and died between January 1, 2012 and December 31, 2018. We identified these patients from the Registry for Catastrophic Illness. In Taiwan, the Registry for Catastrophic Illness requires a peer review of pathohistological reports before a cancer diagnosis is reported16.The outcome was life-sustaining treatments during the last three months of life in cancer patients. Life-sustaining treatments included cardiopulmonary resuscitation, intubation, and defibrillationThe main explanatory variable was EOL discussions with physicians, which was determined by patients’ medical records.17. We calculated the income level from the average monthly income of the insured person and grouped it into three categories: low , intermediate , and high . Type of cancer and the comorbidities in the study subjects were determined according to the International Classification of Diseases, Ninth and Tenth Revision, Clinical Modification (ICD-9-CM and ICD-10-CM) code. The type of cancer included solid tumors and hematologic malignancies. Subjects’ comorbidities include diabetes, chronic kidney disease, congestive heart failure, coronary heart disease, liver cirrhosis, chronic obstructive pulmonary disease, dementia, cerebrovascular disease, and depressive disorder (Supplementary Table S1). A person was considered to have a comorbidity only if the condition occurred in an inpatient setting or in three or more outpatient visits18.The controlling variables included sociodemographic characteristics, type of cancer, and comorbidities. Sociodemographic factors included age, sex, urbanization, and income level. Urbanization described whether subjects resided in urban, suburban, or rural areas2 test where appropriate. We presented continuous data as mean ± standard deviation (SD), and conducted a two-sample t-test to compare outcomes between patients who underwent EOL discussions and those who did not.First, we analyzed the subjects’ demographic data. We then analyzed categorical data using the Pearson χWe assessed the crude associations of EOL discussions and other covariates with the outcome (utilization of life-sustaining treatments during the last three months of life) by computing the odds ratios (ORs) and corresponding 95% confidence intervals (CIs). We then performed a multivariate logistic regression to estimate the association between EOL discussions and the utilization of life-sustaining treatments after adjusting for potential confounders. A variable with p < 0.05 was defined as a significant factor associated with the utilization of life-sustaining treatments in the multivariate analysis. Adjusted odds ratios (AOR) with 95% confidence intervals (CI) indicated the strength and direction of these associations.We conducted subgroup and sensitivity analyses to examine the associations between EOL discussions and the utilization of life-sustaining treatments, after stratifying participants by age and sex. To examine the robustness of the main findings, propensity score analysis was conducted to evaluate the associations between hospice care services and utilization of life-sustaining treatments during the last three months of life. Logistic regression was conducted to calculate the probability of enrolling in a hospice care program in cancer patients according to their age, sex, income level, type of cancer, and comorbidities. A multivariate logistic regression was used to estimate the association between hospice care services and utilization of life-sustaining treatments after adjusting for patients’ propensity score. We performed all data management and analyses using the SAS® v9.4 statistical software package .n = 850) and those with missing data (n = 1071), 381,207 patients were eligible for the purposes of the study. The overall mean (SD) age was 70.5 (14.3) years; 65.6% of the subjects were male; and 14.1% had EOL discussions with healthcare providers towards the end of their lives. The median duration from the EOL discussion to death for the 53,783 patients completing EOL discussions with healthcare providers was 34 days (interquartile range 16–79 days); of these patients, 7382 (13.7%) had such discussions after utilizing life-sustaining treatment.This cohort study involved the raw data of 383,128 deceased cancer patients from 1 January 2012 to 31 December 2018. After excluding those younger than 18 years .Table Table Table Propensity score analysis showed that cancer patients with EOL discussions were less likely to receive life-sustaining treatments during the last three months of life than those without the discussion , including cardiopulmonary resuscitation , endotracheal intubation , and defibrillation .This nationwide cohort study found that 19.4% of cancer patients utilized life-sustaining treatments during the last three months of life. After adjusting for demographic data and comorbidities, cancer patients who underwent EOL discussions were less likely to receive life-sustaining treatments during EOL care. With regard to the treatment types, EOL discussions predicted a lower likelihood of receiving cardiopulmonary resuscitation, endotracheal intubation, and defibrillation towards the end of the patients’ lives.Our study revealed robust associations between EOL discussions and life-sustaining treatments after stratifying patients by age and sex. In all patient subgroups, the discussions significantly lowered the likelihood of receiving life-sustaining treatments near death.8. The culture difference regarding death-related issues between Asia and Western countries may explain the lower rate of completing EOL discussions among Taiwanese cancer patients. In traditional Chinese culture, death-related topics are thought to be taboo, and mentioning it is sacrilegious and to be avoided19. A previous survey in Hong Kong reported that 73% of elderly patients with chronic diseases have never received discussions regarding their EOL treatment19. Since EOL discussions provide patients the opportunity to define their goals and expectations regarding the EOL treatment20, our study suggests that it is imperative to provide such discussions for cancer patients nearing the end of their lives.This study found that 14.1% of cancer patients in Taiwan participated in EOL discussions, which was lower than 37.0% among cancer patients in the US21. Since intensive care in patients with terminal diseases is associated with lower quality of life3, our study suggests that healthcare professionals should proactively provide EOL discussions for terminally ill patients to discuss their preferred treatment during EOL care.This study found that 19.4% of cancer patients in Taiwan received life-sustaining treatments in the last three months of life. A previous report showed that the proportion of cancer patients receiving intensive care in the last six months of life was 40.3% in the US, 17.5% in Belgium, 15.2% in Canada, and 8.2% in Germany22. Another cohort study in the US found that EOL discussions correlated with lower rates of ventilation and resuscitation near death8. Moreover, a study in the US analyzed 145 cancer patients and found that patients who had undergone EOL discussions had lower rates of receiving ventilation and resuscitations in the last week of life2. Our cohort study followed up 381,207 cancer patients and found that EOL discussions associated with a lower utilization of life-sustaining treatments during the last three months of life. With regard to treatment types, cancer patients who had EOL discussions had a lower likelihood of receiving cardiopulmonary resuscitation, endotracheal intubation, and defibrillation during EOL care. Thus the findings of our study suggest that EOL discussions could reduce the utilization of life-sustaining treatments in cancer patients near death.The present cohort study found that cancer patients who underwent EOL discussions had 18% lower rates of receiving life-sustaining treatments in the last three months of life, than those who did not. EOL discussions could allow terminally ill patients to consider their preferences regarding life-sustaining treatments during the EOL care. A previous report showed that EOL discussions significantly increased the rates of do-not-resuscitate order completion among advanced cancer patients7. This may account for the lower rate of receiving life-sustaining treatments at that stage. While cancer patients had EOL discussions with physicians, the benefit and harm of life-sustaining treatments during the EOL care would be discussed and emphasized. Through the EOL discussions with healthcare providers, cancer patients could consider and document their treatment preferences during EOL care. A prior study showed that EOL discussions significantly improved patients’ understanding of their terminal illness and subsequently reduced the likelihood of receiving aggressive treatments during EOL care23. As EOL discussions are associated with less aggressive care7, the findings of our study suggest that it is important to provide them for cancer patients during EOL treatment.The EOL conversations with physicians improve the patients’ understanding of the futility of aggressive therapies during EOL care24. Another US study using administrative data found that EOL discussion was associated with significant hospital cost savings among patients during EOL care25. Since aggressive EOL treatment is associated with higher health care cost and poor quality of EOL care in terminally ill patients2, our study suggests that EOL discussions should be provided for cancer patients to discuss their treatment preference during EOL care.This study showed that cancer patients receiving life-sustaining treatments during EOL care had higher medical expenditures than those not. A previous study involving 314 veterans in the US showed that aggressive EOL treatment was associated with significantly higher inpatient costs during a terminal hospitalizationThis nationwide cohort study has several strengths. First, this study is the largest cohort study to determine the impact of EOL discussions on the utilization of life-sustaining treatments during the last three months of life among cancer patients. The research design enhances the validity of our findings by including unbiased subject selection and strict cancer diagnostic criteria. Moreover, since the Taiwan National Health Insurance covers all medical care of cancer patients, this nationwide population-based study traced all cancer patients, thus minimizing referral bias. Furthermore, the study’s large sample size sufficiently detected the real, albeit subtle, difference between cancer patients who had and those who had not received EOL discussions towards the end of their lives.This cohort study has several limitations. First, there may be important factors  associated with the decision of receiving life-sustaining treatments, which the National Health Insurance Research Database did not record. Second, of the 53,783 patients completing EOL discussions with healthcare providers, 7382 (13.7%) had such discussions after utilizing life-sustaining treatment, which would underestimate the impact of EOL discussions on the utilization of life-sustaining treatments during the last three months of life among cancer patients. Finally, since all our enrollees were Taiwanese, the external validity of our findings may be a concern. Therefore, the generalizability of our results to other non-Asian ethnic groups requires further verification. However, our findings suggest new avenues for future research.In summary, this nationwide, cohort study found that cancer patients who had EOL discussions were less likely to receive life-sustaining treatments during the last three months of life compared to those who did not have EOL discussions. With regard to treatment types, EOL discussions correlated with a lower likelihood of receiving cardiopulmonary resuscitation, endotracheal intubation, and defibrillation during the last three months of life. As end-of-life discussions are associated with less aggressive EOL care, it is important to provide them for cancer patients during EOL treatment.Supplementary Information.


Tyrosine kinase inhibitor (TKI) therapy is often taken indefinitely by chronic myeloid leukemia (CML) patients. However, little is known about the long-term or under-reported TKI side effects due to limited longitudinal clinical data on these relatively new drugs. We utilize novel cross-domain text mining and machine learning to comprehensively assess relationships between TKIs and possible adverse events (AEs) across 30+ million PubMed publications. The top 10% of predicted AEs were mapped to ten physiological function-based foci: hematology, glucose, iron, cardiovascular, thyroid, inflammation, kidney, gastrointestinal, neuromuscular, and others. Study results provided new insight into the breadth of adverse events with TKI usage. Results-based recommendations were devised for proactive patient monitoring protocols as a function of perceived AE risk. Additionally, AEs were mapped to specific TKI types to assist in personalized TKI selection.p < 0.05) AE type: gastrointestinal (bosutinib); edema (imatinib); pulmonary (dasatinib); diabetes (nilotinib); cardiovascular (ponatinib). Next, we propose a novel cross-domain text mining method utilizing a knowledge graph, link prediction, and hub node network analysis to predict new relationships. Cross-domain text mining of 30+ million articles via SemNet predicted and ranked known and novel TKI AEs. Three physiology-based tiers were formed using unsupervised rank aggregation feature importance. Tier 1 ranked in the top 1%: hematology ; glucose ; iron , cardiovascular ; thyroid . Tier 2 ranked in the top 5%: inflammation ; kidney . Tier 3 ranked in the top 10%: gastrointestinal ; neuromuscular ; others . Results suggest proactive TKI patient AE surveillance levels: regular surveillance for tier 1, infrequent surveillance for tier 2, and symptom-based surveillance for tier 3. Tyrosine kinase inhibitors (TKIs) are prescribed for chronic myeloid leukemia (CML) and some other cancers. The objective was to predict and rank TKI-related adverse events (AEs), including under-reported or preclinical AEs, using novel text mining. First, k-means clustering of 2575 clinical CML TKI abstracts separated TKIs by significant ( Chronic myeloid leukemia (CML) is an uncommon type of cancer in the bone marrow that targets early myeloid cells. It results in an increase in impartially mature cells that offsets normal myeloid cells. Comprising approximately 15% of all leukemias, the majority of CML cases are cytogenetically characterized by the presence of the Philadelphia (Ph+) chromosome . In 2021The advent of BCR ABL targeting tyrosine kinase inhibitors (TKI) as a therapy for CML has substantially improved patient outcomes ,4. CurreMore recently, the possibility of treatment-free remission (TFR) has been of great interest. TFR is where patients with a deep molecular response cease to continue TKI therapy if they meet specific criteria. In the United States, the most successful guidelines for TFR patient selection include those CML patients who meet all the following criteria: patients who did not have a high Sokal score at initial diagnosis, never progressed past chronic phase, did not possess TKI resistant mutations, have been on TKI therapy for 8 years, and have had a deep molecular response for >2 years at the time of TFR trial initiation . SeveralWhile TKIs have been very effective, these powerful drugs are not benign. Due to the ubiquitous nature of the drugs’ targets in the body, there is a litany of adverse events (AEs) and side effects associated with TKI usage . StudiesMost TKI therapies are relatively new, and CML is a relatively uncommon leukemia. Thus, there is a limited pool of clinical cohort studies on less common AEs or preclinical AEs that may otherwise go undetected. Here, we propose cross-domain text mining as an innovative opportunity to circumvent the challenges associated with the lack of large-scale longitudinal clinical cohort studies across under-explored physiology. The goal is to utilize integrated text-mined relationships across seemingly disparate domains  to predict new or previously undetected/under-reported AEs. Cross-domain literature mining leverages a heterogeneous information network or “knowledge graph”. The graph connects multifactorial and multi-scalar relationships to genes, proteins, processes, disease or syndromes, drugs, etc. A knowledge graph uses extracted text relationships to create a flowchart of connections. A scientist or clinician can typically deduce relationships that are a couple of connections away from the target node  interest. However, more distant cross-domain relationships further from the target are difficult to manually deduce. Cross-domain text mining is performed with knowledge graph-based text mining software, such as SemNet, to extract relationships from millions of indexed abstracts in the PubMed database ,23.Here, we present a novel cross-domain text mining method with link prediction and hub node network analysis to predict and rank lesser-known AEs relevant to tyrosine kinase regulation. The idea for hub node network analysis was borrowed from bioinformatics where network analysis is used to trace downstream gene relationships to “hub” genes ,25,26. AIn summary, the objective of this study was to perform an in-depth assessment of TKI AEs. Standard bag-of-words text clustering of the CML-specific literature was performed to map the most common AEs to specific TKI drugs. However, novel cross-domain text mining with link prediction and hub node network analysis identified and ranked less obvious or under-reported AEs linked to physiological changes in tyrosine kinase. The relevance of this study’s results is: (1) improved awareness of TKI AEs for surveillance, detection, and management; (2) improved personalized TKI therapy selection based on patient history and specific TKI AE profile; (3) aided design of future TKIs to attenuate or eliminate AEs.The overall goal was to identify and rank potential adverse events (AEs) or side effects due to TKI therapy in CML patients using innovative text mining techniques. Methods consisted of two major analyses: (1) Bag-of-words cluster analysis to connect AEs to specific TKI drug types based on text mining of CML-specific literature; (2) novel cross-domain text mining across all 30+ million biomedical articles in PubMed to identify and rank lesser-known possible AEs linked to tyrosine kinase.First, peer-reviewed CML journal articles in PubMed were extracted to assess the statistical associations between highly occurring AEs and specific TKI drugs  based on the presence of specific terms in a document  and the overall corpus . After conducting PubMed search queries, 2575 abstracts were retrieved through the year 2021. An example query was “CML AND side effects OR adverse events”. All queries included synonyms to look for any associated condition, comorbidity, or toxicity. The abstracts were parsed and common stop words  and punctuation were removed. Abstracts were then tokenized, lemmatized, and cleaned in Python using the Natural Language Toolkit library. A bag-of-words technique  was usedK-means clustering  was usedAfter examining the top 200 terms with the highest term frequency inverse document frequency (TF-IDF) scores in each cluster, clusters 4, 7, 8, 10, and 16 were identified to be relevant to specific TKIs and their associated undesired effects. A list of the top terms related to AEs and toxicity was identified from inspecting the aforementioned terms in each of the five clusters. The highest frequency of occurrence for each term in the clusters was noted to identify specific AE profiles associated with each of the TKIs. For each of these clusters, fold differences were calculated for each term to compare its frequency within the cluster to its frequency within the corpus of abstracts. Pairwise Chi-Square tests were used to determine whether each of the five clusters identified was significantly different from each other. A family-wise alpha of 0.05 was utilized with a Bonferroni correction for multiple comparisons to minimize Type I error.The TKI-specific clusters from the bag-of-word analysis of peer-reviewed CML journal article abstracts are helpful for assessing known drug-specific TKI AEs. However, a different approach is needed to assess potential AEs not yet measured or mentioned in CML literature. One way to assess distant, interconnected relationships across domains is to utilize a knowledge graph. Machine learning algorithms and software, such as SemNet, can be used to rank relationships within a large knowledge graph to one or more targets of interest. This study used the original SemNet  softwareTwo types of knowledge graph text mining were performed: the standard unsupervised rank aggregation algorithm of SemNet to assess published relationships in the knowledge graph  and a liUnlike a clinical meta-analysis, text mining does not select traditional “patient cases”. Rather, text mining traverses a large knowledge graph of interconnected relationships derived from biomedical text to find and rank relationships to a target of interest. An example of an extracted biomedical text relationship is Philadelphia chromosome CAUSES chronic myeloid leukemia. Thus, one of the limitations of cross-domain text mining is that it does not presently allow for the inclusion of specifics such as dose size, disease stage, or time since treatment started. Searching and analyzing the knowledge graph is limited by its organizing ontology. In this study, the biomedical knowledge graph ontology is the Unified Medical Language System (UMLS). On the other hand, the strength of cross-domain text mining is its breadth to integrate massive amounts of relationships across multiple domains. Thus, cross-domain text mining can pinpoint important or novel relationships that might otherwise go undetected in a standard quantitative clinical meta-analysis due to sample size, study inclusion or exclusion criteria, or unintentional human bias. Examination of existing published nodes relating CML and tyrosine kinase was performed in SemNet. SemNet is a semantic inference network and biomedical concept knowledge graph that uses unsupervised ranking algorithms to reveal hidden connections from PubMed’s nearly 30 million indexed abstracts ,23. A usSemNet simulations were utilized to examine diseases and therapeutic substances that might be associated with TKI therapy for CML. The simulation parameters were set to filter for two particular node types in the knowledge graph: Diseases or Syndromes (DSYN) and Therapeutic or Preventive Procedure (TOPP). These parameters were specified to focus on any immediate diseases or therapeutic substances within one connection of the specified target node: CML. After the simulation was run, a comprehensive list of 308 treatments and diseases related to CML were retrieved. The list was subsequently analyzed to look for existing trends or novel relationships derived from the current CML literature. HeteSim scores were utilized to rank conditions that were of most importance to CML and tyrosine kinase.We utilize our previously published link prediction algorithm  in conjuTraditional knowledge graph analysis and link prediction identify links directly connected to a target of interest. For example, SemNet used a standard path link of 2 to compute features for relevance rankings. This means that potentially relevant nodes further from the target may be missed. Expanding the path link, alone, is computationally very expensive and exponentially increases unwanted noise in the resultant rankings.A similar problem has been cited in large bioinformatics gene-gene networks. Bioinformatics network analysis of hub genes effectively enable scientists to tie changes in downstream genes to highly connected gene hubs ,25,26. TSix nodes were specified as “hub nodes” for making the hub node networks: aplastic anemia, anemia, neutropenia, pancytopenia, thrombocytopenia and the more general node, myelosuppression. These nodes were selected as hubs based on their maximal connectivity and their shared overlap between the CML and tyrosine kinase nodes in the initial SemNet simulations described in Once hubs were selected, link prediction was performed using our previously published algorithm . SpecifiThe resultant nodes that comprised the hub neighborhoods became SemNet targets for DSYN conditions associated with tyrosine kinase. Pairwise comparisons were performed in SemNet between mutually highly ranked nodes related to tyrosine kinase and the hub neighborhood. To reduce noise, generic nodes such as “protein” were removed. To enable aggregation across separate hub node simulations, the HeteSim scores were recorded and normalized to fall between 0 and 1.Approximately the top 10% of normalized, highly ranked nodes aggregated from the hub node simulations were isolated for human-in-the-loop validation. The top 10% were chosen on the basis of the most novelty (using the SemNet novelty score) and overall predicted relevance (using the SemNet HeteSim score). Three tiers were used to classify foci of conditions or AEs predicted to be relevant to TKI therapy for CML. Tier 1 included the top 1% of predicted node aggregates, tier 2 the top 5% of predicted node aggregates, and tier 3 the top 10% of predicted node aggregates. The foci were defined using physiology-based UMLS ontology to codify highly ranked node aggregates representing a similar physiological or pathophysiological process or condition.We implemented our previous human-in-the-loop protocol  to validThe primary goal was to identify lesser-known adverse events (AEs) or side effects associated with TKI therapy. A secondary goal was to provide an evidence-based framework to assist clinicians monitoring for AEs and selecting the optimal TKI based on patient history and TKI AE profile.p < 0.05) different from each other, as depicted in The intent of k-means clustering of the CML TKI literature was to identify the most common AEs or side effects among specific TKI drugs. Of the thirty clusters generated in The frequency of side effects or adverse events within each of the clusters are shown in Initial SemNet simulations were conducted to assess which conditions were most associated with CML and TKI therapy in a knowledge graph composed of nearly 30+ million PubMed abstracts. With CML as the target node, and DSYN and TOPP as the UMLS source node types, a list of 308 treatments and diseases related to CML was generated. The two SemNet features that were examined were HeteSim score and novelty score. HeteSim score represents the strength of the relationship to the target. Here, a low HeteSim score indicates a stronger relationship between source and target node. The novelty score indicates how potentially novel a connection may be. The resultant TOPP (Therapeutic or Preventive Procedure) source nodes yielded a list of broad procedures without specific processes or drug names and thus were not of interest. The resultant DSYN (Disease or Syndrome) nodes were sorted by their HeteSim scores and novelty scores and compared. The top 20 nodes by HeteSim score and the top 20 nodes by novelty score are shown in The k-means clustering examined only abstracts that specifically included CML and a TKI drug, whereas SemNet examined the entire knowledge graph of cross-domain relationships from all of PubMed. The advantage of cross-domain text mining was that it identified physiological relationships to tyrosine kinase or tyrosine kinase inhibitors that otherwise go undetected if only the CML literature was examined. This extensive heterogeneous information network enables distant or novel relationships to be identified by leveraging the comprehensive biomedical literature. Yet, hematological conditions remained frequent and highly ranked in relevance in both CML text mining and cross-domain text mining. Some of these conditions shown in Initial SemNet simulations examined relationships tied to the target node, CML. However, the inclusion of CML as a target constrained the identification of conditions related to tyrosine kinase pathophysiology that may not have yet been published in the CML literature or where frequency counts are under-represented. In order to examine deeper relationships of potential importance, link prediction  and hub The SemNet feature scores for link prediction with hub node network analysis HeteSim scores were normalized to fall between 0 and 1 to enable uniform comparison and aggregation. As such, the mean occurrence rate and normalized HeteSim scores were aggregated to predict which conditions were most likely to be relevant to TKI therapy. Foci were determined based on three tiers of aggregated cross-domain text mining rankings of conditions predicted as most relevant to tyrosine kinase: tier 1 approximated the top 1% of predicted conditions, tier 2 approximated the top 5% of predicted conditions, and tier 3 approximated the top 10% of predicted conditions. Foci names were UMLS-inspired functional classifications that best represented the associative physiology of the nodes within the foci.Tier 1 included the top 1% of conditions predicted as most relevant to the tyrosine kinase node: hematology condition (1), glucose regulation (2), iron homeostasis (3), cardiovascular conditions (4), and thyroid conditions (5). Tier 2 included the top 5% of conditions predicted as most relevant to the tyrosine kinase node: inflammation (6) and kidney disorders (7). Tier 3 included the top 10% of conditions predicted as most relevant to the tyrosine kinase node: gastrointestinal disorders (8) neuromuscular disorders (9), and other (10). “Other” denoted conditions could not be reasonably described by a single, cohesive physiological category (or foci). Hematology, cardiovascular, and gastrointestinal conditions were expected to be present based on the results of k-means clustering of frequent terms in the CML-specific literature. However, some of the other conditions identified as relevant to tyrosine kinase in the cross-domain text mining were less obvious. For example, diabetes and kidney disorders only appeared in a single k-means CML literature cluster . Thyroid disorders, iron homeostasis, and inflammation were not among the most frequent terms in the k-means clustering of CML-specific literature.The three tiers reflect both the prevalence of conditions in the text mined foci, as well as their predicted HeteSim feature relevance to tyrosine kinase. As such, the assigned tier was used to suggest the level of clinical surveillance for CML patients undergoing TKI therapy. Surveillance entails testing for the presence and degree of clinical or subclinical conditions associated with or possibly worsened by TKI therapy. Tier 1 foci are predicted in the present analysis to be prevalent and relevant enough that regularly scheduled surveillance is warranted regardless of patient history. Tier 2 foci are predicted to need periodic surveillance; periodicity is expected to be infrequent, unless a patient has relevant antecedent disease or comorbidities that increase susceptibility to tier 2 conditions. Tier 3 suggests surveillance only when overt or persistent symptoms are present. As such, tier 3 surveillance would be similar to the age-matched general population of non-CML patients.Specific literature evidence is presented below to provide context and support for CML-specific TKI relationships and cross-domain text mining link predictions between tyrosine kinase and other diseases or syndromes (DSYN). Recall that conditions ranked by cross-domain text mining as “most important” to tyrosine kinase were determined using the normalized HeteSim relevance feature scores to the tyrosine kinase node and connected node neighborhoods. The highly ranked conditions are discussed in the context of possible adverse events or conditions due to tyrosine kinase inhibitor (TKI) therapy. However, as with all relationship-based statistical models, the predictions of cross-domain text mining are associative and not causal. As such, highly ranked conditions related to tyrosine kinase cannot explicitly be interpreted as adverse events caused by tyrosine kinase therapy. Nonetheless, the predictions of associated conditions with tyrosine kinase provide insight for current TKI patient management and future research.As noted in K-means clustering of CML-specific TKI literature and cross-domain text mining with tyrosine kinase  found myIn summary, the mechanism by which TKIs work means that myelosuppression is an expected possibility. Thus, the goal is to adjust the dose of TKI to minimize myelosuppression that causes anemia, neutropenia, or thrombocytopenia. For patients who are more susceptible to myelosuppression due to other comorbidities or antecedent disease, physicians should select a TKI where myelosuppressive AEs are not as pervasive. In this study, nilotinib was predicted to have the fewest hematological AEs. A regularly performed peripheral complete blood count test can identify signs of myelosuppression. Such a CBC every 4–6 months is currently a common CML standard of care practice. When overt symptoms are present, more specific testing may be warranted to determine if hematological events are being worsened by other conditions, comorbidities, or TKI-related AEs.Glucose-related conditions were predicted by cross-domain text mining to be the second most relevant AE with TKI therapy. In the case of glucose, the impact appears to depend on habituation to the drug. Early on, patients on TKIs tend to have lower blood sugar levels or A1c. In fact, imatinib was recently examined in a study as a possible therapeutic for Type I diabetes . While tThe iron foci ranked number 3 in the cross-domain text mining analysis in its relationship importance to tyrosine kinase. Once again, opposing conditions are identified: iron deficiency (too little iron) and iron overload (too much iron). It is possible both are relevant to TKI therapy. However, it is plausible that iron overload is simply a noisy artifact in this analysis due to its strong relationship with blood transfusions. “Blood transfusion” is a UMLS TOPP node that was strongly connected with the hub nodes used to generate the neighborhood rankings for determining the foci.Iron deficiency can impact the thyroid , which iThe cardiovascular foci ranked fourth in the cross-domain text mining analysis. However, cardiovascular event terms were even more frequent in the k-means clustering of CML-specific literature. Hypertension AE prevalence is approximately 10% for those treated with imatinib, dasatinib, bosutinib, nilotinib  but is aThe thyroid focus was ranked number five in the cross-domain text mining analysis. Again, opposing conditions are identified as hypothyroidism (too little thyroid hormone) and hyperthyroidism (too much thyroid hormone) were the top two conditions in the thyroid foci. In the general [non-CML] population, hyperthyroidism is typically attributed to Grave’s disease, an autoimmune disorder. However, neutropenia is also associated with hyperthyroidism. Certain types of TKIs can cause hyperthyroidism due to their mechanism of action in the down-regulation of tyrosine kinase. Hyperthyroidism was initially thought to be the more common AE during early TKI therapy . HoweverCross-doming text mining also predicted parathyroid function as relatively important to the tyrosine kinase node. However, according to normalized HeteSim feature importance scores, the predicted tie between tyrosine kinase and the parathyroid was not as strong as the thyroid, itself. Secondary hyperparathyroidism has been associated with bone marrow fibrosis (hypocelluar bone marrow), which can cause pancytopenia, anemia, thrombocytopenia, or neutropenia. Patients with hyperparathyroidism may not exhibit overt symptoms early in the disease course, making monitoring all the more important. Changes in blood calcium  or phosphatase (namely hypophosphatemia) due to hyperparathyroidism can impact cardiovascular AEs . In one Finally, there are key relationships between anemia, iron homeostasis, and thyroid function which complicates this triad of tier 1 foci of TKI-related AEs. Anemia caused by iron deficiency  impairs thyroid metabolism function. Both overt and subclinical hypothyroidism are associated with anemia. Previous studies have shown improvement in both conditions with the addition of iron to thyroxine therapy . In concAs noted in Cluster 16 from the clustering methods, which was dominated by nilotinib, had the term “kidney” occur at a high frequency within the cluster. All text mining analyses revealed a connection between kidney conditions and hematological conditions, namely anemia. SemNet simulations predicted glomerulonephritis, glomerulopathy, toxic nephropathy, and chronic kidney disease as kidney conditions relevant to tyrosine kinase.Chronic kidney disease (CKD) is characterized by excessive fibroblast activation, and it is hypothesized that tyrosine kinase can increase fibroblast activation and contribute to CKD development. Therefore, it may be valuable to consider the impact of TKIs on fibroblast activation by reversing the effect of tyrosine kinases, and in turn evaluate the impact of TKI treatment on the kidney health of patients. However, most TKIs inhibit more than one kinase, making their exact effect unclear and their individual impact on kidney health difficult to determine . Some stFive nodes were identified as relevant to kidney function via analysis of the hub neighborhoods: iron deficiency, PTH, urea, uric acid, and C-reactive protein. While these nodes have clear and heavily weighted ties to the hematological hub nodes, it is unclear whether they are truly important to CML patients on TKI therapy who do not have a history of pre-existing kidney disease. It is possible that the hub node network methodology resulted in the overweighting of the relevance of kidney disease due to its strong connections in each hub’s neighborhood. However, the well-known impact of fluid retention  and fluiIn summary, the results of the present study suggest TKI patients undergo periodic kidney testing, with the periodicity based on the presence of relevant antecedent disease or other risk factors that impact susceptibility. Standard metrics such as serum creatinine, glomerular filtration rate, and blood urea nitrogen are suitable candidates to test for proper kidney function in patients taking TKIs.Inflammation was most represented in cluster 10 (dasatinib) but was also represented in cluster 7 (imatinib) and cluster 16 (nilotinib). “Inflammation” could represent many different types of symptoms. The three highest ranked types of inflammatory disorders in the cross-domain text mining analysis were chronic inflammatory disorder (CID), autoimmune diseases, and periodontitis. Autoimmune disease has been associated with and identified as a predisposing risk factor for getting CML; one study found the odds ratio of getting CML was 1.55 (compared to 1) for patients that had an autoimmune disease prior to being diagnosed with CML . There hIn summary, it appears that inflammation has connections to CML predisposition. Inflammation is most likely a relevant adverse risk factor for patients who have pre-existing inflammatory or autoimmune disorders. Based on the cross-domain text mining predictions of this study and supporting direct literature evidence, it is recommended that inflammatory markers be periodically monitored based on the presence of relevant antecedent disease or other pertinent risk factors that impact susceptibility. Moreover, patients more at risk for clotting should have inflammation markers monitored given inflammation and clotting are known comorbidities even in the general [non-CML] population.As noted in For the cross-domain text mining analysis, bowel regulation (diarrhea or constipation), liver dysfunction, and pancreatitis were among the most highly ranked gastrointestinal events. K-means clustering of CML literature found that “gastrointestinal” was among the most frequent terms and appeared with all TKIs. Gastrointestinal AEs are some of the most common symptoms reported by CML patients. Many patients report nausea, vomiting, and diarrhea. A recent large cross-cohort meta-analysis extensively examined gastrointestinal AEs with TKI therapy . BrieflyIn summary, the gastrointestinal focus was a tier 3 focus based on cross-domain text mining predictions. Based on the results of this study and supporting clinical evidence, gastrointestinal AEs should be monitored based primarily on the presence of overt symptoms. Basic liver function can be evaluated via a standard peripheral blood chemistry test. The same standard blood chemistry panel was already recommended for regular monitoring to evaluate some of the TKI AEs within the tier 1 foci. If symptoms warrant, a peripheral blood test of amylase can provide more specific evidence of pancreatitis.Based on cross-domain text mining analysis, the most highly ranked neuromuscular TKI AEs included autonomia, neuropathy, muscle pain, and cognitive dysfunction. “Neurological disorders” did not show up as a frequent term in the k-means clustering of CML literature. “Musculoskeletal” appeared relatively often even though the term did not make the top terms list shown in There are mixed clinical findings on the impact of pre-existing or antecedent neurological autoimmune diseases versus neurological autoimmune AEs caused by TKI therapy. Autoimmune neurological diseases, such as myasthenia gravis, have a strong enough association with CML that some have suggested that they should be classified as paraneoplastic neurologic syndrome ; howeverIn summary, based on the predictions of the present study and corroborating clinical evidence, most neurological or neuromuscular AEs would only require assessment when the patient presents with overt symptoms.In the present study, the “other” focus was used to categorize conditions that were found among the top 10% of predicted relevant conditions to tyrosine kinase. Secondary cancers were frequently occurring nodes. Secondary cancers have been associated with CML both before and after CML diagnosis ,79,80,81Other foci conditions predicted as relevant were various forms of vitamin deficiency such as vitamins B6, B12, D, C, and of course, iron, which was ranked enough to be its own tier 1 focus. The majority of these vitamins are tied to hematopoiesis, which explains why they are likely present in these tier 3 foci. Beyond ties to hematopoiesis, there are presently no widespread hypotheses as to how or why vitamin deficiency may be associated with TKI therapy. It is possible TKIs may reduce innate absorption.Edema was another condition ranked in the top 10% in the cross-domain text mining analysis. Edema was also a frequent term in the k-means clustering of CML literature. Imatinib and dasatinib had strong associations with edema . MoreoveDermatological or skin conditions were another predicted TKI AE type that belonged to the “other” tier 3 foci. Imatinib has been documented to contribute to the development of rash and skin lesions , as is sPleural effusion is perhaps one of the most well-known acute adverse events with TKI therapy . DasatinIn summary, most conditions within the “other” foci only require monitoring when overt symptoms are present. Nonetheless, given the higher prevalence of secondary malignancies ,80,85, pCross-domain text mining via natural language processing (NLP) and machine learning enable expanded types of exploratory analyses that would not be otherwise possible. That is, mining across different domains allows comprehensive aggregation of relationships and perspectives. Compared to traditional manual literature reviews of select studies, cross-domain text mining utilizes machine learning approaches, which minimize the interjection of human bias into the results. However, cross-domain text mining’s current major limitation is that nuanced information is difficult to include in automated analysis. For example, the present cross-domain text mining study could not specify certain features for inclusion, such as TKI dose, length of TKI treatment, etc. Future work with patient-intervention-outcome (PIO) NLP models  could prp < 0.05) differences in AE term frequency by TKI type: gastrointestinal (bosutinib); edema (imatinib); pulmonary (dasatinib); diabetes (nilotinib); cardiovascular (ponatinib). The novel, cross-domain text mining using link prediction and hub node network analysis predicted three tiers of TKI AEs spanning ten physiological foci. Tier 1 foci (top 1% by predicted relevance to tyrosine kinase) included hematological events, glucose, iron, cardiovascular, and thyroid conditions. Tier 2 foci (top 5% by predicted relevance to tyrosine kinase) included inflammation and kidney conditions. Tier 3 foci (top 10% by predicted relevance to tyrosine kinase) include gastrointestinal, neuromuscular or “other” conditions. In summary, while TKIs have been pivotal in changing the outcome of CML, these medications are not benign. Careful proactive monitoring and selection of TKI to minimize patient-specific AEs is necessary to optimize clinical management and patient quality of life.The need for long-term tyrosine kinase inhibitor (TKI) therapy to treat CML warrants careful patient monitoring for adverse events or side effects. Assessment of CML TKI literature revealed hematological adverse events  were frequently cited with all TKIs. Clustering revealed significant (


Acute and chronic complications in esophago-colonic anastomosis have a significant impact in the postoperative course of patients with colonic transposition. Evidence about their management is poor and surgical treatment is mostly based on tailored approaches, so each new experience could be useful to improve knowledge about this peculiar condition. We report a unique case of an esophago-colonic resection and re-anastomosis without sternal approximation after recurrent anastomosis failure and strictures.A 69-year-old woman was referred to our hospital for worsening dysphagia. The patient had undergone esophago-gastrectomy with right colon interposition 12 years prior due to caustic ingestion. The esophago-colonic anastomosis was initially complicated by an enterocutaneous fistula, which was treated with anastomosis resection and left colon transposition. This was then further complicated by dehiscence and sternal infection treated with resection of the distal portion of the sternum and a new colo-jejunal anastomosis. Finally, a chronic anastomotic stricture occurred, refractory to endoscopic dilatation and prothesis positioning. We planned a new colonic-esophageal resection and re-anastomosis. The main technical challenges were addressing the adhesions resulting from previous surgery and mobilizing an adequate length of the intestinal tract to allow conduit continuity restoration. Blood supply was assessed through Indocyanine Green Fluorescence. To avoid compression of the digestive conduit sternal margins were not re-approximated, and the transposed tube was covered and protected using both pectoralis major muscles flap. We decided to avoid the use of any prosthetic material to reduce the risk of infection. The patient was able to resume oral food intake on the 12th day postoperatively after a barium swallowing test showed an adequate conduit caliber.Esophago-colonic anastomosis complications represent a life-threatening condition. Therefore, reports and sharing of knowledge are important to improve expertise in management of these conditions. Esophago-colonic anastomosis complications embrace a variety of chronic and acute disorders including redundancy, stricture, fistula, anastomotic dehiscence, and others . Acute aWe describe a unique case of retrosternal esophago-colonic resection and re-anastomosis for chronic refractory stricture after recurrent dehiscence in a patient who had undergone esophago-gastrectomy 12 years prior due to caustic injury.A 69-year-old woman was referred to our hospital because of worsening dysphagia and weight loss in the last year. Twelve years prior the patient had undergone esophago-gastrectomy for caustic ingestion, at another institution. The restoration of the alimentary tract was obtained initially with a retrosternal right colon interposition and esophago-colonic anastomosis since the severity of the caustic injuries did not allow the use of a gastric tube. The postoperative course was characterized by esophago-colonic anastomotic leakage and entero-cutaneous fistula treated with antibiotics and cervical abscess drainage. Thus, the right colonic tract was removed and replaced with left colon transposition through a median sternotomy two months after the first operation. Over the years, the patient presented severe stricture of the colo-jejunal anastomosis, complicated with mediastinal and sternal infection due to a new entero-cutaneous fistula. This was treated surgically with resection of the distal portion of the sternum and a new colo-jejunal anastomosis. Since then, the patient underwent repeated endoscopic dilatation for secondary esophago-colonic anastomotic stricture. A self-expandable endoprosthesis was positioned for worsening dysphagia, however it was removed after 10 days due to severe patient’s discomfort and pain.Upon presentation at our hospital, the patient complained of severe dysphagia with almost no capability of oral intake. Body weight was 38 kg and body mass index 13.5. A barium swallow test revealed a severe stricture of nearly 90% of the esophageal lumen at the level of the esophago-colonic anastomosis. That completely precluded solid oral intake and severely compromised liquid intake, which resulted in frequent episodes of inhalation (Fig. Re-median sternotomy was cautiously performed. The anastomotic tract appeared completely encased by fibro-calcific tissue probably due to chronic inflammation and previous surgery Fig. . Since iThe postoperative course was characterized by Klebsiella pneumoniae pulmonary infection successfully treated with antibiotics. No anastomotic complication or chest wall instability were observed. The postoperative barium swallowing test performed on day 10 revealed a proper caliber of the upper digestive tract and absence of strictures and leaks Fig. . TherefoRetrosternal colonic transposition is considered a feasible and effective option in case of esophagectomy and gastrectomy for caustic injury . Re-operBecause of its exceptional nature, we propose some general tips that could be useful for further similar experiences:Caution in re-sternotomy In case of re-sternotomy, fibrosis and tenacious mediastinal adhesions are expected. In order to avoid conduit damage, sternal division must be performed while carefully preserving underlying tissues.Tension-free anastomosis Intestinal loops are often encased in fibrous tissue due to previous surgery and their mobilization could represent a surgical challenge. Radial cuts on the mesentery are useful to reduce tension between loops and their vascular arch to accomplish a tension free anastomosis. It is advisable to use vascular structure as an anatomic guide to avoid unintentional damage.ICG fluorescence for vascularization assessment An adequate blood supply is crucial for the anastomosis outcome. ICG fluorescence could represent an effective way to assess vascularization of both colonic and esophageal ends.Avoid conduit compression Due to previous sternotomy and fibrotic mediastinal adhesions, the risk of retrosternal conduit compression is high [ is high ; in thisEsophago-colonic anastomosis complications represent a life-threatening condition and a challenge for surgeons. Due to the exceptionality of cases, highly personalized treatment is required. Reports of single cases and sharing of experiences could be helpful in the management of future similar circumstances.


The CRISPR/Cas9  method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy. In agroecology, the integrated approach in production of crops and conceptual marketing management draws holistic economic concern. As reported by “Food and Agriculture Organization” , the croThe customary methods have certain drawbacks such as non-specificity and the generation of mutations with abundance of nucleotides . NaturalThe targeted genomic engineering can be extremely beneficial to agriculture. If the function of a specific gene is known, it can be over expressed or suppressed to obtain the desired trait. Eventually, the crops that are capable of withstanding biotic and abiotic stresses can be easily developed using CRISPR/Ca9 and nanotechnology. Similarly, undesired genes can also be silenced by using these technologies, which would allow expression of only the desirable traits to eventually obtain higher yield. It will be an extremely difficult task to improve crop refinement without genomic engineering. Conventional breeding programs would require longer duration to introduce new quality-related traits or disease-tolerance traits. Therefore, genomic engineering is a striking technology for the future development of agricultural crops with nutrition. Nanotechnology-based protocols has new sets of advanced applications in agriculture and biomedicine; typically, the nano-sized particles are used to deliver the task obtain desirable results in crop development. Coalescing biotechnology and nanotechnology approaches, including GE, have more benefits than customary breeding to improve the development of food crops, which can naturally overcome biotic and abiotic stress along with enhancing the yield. This brief review mainly focuses the importance of genomic engineering in agriculture, and the progress in developing mutant plants using sequence-specific nucleases (SSNs). Furthermore, the procreation of genomically edited crops are already developed in agricultural biotechnology, the main objective, limitations and prospective challenges of GE are highlighted including the role of nanotechnology-based methods in crop refinement.via addition, deletion, and alternation of sequences  sequence comprising of twenty nucleotides that are essential to balance to the target DNA and the details of sgRNAs designing is well explained by The lost DNA part cannot be recollected in this NHEJ pathway. In this repair pathway, the dimeric protein complex (Ku) binds at the end of the broken DNA and later to DNA protein kinase catalytic subunits (DNA-PKCs). Artemis proteins are also come in to play and bind at the DNA terminal to make a complex; allowing phosphorylation and eventually the synthesis of DNA begin. This double-stranded DNA converted to blunt-ended double-stranded DNA by catalytic DNA ligase reaction, forming covalent linkage of phosphodiesters . This reThe HDR pathway use the autologous donor DNA sequences from sister chromatids or foreign DNA to create precise insertion and substitution between DNA double-strand break (DSB) sites for further alterations. Considerable research has been done previously on proteins involved in the HDR pathway, MRE11-Rad50-Nbs1 (MRN) complex binds at the 5′ end of the DSBs and forms the 3′ overhangs. Later the replication protein A (RPA) binds to the single-strand DNA to prevent the nuclease activity. RAD-51 protein involves in search of homologous DNA and eventually the invasion occurs to complete the homologs-directed repair . El-MounTransgenesis profoundly involving genetic addition without changing the genetic pool to create specific traits for agricultural/agroeconomical benefits. In the present scenario, providing food security to a mounting populace is one of the major challenges in this modern world. Thenceforth, the food fructification needs to be increased over 80–90%. Furthermore, the food production is declining every year due to extreme weather conditions, climate change, global warming, farmland availability, and cumulative biotic and abiotic problems. To overcome these challenging obstacles, gene modification technique in food crops will be the superlative method to achieve the targeted tasks . The genHomologous recombination is a challenging process wherein chromosome can chasm by the nuclease that must be coordinated with the distribution of the DNA repair template. Initially, HR in plants was confirmed by the incorporation of marker genes at detailed chromosomal sites. Targeted transgene insertion into the euchromatin should provide promising results in plants with high transgene expression; therefore, it is a great improvement over the integration by the traditional Transgenesis . MoreoveXanthomonas oryzae pv. oryzae (Xoo), the yield and rice quality will be deprived from its authentic taste. By CRISPR/Cas9 GE technique, the genes namely OsSWEET11, OsSWEET13, and OsSWEET14 could be possibly edited to overcome the bacterial blight disease (via agrobacterium mediated transformation. The mutated rice varieties exhibited prolonged basic vegetative growth (BVG) period at latitudes  gene was modified to develop the fragrance in non-aromatic rice grains for better marketing  for the development of haploid plants in wheat crops. Among these three promotors, TaU3 showed better results (via symbiotic relationship with rhizobia. In this process NFR (Nod Factor Receptor) play a major role in nitrogen fixation cycle. Thence, AhNFR1 and AhNFR5 genes were mutated by CRISPR/Cas9 to proliferate the root nodules via hairy root transformation system (via Biolistic bombardment resulted in enhanced biosynthesis of carotenoid and chlorophylls (MATRILINEAL/NOT-LIKE-DAD/PHOSPHOLIPASE A (MTL/NLD/ZmPLA) gene is edited by CRISPER/Cas9 with OsU3 promotor via Agrobacterium for the haploid induction in foxtail millet  causes Red Blotch Disease (Xanthomonas axonopodis. It is threatening to citrus family crops worldwide. The CsWRKY22 gene was edited by CRISPR/Cas9 with AtU6-1 promotor via Agrobacterium methodology to produce the Canker disease-free citrus in Wanjincheng orange plants. PDS (phytoene desaturase) gene was mutated for the development of Albino phenotype and carotenoid biosynthesis in banana crop (Fusarium oxysporum is a dangerous pathogen for watermelon. The editing of Clpsk1 gene that encode Phytosulfokine (PSK) precursor could be conferred to enhance resistance of Fusarium oxysporum to watermelon, the gene was efficiently edited by CRISPR/Cas9 system via Agrobacterium method to produce the Fusarium oxysporum resistant watermelons in appreciable yield  and MYBA7 (Transcription factor) genes are edited by CRISPR/Cas9  Disease . Citrus ana crop . Fusariule yield .via Agrobacterium (Phelipanche aegyptiaca and Orobanche spp.), a kind of plant parasite can cause severe damage to the tomato plants. Thus, the CCD8 (Carotenoid Cleavage Dioxygenase 8) gene was edited to afford the Phelipanche aegyptiaca parasite resistant tomatoes (Camelina sativa CRUCIFERIN C) gene encodes the seed proteins in Camelina sativa and this gene was edited by CRISPR/Cas9 to enhance the seed storage protein and enriched saturated fatty acids contents  in the stomatal guard cells of tomato fruit. This gene was edited for the development of bacterial speck disease resistance acterium . Broomratomatoes . SlMlo1 tomatoes . Steroidtomatoes . BoaCRTItomatoes . CsCRUC contents . Powderycontents . Thencefcontents . Assured14 genes . To cont14 genes . The amy14 genes , thereby14 genes . Tiller-14 genes . OsRR22 14 genes  and the 14 genes  and vege14 genes  along wiCiPDS (chicory phytoene desaturase) gene was edited by under U6 promotor via Agrobacterium mediated and protoplast transfection methods. Among these two methods, Agrobacterium mediated route showed 31.25% transformation efficiency in chicory and the mutated chicory plants showed better Albino phenotype content  gene was modified to check the nitrogen uptake and nitrate metabolism in petunia plants. Mutated plants showed better nitrogen uptake efficiency . CiPDS  recognizes an 8-mer PAM (5′-NNNNGATT) sequence hence it can progress the target particularity, whereas SaCas9 recognizes a 6-mer PAM sequence (5′-NNGRRT) (Oriza sativa snoRNA U3), AtU6 (Arabidopsis U6), OsUBI (Oriza sativa Ubiquitin), ZmUBI (Zea mays UBI), cauliflower mosaic virus 35S promoters have been used to promote Cas9 expression in plants and, more than 30 empty gRNA backbones in binary vectors was supplied by Addgene  . This te Addgene . Tissue  Addgene . The pro Addgene . The pLA Addgene , and pDD Addgene , INCURVA Addgene , and the Addgene . In orde Addgene . Althoug Addgene . To over Addgene .in vitro and in vivo  have been employed to identify specific locations in the genome that can anchorage polygenic diseases such as Alzheimer’s, diabetes, autism, and schizophrenia. This technique is crucial in biomedical field to treat various diseases, including the removal of HIV genome . The ex  in mice , which asquitoes . Cancer squitoes . Furthersquitoes . GE techsquitoes , hemophisquitoes  cystic fsquitoes , and sicsquitoes . The Cassquitoes .Capsicum annuum L. syn. chilli) was developed by editing NAC72 gene via gene therapy.This GE technology has been used to treat hematologic diseases, infectious diseases, and malignant tumors (2)Gene pyramids and gene knockouts can be created by inserting foreign genes through this approach.(3)Repression/activation of gene expression.(4)Delivery of proteins to genomic loci.(5)Gene expression can be regulated with this technology. It also plays a major role in the progress of new mutant diversities to help the breeders.(6)Gene silencing is an important aspect in the crop improvement program based on CRISPR intrusion (CRISPRi) .(7)It is a promising technique to study the new gene’s function.(8)Plants that are lenient to biotic and abiotic stresses, as well as herbicides, can be easily developed.(9)Researchers are already using this technology in gene therapy .(10)Currently, nanotechnology is being used to prepare nano-fertilizers, nano-pesticides, and to enhancing the abiotic stress tolerance, thereby protecting the crops.(11)Different types of NPs have also been used for the transformation, editing, and silencing of genes to improve crop yield and quality.CRISPR/Cas9 technology is among the best and most cost-effective methods for genomic editing in plants. However, some of its limitations are mentioned below.(1)Genomic editing is inefficient and slow by the presence of larger protein sizes. Therefore, protein size should be small to ensure speedy and efficient genomic editing.(2)It contains limited number of PAM sites at limited loci.(3)CRISPR/CAS9 can introduce multiple random mutations, as well as mutations at unspecific loci.(4)It has low HDR efficiency.(5)It exhibits low efficiency against viruses.(6)It has become difficult to commercialize transgenic crops developed using CRISPR/Cas9 technology in many countries because different countries have different rules and regulations.(7)In backward and developing countries, there is a lack of proper understanding of pesticides, fertilizers, and other products developed by nanotechnology; therefore, it is impossible to grow better crops.At present, this technology is helping researchers in agriculture and breeders in developing crops that can overcome biotic and abiotic stress, with high nutritional values, and optimal yield parameters, thereby providing adequate food grains, vegetables, and fruits to current world population. Even with the availability of all types of biotechnological and bioinformatics tools, there are enduring challenges in developing genetically modified plants using the CRISPR system. Owing to unavailability of complete genome sequence information and the large genome size of some tropical, medicinally valuable crops, and fruits, some studies have been unable to edit genes to obtain desirable traits . TherefoScientists and plant breeding researchers are working to develop high yielding and biotic/abiotic stress resistant variety. CRISPR/Cas9 GE in consolidation with nanotechnology have emerged as an important platform to improve the quality and desirable quality of agricultural crops with appreciable yield. These technologies are significantly susceptible and open new prospects in plant genetics. The nutritional values and quality of health prospects of plants and human could be enriched with broad spectrum of applications including in biomedical domain. The imminent fertility and diminishing useful prokaryotic microorganism issues in soil are delicate issues in addition to biotic problems. Relapsing the aforesaid issues could be feasible using CRISPR/Cas9 GE and nanotechnology aspects, it will be challenging and greatly influence to the crop refinement. Skillful editing of genetic sequence of plant genome could progressively improve the agronomic traits, photosynthetic capacity, and nutritional values. Furthermore, biotic and abiotic stress-induced issues in plants could be configured and minimized. The methodologies can also be diversified to characterize the individual gene functions, thereby improving the genomic sequences of agricultural crops to produce exceptional yield. These findings could point new strategies in agroecology facilitating the sustainable production of nutritional quality food to satisfy the increasing demand of ever-growing population.Agrobacterium tumefaciens is quite low in some specified plant tissues. Hence, an alternative bacterial system to gene transfer is necessary for ease genome editing in all crops by adopting CRISPR/Cas9-Nanotechnology system. Furthermore, the development of tissue culture free delivery protocols involving direct genomic editing in germplasms and meristematic cells of plants, can yield propitious results. To date, numerous crops have been developed with this combined CRISPR/Cas9-Nanoparticle complex system. It is advisable to framework on the products already developed by this method and ensure their recurrent use in agricultural locales. Extensive studies are recommended to elucidate the complete interactions (plant cell mechanisms) of nanoparticles/nanocomposites in all types of crops. We strongly believe that the products developed by conjoining these technologies will beneficially assist the agro-based researchers to bloom their ideas for innovative crop development/refinement.CRISPR/Cas9 and nanoparticle complex system is an advanced innovative technique in agricultural crop development/refinement. Thus far, CRISPR system in connotation with nanotechnology has been used to improve the quality and yield of many valuable crops for future benefits. Using nanoparticle based fertilizers/additives; extinct nutrients could be regained, ensuring that the soil nutrients could be maintained. The green, non-toxic nanoparticles is a sagacious approach to increase micro and macronutrient levels in the soil for healthy growth of crops. Chemically derived nanoparticle usage should be eliminated; these can harm not only the crops but also to the environment. Zinc oxide-based nanocomposites and nano-fertilizers have shown appreciable results in crop growth; maintaining the soil salinity and fertility with robust yield. The green protocols to develop Zinc oxide-based green nanocomposites draws the attention of agro-scientific community and it should be given prime importance, so that toxic free effective nano-priming techniques can reduce the soil contamination and improves the seed quality. Metal organic frameworks (MOF) have been recently investigated as delivery systems for CRISPR/Cas9. Non-toxic and eco-friendly MOF 3-dimentional structures with biopolymer conjugates are potentially promising. Furthermore, CRISPR/Cas9-associated nanoparticle complex has been successfully utilized for transformation, silencing, and modification of genes to overcome the existing and expected critical biotic and abiotic issues, thereby producing nutritional-rich crops. This technology can be used to alter the metabolic pathways in plants to obtain desired high-quality secondary metabolites for future usage. Recently, revolutionary changes in this crop refinement program witnessed auspicious results. Nod factors have been shown to increase nitrogen efficiency in legume crops using CRISPR/Cas9 system with nano-technological contrivance. Modifying the Nod signaling pathway in cereal crops should eliminates the use of toxic inorganic fertilizers. The transformation efficiency by BN planned the manuscript outline, wrote the draft, and prepared the tables. GS contributed in writing, reshaping/editing the manuscript and modifying the tables. GS, S-CK, MM, CS, RP, and MK proofread the manuscript. S-YK acquired the funding. S-YK and S-HL supervised the study and revised the manuscript. All the authors reviewed and approved the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Vaccinium myrtillus) plants grown under different light regimes supports the hypothesis.Global warming is predicted to change the growth conditions for plants and crops in regions at high latitudes (>60° N), including the Arctic. This will be accompanied by alterations in the composition of natural plant and pest communities, as herbivorous arthropods will invade these regions as well. Interactions between previously non-overlapping species may occur and cause new challenges to herbivore attack. However, plants growing at high latitudes experience less herbivory compared to plants grown at lower latitudes. We hypothesize that this finding is due to a gradient of constitutive chemical defense towards the Northern regions. We further hypothesize that higher level of defensive compounds is mediated by higher level of the defense-related phytohormone jasmonate. Because its biosynthesis is light dependent, Arctic summer day light conditions can promote jasmonate accumulation and, hence, downstream physiological responses. A pilot study with bilberry ( Steadily rising worldwide greenhouse gases emissions have caused an increase of the global temperature of >1 °C within the last 50 years . The pre-1  ecosystems, for example by changing the distribution of species and their interactions , as well-1 . Thus, i-1 . For exa-1 , and loc-1  but for -1 . Thus, vAcidovorax radices N35) in the soil increased crop  growth and simultaneously reduced insect pests  under environmental condition simulating climate change-related elevated ozone (O3) levels , showed that at ambient temperatures-increased resistance was costly, whereas warming promoted better defended plants  levels . A recend plants . This inPlant protection against pathogens and herbivores may be either constitutively present  or induced upon stress  . While sThus, it is tempting to speculate that plants living at high latitudes might have a certain yet unknown intrinsic potential for defending themselves against pathogens and pests. Besides temperature and precipitation, the light conditions at high latitudes with extremely long daylight in summer may have a yet neglected role by causing a higher constitutive defense level.Jasmonates (JAs) are lipid-derived phytohormones that regulate a broad range of biological processes in plants, including plant growth, development, tolerance to abiotic stresses, and the production of secondary metabolites . In partIn the absence of stress, only low levels of JA-Ile are present in the cell. In this situation, the Topless (TPL)-Novel Interactor of JAZ adapter proteins (NINJA)-JA-ZIM-domain (JAZ) complex represses MYC transcription factors, which are involved in the transcription of JAs-responsive genes. Upon stimuli such as herbivory or wounding, JA-Ile accumulates and binds to the receptor CORONATINE-INSENSITIVE1 (COI1) . COI1 isOryza sativa) (Zea mays)   and maizea mays) . In riceea mays)  or JAR1 ea mays)  showed cea mays) .Arabidopsis thaliana  as well as additional plant hormones contribute to these responses . In partSpodoptera frugiperda larvae) performed better and gained more weight than under ambient light conditions. Moreover, herbivory is reduced in plants grown in full sunlight compared with plants grown in shade (Antirrhinum majus), the biosynthesis regulation of floral fragrance by light quality is mediated by JAs and calcium ions  plants were collected in Northern Norway close to Tromsø (69° 29’ N) and grown under arctic (24 h light) and Central European (12 h light/12 h dark) light regimes. After two weeks, the leaf samples were collected every 6 hours in liquid nitrogen and stored at -80 °C. Eventually, samples were freeze dried, grinded and used for phytohormone analyses. We found that the levels of jasmonic acid (Chenopodium ficifolium grown either under long-day (18 h light/6 h dark) and short-day (6 h light/18 h dark) regimes also showed that after three weeks the levels of JAs but also of abscisic and salicylic acids were significantly higher in long-day plants. The same was demonstrated for many stress-related genes (In order to test this hypothesis, we conducted a pilot study where naturally occurring bilberry (nic acid , and counic acid . A very ed genes .via the jasmonate pathway, including the defense against nectrotrophic fungi. This might also be true for other phytohormones signaling pathways that directly or indirectly interact with JA signaling. Given that during evolution plants adapted to various light qualities and intensities, it is not surprising that light interacts with the action of phytohormones such as JAs that affect both development and defense. Our controlled pilot study was performed with local wild bilberry ecotype adapted to long day light conditions during the growth season. To further explore the response of this species to different day length conditions, controlled experiments with plants originating from different latitudinal locations will be performed. Additional, comprehensive studies to better understand the underlying molecular mechanisms in bilberry and other plants would lead to potential agricultural benefits for crops grown in the far North, which could become important in the future, especially under climate change conditions.These findings suggest that at high latitudes light is an important factor for JAs accumulation and, consequently, affects JA-dependent downstream defenses (summarized in The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.Concept: AMi. CF, LJ, AMi performed the experiments. AMi and MR wrote the manuscript with contribution of all authors. All authors contributed to the article and approved the submitted version.AMr received a Martina Roeselova memorial fellowship. The Max Planck Society covered the open access fee.We thank the Max Planck Society. We also thank Michael Reichelt for phytohormone measurements. The staff of the Climate laboratory Holt at UiT The Arctic University of Norway is acknowledged for running the controlled growth experiment. AMr thanks Martina Roeselova memorial fellowship.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. 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The link between cancer and autoimmunity is well-established. For example, increased levels of autoantibodies are frequently found in cancer patients, and autoimmune diseases are linked to an increased risk for certain neoplasms. However, the extent to which chemotherapy induces autoimmune reactions remains largely elusive. Here, we quantified immunoglobulin M (IgM) responses to various human tissues and the patient’s tumor before and during adjuvanted chemotherapy (seven cycles of the FOLFIRI regimen (folinic acid/fluorouracil/irinotecan) plus cetuximab) of a patient with metastasized colon cancer. IgM levels against all investigated tissues increased shortly after the first cycle and were further boosted by cycles two and three. Autoimmune responses then decreased during cycles four to seven but remained above baseline levels for most tissues. Our findings suggest that chemotherapy can induce broadly reactive autoimmune responses. Monitoring self-reactive IgM responses during treatment may help alleviate autoimmunity-related adverse events. Malignant disease is a known cause of autoimmune responses that include the generation of autoantibodies . Cancer-In contrast, little is known about the effect of chemotherapy on autoimmune responses. Chemotherapy-induced cell death leads to the release of tumor antigens from dying tumor cells along with damage-associated molecular pattern molecules (DAMPs), which bind receptors on immune cells, stimulating immune responses . HoweverA 55-year-old woman was diagnosed with cancer of the sigmoid colon via a colonoscopy that was performed because of reported periodic bleeding during defecation. There was no evidence of dissemination of the tumor. A sigmoidectomy was performed. Histological examination revealed a moderately differentiated colorectal adenocarcinoma penetrating adipose tissue, with extensive lymphovascular invasion. The patient received eight cycles of chemotherapy ). Positron emission tomography-computed tomography (PET-CT) and magnetic resonance imaging (MRI) scans detected no distant metastases.About one year after the initial diagnosis, abdominal ultrasound and a PET-CT scan revealed ovarian cancer of potential metastatic origin. Further suspected metastases were identified in the lung as well as an axillary lymph node. The patient underwent extirpation of the uterus with appendages and the omentum. Histology of the removed organs revealed a moderately differentiated adenocarcinoma of the left ovary, likely of metastatic origin. Immunohistochemistry revealed that the phenotype of the tumor was consistent with colorectal carcinoma. A follow-up CT scan showed metastasis in the left lung. Consequently, the patient received radiotherapy treatment for this metastasis, which was shown to be successful by following PET-CT scans.About nine months later, a PET-CT scan revealed a new hypermetabolic nodule in the left lung and hypermetabolic lymphadenopathy in a subcarinal lymph node, most likely of neoplastic nature. Hypermetabolic foci were identified in the rectus abdominis muscle and the right iliac region. A total biopsy of the metastatic focus of the anterior abdominal wall with partial resection of the rectus abdominis muscle on the left was performed. Histological findings were consistent with adenocarcinoma metastasis.The patient received seven cycles of chemotherapeutic treatment with the FOLFIRI regimen plus cetuximab over a time period of about three months. PET-CT evaluation confirmed the stabilization of the patient. To monitor the patient’s health status and the autoimmune response to chemotherapy, we quantified self-reactive IgM responses at organ-level resolution using an investigational diagnostic approach. Briefly, soluble components of various human organ homogenates, and of the patient’s tumor tissue, were immobilized on the surface of goat red blood cells (RBCs). The human antigen-functionalized RBCs were incubated with serial dilutions of the patient’s serum, whereby organ-specific IgM, due to its oligomeric nature, cross-links the RBCs Figure . The serFor all organs and the tumor tissue, we observed a fast initial increase in IgM levels (four- to eightfold increases compared to baseline). The following day the titers decreased, but then increased again and stabilized at above baseline at six to nine days post the first cycle of chemotherapy. IgM titers to the lungs  and stomach  were especially high Figure . During Shortly after the seventh cycle of chemotherapy, the patient was hospitalized with symptoms of acute respiratory infection. A polymerase chain reaction (PCR) test for coronavirus disease 2019 (COVID-19) was positive. The patient passed away due to severe pneumonia about three weeks later.We observed an increase in autoreactive and cancer-specific IgM antibodies following chemotherapy with the FOLFIRI regimen plus cetuximab. Although this is merely a correlation, the steep and substantial increase in IgM titers observed immediately after the second cycle provided evidence that chemotherapy had a causative effect on elevated autoantibodies in this case. Moreover, chemotherapeutic drugs, in general, exert cytotoxicity and therefore can damage cells of vital organs. This may induce autoimmune responses through various mechanisms. For example, cell death can lead to the release of autoantigens along with DAMPs, which can stimulate immune responses . FurtherThis study concluded that self-reactive IgM against various organs can be induced by chemotherapy. An experimental agglutination-based assay was able to quickly quantitate these IgM responses at organ-level specificity. Monitoring IgM responses may improve the prognosis of patients with cancer or other diseases associated with increased autoantibody levels.


Antral follicle Count (AFC) is a non-invasive biomarker used to assess ovarian reserves through transvaginal ultrasound (TVUS) imaging. Antral follicles’ diameter is usually in the range of 2–10 mm. The primary aim of ovarian reserve monitoring is to measure the size of ovarian follicles and the number of antral follicles. Manual follicle measurement is inhibited by operator time, expertise and the subjectivity of delineating the two axes of the follicles. This necessitates an automated framework capable of quantifying follicle size and count in a clinical setting. This paper proposes a novel Harmonic Attention-based U-Net network, HaTU-Net, to precisely segment the ovary and follicles in ultrasound images. We replace the standard convolution operation with a harmonic block that convolves the features with a window-based discrete cosine transform (DCT). Additionally, we proposed a harmonic attention mechanism that helps to promote the extraction of rich features. The suggested technique allows for capturing the most relevant features, such as boundaries, shape, and textural patterns, in the presence of various noise sources . We evaluated the proposed model on our in-house private dataset of 197 patients undergoing TransVaginal UltraSound (TVUS) exam. The experimental results on an independent test set confirm that HaTU-Net achieved a Dice coefficient score of  Ovarian reserve, defined as the total number of ovarian follicles, indicates the quality and quantity of the primordial follicular pool in the ovaries . PatientThe primary aim of ovarian reserve monitoring is to measure the number and size of ovarian follicles and the number of antral follicles, which are, on average, 2–10 mm in diameter . FolliclDeveloping an automated solution for ovary and follicle segmentation incorporates numerous challenges. Convolutional neural networks (CNNs) have shown substantial performance, and accuracy advancements over conventional methods . With thRecently, many deep learning-based methods have been developed for analyzing medical images ,22. SpecVarious deep learning-based methods have been used to detect and segment ovary, and antral follicles ,30. Li, We propose a segmentation network called HaTU-Net to segment ovaries and follicles from TVUS images.We propose using harmonic convolution  to replaWe developed harmonic attention (HA) block to improve feature discriminability between the target and background pixels in the segmentation stage. The HA block encourages the features by avoiding the artifacts, and support for the HaTU-Net leads to improved segmentation results.Our experimental results confirm HaTU-Net has shown significant improvement compared to the various state-of-the-art segmentation methods   could noThe remainder of this paper is organized as follows: This section presents a detailed description of the ovary US dataset and architecture details of the proposed HaTU-Net as depicted in The Institutional Review Board approved the retrospective study (IRB), and the requirement for informed consent was waived. The radiology reports of adult patients who underwent transvaginal ultrasound (TVUS) exams between 2005 and 2019 in a single institution were reviewed, and a total of 197 eligible patients were identified and selected. The inclusion criteria were: (1) premenopausal female adult patients, (2) underwent TVUS exams, (3) normal ovary on the pelvic ultrasound, and (4) available B-mode static images of the ovary. Patients with the following criteria were excluded: (1) low-quality US images with obscure boundaries of the ovary, (2) abnormal ovary findings on the ultrasound, or (3) known ovarian pathologies or ovarian surgical history.All TVUS exams were performed using GE LOGIQ E9  ultrasonic system equipped with a transvaginal IC5-9 transducer. US exams were reviewed in a picture archiving and communication system (PACS) to extract the DICOM images of ovaries in sagittal and coronal planes. Using the MicroDicom Viewer tool , a radiologist who had ten years of experience in pelvic ultrasound annotated the contours of the ovary and follicles following a specific protocol, (1) annotated all follicles of 2–28 mm  in diameconv-transpose2D operation. Each encoder layer’s features are concatenated with the corresponding features in the decoding layer (skip connections). A threshold of 0.5 is used to generate the final predicted mask for ovary and follicles segmentation.rization , allowinI of size u and v in the two orthogonal directions. Here Motivated by , we repl follows : (1)Tu,vd is represented as a weighted linear aggregation of DCT coefficients on all input channels C as follows:u, v and The input image features are decomposed using the DCT transform to perform the convolution operation. A kernel size of T ∈ C, which is the channel statistics. This generates r refers to the reduction ratio), then the channel attention map can be formulated as:To advance the feature discriminability between the small targeted region and background pixels, T and O:The use of skip connections between the input feature map We use a weighted sum of the binary cross-entropy (BCE) and focal loss y is the target binary mask, and The final loss is expressed as follows:In the third stage, segmented follicles are used to measure the follicle size. Input: Single ground truth follicle segmentation mask and predicted follicle segmentation mask.Load ground truth mask and predicted mask images.Measure follicle diameters on both images in pixels.Convert pixel diameters to physical measurements.Exclude follicles sized outside the recruitable range of 2–10 mm in diameter by converting pixels black, as counting antral follicles < 2 mm in diameter might heighten the chances of counting small anechoic structures like vessels or artifacts; whereas counting dominant follicles > 10 mm lack the evidence of clinical practicality .Compute the dice similarity coefficient (DSC) between the ground truth mask and predicted mask images.Calculate the number of correctly detected follicles from the predicted mask (follicles with >0.5 Dice coefficient score are considered).Calculate the number of detected follicles from the predicted mask.Calculate the number of actual follicles from the ground truth mask.Evaluate the precision and recall of our predicted follicle counting with the formula from .All the methods are implemented in PyTorch . We use This paper organizes our experiments into three key stages: 1. ovary segmentation, 2. follicle segmentation, and 3. follicle counting. To measure the effectiveness of the proposed model on segmentation stages, five evaluation metrics are used, i.e., accuracy, dice similarity coefficient (Dice), intersection over union (IoU), sensitivity, and specificity . The preWe define our baseline model as a U-Net where it replaces the standard 2D convolutions layers with harmonic convolutions. Since the ovary occupies a large part of an ultrasound image, we enforce fine boundary segmentation while retaining shape information through an HA block (BL + HA). Therefore, adding the harmonic attention block to BL leads to better segmentation results. Finally, HaTU-Net improves the DSC and IoU scores by approximately Further, qualitative analysis plays a crucial role in visually determining segmentation results. We have proposed an efficient segmentation model to segment the ovary and follicle in TVUS images. For this purpose, we replaced the standard convolutional filter using harmonic convolution. The input image was first decomposed using the discrete cosine transform (DCT), and these transformed signals merged using learned weights. We utilized the proposed harmonic attention block that provides a better feature representation of the targeted region  by ignoring the unwanted features that could infer the segmentation performance. Although the existing methods achieved acceptable results, they failed to capture the precise boundaries of the ovary and follicles from noisy US images. We found that the proposed model ignored the imaging artifacts in the presence of shadows, speckle noise, and poor contrast images, leading to better segmentation results than existing approaches. It also produced fewer false-positive pixels and provided a more robust segmentation performance with less error rate. However, our proposed model has the limitation of poorly segmenting the ambiguous boundaries of ovaries and follicles.In this paper, we proposed an automated solution for ovarian ultrasound quantification. We have developed a novel method named HaT-UNet that provides accurate segmentation of ovaries and follicles from TVUS images. The proposed HaTU-Net employed harmonic convolution with discrete cosine transform (DCT) and enhanced feature discriminability through HA block to handle ambiguous boundaries. Experimental results proved that the HaTU-Net tackles the presence of imaging artifacts by achieving DSC score improvement of