Does Synthetic Data Generation of LLMs Help Clinical Text Mining?

Recent advancements in large language models (LLMs) have led to the development of highly potent models like OpenAI's ChatGPT. These models have exhibited exceptional performance in a variety of tasks, such as question answering, essay composition, and code generation. However, their effectiveness in the healthcare sector remains uncertain. In this study, we seek to investigate the potential of ChatGPT to aid in clinical text mining by examining its ability to extract structured information from unstructured healthcare texts, with a focus on biological named entity recognition and relation extraction. However, our preliminary results indicate that employing ChatGPT directly for these tasks resulted in poor performance and raised privacy concerns associated with uploading patients' information to the ChatGPT API. To overcome these limitations, we propose a new training paradigm that involves generating a vast quantity of high-quality synthetic data with labels utilizing ChatGPT and fine-tuning a local model for the downstream task. Our method has resulted in significant improvements in the performance of downstream tasks, improving the F1-score from 23.37% to 63.99% for the named entity recognition task and from 75.86% to 83.59% for the relation extraction task. Furthermore, generating data using ChatGPT can significantly reduce the time and effort required for data collection and labeling, as well as mitigate data privacy concerns. In summary, the proposed framework presents a promising solution to enhance the applicability of LLM models to clinical text mining.Comment: 10 pages, 8 tables, 4 figure

Large Language Model Soft Ideologization via AI-Self-Consciousness

Large language models (LLMs) have demonstrated human-level performance on a vast spectrum of natural language tasks. However, few studies have addressed the LLM threat and vulnerability from an ideology perspective, especially when they are increasingly being deployed in sensitive domains, e.g., elections and education. In this study, we explore the implications of GPT soft ideologization through the use of AI-self-consciousness. By utilizing GPT self-conversations, AI can be granted a vision to "comprehend" the intended ideology, and subsequently generate finetuning data for LLM ideology injection. When compared to traditional government ideology manipulation techniques, such as information censorship, LLM ideologization proves advantageous; it is easy to implement, cost-effective, and powerful, thus brimming with risks

Tapered Optical Fiber Sensor for Label-Free Detection of Biomolecules

This paper presents a fast, highly sensitive and low-cost tapered optical fiber biosensor that enables the label-free detection of biomolecules. The sensor takes advantage of the interference effect between the fiber’s first two propagation modes along the taper waist region. The biomolecules bonded on the taper surface were determined by demodulating the transmission spectrum phase shift. Because of the sharp spectrum fringe signals, as well as a relatively long biomolecule testing region, the sensor displayed a fast response and was highly sensitive. To better understand the influence of various biomolecules on the sensor, a numerical simulation that varied biolayer parameters such as thickness and refractive index was performed. The results showed that the spectrum fringe shift was obvious to be measured even when the biolayer was only nanometers thick. A microchannel chip was designed and fabricated for the protection of the sensor and biotesting. Microelectromechanical systems (MEMS) fabrication techniques were used to precisely control the profile and depth of the microchannel on the silicon chip with an accuracy of 2 μm. A tapered optical fiber biosensor was fabricated and evaluated with an Immune globulin G (IgG) antibody-antigen pair

Implantable and Biodegradable Macroporous Iron Oxide Frameworks for Efficient Regeneration and Repair of Infracted Heart

The construction, characterization and surgical application of a multilayered iron oxide-based macroporous composite framework were reported in this study. The framework consisted of a highly porous iron oxide core, a gelatin-based hydrogel intermediary layer and a matrigel outer cover, which conferred a multitude of desirable properties including excellent biocompatibility, improved mechanical strength and controlled biodegradability. The large pore sizes and high extent of pore interconnectivity of the framework stimulated robust neovascularization and resulted in substantially better cell viability and proliferation as a result of improved transport efficiency for oxygen and nutrients. In addition, rat models with myocardial infraction showed sustained heart tissue regeneration over the infract region and significant improvement of cardiac functions following the surgical implantation of the framework. These results demonstrated that the current framework might hold great potential for cardiac repair in patients with myocardial infraction

Worldwide Variations in Demographics, Management, and Outcomes of Acute Pancreatitis

Background & Aims Few studies have compared regional differences in acute pancreatitis. We analyzed data from an international registry of patients with acute pancreatitis to evaluate geographic variations in patient characteristics, management, and outcomes. Methods We collected data from the APPRENTICE registry of patients with acute pancreatitis, which obtains information from patients in Europe (6 centers), India (3 centers), Latin America (5 centers), and North America (8 centers) using standardized questionnaires. Our final analysis included 1,612 patients with acute pancreatitis (median age, 49 years; 53% male, 62% white) enrolled from August 2015 through January 2018. Results Biliary (45%) and alcoholic acute pancreatitis (21%) were the most common etiologies. Based on the revised Atlanta classification, 65% of patients developed mild disease, 23% moderate, and 12% severe. The mean age of patients in Europe (58 years) was older than mean age for all 4 regions (46 years) and a higher proportion of patients in Europe had comorbid conditions (73% vs 50% overall). The predominant etiology of acute pancreatitis in Latin America was biliary (78%), whereas alcohol-associated pancreatitis accounted for the highest proportion of acute pancreatitis cases in India (45%). Pain was managed with opioid analgesics in 93% of patients in North America versus 27% of patients in the other 3 regions. Cholecystectomies were performed at the time of hospital admission for most patients in Latin America (60% vs 15% overall). A higher proportion of European patients with severe acute pancreatitis died during the original hospital stay (44%) compared with the other 3 regions (15%). Conclusions We found significant variation in demographics, etiologies, management practices, and outcomes of acute pancreatitis worldwide

Mortality in acute pancreatitis with persistent organ failure is determined by the number, type, and sequence of organ systems affected

Background: Persistent organ failure (POF) is the strongest determinant of mortality in acute pancreatitis (AP). There is a paucity of data regarding the impact of different POF attributes on mortality and the role of different characteristics of systemic inflammatory response syndrome (SIRS) in the risk of developing POF. Objective: We aimed to assess the association of POF dynamic features with mortality and SIRS characteristics with POF. Methods: We studied 1544 AP subjects prospectively enrolled at 22 international centers (APPRENTICE consortium). First, we estimated the association of onset, duration, and maximal score of SIRS with POF. Then, we evaluated the risk of mortality based on POF onset, duration, number, type, and sequence of organs affected. Analyses were adjusted for potential confounders. Results: 58% had SIRS, 11% developed POF, and 2.5% died. Early SIRS, persistent SIRS, and maximal SIRS score ≥ 3 were independently associated with higher risk of POF (p < 0.05). Mortality risk in POF was higher with two (33%, odds ratio [OR] = 10.8, 3.3-34.9) and three (48%, OR = 20.2, 5.9-68.6) organs failing, in comparison to single POF (4%). In subjects with multiple POF, mortality was higher when the cardiovascular and respiratory systems failed first or concurrently as compared to when the renal system failed first or concurrently with other organ (p < 0.05). In multivariate regression model, the number and sequence of organs affected in POF were associated with mortality (p < 0.05). Onset and duration of POF had no impact mortality. Conclusion: In AP patients with POF, the risk of mortality is influenced by the number, type, and sequence of organs affected. These results are useful for future revisions of AP severity classification systems

Worldwide trends in underweight and obesity from 1990 to 2022: a pooled analysis of 3663 population-representative studies with 222 million children, adolescents, and adults

Background Underweight and obesity are associated with adverse health outcomes throughout the life course. We estimated the individual and combined prevalence of underweight or thinness and obesity, and their changes, from 1990 to 2022 for adults and school-aged children and adolescents in 200 countries and territories. Methods We used data from 3663 population-based studies with 222 million participants that measured height and weight in representative samples of the general population. We used a Bayesian hierarchical model to estimate trends in the prevalence of different BMI categories, separately for adults (age ≥20 years) and school-aged children and adolescents (age 5–19 years), from 1990 to 2022 for 200 countries and territories. For adults, we report the individual and combined prevalence of underweight (BMI &lt;18·5 kg/m2) and obesity (BMI ≥30 kg/m2). For school&#x2;aged children and adolescents, we report thinness (BMI &lt;2 SD below the median of the WHO growth reference) and obesity (BMI &gt;2 SD above the median). Findings From 1990 to 2022, the combined prevalence of underweight and obesity in adults decreased in 11 countries (6%) for women and 17 (9%) for men with a posterior probability of at least 0·80 that the observed changes were true decreases. The combined prevalence increased in 162 countries (81%) for women and 140 countries (70%) for men with a posterior probability of at least 0·80. In 2022, the combined prevalence of underweight and obesity was highest in island nations in the Caribbean and Polynesia and Micronesia, and countries in the Middle East and north Africa. Obesity prevalence was higher than underweight with posterior probability of at least 0·80 in 177 countries (89%) for women and 145 (73%) for men in 2022, whereas the converse was true in 16 countries (8%) for women, and 39 (20%) for men. From 1990 to 2022, the combined prevalence of thinness and obesity decreased among girls in five countries (3%) and among boys in 15 countries (8%) with a posterior probability of at least 0·80, and increased among girls in 140 countries (70%) and boys in 137 countries (69%) with a posterior probability of at least 0·80. The countries with highest combined prevalence of thinness and obesity in school-aged children and adolescents in 2022 were in Polynesia and Micronesia and the Caribbean for both sexes, and Chile and Qatar for boys. Combined prevalence was also high in some countries in south Asia, such as India and Pakistan, where thinness remained prevalent despite having declined. In 2022, obesity in school-aged children and adolescents was more prevalent than thinness with a posterior probability of at least 0·80 among girls in 133 countries (67%) and boys in 125 countries (63%), whereas the converse was true in 35 countries (18%) and 42 countries (21%), respectively. In almost all countries for both adults and school-aged children and adolescents, the increases in double burden were driven by increases in obesity, and decreases in double burden by declining underweight or thinness. Interpretation The combined burden of underweight and obesity has increased in most countries, driven by an increase in obesity, while underweight and thinness remain prevalent in south Asia and parts of Africa. A healthy nutrition transition that enhances access to nutritious foods is needed to address the remaining burden of underweight while curbing and reversing the increase in obesit

Molecular Interactions Between ‘Candidatus Liberibacter Solanacearum’ and the Potato Psyllid, Bactericera Cockerelli, at the Gut Interface

‘Candidatus Liberibacter solanacearum’ (Lso), is an emerging and serious bacterial pathogen of solanaceous crops, and it can cause very damaging plant diseases (e.g., zebra chip in potatoes). Presently, two haplotypes of Lso (LsoA and LsoB) are present in North America; both are transmitted by potato psyllid, Bactericera cockerelli (Šulc), in a circulative and persistent manner. The psyllid gut is the first organ Lso encounters and could be a barrier for its transmission. However, the molecular mechanisms involved in Lso acquisition and transmission by the potato psyllid are largely unknown. This dissertation aims to understand the molecular interactions between Lso and the potato psyllid at the gut interface. First, the acquisition and transmission of LsoA or LsoB by potato psyllid were investigated. Second, I investigated the global transcriptional responses of the adult psyllid gut upon infection of the two Lso haplotypes using Illumina sequencing. Third, I explored whether any of these two Lso haplotypes triggered an apoptotic or autophagic response in the gut of the adult potato psyllid. The results indicated that LsoB relative abundance increased faster in the psyllid gut than that of LsoA, and LsoB had a shorter latent period than LsoA. In addition, the transcriptome analyses showed that each haplotype triggers a unique transcriptional response, with most of the distinct gene expression changes being elicited by the highly virulent LsoB. Furthermore, Lso might repress the apoptotic response in the adult psyllid gut by inducing the anti-apoptotic gene IAPP5.2 at the early stage of the infection, which may favor Lso acquisition and colonization of the psyllid gut cells. However, Lso might induce an autophagic response in the adult psyllid gut since the majority of autophagy-related genes (ATGs) are sensitive and responsive to the exposure or infection of both LsoA and LsoB. Further investigation needs to be conducted to deepen the study of autophagic response of potato psyllid to Lso infection. This dissertation is therefore an important contribution to a mechanistic understanding of Lso transmission, provides insights into understanding the adaptive significance of the immune response and has the potential to create new approaches for disrupting Lso transmission

Molecular Interactions Between ‘Candidatus Liberibacter Solanacearum’ and the Potato Psyllid, Bactericera Cockerelli, at the Gut Interface

‘Candidatus Liberibacter solanacearum’ (Lso), is an emerging and serious bacterial pathogen of solanaceous crops, and it can cause very damaging plant diseases (e.g., zebra chip in potatoes). Presently, two haplotypes of Lso (LsoA and LsoB) are present in North America; both are transmitted by potato psyllid, Bactericera cockerelli (Šulc), in a circulative and persistent manner. The psyllid gut is the first organ Lso encounters and could be a barrier for its transmission. However, the molecular mechanisms involved in Lso acquisition and transmission by the potato psyllid are largely unknown. This dissertation aims to understand the molecular interactions between Lso and the potato psyllid at the gut interface. First, the acquisition and transmission of LsoA or LsoB by potato psyllid were investigated. Second, I investigated the global transcriptional responses of the adult psyllid gut upon infection of the two Lso haplotypes using Illumina sequencing. Third, I explored whether any of these two Lso haplotypes triggered an apoptotic or autophagic response in the gut of the adult potato psyllid. The results indicated that LsoB relative abundance increased faster in the psyllid gut than that of LsoA, and LsoB had a shorter latent period than LsoA. In addition, the transcriptome analyses showed that each haplotype triggers a unique transcriptional response, with most of the distinct gene expression changes being elicited by the highly virulent LsoB. Furthermore, Lso might repress the apoptotic response in the adult psyllid gut by inducing the anti-apoptotic gene IAPP5.2 at the early stage of the infection, which may favor Lso acquisition and colonization of the psyllid gut cells. However, Lso might induce an autophagic response in the adult psyllid gut since the majority of autophagy-related genes (ATGs) are sensitive and responsive to the exposure or infection of both LsoA and LsoB. Further investigation needs to be conducted to deepen the study of autophagic response of potato psyllid to Lso infection. This dissertation is therefore an important contribution to a mechanistic understanding of Lso transmission, provides insights into understanding the adaptive significance of the immune response and has the potential to create new approaches for disrupting Lso transmission