CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.

Over a decade has passed since the development of the Hi-C method for genome-wide analysis of 3D genome organization. Hi-C utilizes next-generation sequencing (NGS) technology to generate large-scale chromatin interaction data, which has accumulated across a diverse range of species and cell types, particularly in eukaryotes. There is thus a growing need to streamline the process of Hi-C data analysis to utilize these data sets effectively. Hi-C generates data that are much larger compared to other NGS techniques such as chromatin immunoprecipitation sequencing (ChIP-seq) or RNA-seq, making the data reanalysis process computationally expensive. In an effort to bridge this resource gap, the 4D Nucleome (4DN) Data Portal has reanalyzed approximately 600 Hi-C data sets, allowing users to access and utilize the analyzed data. In this chapter, we provide detailed instructions for the implementation of the common workflow language (CWL)-based Hi-C analysis pipeline adopted by the 4DN Data Portal ecosystem. This reproducible and portable pipeline generates standard Hi-C contact matrices in formats such as .hic or .mcool from FASTQ files. It enables users to output their own Hi-C data in the same format as those registered in the 4DN Data portal, facilitating comparative analysis using data registered in the portal. Our custom-made scripts are available on GitHub at https://github.com/kuzobuta/4dn_cwl_pipeline .

Language Matters: Exploring Preferred Terms for Diverse Populations.

This article explores the significance of employing preferred terms and inclusive language in research practices concerning diverse populations. It highlights how inappropriate terminology can lead to labeling, stereotyping, and stigma, particularly for equity-denied groups. The study aimed to identify and analyze terminology preferences for diverse communities by major international organizations. Through a systematic environmental scan methodology, data were collected from 12 prominent organizations. The results indicate a concerted effort toward adopting inclusive language, with organizations favoring respectful and accurate terminology. For instance, terms like "people made vulnerable by systemic inequities" and "migrant workers" were preferred over outdated or stigmatizing alternatives. The discussion emphasizes the importance of identifying conflicting terms and trends in terminology preferences over time. We recommend prioritizing the use of preferred terms to promote respectful and accurate discourse, with a focus on person-centered language. Ultimately, the findings underscore the critical role of language in shaping perceptions and attitudes toward diverse communities, and advocate for continued efforts to promote inclusivity and equity in research, policy, and practice.

Enhancing lexical tone learning for second language speakers: effects of acoustic properties in Mandarin tone perception.

Understanding the challenges faced by second language (L2) learners in lexical tone perception is crucial for effective language acquisition. This study investigates the impact of exaggerated acoustic properties on facilitating Mandarin tone learning for English speakers. Using synthesized tone stimuli, we systematically manipulated pitch contours through three key modifications: expanding the fundamental frequency (F0), increasing F0 (female voice), and extending the overall duration. Our objectives were to assess the influence of F0 expansion, higher F0, longer duration, and varied syllables on Mandarin tone learning and generalization. Participants engaged in a non-adaptive trial-by-trial tone identification task. Mixed-effects logistic regression modeling was used to analyze accuracy across learning phases, acoustic factors, and tones. Findings reveal improvements in accuracy from training to testing and generalization phases, indicating the effectiveness of perceptual training to tone perception for adult English speakers. Tone 1 emerged as the easiest to perceive, while Tone 3 posed the most challenge, consistent with established hierarchies of tonal acquisition difficulty. Analysis of acoustic factors highlighted tone-specific effects. Expanded F0 was beneficial for the identification of Tone 2 and Tone 3 but posed challenges for Tone 1 and Tone 4. Additionally, longer durations also exhibited varied effects across tones, aiding in the identification of Tone 3 and Tone 4 but hindering Tone 1 identification. The higher F0 was advantageous for Tone 2 but disadvantageous for Tone 3. Furthermore, the syllable ma facilitated the identification of Tone 1 and Tone 2 but not for Tone 3 and Tone 4. These findings enhance our understanding of the role of acoustic properties in L2 tone perception and have implications for the design of effective training programs for second language acquisition.

The influence of home environment on 2-year-old Chinese children's language development: the mediating effect of executive function and the moderating effect of temperament.

Prior research highlighted the effect of home environment on the language development of young children. Recent research has mainly discussed the moderating effect of personality traits like temperament. Nevertheless, the precise mechanism about the relationship between home environments to children's language development remains incompletely understood. This study explored how home environment impacts the language development of 2-year-old toddlers and the role of temperament and executive function in this relationship. We used the Chinese Child Adaptive Behavior Scale, the Temperament Scale for 1-3 years old of toddlers and the Home Environment Scale for Infants' and Toddlers' families to assess children's language development, temperament, and home environment. Simultaneously, the research used the Stroop-like day-night task and the multiple location search task to evaluate children's executive function. A total of 117 2-year-old children as well as their parents were involved in the study. The results revealed that home environment significantly predicts children's language ability with executive function as a mediating role. Temperament dimensions including extraversion, independence, reactivity, and social inhibition play a moderating role between home environment and executive function. The findings contributed to the improved implementation of home education tailored to children with different temperament traits, offering effective support for the cognitive and language development of young children.

Unravelling the Silence: A Case Report on the Late Diagnosis of Language-Predominant Frontotemporal Dementia in a Rural Tertiary Hospital.

Frontotemporal dementia (FTD) is one of the significant neurological disorders that mostly affects over-60-year-old adults. In essence, FTD, which results from frontal and temporal lobe damages, manifests itself in several ways that include behavioral modifications as well as linguistic loss. These are behavioral variant FTD (bvFTD), primary progressive aphasia (PPA), or various movement disorders with genetic links. FTD takes, on average, three years to be diagnosed since there are no definitive diagnostic tests for this disease. MRI and PET scans use brain imaging techniques to observe damaged parts of the brain. The case study shows a lot of deep-seated language deficits and memory impairments, which ultimately point to the involvement of the temporal lobe. Understanding about FTD and early detection are crucial in enhancing intervention as well as management efforts.

Adapting Novel Augmented Reality Devices for Patient Simulations in Medical Education.

Extended reality (XR) simulations are becoming increasingly common in educational settings, particularly in medical education. Advancing XR devices to enhance these simulations is a booming field of research. This study seeks to understand the value of a novel, non-wearable mixed reality (MR) display during interactions with a simulated holographic patient, specifically in taking a medical history. Twenty-one first-year medical students at the University of North Carolina at Chapel Hill participated in the virtual patient (VP) simulations. On a five-point Likert scale, students overwhelmingly agreed with the statement that the simulations helped ensure they were progressing along learning objectives related to taking a patient history. However, they found that, at present, the simulations can only partially correct mistakes or provide clear feedback. This finding demonstrates that the novel hardware solution can help students engage in the activity, but the underlying software may need adjustment to attain sufficient pedagogical validity.

In the heart of Swahili: An exploration of data collection methods and corpus curation for natural language processing.

Swahili corpus is a dataset generated by collecting written Kiswahili sentences from different sectors that deals with Kiswahili documents. Corpus of intended language is needed in Natural Language Processing (NLP) task to fit algorithm in order to understand that language before training the model. Swahili corpus dataset generated contained 1,693,228 sentences with 39,639,824 words and 871,452 unique words. Corpus exported in text file format with storage size of 168 MB. These sentences collected from different sources in different categories as follows: - Health (AFYA), Business and Industries (BIASHARA), Parliament (BUNGE), Religion (DINI), Education (ELIMU), News (HABARI), Agriculture (KILIMO), Social Media (MITANDAO), Non-Governmental Organizations (MASHIRIKA YA KIRAIA), Government (SERIKALI), Laws (SHERIA) and Politics (SIASA). This abstract outlines the systematic data collection process employed for the creation of a Swahili corpus derived from multiple public websites and reports. The compilation of this corpus involves a meticulous and comprehensive approach to ensure the representation of diverse linguistic contexts and topics relevant to the Swahili language. The data collection process commenced with the identification of suitable sources across various domains, including news articles, health publications, online forums, and Governmental public reports. Websites and platforms with publicly available Swahili content were systematically crawled and archived to capture a broad spectrum of linguistic expressions. Furthermore, special attention was given to reputable sources to maintain the authenticity of the corpus and linguistic richness. The inclusion of diverse sources ensures that the corpus reflects the linguistic nuances inherent in different contexts and registers within the Swahili language. Additionally, efforts were made to incorporate variations in domain dialects, acknowledging the linguistic diversity present in Swahili. The potential for reusing this Swahili corpus is vast. Researchers, linguists, and language enthusiasts can leverage the diverse and extensive dataset for a multitude of applications, including NLP tasks such as sentiment analysis, textual data clustering, classifications tasks and machine translation. The Corpus can serve as training data for developing and evaluating NLP algorithms, including part-of-speech tagging, and named entity recognition. Also, text mining techniques can be applied to corpus and enable researchers to extract valuable insights, identify patterns, and discover knowledge from large textual datasets.

Exercise and Language Performance in Healthy Aging, Stroke and Neurodegenerative Conditions: a Scoping Review.

Background: While the benefits of exercise on cognitive functions have already been reviewed, little is known about the impact of exercise on language performance. This scoping review was conducted to identify existing evidence on exercise-induced changes in language performance in healthy aging individuals and adults with stroke or neurodegenerative conditions. Methods & Results: Using the Arksey and O'Malley framework, 29 studies were included. Eleven studies in healthy aging indicated enhanced language performance, with 72.72% having significant improvement in semantic/phonological Verbal Fluency (VF) following exercise. Among 18 studies on older adults with stroke or neurodegenerative conditions, 11 reported better language performance, with 44.44% having significant improvement in picture naming/description and semantic/phonological VF by exercise. The seven remaining studies reported no significant change in language performance in persons with stroke or neurodegenerative conditions. Conclusion: Overall, exercise interventions showed improvement in language performance in healthy aging, while selective enhancement was shown for language performance in persons with either stroke or neurodegenerative conditions.

Exploring L2 educators' training and professional development needs in VR English language learning.

Virtual Reality technology has garnered increasing attention and utilization within language education. The research explored the multifaceted challenges and opportunities L2 educators encounter in Iran when integrating VR technology into language instruction and when focusing on educators' perceptions of VR technology and the training gaps they identify. The researchers adopted a qualitative case study design. The selection of cases involved purposive sampling. The study included a total number of 23 L2 educators from language institutions in Iran. In the current study the researchers administered a qualitative case study design, focusing on the experiences of educators in real-world settings where VR technology was being used or considered for language instruction. Research findings reveal that educators encounter significant training gaps related to VR technology, emphasizing the critical need for comprehensive training programs. The implications of this study underscore the importance of equipping educators with the knowledge and skills required to harness VR's potential for enhancing language instruction. Training programs should encompass technical proficiency, pedagogical competence, administrative navigation, collaborative learning, alignment with learning goals, and ongoing professional development. By addressing these multifaceted needs, institutions and organizations can empower educators to leverage VR effectively, fostering engaging and effective language learning experiences for students.

Enjoyment in foreign language learning: A systematic review.

In recent years, research on enjoyment in foreign language (FL) learning has flourished. To help illuminate the existing scope of inquiry and guide future research, this paper presents a systematic review of 118 empirical studies on FL learning enjoyment published between 2014 and 2023. Each study was coded according to its research context, methodological features, and research focus. The results indicate (1) a heavy focus on adult English as a foreign language (EFL) learners whose first languages are Chinese or Persian within traditional classroom learning settings; (2) a strong preference for quantitative methods; and (3) a prominent focus on enjoyment's antecedents and effects. Drawing upon these findings, we recommend that future research (1) addresses the experiences of language learners from diverse demographic backgrounds in a wider variety of learning settings; (2) applies multimodal methods to thoroughly assess the experience of enjoyment from both objective and subjective perspectives; and (3) explores the nature of enjoyable teacher-student or student-student socio-emotional interaction in greater depth.

Socratic Artificial Intelligence Learning (SAIL): The Role of a Virtual Voice Assistant in Learning Orthopedic Knowledge.

OBJECTIVE: We hypothesized that learning through multiple sensory modalities would improve knowledge recall and recognition in orthopedic surgery residents and medical students. DESIGN: We developed a virtual study assistant, named Socratic Artificial Intelligence Learning (SAIL), based on a custom-built natural language processing algorithm. SAIL draws from practice questions approved by the American Board of Orthopaedic Surgery and quizzes users through a conversational, voice-enabled Web interface. We performed a randomized controlled study using a within-subjects, repeated measures design. SETTING: Participants first took a pretest to assess their baseline knowledge. They then underwent 10 days of spaced repetition training with practice questions using 3 modalities: oral response, typed response, and multiple-choice. Recall and recognition of the practiced knowledge were assessed via a post-test administered on the first day, first week, and 2 months after the training period. PARTICIPANTS: Twenty-four volunteers, who were medical students and orthopedic surgery residents at multiple US medical institutions. RESULTS: The oral, typed, and multiple-choice modalities produced similar recall and recognition rates. Although participants preferred using the traditional multiple-choice modality to study for standardized examinations, many were interested in supplementing their study routine with SAIL and believe that SAIL may improve their performance on written and oral examinations. CONCLUSIONS: SAIL is not inferior to the multiple-choice modality for learning orthopedic core knowledge. These results indicate that SAIL can be used to supplement traditional study methods. COMPETENCIES: medical knowledge; practice-based learning and improvement.

The Impact of Collaborative Documentation on Person-Centered Care: Textual Analysis of Clinical Notes.

Background: Collaborative documentation (CD) is a behavioral health practice involving shared writing of clinic visit notes by providers and consumers. Despite widespread dissemination of CD, research on its effectiveness or impact on person-centered care (PCC) has been limited. Principles of PCC planning, a recovery-based approach to service planning that operationalizes PCC, can inform the measurement of person-centeredness within clinical documentation. Objective: This study aims to use the clinical informatics approach of natural language processing (NLP) to examine the impact of CD on person-centeredness in clinic visit notes. Using a dictionary-based approach, this study conducts a textual analysis of clinic notes from a community mental health center before and after staff were trained in CD. Methods: This study used visit notes (n=1981) from 10 providers in a community mental health center 6 months before and after training in CD. LIWC-22 was used to assess all notes using the Linguistic Inquiry and Word Count (LIWC) dictionary, which categorizes over 5000 linguistic and psychological words. Twelve LIWC categories were selected and mapped onto PCC planning principles through the consensus of 3 domain experts. The LIWC-22 contextualizer was used to extract sentence fragments from notes corresponding to LIWC categories. Then, fixed-effects modeling was used to identify differences in notes before and after CD training while accounting for nesting within the provider. Results: Sentence fragments identified by the contextualizing process illustrated how visit notes demonstrated PCC. The fixed effects analysis found a significant positive shift toward person-centeredness; this was observed in 6 of the selected LIWC categories post CD. Specifically, there was a notable increase in words associated with achievement (ß=.774, P<.001), power (ß=.831, P<.001), money (ß=.204, P<.001), physical health (ß=.427, P=.03), while leisure words decreased (ß=-.166, P=.002). Conclusions: By using a dictionary-based approach, the study identified how CD might influence the integration of PCC principles within clinical notes. Although the results were mixed, the findings highlight the potential effectiveness of CD in enhancing person-centeredness in clinic notes. By leveraging NLP techniques, this research illuminated the value of narrative clinical notes in assessing the quality of care in behavioral health contexts. These findings underscore the promise of NLP for quality assurance in health care settings and emphasize the need for refining algorithms to more accurately measure PCC.

Evaluating a Natural Language Processing-Driven, AI-Assisted International Classification of Diseases, 10th Revision, Clinical Modification, Coding System for Diagnosis Related Groups in a Real Hospital Environment: Algorithm Development and Validation Study.

BACKGROUND: International Classification of Diseases codes are widely used to describe diagnosis information, but manual coding relies heavily on human interpretation, which can be expensive, time consuming, and prone to errors. With the transition from the International Classification of Diseases, Ninth Revision, to the International Classification of Diseases, Tenth Revision (ICD-10), the coding process has become more complex, highlighting the need for automated approaches to enhance coding efficiency and accuracy. Inaccurate coding can result in substantial financial losses for hospitals, and a precise assessment of outcomes generated by a natural language processing (NLP)-driven autocoding system thus assumes a critical role in safeguarding the accuracy of the Taiwan diagnosis related groups (Tw-DRGs). OBJECTIVE: This study aims to evaluate the feasibility of applying an International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM), autocoding system that can automatically determine diagnoses and codes based on free-text discharge summaries to facilitate the assessment of Tw-DRGs, specifically principal diagnosis and major diagnostic categories (MDCs). METHODS: By using the patient discharge summaries from Kaohsiung Medical University Chung-Ho Memorial Hospital (KMUCHH) from April 2019 to December 2020 as a reference data set we developed artificial intelligence (AI)-assisted ICD-10-CM coding systems based on deep learning models. We constructed a web-based user interface for the AI-assisted coding system and deployed the system to the workflow of the certified coding specialists (CCSs) of KMUCHH. The data used for the assessment of Tw-DRGs were manually curated by a CCS with the principal diagnosis and MDC was determined from discharge summaries collected at KMUCHH from February 2023 to April 2023. RESULTS: Both the reference data set and real hospital data were used to assess performance in determining ICD-10-CM coding, principal diagnosis, and MDC for Tw-DRGs. Among all methods, the GPT-2 (OpenAI)-based model achieved the highest F1-score, 0.667 (F1-score 0.851 for the top 50 codes), on the KMUCHH test set and a slightly lower F1-score, 0.621, in real hospital data. Cohen κ evaluation for the agreement of MDC between the models and the CCS revealed that the overall average κ value for GPT-2 (κ=0.714) was approximately 12.2 percentage points higher than that of the hierarchy attention network (κ=0.592). GPT-2 demonstrated superior agreement with the CCS across 6 categories of MDC, with an average κ value of approximately 0.869 (SD 0.033), underscoring the effectiveness of the developed AI-assisted coding system in supporting the work of CCSs. CONCLUSIONS: An NLP-driven AI-assisted coding system can assist CCSs in ICD-10-CM coding by offering coding references via a user interface, demonstrating the potential to reduce the manual workload and expedite Tw-DRG assessment. Consistency in performance affirmed the effectiveness of the system in supporting CCSs in ICD-10-CM coding and the judgment of Tw-DRGs.

Neural Conversational Agent for Weight Loss Counseling: Protocol for an Implementation and Feasibility Study.

BACKGROUND: Obesity is a common, serious and costly chronic disease. Current clinical practice guidelines recommend that providers augment the longitudinal care of people living with obesity with consistent support for the development of self-efficacy and motivation to modify their lifestyle behaviors. Lifestyle behavior change aligns with the goals of motivational interviewing (MI), a client-centered yet directive counseling modality. However, training health care providers to be proficient in MI is expensive and time-consuming, resulting in a lack of trained counselors and limiting the widespread adoption of MI in clinical practice. Artificial intelligence (AI) counselors accessible via the internet can help circumvent these barriers. OBJECTIVE: The primary objective is to explore the feasibility of conducting unscripted MI-consistent counseling using Neural Agent for Obesity Motivational Interviewing (NAOMI), a large language model (LLM)-based web app for weight loss counseling. The secondary objectives are to test the acceptability and usability of NAOMI's counseling and examine its ability to shift motivational precursors in a sample of patients with overweight and obesity recruited from primary care clinics. METHODS: NAOMI will be developed based on recent advances in deep learning in four stages. In stages 1 and 2, NAOMI will be implemented using an open-source foundation LLM and (1) few-shot learning based on a prompt with task-specific instructions and (2) domain adaptation strategy based on fine-tuning LLM using a large corpus of general psychotherapy and MI treatment transcripts. In stages 3 and 4, we will refine the best of these 2 approaches. Each NAOMI version will be evaluated using a mixed methods approach in which 10 adults (18-65 years) meeting the criteria for overweight or obesity (25.0≥BMI≤39.9) interact with NAOMI and provide feedback. NAOMI's fidelity to the MI framework will be assessed using the Motivational Interviewing Treatment Integrity scale. Participants' general perceptions of AI conversational agents and NAOMI specifically will be assessed via Pre- and Post-Interaction Questionnaires. Motivational precursors, such as participants' confidence, importance, and readiness for changing lifestyle behaviors (eg, diet and activity), will be measured before and after the interaction, and 1 week later. A qualitative analysis of changes in the measures of perceptions of AI agents and counselors and motivational precursors will be performed. Participants will rate NAOMI's usability and empathic skills post interaction via questionnaire-based assessments along with providing feedback about their experience with NAOMI via a qualitative interview. RESULTS: NAOMI (version 1.0) has been developed. Participant recruitment will commence in September 2024. Data collection activities are expected to conclude in May 2025. CONCLUSIONS: If proven effective, LLM-based counseling agents can become a cost-effective approach for addressing the obesity epidemic at a public health level. They can also have a broad, transformative impact on the delivery of MI and other psychotherapeutic treatment modalities extending their reach and broadening access. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/60361.

Evaluating the Capabilities of Generative AI Tools in Understanding Medical Papers: Qualitative Study.

BACKGROUND: Reading medical papers is a challenging and time-consuming task for doctors, especially when the papers are long and complex. A tool that can help doctors efficiently process and understand medical papers is needed. OBJECTIVE: This study aims to critically assess and compare the comprehension capabilities of large language models (LLMs) in accurately and efficiently understanding medical research papers using the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) checklist, which provides a standardized framework for evaluating key elements of observational study. METHODS: The study is a methodological type of research. The study aims to evaluate the understanding capabilities of new generative artificial intelligence tools in medical papers. A novel benchmark pipeline processed 50 medical research papers from PubMed, comparing the answers of 6 LLMs (GPT-3.5-Turbo, GPT-4-0613, GPT-4-1106, PaLM 2, Claude v1, and Gemini Pro) to the benchmark established by expert medical professors. Fifteen questions, derived from the STROBE checklist, assessed LLMs' understanding of different sections of a research paper. RESULTS: LLMs exhibited varying performance, with GPT-3.5-Turbo achieving the highest percentage of correct answers (n=3916, 66.9%), followed by GPT-4-1106 (n=3837, 65.6%), PaLM 2 (n=3632, 62.1%), Claude v1 (n=2887, 58.3%), Gemini Pro (n=2878, 49.2%), and GPT-4-0613 (n=2580, 44.1%). Statistical analysis revealed statistically significant differences between LLMs (P<.001), with older models showing inconsistent performance compared to newer versions. LLMs showcased distinct performances for each question across different parts of a scholarly paper-with certain models like PaLM 2 and GPT-3.5 showing remarkable versatility and depth in understanding. CONCLUSIONS: This study is the first to evaluate the performance of different LLMs in understanding medical papers using the retrieval augmented generation method. The findings highlight the potential of LLMs to enhance medical research by improving efficiency and facilitating evidence-based decision-making. Further research is needed to address limitations such as the influence of question formats, potential biases, and the rapid evolution of LLM models.

Improving Prediction of Complications Post-Proton Therapy in Lung Cancer Using Large Language Models and Meta-Analysis.

PURPOSE: This study enhances the efficiency of predicting complications in lung cancer patients receiving proton therapy by utilizing large language models (LLMs) and meta-analytical techniques for literature quality assessment. MATERIALS AND METHODS: We integrated systematic reviews with LLM evaluations, sourcing studies from Web of Science, PubMed, and Scopus, managed via EndNote X20. Inclusion and exclusion criteria ensured literature relevance. Techniques included meta-analysis, heterogeneity assessment using Cochran's Q test and I2 statistics, and subgroup analyses for different complications. Quality and bias risk were assessed using the PROBAST tool and further analyzed with models such as ChatGPT-4, Llama2-13b, and Llama3-8b. Evaluation metrics included AUC, accuracy, precision, recall, F1 score, and time efficiency (WPM). RESULTS: The meta-analysis revealed an overall effect size of 0.78 for model predictions, with high heterogeneity observed (I2 = 72.88%, P < 0.001). Subgroup analysis for radiation-induced esophagitis and pneumonitis revealed predictive effect sizes of 0.79 and 0.77, respectively, with a heterogeneity index (I2) of 0%, indicating that there were no significant differences among the models in predicting these specific complications. A literature assessment using LLMs demonstrated that ChatGPT-4 achieved the highest accuracy at 90%, significantly outperforming the Llama3 and Llama2 models, which had accuracies ranging from 44% to 62%. Additionally, LLM evaluations were conducted 3229 times faster than manual assessments were, markedly enhancing both efficiency and accuracy. The risk assessment results identified nine studies as high risk, three as low risk, and one as unknown, confirming the robustness of the ChatGPT-4 across various evaluation metrics. CONCLUSION: This study demonstrated that the integration of large language models with meta-analysis techniques can significantly increase the efficiency of literature evaluations and reduce the time required for assessments, confirming that there are no significant differences among models in predicting post proton therapy complications in lung cancer patients.

Using Advanced AI to Improve Predictions of Treatment Side Effects in Lung Cancer: This research uses cutting-edge artificial intelligence (AI) techniques, including large language models like ChatGPT-4, to better predict potential side effects in lung cancer patients undergoing proton therapy. By analyzing extensive scientific literature quickly and accurately, this approach has proven to enhance the evaluation process, making it faster and more reliable in foreseeing complications from treatments.

The Accurate Prediction of Antibody Deamidations by Combining High-Throughput Automated Peptide Mapping and Protein Language Model-Based Deep Learning.

Therapeutic antibodies such as monoclonal antibodies (mAbs), bispecific and multispecific antibodies are pivotal in therapeutic protein development and have transformed disease treatments across various therapeutic areas. The integrity of therapeutic antibodies, however, is compromised by sequence liabilities, notably deamidation, where asparagine (N) and glutamine (Q) residues undergo chemical degradations. Deamidation negatively impacts the efficacy, stability, and safety of diverse classes of antibodies, thus necessitating the critical need for the early and accurate identification of vulnerable sites. In this article, a comprehensive antibody deamidation-specific dataset (n = 2285) of varied modalities was created by using high-throughput automated peptide mapping followed by supervised machine learning to predict the deamidation propensities, as well as the extents, throughout the entire antibody sequences. We propose a novel chimeric deep learning model, integrating protein language model (pLM)-derived embeddings with local sequence information for enhanced deamidation predictions. Remarkably, this model requires only sequence inputs, eliminating the need for laborious feature engineering. Our approach demonstrates state-of-the-art performance, offering a streamlined workflow for high-throughput automated peptide mapping and deamidation prediction, with the potential of broader applicability to other antibody sequence liabilities.

Gamify4LexAmb: a gamification-based approach to address lexical ambiguity in natural language requirements.

Ambiguity is a common challenge in specifying natural language (NL) requirements. One of the reasons for the occurrence of ambiguity in software requirements is the lack of user involvement in requirements elicitation and inspection phases. Even if they get involved, it is hard for them to understand the context of the system, and ultimately unable to provide requirements correctly due to a lack of interest. Previously, the researchers have worked on ambiguity avoidance, detection, and removal techniques in requirements. Still, less work is reported in the literature to actively engage users in the system to reduce ambiguity at the early stages of requirements engineering. Traditionally, ambiguity is addressed during inspection when requirements are initially specified in the SRS document. Resolving or removing ambiguity during the inspection is time-consuming, costly, and laborious. Also, traditional elicitation techniques have limitations like lack of user involvement, inactive user participation, biases, incomplete requirements, etc. Therefore, in this study, we have designed a framework, Gamif ication for Lex ical Amb iguity (Gamify4LexAmb), for detecting and reducing ambiguity using gamification. Gamify4LexAmb engages users and identifies lexical ambiguity in requirements, which occurs in polysemy words where a single word can have several different meanings. We have also validated Gamify4LexAmb by developing an initial prototype. The results show that Gamify4LexAmb successfully identifies lexical ambiguities in given requirements by engaging users in requirements elicitation. In the next part of our research, an industrial case study will be performed to understand the effects of gamification on real-time data for detecting and reducing NL ambiguity.