bluuebunny/crossref_metadata_2025_split huggingface dataset:
Policies on Artificial Intelligence Chatbots Among Academic Publishers: A Cross-Sectional Audit
Authors: Bhavsar Daivat , Duffy Laura , Jo Hamin , Lokker Cynthia , Haynes R. Brian , Iorio Alfonso , Marusic Ana , Ng Jeremy Y. 
Published: June 2024

AbstractBackgroundArtificial intelligence (AI) chatbots are novel computer programs that can generate text or content in a natural language format. Academic publishers are adapting to the transformative role of AI chatbots in producing or facilitating scientific research. This study aimed to examine the policies established by scientific, technical, and medical academic publishers for defining and regulating the responsible authors’ use of AI chatbots.MethodsThis study performed a cross-sectional audit on the publicly available policies of 163 academic publishers, indexed as members of the International Association of the Scientific, Technical, and Medical Publishers (STM). Data extraction of publicly available policies on the webpages of all STM academic publishers was performed independently in duplicate with content analysis reviewed by a third contributor (September 2023 - December 2023). Data was categorized into policy elements, such as ‘proofreading’ and ‘image generation’. Counts and percentages of ‘yes’ (i.e., permitted), ‘no’, and ‘N/A’ were established for each policy element.ResultsA total of 56/163 (34.4%) STM academic publishers had a publicly available policy guiding the authors’ use of AI chatbots. No policy allowed authorship accreditations for AI chatbots (or other generative technology). Most (49/56 or 87.5%) required specific disclosure of AI chatbot use. Four policies/publishers placed a complete ban on the use of AI tools by authors.ConclusionsOnly a third of STM academic publishers had publicly available policies as of December 2023. A re-examination of all STM members in 12-18 months may uncover evolving approaches toward AI chatbot use with more academic publishers having a policy.
Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression
Authors: Forte Eleonora , Sanders Jes M. , Pla Indira , Kanchustambham Vijaya Lakshmi , Hollas Michael A. R. , Huang Che-Fan , Sanchez Aniel , Peterson Katrina N. , Melani Rafael D. , Huang Alexander , Polineni Praneet , Doll Julianna M. , Dietch Zachary , Kelleher Neil L. , Ladner Daniela P. 
Published: June 2024

AbstractCirrhosis, advanced liver disease, affects 2-5 million Americans. While most patients have compensated cirrhosis and may be fairly asymptomatic, many decompensate and experience life-threatening complications such as gastrointestinal bleeding, confusion (hepatic encephalopathy), and ascites, reducing life expectancy from 12 to less than 2 years. Among patients with compensated cirrhosis, identifying patients at high risk of decompensation is critical to optimize care and reduce morbidity and mortality. Therefore, it is important to preferentially direct them towards specialty care which cannot be provided to all patients with cirrhosis. We used discovery Top-down Proteomics (TDP) to identify differentially expressed proteoforms (DEPs) in the plasma of patients with progressive stages of liver cirrhosis with the ultimate goal to identify candidate biomarkers of disease progression. In this pilot study, we identified 209 DEPs across three stages of cirrhosis (compensated, compensated with portal hypertension, and decompensated), of which 115 derived from proteins enriched in the liver at a transcriptional level and discriminated the three stages of cirrhosis. Enrichment analyses demonstrated DEPs are involved in several metabolic and immunological processes known to be impacted by cirrhosis progression. We have preliminarily defined the plasma proteoform signatures of cirrhosis patients, setting the stage for ongoing discovery and validation of biomarkers for early diagnosis, risk stratification, and disease monitoring.Graphical AbstractHighlightsPerformed a pilot top-down LC-MS/MS analysis to identify proteoforms (PFRs) in the plasma of patients with 3 progressive stages of liver cirrhosis.Identified 2867 proteoforms (PFRs) and 209 differentially regulated proteoforms (DRPs) in the different stages of the disease.Identified DRP profiles able to potentially distinguish early from late stages of the disease, including 115 liver-derived DRPs.Fibrinogen alpha chain, haptoglobin, and Apo A-I are the proteins with the highest number of DRPs and represent potential candidate biomarkers of liver cirrhosis progression.
Scaling text de-identification using locally augmented ensembles
Authors: Murugadoss Karthik , Killamsetty Saivikas , Doddahonnaiah Deeksha , Iyer Nakul , Pencina Michael , Ferranti Jeffrey , Halamka John , Malin Bradley A. , Ardhanari Sankar 
Published: June 2024

AbstractThe natural language text in electronic health records (EHRs), such as clinical notes, often contains information that is not captured elsewhere (e.g., degree of disease progression and responsiveness to treatment) and, thus, is invaluable for downstream clinical analysis. However, to make such data available for broader research purposes, in the United States, personally identifiable information (PII) is typically removed from the EHR in accordance with the Privacy Rule of the Health Insurance Portability and Accountability Act (HIPAA). Automated de-identification systems that mimic human accuracy in identifier detection can enable access, at scale, to more diverse de-identified data sets thereby fostering robust findings in medical research to advance patient care.The best performing of such systems employ language models that require time and effort for retraining or fine tuning for newer datasets to achieve consistent results and revalidation on older datasets. Hence, there is a need to adapt text de-identification methods to datasets across health institutions. Given the success of foundational large language models (LLMs), such as ChatGPT, in a wide array of natural language processing (NLP) tasks, they seem a natural fit for identifying PII across varied datasets.In this paper, we introduce locally augmented ensembles, which adapt an existing PII detection ensemble method trained at one health institution to others by using institution-specific dictionaries to capture location specific PII and recover medically relevant information that was previously misclassified as PII. We augment an ensemble model created at Mayo Clinic and test it on a dataset of 15,716 clinical notes at Duke University Health System. We further compare the task specific fine tuned ensemble against LLM based prompt engineering solutions on the 2014 i2b2 and 2003 CoNLL NER datasets for prediction accuracy, speed and cost.On the Duke notes, our approach achieves increased recall and precision of 0.996 and 0.982 respectively compared to 0.989 and 0.979 respectively without the augmentation. Our results indicate that LLMs may require significant prompt engineering effort to reach the levels attained by ensemble approaches. Further, given the current state of technology, they are at least 3 times slower and 5 times more expensive to operate than the ensemble approach.
PCCA variant rs16957301 is a novel AKI risk genotype-specific for patients who receive ICI treatment: Real-world evidence from All of Us cohort
Authors: Wang Yanfei , Xiong Chenxi , Yu Weifeng , Zhou Minghao , Shugg Tyler A. , Hsu Fang-Chi , Eadon Michael T. , Su Jing , Song Qianqian 
Published: June 2024

ABSTRACTBackgroundImmune checkpoint inhibitors (ICIs) enhance the immune system’s ability to target and destroy cancer cells by blocking inhibitory pathways. Despite their efficacy, these treatments can trigger immune-related adverse events (irAEs), such as acute kidney injury (ICI-AKI), complicating patient management. The genetic predispositions to ICI-AKI are not well understood, necessitating comprehensive genomic studies to identify risk factors and improve therapeutic strategies.ObjectiveTo identify genetic predispositions for ICI-AKI using large-scale real-world data.MethodsA systematic literature search led to 14 candidate variants related to irAEs. We performed a candidate variant association study with these 14 variants using the All of Us cohort (AoU, v7, cutoff date: 7/1/2022). A cohort for cancer patients receiving ICI and a general cohort were established to evaluate ICI-AKI risk. Logistic regression, adjusted for sex, was used to evaluate the impact of each candidate genotype, separately for self-reported and ancestry-estimated race. Kaplan-Meier survival analysis assessed the genetic effects on AKI-free survival.ResultsThe ICI cohort (n=414) showed a one-year AKI incidence rate of 23.2%, significantly higher than the general cohort (6.5%, n=213,282). The rs16957301 variant (chr13:100324308, T>C) in the PCCA gene was a significant risk genotype for ICI-AKI among self-reported Caucasians (Beta=0.93, Bonferroni-corrected P-value=0.047) and ancestry estimated Caucasians (Beta = 0.94, Bonferroni-corrected P-value=0.044). Self-reported Caucasians with the rs16957301 risk genotypes (TC/CC) developed AKI significantly earlier (3.6 months) compared to the reference genotype (TT, 7.0 months, log-rank P=0.04). Consistent results were found in ancestry-estimated Caucasians. This variant did not present significant AKI risks in the general cohort (Beta: -0.008–0.035, FDR: 0.75–0.99).ConclusionReal-world evidence from the All of Us cohort suggests that, in Caucasians, PCCA variant rs16957301 is a novel AKI risk genotype specific to ICI treatment. Additional studies are warranted to validate rs16957301 as risk marker for AKI in Caucasian patients treated with ICIs and to assess its risk in other ancestral populations.
Added value of cell-free DNA over clinical and ultrasound information for diagnosing ovarian cancer
Authors: Vanderstichele Adriaan , Ceusters Jolien , Fischerova Daniela , Testa Antonia , Froyman Wouter , Landolfo Chiara , Heremans Ruben , Moro Francesca , Van Rompuy Anne-Sophie , Baert Thaïs , Van Nieuwenhuysen Els , Van Gorp Toon , Vergote Ignace , Busschaert Pieter , Venken Tom , Lambrechts Diether , Vermeesch Joris Robert , Bourne Tom , Coosemans An , Van Calster Ben , Timmerman Dirk 
Published: June 2024

ABSTRACTBackgroundWe previously proposed two cfDNA-based scores (genome-wide z-score and nucleosome score) as candidate non-invasive biomarkers to further improve pre-surgical diagnosis of ovarian malignancy. We aimed to investigate the added value of these cfDNA-based scores to the predictors of the ADNEX model (Assessment of Different NEoplasias in the adnexa) to estimate the risk of ovarian malignancy.Methods526 patients with an adnexal mass scheduled for surgery were consecutively recruited in three oncology referral centers. cfDNA-based scores were calculated in pre-operative plasma samples. Logistic regression models were fitted for ADNEX predictors alone and after adding cfDNA scores. We reported likelihood ratio tests, the area under the Receiver Operating Characteristic curve (AUC), sensitivity, specificity, and Net Benefit for thresholds between 5% and 40%.ResultsThe study included 272 benign, 86 borderline, 36 stage I invasive, 113 stage II-IV invasive, and 19 secondary metastatic tumors. The likelihood ratio tests for adding the cfDNA variables to the ADNEX model were statistically significant (p<0.001 for ADNEX without CA125, p=0.001 for ADNEX with CA125). The accompanying increases in AUC were 0.013 and 0.003. Net Benefit, sensitivity and specificity were similar for all models. The increase in Net Benefit at the recommended 10% threshold estimated risk of malignancy was 0.0017 and 0.0020, respectively. According to these results, adding cfDNA markers required at least 453 patients per additional true positive.ConclusionAlthough statistically significant, the addition of the cfDNA scores to the ADNEX model do not improve the ADNEX model in a clinically meaningful way.
Decreased central corpus callosum volume is associated with repetitive behaviours and motor difficulties in autistic children
Authors: Scaccabarozzi Gaia , Peruzzo Denis , Arrigoni Filippo , Ceccarelli Silvia Busti , Villa Laura , Mani Elisa , Maggioni Eleonora , Brambilla Paolo , Nobile Maria , Molteni Massimo , Crippa Alessandro 
Published: June 2024

AbstractAlong with the core characteristics of the condition, autistic individuals commonly experience motor coordination difficulties, potentially related to a reduced cortical connectivity. Being the largest human commissure, the corpus callosum (CC) plays an essential role in interhemispheric connectivity and has been often involved among autistic atypicalities. This study aimed to investigate the volumes of corpus callosum subregions in a group of drug-naïve, autistic children and to explore its possible associations with both core features and motor coordination skills. Thirty-five autistic children (2.5-12 years) were compared with a group of 35 closely IQ-matched, non-autistic peers. CC was identified and segmented into five subregions using Freesurfer. Callosal volumes were compared between the two groups and correlated with parental ratings of core autistic features as assessed by the Social Responsiveness Scale and with motor features as assessed by the Developmental Coordination Disorder Questionnaire. Associations between CC volume and Autism Diagnostic Observation Schedule scores were also explored in autistic participants. Autistic children showed a reduced volume of the central segment of the CC, in the context of a comparable CC total volume. This reduction appeared to be correlated with symptoms of restricted and repetitive behaviours in autistic children, and to parental ratings of autistic mannerisms and motor skills across participants. These findings expand the current knowledge about the neural mechanisms underlying autism, suggesting that the reduced connectivity through the CC might have implications for both core and motor features of autistic individuals.Lay SummaryDifferences in brain development have been widely outlined in autism. Exploring brain scans of 35 autistic and non-autistic children aged 2.5-12 years and closely matched for cognitive functioning, we found that the central part of the corpus callosum was smaller for the autistic group. This reduction was associated with the level of restricted and repetitive behaviours in autistic children, and to parental ratings of autistic mannerisms and motor coordination skills across participants. This work offers new empirical evidence that interhemispheric connectivity is atypical in autism and that the corpus callosum can be involved in the manifestation of both core and motor characteristics of autistic children.
Gender, religion and politics: a qualitative analysis on the role of women to a sustainable quality of work-life (QWL)
Authors: Akinwale Olayombo Elizabeth , Akinwale Olusegun Emmanuel , Kuye Owolabi Lateef 
Published: June 2024

Purpose Employability skills have transformed from the acquisition of university degrees to possessions of cognate skills other than only degrees that can help employees secure employment in contemporary work environments. This study evaluates essential skills that will prepare millennia of youths and graduates for employment in the present job market. The study investigated four major hypotheses to underscore the employability opportunities of graduates in challenging 21st-century work environments.Design/methodology/approach To clearly gain an understanding of women’s disparity in society, the study employed a qualitative approach to evaluate the incidence of gender prejudice in a men’s dominant world. The study utilised two distinguished sampling strategies, purposive and snowballing sampling techniques, which were deemed suitable and useful due to the nature of the study. The study recruited 42 participants by conducting semi-structured interview sessions for the study. The study employed a deductive approach to analyse the data obtained from participants. A thematic content analysis was used to take away prejudice and establish an overarching impression of the interviewed data. Atlas.ti was used to analyse the transcribed interview data from the participants to establish common themes from the surveyed informants.Findings The results of this investigation indicated that there is a deep-rooted trend of institutionalised men’s dominance in politics and religious leadership. Women perceived less representation and men dominated the two domains of existence in their local environment. The study established that women are optimistic about a turnaround narrative on gender equality in politics and religious leadership. They expressed their concern about strengthened public debate and campaigns on women’s representation, and against gender discrimination. The study further shows that women are influencing the ethical and moral sense for change against women’s neglect in society. They expressed their concerns against the selection of people into political offices for elected political posts and observed the peculiarity of political godfathers fixing their favourite men into those offices.Originality/value The study discovered that women are leading campaigns for their representation in politics as well as church leadership today. The novelty of this study bothering around two domains of women’s lives – politics and religion, in particular, church leadership. These have not been evidence before in a study.
Collaborative care for mental health of children and young people: a qualitative study of the experiences of mental health professionals
Authors: Fatima Sarrah , Brenisin Kristina , Doyle Isobel , Gathii Esther , Breen Kieran 
Published: June 2024

PurposeThe development and implementation of a provider collaborative (PC) represents an ambitious and complex piece of work to be delivered across a geographical area for a vulnerable patient cohort. The UK East Midlands Children and Adolescent Mental Health Services (CAMHS) PC was established in April 2021, and the current study aimed to explore the views of a variety of staff members about its functioning over the first twelve months. Specifically, it explored whether the intended aims has been achieved and identified the challenges that it faced during its introduction.Design/methodology/approachFeedback was collected through in-depth qualitative interviews and surveys with frontline (n = 20) and senior staff (n = 19) that were conducted to explore the experiences of a variety of stakeholders within the collaborative.FindingsTwo main themes were identified – the achievement of the key aims and the barriers to success. A thematic analysis has shown that whilst the aim of the PC is well intentioned and is generally welcomed by the multiple stakeholders across the geographical region, it is clear that changes are required in order to ensure the inception of an efficient care service that is able to achieve the ultimate goal of providing the ultimate goal of “right care at the right time”.Originality/valueThis is the first study, to the authors' knowledge, to explore collaborative working in CAMHs services. The study involved staff feedback from Phases 1 and 2 of a 4-years-long evaluation. The findings demonstrate the overall aims are being met as well as identifying areas of concern; this, in turn, allows the authors to develop a series of recommendations to implement and improve collaborative working before assessing their impact in the subsequent phase.
UICF: a new user-item composite filtering recommendation framework by leveraging temporal semantics
Authors: Wei Qingting , Liu Xing , Xian Daming , Xu Jianfeng , Liu Lan , Long Shiyang 
Published: June 2024

PurposeThe collaborative filtering algorithm is a classical and widely used approach in product recommendation systems. However, the existing algorithms rely mostly on common ratings of items and do not consider temporal information about items or user interests. To solve this problem, this study proposes a new user-item composite filtering (UICF) recommendation framework by leveraging temporal semantics.Design/methodology/approachThe UICF framework fully utilizes the time information of item ratings for measuring the similarity of items and takes into account the short-term and long-term interest decay for computing users’ latest interest degrees. For an item to be probably recommended to a user, the interest degrees of the user on all the historically rated items are weighted by their similarities with the item to be recommended and then added up to predict the recommendation degree.FindingsComprehensive experiments on the MovieLens and KuaiRec datasets for user movie recommendation were conducted to evaluate the performance of the proposed UICF framework. Experimental results show that the UICF outperformed three well-known recommendation algorithms Item-Based Collaborative Filtering (IBCF), User-Based Collaborative Filtering (UBCF) and User-Popularity Composite Filtering (UPCF) in the root mean square error (RMSE), mean absolute error (MAE) and F1 metrics, especially yielding an average decrease of 11.9% in MAE.Originality/valueA UICF recommendation framework is proposed that combines a time-aware item similarity model and a time-wise user interest degree model. It overcomes the limitations of common rating items and utilizes temporal information in item ratings and user interests effectively, resulting in more accurate and personalized recommendations.
Voting with the wallet: a principal–agent framework for the analysis of sustainable supply chains
Authors: Varella Miranda Bruno , Monteiro Guilherme Fowler A. , Oliveira Gustavo Magalhães de , Rodrigues Vinicius Picanço 
Published: June 2024

Purpose
This paper aims to investigate delegation decisions in supply chains, exploring the metaphor that consumers who make environmentally and socially responsible choices are equivalent to voters in an election.

Design/methodology/approach
This theoretical paper relies on the principles of agency theory to shed light on fundamental challenges that shape our ability to transform supply chains.

Findings
This paper unravels two puzzles linked to delegation decisions within sustainable supply chains. It shows that as firms adopt sustainable production systems, their ability to convey relevant information that convinces consumers to enter in a delegation relationship diminishes, ceteris paribus; and once a delegation relationship is established, complementarity within the dimensions of the contract is necessary to guarantee the delivery of sustainability attributes.

Research limitations/implications
The findings of this paper offer insights that can inspire empirical research on sustainable supply chain management.

Practical implications
Policymakers and entrepreneurs willing to incentivize the transformation of supply chains must think about the nature of the relationship between firms and consumers. This paper provides a metaphor that can help practitioners to reinterpret their role as providers or consumers of products and services with sustainability attributes.

Social implications
This paper provides insights that may enhance the understanding of how individual consumption decisions may contribute to transforming supply chains.

Originality/value
This paper expands the repertoire of theoretical tools that can be applied to study the emergence and resilience of sustainable supply chains.