bluuebunny/crossref_metadata_2025_split huggingface dataset:
New implementation of data standards for AI in oncology. Experience from the EuCanImage project
Authors: García-Lezana Teresa , Bobowicz Maciej , Frid Santiago , Rutherford Michael , Recuero Mikel , Riklund Katrine , Cabrelles Aldar , Rygusik Marlena , Fromont Lauren , Francischello Roberto , Neri Emanuele , Capella Salvador , Navarro Arcadi , Prior Fred , Bona Jonathan , Nicolas Pilar , Starmans Martijn P. A. , Lekadir Karim , Rambla Jordi ,   EuCanImage Consortium
Published: March 2024

ABSTRACTBackgroundAn unprecedented amount of personal health data, with the potential to revolutionise precision medicine, is generated at healthcare institutions worldwide. The exploitation of such data using artificial intelligence relies on the ability to combine heterogeneous, multicentric, multimodal and multiparametric data, as well as thoughtful representation of knowledge and data availability. Despite these possibilities, significant methodological challenges and ethico-legal constraints still impede the real-world implementation of data models.Technical detailsThe EuCanImage is an international consortium aimed at developing AI algorithms for precision medicine in oncology and enabling secondary use of the data based on necessary ethical approvals. The use of well-defined clinical data standards to allow interoperability was a central element within the initiative. The consortium is focused on three different cancer types and addresses seven unmet clinical needs. We have conceived and implemented an innovative process to capture clinical data from hospitals, transform it into the newly developed EuCanImage data models and then store the standardised data in permanent repositories. This new workflow combines recognized software (REDCap for data capture), data standards (FHIR for data structuring) and an existing repository (EGA for permanent data storage and sharing), with newly developed custom tools for data transformation and quality control purposes (ETL pipeline, QC scripts) to complement the gaps.ConclusionThis article synthesises our experience and procedures for healthcare data interoperability, standardisation and reproducibility.
Ambulatory Blood Pressure and Number of Subclinical Target Organ Injury Markers in Youth: The SHIP AHOY Study
Authors: Hamdani Gilad , Urbina Elaine M. , Daniels Stephen R. , Falkner Bonita E. , Ferguson Michael A. , Flynn Joseph T. , Hanevold Coral D. , Ingelfinger Julie R. , Khoury Philip R. , Lande Marc B. , Meyers Kevin E. , Samuels Joshua , Mitsnefes Mark 
Published: March 2024

AbstractBackgroundHypertension in adolescence is associated with subclinical target organ injury (TOI). We aimed to determine whether different blood pressure (BP) thresholds were associated with increasing number of TOI markers in healthy adolescents.Methods244 participants (mean age 15.5±1.8 years, 60.1% male) were studied. Participants were divided based on both systolic clinic and ambulatory BP (ABP), into low- (<75thpercentile), mid- (75th-90thpercentile) and high-risk (>90thpercentile) groups. TOI assessments included left ventricular mass, systolic and diastolic function, and vascular stiffness. The number of TOI markers for each participant was calculated. A multivariable general linear model was constructed to evaluate the association of different participant characteristics with higher numbers of TOI markers.Results47.5% of participants had at least one TOI marker: 31.2% had one, 11.9% two, 3.7% three, and 0.8% four. The number of TOI markers increased according to the BP risk groups: the percentage of participants with more than one TOI in the low-, mid-, and high groups based on clinic BP was 6.7%, 19.1%, and 21.8% (p=0.02), and based on ABP was 9.6%, 15.8%, and 32.2% (p<0.001). In a multivariable regression analysis, both clinic BP percentile and ambulatory SBP index were independently associated with the number of TOI markers. When both clinic and ABP were included in the model, only the ambulatory SBP index was significantly associated with the number of markers.ConclusionHigh SBP, especially when assessed by ABPM, was associated with an increasing number of subclinical cardiovascular injury markers in adolescents.
The impact of a conditional financial incentive on linkage to HIV care: Findings from the HITS cluster randomized clinical trial in rural South Africa
Authors: Kim Hae-Young , Inghels Maxime , Mathenjwa Thulile , Shahmanesh Maryam , Seeley Janet , Matthews Phillippa , McGrath Nuala , Adeagbo Oluwafemi , Gareta Dickman , Yapa H. Manisha , Zuma Thembelihle , Dobra Adrian , Bärnighausen Till , Tanser Frank 
Published: March 2024

AbstractIntroductionHIV elimination requires innovative approaches to ensure testing and immediate treatment provision. We investigated the effectiveness of conditional financial incentives on increasing linkage to HIV care in a 2×2 factorial cluster randomized controlled trial-Home-Based Intervention to Test and Start (HITS) - in rural South Africa.MethodsOf 45 communities in uMkhanyakude, KwaZulu-Natal, 16 communities were randomly assigned to the arms to receive financial incentives for home-based HIV counseling and testing (HBHCT) and linkage to care within 6 weeks (R50 [US$3] food voucher each) and 29 communities to the arms without financial incentives. We examined linkage to care (i.e., initiation or resumption of antiretroviral therapy after >3 months of care interruption) at local clinics within 6 weeks of a home visit, the eligibility period to receive the second financial incentive. Linkage to care was ascertained from individual clinical records. Intention-to-treat analysis (ITT) was performed using modified Poisson regression with adjustment for receiving another intervention (i.e., male-targeted HIV-specific decision support app) and clustering of standard errors at the community level.ResultsAmong 13,894 eligible men (i.e., ≥15 years and resident in the 45 communities), 20.7% received HBHCT, which resulted in 122 HIV-positive tests. Of these, 27 linked to care within 6 weeks of HBHCT. Additionally, of eligible men who did not receive HBHCT, 66 linked to care. In the ITT analysis, the proportion of linkage to care among men did not differ in the arms which received financial incentives and those without financial incentives (adjusted Risk Ratio [aRR]=0.78, 95% CI: 0.51-1.21). Among 19,884 eligible women, 29.1% received HBHCT, which resulted in 375 HIV-positive tests. Of these, 75 linked to care. Among eligible women who did not receive HBHCT, 121 linked to care within 6 weeks. Women in the financial incentive arms had a significantly higher probability of linkage to care, compared to those in the arms without financial incentives (aRR=1.50; 95% CI: 1.03-2.21).ConclusionWhile a small once-off financial incentive did not increase linkage to care among men during the eligibility period of 6 weeks, it significantly improved linkage to care among women over the same period.Clinical Trial Number:ClinicalTrials.gov#NCT03757104
Accelerating precision medicine: a proposed framework for large-scale multiomics data integrity, interoperability, analysis, and collaboration in biomedical discovery
Authors: Sriram Vivek , Conard Ashley Mae , Rosenberg Ilyana , Kim Dokyoon , Hall Amanda K 
Published: March 2024

ABSTRACTObjectiveTo identify and define a process and framework for biomedical discovery research. Our study aim was to characterize the biomedical discovery lifecycle across data modalities and professional stakeholders involved in biomedical research to address the multiomics data challenges of precision medicine.Materials and MethodsWe recruited fifteen professionals from various biomedical roles and industries to participate in 60-minute semi-structured interviews, which involved an assessment of common challenges, needs, tasks, and data management methods and a brainstorm exercise to validate each professional’s biomedical research process. We applied a qualitative analysis of individual interviews using a constant comparative approach for emerging themes.ResultsWe found a general process of biomedical discovery across all participants that consisted of four key stages: data plan, data integrity, data analysis, and data-driven discovery. Within each stage of the process, participants highlighted their challenges and needs and emphasized the importance of data integrity and interoperability, particularly during data hand-offs. The process extends across three general levels of data, including non-human, non-clinical human, and clinical human data, to define an overarching framework for biomedical discovery research.ConclusionsThe proposed framework provides researchers with an opportunity to align workstreams and converge on a single process to conduct biomedical research across stakeholders and data types. Key opportunities were found that can be explored in the health technology space, including generative artificial intelligence, to help tackle multiomics data challenges to advance precision medicine.
Postpartum suicidal ideation in Austria and Germany during the COVID-19 pandemic
Authors: Florea C. , Preiß J. , Angerer M. , Schabus M. 
Published: March 2024

AbstractIntroductionPostpartum suicidal ideation is a significant concern, as it poses a risk for future suicide attempts, particularly in high income countries, where suicide ranks among the leading causes of death for postpartum mothers. The literature indicates a global average prevalence of postpartum suicidal ideation of approximately 7%, but for Austria and Germany there are few studies on this subject.MethodsIn a web-based survey for Austrian and German mothers of children born during the COVID-19 pandemic, several measures of mental health (depression, stress), social support and other parenting and pandemic-related questions were assessed in 1964 mothers. Based on the answers for the last item of the Edinburgh Postpartum Depression Scale, the suicidality risk and the presence or absence of suicidal ideation were computed. Furthermore, possible risk or protective factors for suicidality were investigated.ResultsThe prevalence of suicidal ideation was 7.3%, which is in the range of the global prevalence reported in the literature, but two times higher than previous reports on German mothers. The three strongest risk factors for suicidal ideation were (i) high levels of stress (increased risk by 350%), (ii) a lack of perceived social support (increased risk by 265%), and (iii) a perceived negative effect of the pandemic on the relationship with the partner (increased risk by 223%). Not receiving help from family and friends, having a lower income, and feeling negatively impacted by the pandemic also significantly increased the risk of suicidal ideation.Discussion and conclusionThe results indicate a higher prevalence of suicidality than previously reported in German mothers, and confirm the risk factors previously associated with depression and suicidality. These risk and protective factors could be targets of social and public health policies, while the first step should be a general screening program for suicidality in this population group.
Smad4and TGF-β1 dependent gene expression biomarkers in conditional intestinal adenoma, organoids and colorectal cancer
Authors: Surakhy Mirvat , Matheson Julia , Barnes David , Carter Emma J. , Hughes Jennifer , Bühnemann Claudia , Sanegre Sabina , Morreau Hans , Metz Paul , Imianowski Charlotte J. , Hassan A. Bassim 
Published: March 2024

AbstractTGF-β ligand activation suppresses cell growth yet can paradoxically and potently promote cancer invasion and metastasis depending on downstream pathway mutational context. Here, we evaluated the basis of this observation in conditional murine intestinal adenoma models with and without loss of Mothers against decapentaplegic homolog 4 (Smad4), with the aim of identifying TGF-β-BMP-SMAD4 pathway dependent gene expression biomarkers for translational application. ConditionalLgr5-CreERT2activation inApcfl/flSmad4fl/flresulted in adenoma formation with recombined homozygote floxed alleles(ApcΔ/ΔSmad4Δ/Δ). The adenoma phenotype was discordant, with a reduced small intestinal adenoma burden yet development of large non-metastatic caecal adenoma with nuclear localisation of phospho-Smad2/3. DerivedApcΔ/ΔSmad4Δ/Δadenoma organoids resisted TGF-β1 dose dependent growth arrest and cell death (IC50534pM) compared toApcΔ/ΔSmad4+/+(IC 24pM). TGF-β1 (390pM) modified adenoma mRNA expression (bulk RNA-Seq) most significantly forId1lowandSpp1highinApcΔ/ΔSmad4Δ/Δ. Single cell RNAseq of caecal adenoma identified expansion ofLgr5low, Pak3highandId1lowprogenitor populations inApcΔ/ΔSmad4Δ/Δ. Of the 76Smad4and TGF-β1 dependent genes identified in adenoma organoids, 7 human equivalent genes were also significantly differentially expressed in colorectal cancer, includingID1low,SPP1highandPAK3highthat also correlated with poorer survival (TCGA cohorts). Murine conditional models identifiedSmad4loss of function mRNA expression biomarkers that require further evaluation as functional classifiers of colorectal cancer subtypes.
The Origin of Movement Biases During Reaching
Authors: Wang Tianhe , Morehead Ryan J. , Tsay Jonathan S. , Ivry Richard B. 
Published: March 2024

AbstractGoal-directed movements can fail due to errors in our perceptual and motor systems. While these errors may arise from random noise within these sources, they also reflect systematic motor biases that vary with the location of the target. The origin of these systematic biases remains controversial. Drawing on data from an extensive array of reaching tasks conducted over the past 30 years, we evaluated the merits of various computational models regarding the origin of motor biases. Contrary to previous theories, we show that motor biases do not arise from systematic errors associated with the sensed hand position during motor planning or from the biomechanical constraints imposed during motor execution. Rather, motor biases are primarily caused by a misalignment between eye-centric and the body-centric representations of position. This model can account for motor biases across a wide range of contexts, encompassing movements with the right versus left hand, proximal and distal effectors, visible and occluded starting positions, as well as before and after sensorimotor adaptation.
Splice site andde novomutations can cause mixed dominant negative/gain of functionPLCG2-associated immune dysregulation with cold urticaria (CU-PLAID)
Authors: Chou Sophia R. , Bailey Alexis C. , Baysac Kathleen , Oler Andrew J. , Milner Joshua D. , Ombrello Michael J. 
Published: March 2024

AbstractBackgroundPhospholipase Cγ2 (PLCγ2) is an important signaling molecule that receives and transmits signals from various cell surface receptors in most hematopoietic lineages. Variants ofPLCG2cause PLCγ2-associated immune dysregulation (PLAID), a family of conditions that are classified by mutational effect. PLAID with cold urticaria (CU-PLAID) is caused by in-frame deletions ofPLCG2that are dominant negative at physiologic temperatures but become spontaneously active at sub-physiologic temperatures.ObjectiveTo identify genetic lesions that cause PLAID by combining RNA sequencing of full-lengthPLCG2with whole genome sequencing.MethodsWe studied nine probands with antibody deficiency and a positive evaporative cooling test, together with two known CU-PLAID patients and three healthy subjects. Illumina sequencing was performed on full-lengthPLCG2cDNA synthesized from peripheral blood mononuclear cell RNA and whole genome sequencing was used to identify genetic lesions. Novel alternate transcripts were overexpressed in thePlcg2-deficient DT40 cell overexpression system. ERK phosphorylation was quantified by flow cytometry with and without BCR crosslinking.ResultsTwo probands expressed novel alternative transcripts ofPLCG2with in-frame deletions. The first, expressingPLCG2without exons 18-19, carried a splice site mutation in intron 19. The second, expressingPLCG2without exons 19-22, carried a 14kbde novodeletion ofPLCG2. DT40 cells overexpressing the exon 18-19 or exon 19-22 deletions failed to phosphorylate ERK in response to BCR crosslinking.ConclusionIn addition to autosomal dominant genomic deletions,de novodeletions and splice site mutations ofPLCG2can also cause CU-PLAID. All of these can be identified by cDNA-based sequencing.Capsule SummaryBy identifying both the firstde novoand splice site variants to causePLCG2-associated immune dysregulation with cold urticaria (CU-PLAID), we demonstrate the diagnostic utility ofPLCG2-specific RNA-sequencing.
Reporting of Fairness Metrics in Clinical Risk Prediction Models: A Call for Change
Authors: Rountree Lillian , Lin Yi-Ting , Liu Chuyu , Salvatore Maxwell , Admon Andrew , Nallamothu Brahmajee K , Singh Karandeep , Basu Anirban , Mukherjee Bhramar 
Published: March 2024

AbstractClinical risk prediction models integrated in digitized healthcare systems hold promise for personalized primary prevention and care. Fairness metrics are important tools for evaluating potential disparities across sensitive features in the field of prediction modeling. In this paper, we seek to assess the uptake of fairness metrics in clinical risk prediction modeling by conducting a scoping literature review of recent high impact publications in the areas of cardiovascular disease and COVID-19. Our review shows that fairness metrics have rarely been used in clinical risk prediction modeling despite their ability to identify inequality and flag potential discrimination. We also find that the data used in clinical risk prediction models remain largely demographically homogeneous, demonstrating an urgent need for collecting and using data from diverse populations. To address these issues, we suggest specific strategies for increasing the use of fairness metrics while developing clinical risk prediction models.
Macular Structure Characteristics in Unilateral Idiopathic Full-Thickness Macular Hole and the Healthy Fellow Eyes
Authors: Hou Yi-Ting , Yang Chung-May , Hsieh Yi-Ting 
Published: March 2024

ABSTRACTAimsTo investigate the characteristics of the macular structure and foveal pit in eyes with lesions and healthy fellow eyes of patients with unilateral full-thickness macular holes (FTMH).MethodsPatients with unilateral FTMH were retrospectively enrolled as the study group, and their age- and sex-matched individuals with no vitreomacular diseases as the control group in a medical center. FTMHs were classified as FTMH with lamellar hole-associated epiretinal proliferation (LHEP), FTMH without LHEP or FTMH without vitreomacular separation. Macular structure parameters, including foveal base width (FBW), central foveolar thickness (CFT), central subfield thickness (CST), central subfield volume (CSV), and retinal artery trajectory (RAT), were measured using optical coherence tomography and fundus photography. These parameters were compared among different FTMH groups.ResultsA total of 68 patients (39 women) with unilateral FTMH and 68 healthy controls were enrolled. The RAT of the lesioned eyes (0.19±0.06) and the healthy fellow eyes (0.14±0.04) were both smaller than those of the normal controls (0.37±0.14) (P<0.001 for both). The FBW of the healthy fellow eyes (446.8±98.2 µm) were significantly larger than those in the control group (338.4±80.6 µm,P<0.001). No significant differences in any macular parameters were noted among the three different types of FTMH.ConclusionsPatients with unilateral FTMH had a wider RAT in both the lesioned and healthy eyes, and a wider foveal base in their healthy fellow eyes than in normal controls. Such macular structure characteristics may be prone to macular hole formation.
A Survey on Optimization and Machine Learning-Based Fair Decision Making in Healthcare
Authors: Chen Zequn , Marrero Wesley J. 
Published: March 2024

AbstractThe unintended biases introduced by optimization and machine learning (ML) models are a topic of great interest to medical professionals. Bias in healthcare decisions can cause patients from vulnerable populations (e.g., racially minoritized, low-income, or living in rural areas) to have lower access to resources and inferior outcomes, thus exacerbating societal unfairness. In this systematic literature review, we present a structured overview of the literature regarding fair decision making in healthcare until April 2024. After screening 782 unique references, we identified 103 articles within the scope of our review. We categorize the identified articles into the following three sections: algorithmic bias, fairness metrics, and bias mitigation techniques. Specifically, we identify examples of algorithmic, data, and publication bias as they are typically encountered in research and practice. Subsequently, we define and discuss the fairness metrics previously considered in the literature, including notions of fairness through unawareness, demographic parity, equal opportunity, and equal odds. Lastly, we summarize the bias mitigation techniques available in the optimization and ML literature by classifying them into pre-processing, in-processing, and post-processing approaches. Fairness in decision making is an emerging field, poised to substantially reduce social inequities and improve the overall well-being of underrepresented groups. Our review aims to increase awareness of fairness in healthcare decision making and facilitate the selection of appropriate approaches under varying scenarios.
A brain-to-text framework of decoding natural tonal sentences
Authors: Zhang Daohan , Wang Zhenjie , Qian Youkun , Zhao Zehao , Liu Yan , Hao Xiaotao , Li Wanxin , Lu Shuo , Zhu Honglin , Chen Luyao , Xu Kunyu , Li Yuanning , Lu Junfeng 
Published: March 2024

AbstractSpeech brain-computer interfaces (BCIs) directly translate brain activity into speech sound and text, yet decoding tonal languages like Mandarin Chinese poses a significant, unexplored challenge. Despite successful cases in non-tonal languages, the complexities of Mandarin, with its distinct syllabic structures and pivotal lexical information conveyed through tonal nuances, present challenges in BCI decoding. Here we designed a brain-to-text framework to decode Mandarin tonal sentences from invasive neural recordings. Our modular approach dissects speech onset, base syllables, and lexical tones, integrating them with contextual information through Bayesian likelihood and the Viterbi decoder. The results demonstrate accurate tone and syllable decoding under variances in continuous naturalistic speech production, surpassing previous intracranial Mandarin tonal syllable decoders in decoding accuracy. We also verified the robustness of our decoding framework and showed that the model hyperparameters can be generalized across participants of varied gender, age, education backgrounds, pronunciation behaviors, and coverage of electrodes. Our pilot study shed lights on the feasibility of more generalizable brain-to-text decoding of natural tonal sentences from patients with high heterogeneities.