cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30645797
title: Supplementary Material for: Clinical utility of intestinal ultrasound for guiding therapy in IBD: A retrospective real-world cohort from a Swiss tertiary center

description: Background: Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), are chronic immune-mediated disorders that significantly impact patients' quality of life. Proper IBD management often requires invasive diagnostic procedures such as endoscopy. Transabdominal intestinal ultrasound (IUS) offers a promising alternative due to its non-invasive, inexpensive, and widely available nature. This study aims to evaluate the effectiveness of IUS combined with clinical parameters in guiding treatment decisions for IBD patients in remission or relapse.
Methods: Retrospective cohort study of University Hospital Zurich (January-August 2022), which included consecutive adult IBD patients undergoing a single transabdominal IUS for treatment decision-making. IUS influenced clinical decisions by guiding therapy continuation, modification, or cessation and addressing complications.
Results: The study analyzed 103 consecutive IBD patients, 66% diagnosed with CD and 34% with UC. The majority (69.9%) were in clinical remission, and two-third of the remission patients claimed also no symptoms. (32% of the whole cohort were asymptomatic). Bowel wall thickness (BWT) in the terminal ileum and left colon also significantly influenced treatment decisions (p = 0.014 and p = 0.042, respectively). In a multivariable logistic regression, both diarrhea (p = 0.013) and maximal BWT (p = 0.020) remained statistically significant predictors for a change in treatment.
Conclusion: The study demonstrates that IUS, along with clinical symptoms such as diarrhea, plays a significant role in guiding treatment decisions for IBD patients. Diarrhea and BWT were strong predictors for adjusting therapy, highlighting the value of integrating non-invasive imaging with clinical assessment to optimize IBD management.
DOI: 10.6084/m9.figshare.30645797.v1
title: Supplementary Material for: Clinical utility of intestinal ultrasound for guiding therapy in IBD: A retrospective real-world cohort from a Swiss tertiary center

description: Background: Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), are chronic immune-mediated disorders that significantly impact patients' quality of life. Proper IBD management often requires invasive diagnostic procedures such as endoscopy. Transabdominal intestinal ultrasound (IUS) offers a promising alternative due to its non-invasive, inexpensive, and widely available nature. This study aims to evaluate the effectiveness of IUS combined with clinical parameters in guiding treatment decisions for IBD patients in remission or relapse.
Methods: Retrospective cohort study of University Hospital Zurich (January-August 2022), which included consecutive adult IBD patients undergoing a single transabdominal IUS for treatment decision-making. IUS influenced clinical decisions by guiding therapy continuation, modification, or cessation and addressing complications.
Results: The study analyzed 103 consecutive IBD patients, 66% diagnosed with CD and 34% with UC. The majority (69.9%) were in clinical remission, and two-third of the remission patients claimed also no symptoms. (32% of the whole cohort were asymptomatic). Bowel wall thickness (BWT) in the terminal ileum and left colon also significantly influenced treatment decisions (p = 0.014 and p = 0.042, respectively). In a multivariable logistic regression, both diarrhea (p = 0.013) and maximal BWT (p = 0.020) remained statistically significant predictors for a change in treatment.
Conclusion: The study demonstrates that IUS, along with clinical symptoms such as diarrhea, plays a significant role in guiding treatment decisions for IBD patients. Diarrhea and BWT were strong predictors for adjusting therapy, highlighting the value of integrating non-invasive imaging with clinical assessment to optimize IBD management.
DOI: 10.6084/m9.figshare.30645800
title: Supplementary Material for: Liquid-based oral brush cytology: evaluation of two artificial intelligence models in Papanicolaou and Silver-Stained Nucleolar Organizer Region (AgNOR) analyses

description: Introduction: Oral squamous cell carcinoma (OSCC) is the most prevalent oral malignant neoplasm. Cytopathology may represent an important tool in the screening of OSCC, and liquid-based oral brush cytology (LBOBC) has been widely studied because of its clearer cell sample results. These cytopathological analyses could be more efficient with the aid of artificial intelligence (AI). The objective of this study was to analyze the effectiveness of two AI models (Papanicolaou and AgNOR Slide Image Examiners) in LBOBC analyses. Methods: Two human evaluators and the AI models performed cell maturation pattern analysis and mean nucleolar organizer region (NOR) per nucleus count in Papanicolaou and silver-stained nucleolar organizer region (AgNOR) oral cytopathological samples of 20 individuals, respectively. Inter-evaluator agreement was evaluated by kappa and intraclass correlation coefficient (ICC). Chi-square and Wilcoxon matched-pairs/Friedman tests analyzed differences between the conventional and LBOBC methods, and among evaluators. Results: Kappa between the Papanicolaou AI model and each human researcher was substantial (k = 0.69) for the conventional method, and moderate for the LBOBC (k = 0.55-0.53. There were statistical differences in the cellular type analysis between cytology methods and among evaluators (p &lt; 0.001). The automated AgNOR model showed an excellent/highly good agreement with human evaluators for NOR count in both cytology methods, with and without bounding boxes. There was no statistical difference in the NOR count between methods (p &gt; 0.05). In the conventional method, there were differences among evaluators (p &lt; 0.05); in the LBOBC, there were not (p &gt; 0.05). Conclusions: The AgNOR automated model is reliable when assessing NOR count in oral samples processed by different cytological methods, when compared to the human analysis. The Papanicolaou model still needs more training with LBOBC samples.
DOI: 10.6084/m9.figshare.30645800.v1
title: Supplementary Material for: Liquid-based oral brush cytology: evaluation of two artificial intelligence models in Papanicolaou and Silver-Stained Nucleolar Organizer Region (AgNOR) analyses

description: Introduction: Oral squamous cell carcinoma (OSCC) is the most prevalent oral malignant neoplasm. Cytopathology may represent an important tool in the screening of OSCC, and liquid-based oral brush cytology (LBOBC) has been widely studied because of its clearer cell sample results. These cytopathological analyses could be more efficient with the aid of artificial intelligence (AI). The objective of this study was to analyze the effectiveness of two AI models (Papanicolaou and AgNOR Slide Image Examiners) in LBOBC analyses. Methods: Two human evaluators and the AI models performed cell maturation pattern analysis and mean nucleolar organizer region (NOR) per nucleus count in Papanicolaou and silver-stained nucleolar organizer region (AgNOR) oral cytopathological samples of 20 individuals, respectively. Inter-evaluator agreement was evaluated by kappa and intraclass correlation coefficient (ICC). Chi-square and Wilcoxon matched-pairs/Friedman tests analyzed differences between the conventional and LBOBC methods, and among evaluators. Results: Kappa between the Papanicolaou AI model and each human researcher was substantial (k = 0.69) for the conventional method, and moderate for the LBOBC (k = 0.55-0.53. There were statistical differences in the cellular type analysis between cytology methods and among evaluators (p &lt; 0.001). The automated AgNOR model showed an excellent/highly good agreement with human evaluators for NOR count in both cytology methods, with and without bounding boxes. There was no statistical difference in the NOR count between methods (p &gt; 0.05). In the conventional method, there were differences among evaluators (p &lt; 0.05); in the LBOBC, there were not (p &gt; 0.05). Conclusions: The AgNOR automated model is reliable when assessing NOR count in oral samples processed by different cytological methods, when compared to the human analysis. The Papanicolaou model still needs more training with LBOBC samples.
DOI: 10.6084/m9.figshare.30645806
title: Supplementary Material for: Do income inequalities influence the relationship between dental caries experience and nutritional status in children and adolescents? Scoping review.

description: Objective: To demonstrate the state of the art in the effect of income inequalities on the relationship between dental caries and nutritional status in children and adolescents, and provide an overview of the countries investigated.
Methods: Seven databases, along with gray literature (Google Scholar), were searched to identify studies based on the acronym PCC (Population: children and/or adolescents; Concept: relationship of nutritional status with dental caries experience; Context: income classifications (high, middle, and low) and the countries considered. Two independent reviewers performed study selection and data collection. The results were presented in table, graphic, and narrative formats.
Results: After the eligibility assessment, 37 studies were included in 21 countries. Nineteen studies indicated that income inequalities may have repercussions on the relationship between nutritional status and dental caries, while 11 studies suggested a possible absence of effect on the relationship between these variables. Seven studies were considered inconclusive regarding children and adolescents. 
Conclusion: Although the evidence remains inconclusive in specific contexts, most of the included studies suggest a potential influence of income inequalities on the relationship between dental caries experience and nutritional status in children and adolescents.
DOI: 10.6084/m9.figshare.30645806.v1
title: Supplementary Material for: Do income inequalities influence the relationship between dental caries experience and nutritional status in children and adolescents? Scoping review.

description: Objective: To demonstrate the state of the art in the effect of income inequalities on the relationship between dental caries and nutritional status in children and adolescents, and provide an overview of the countries investigated.
Methods: Seven databases, along with gray literature (Google Scholar), were searched to identify studies based on the acronym PCC (Population: children and/or adolescents; Concept: relationship of nutritional status with dental caries experience; Context: income classifications (high, middle, and low) and the countries considered. Two independent reviewers performed study selection and data collection. The results were presented in table, graphic, and narrative formats.
Results: After the eligibility assessment, 37 studies were included in 21 countries. Nineteen studies indicated that income inequalities may have repercussions on the relationship between nutritional status and dental caries, while 11 studies suggested a possible absence of effect on the relationship between these variables. Seven studies were considered inconclusive regarding children and adolescents. 
Conclusion: Although the evidence remains inconclusive in specific contexts, most of the included studies suggest a potential influence of income inequalities on the relationship between dental caries experience and nutritional status in children and adolescents.
DOI: 10.6084/m9.figshare.30645809
title: Supplementary Material for: Inflammatory bowel like disease with ileocolic and perianal involvement induced by ocrelizumab: a case report

description: Immune-mediated colitis (IMC) is a common immune related adverse event associated with immune checkpoint inhibitors. Other classes of biological therapy, such as monoclonal antibody with anti-CD20 activity, have also been associated with drug-induced gastrointestinal injuries, although through different immunomechanisms. In the literature, there are some previously described cases reporting on entero-colitis induced by rituximab and ocrelizumab highlighting its potential severity. Consequently, recently, the FDA amended the Prescribing Information of ocrelizumab to include immune-mediated colitis in the Warnings and Precautions section.
We present the case of a patient with immune-mediated enterocolitis, markedly resembling Crohn’s disease with ileocolic and perianal involvement induced by ocrelizumab. Endoscopically, this condition is indistinguishable from inflammatory bowel disease with significant overlap in histology. With discontinuation of ocrelizumab, the lesions and the symptoms disappeared. 
There are no clear recommendations on how to manage these patients. Clinicians must be aware of this entity and report on these unquestionably increasing conditions.
DOI: 10.6084/m9.figshare.30645809.v1
title: Supplementary Material for: Inflammatory bowel like disease with ileocolic and perianal involvement induced by ocrelizumab: a case report

description: Immune-mediated colitis (IMC) is a common immune related adverse event associated with immune checkpoint inhibitors. Other classes of biological therapy, such as monoclonal antibody with anti-CD20 activity, have also been associated with drug-induced gastrointestinal injuries, although through different immunomechanisms. In the literature, there are some previously described cases reporting on entero-colitis induced by rituximab and ocrelizumab highlighting its potential severity. Consequently, recently, the FDA amended the Prescribing Information of ocrelizumab to include immune-mediated colitis in the Warnings and Precautions section.
We present the case of a patient with immune-mediated enterocolitis, markedly resembling Crohn’s disease with ileocolic and perianal involvement induced by ocrelizumab. Endoscopically, this condition is indistinguishable from inflammatory bowel disease with significant overlap in histology. With discontinuation of ocrelizumab, the lesions and the symptoms disappeared. 
There are no clear recommendations on how to manage these patients. Clinicians must be aware of this entity and report on these unquestionably increasing conditions.
DOI: 10.6084/m9.figshare.30645812
title: Supplementary Material for: Phenotypes and Natural Course of Atopic Dermatitis: A pathway to the Atopic March

description: Introduction
Atopic dermatitis (AD) is a chronic inflammatory skin disorder that may progress to asthma and/or allergic rhinitis (AR) in children, a progression known as the "atopic march." 
Methods
This study aimed to evaluate the natural history of AD, its clinical phenotypes, and the risk of progression to atopic march over a 10-year period. A retrospective review of medical records was performed for children diagnosed with AD and those with respiratory allergies who had prior AD. Patients were categorized into early transient, early persistent, and late-onset phenotypes based on eczema onset age and disease course. Disease progression, atopic march development, and related risk factors were analyzed
Results
The study included 894 children (375 females, 519 males) with a mean presentation age of 3.54 ± 3.31 years, mean follow-up of 3.65 ± 2.84 years. Based on clinical phenotypes, 61% (n=545) were early transient, 15.2% (n=136) early persistent, and 23.8% (n=213) late-onset. Asthma and AR rates were 8.6–11.2% in early transient, 14.0–22.8% in early persistent, and 16.0–24.9% in late-onset phenotypes respectively. Overall, 29.9% (n=267) exhibited the atopic march; 56.3% (n=503) were in remission and 43.7% (n=391) had persistent AD. Aeroallergen sensitization was significantly associated with persistent disease (p=0.016) and atopic march progression (p=0.001). Family history of atopy correlated with disease persistence (p=0.033)
Conclusion
Nearly one-third of children with AD are at risk of developing additional allergic diseases constituting the atopic march. Children with AD who exhibit aeroallergen sensitization should be closely monitored for the development of respiratory allergies.
DOI: 10.6084/m9.figshare.30645812.v1
title: Supplementary Material for: Phenotypes and Natural Course of Atopic Dermatitis: A pathway to the Atopic March

description: Introduction
Atopic dermatitis (AD) is a chronic inflammatory skin disorder that may progress to asthma and/or allergic rhinitis (AR) in children, a progression known as the "atopic march." 
Methods
This study aimed to evaluate the natural history of AD, its clinical phenotypes, and the risk of progression to atopic march over a 10-year period. A retrospective review of medical records was performed for children diagnosed with AD and those with respiratory allergies who had prior AD. Patients were categorized into early transient, early persistent, and late-onset phenotypes based on eczema onset age and disease course. Disease progression, atopic march development, and related risk factors were analyzed
Results
The study included 894 children (375 females, 519 males) with a mean presentation age of 3.54 ± 3.31 years, mean follow-up of 3.65 ± 2.84 years. Based on clinical phenotypes, 61% (n=545) were early transient, 15.2% (n=136) early persistent, and 23.8% (n=213) late-onset. Asthma and AR rates were 8.6–11.2% in early transient, 14.0–22.8% in early persistent, and 16.0–24.9% in late-onset phenotypes respectively. Overall, 29.9% (n=267) exhibited the atopic march; 56.3% (n=503) were in remission and 43.7% (n=391) had persistent AD. Aeroallergen sensitization was significantly associated with persistent disease (p=0.016) and atopic march progression (p=0.001). Family history of atopy correlated with disease persistence (p=0.033)
Conclusion
Nearly one-third of children with AD are at risk of developing additional allergic diseases constituting the atopic march. Children with AD who exhibit aeroallergen sensitization should be closely monitored for the development of respiratory allergies.
DOI: 10.6084/m9.figshare.30645815
title: Supplementary Material for: Trajectories of Sleep, psychological, cognitive, and quality of life outcomes following CPAP initiation: A sex-sensitive longitudinal study

description: Objectives: Continuous Positive Airway Pressure (CPAP) is the standard treatment for obstructive sleep apnea (OSA), yet diagnostic and treatment models have historically overlooked sex-specific responses. This study aimed to examine sex differences in changes in sleep-related symptoms, cognitive functions and quality of life (QOL) following CPAP initiation in individuals with OSA.
Methods: A prospective repeated-measures study was conducted at a sleep clinic. Adults diagnosed with OSA (apnea-hypopnea index ≥ 5) were assessed at four time points after CPAP initiation. Outcomes measures included Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Mini-Mental State Examination, Hospital Anxiety and Depression Scale, and QOL. Generalized estimating equations were used for longitudinal analysis.
Results: Of 121 participants (mean age: 50.8 years; 15.7% female). CPAP adherence did not differ by sex. At baseline, women reported significantly poorer sleep quality and physical functions. Adjusted analyses revealed women exhibited poorer sleep quality (β = 3.23, p &lt; .00001) but better cognitive function (β = 0.70, p = .025) compared to men after receiving CPAP treatment. When examining sex differences over time, women showed progressive improvements in sleep quality (β = -1.12, p = .001), depressive symptoms (β = -0.90, p = .004), and the physical domain of quality of life (β = 0.49, p = .019) throughout the treatment period.
Conclusions: CPAP therapy significantly improved sleep quality, depressive symptoms, cognitive function, and physical well-being in female patients with OSA. Implementing sex-specific treatment and support strategies may strengthen patient engagement, improve adherence, and optimize therapeutic outcomes.
DOI: 10.6084/m9.figshare.30645815.v1
title: Supplementary Material for: Trajectories of Sleep, psychological, cognitive, and quality of life outcomes following CPAP initiation: A sex-sensitive longitudinal study

description: Objectives: Continuous Positive Airway Pressure (CPAP) is the standard treatment for obstructive sleep apnea (OSA), yet diagnostic and treatment models have historically overlooked sex-specific responses. This study aimed to examine sex differences in changes in sleep-related symptoms, cognitive functions and quality of life (QOL) following CPAP initiation in individuals with OSA.
Methods: A prospective repeated-measures study was conducted at a sleep clinic. Adults diagnosed with OSA (apnea-hypopnea index ≥ 5) were assessed at four time points after CPAP initiation. Outcomes measures included Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Mini-Mental State Examination, Hospital Anxiety and Depression Scale, and QOL. Generalized estimating equations were used for longitudinal analysis.
Results: Of 121 participants (mean age: 50.8 years; 15.7% female). CPAP adherence did not differ by sex. At baseline, women reported significantly poorer sleep quality and physical functions. Adjusted analyses revealed women exhibited poorer sleep quality (β = 3.23, p &lt; .00001) but better cognitive function (β = 0.70, p = .025) compared to men after receiving CPAP treatment. When examining sex differences over time, women showed progressive improvements in sleep quality (β = -1.12, p = .001), depressive symptoms (β = -0.90, p = .004), and the physical domain of quality of life (β = 0.49, p = .019) throughout the treatment period.
Conclusions: CPAP therapy significantly improved sleep quality, depressive symptoms, cognitive function, and physical well-being in female patients with OSA. Implementing sex-specific treatment and support strategies may strengthen patient engagement, improve adherence, and optimize therapeutic outcomes.
DOI: 10.6084/m9.figshare.30645818
title: Supplementary Material for: Ningmitai Capsule Facilitates Residual Fragment Clearance after Ureteroscopic Holmium Laser Lithotripsy: A Multicenter Randomized Controlled Trial

description: Objective To evaluate the efficacy of Ningmitai capsule (NMT), a traditional Chinese medicine, alone or combined with tamsulosin, in promoting residual stone fragment clearance after Ureteroscopic Holmium Laser Lithotripsy (Ho:YAG-URS).
Methods In this multicenter, prospective, randomized controlled trial, 222 patients with distal ureteral residual fragments (3.18 ± 1.14 mm) post-Ho:YAG-URS were assigned to three groups: control (no medication), NMT (0.38g × 4 capsules, 3 times/day), or NMT + tamsulosin (0.4 mg/day). Primary outcome was the stone-free rate (SFR) at 4 weeks. Secondary outcomes included stone expulsion rate, stone-free time, and expulsion time.
Results At 4 weeks, SFRs were 76.19% (control), 92.21% (NMT; p = 0.023 vs. control), and 98.91% (combination; p &lt; 0.001 vs. control). The combination group achieved significantly shorter stone-free time (6.37 ± 2.25 vs. 15.82 ± 21.62 days, p &lt; 0.0001) and expulsion time (2.27 ± 1.17 vs. 6.64 ± 10.56 days, p &lt; 0.0001) compared to the control group. No drug-related adverse events were reported.
Conclusions NMT significantly accelerates residual fragment expulsion post-Ho:YAG-URS, with synergistic effects observed when combined with tamsulosin. This study demonstrates that patients can benefit from Ningmitai capsules alone or combined with tamsulosin, particularly for small fragments where alpha-blockers show limited efficacy.