cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24080373
title: Supplementary Material for: Burgers, fast foods, and increased associated risk for atopic dermatitis: A cross-sectional study of dietary habits among young Chinese adults in Singapore/Malaysia

description: Background: We see increasing evidence that dietary and nutrients factors play a pivotal role in allergic diseases and recent global findings suggest that dietary habits influence the pathogenesis of atopic dermatitis (AD). Frequent consumption of fast food diets are associated with AD development. Despite the rising prevalence of AD in Asia, efforts in investigating the role of dietary habits and AD in adults are still lacking. Methods: We evaluated the association of foods and dietary habits with AD presentation using our population established for the Singapore/Malaysia Cross-sectional Genetics Epidemiology Study (SMCGES). Dietary habits profiles of 11494 young Chinese adults (1550 AD cases/ 2978 non-atopic controls/6386 atopic controls) were assessed by an investigator-administered questionnaire. AD cases were further evaluated for their chronicity (550 chronic) and severity (628 moderate-to-severe). Additionally, we derived a novel food index, Quality of Diet based on Glycaemic Index Score (QDGIS), to examine the association of dietary habits of GI and foods with AD and various AD phenotypes. Results: The majority of AD subjects are distributed in the good (37.1%) and moderate (36.2%) QDGIS classes. From the multivariate analyses for age and gender, a moderate QDGIS class was significantly associated with a lower odds of AD (Adjusted Odds Ratio (AOR): 0.844; 95% Confidence Interval (CI): 0.719-0.991; p &lt;0.05) and moderate/severe AD (AOR: 0.839; 95% CI: 0.714-0.985; p &lt;0.05). A good QDGIS class was only significantly associated with a lower odds of chronic AD (AOR: 0.769; 95% CI: 0.606-09761; p &lt;0.05). Among high GI foods, frequent consumption of burgers/fast food was strongly associated with an increased risk of chronic and severe AD. Among low GI foods, increased intake frequencies of fruits, vegetables, and pulses decreased the odds of AD. Finally, we identified significant associations between frequent seafood, margarine, butter, and pasta consumption with an increased odds of AD despite them having little GI values. Conclusion: While genetic components are well-established in their risks associated with increased AD prevalence, there is still a lack of a focus epidemiology study associating dietary influence with AD. Based on the first allergic epidemiology study conducted here in Singapore and Malaysia, it laid the groundwork to guide potential dietary interventions from changing personal eating habits.
DOI: 10.6084/m9.figshare.24080436
title: Supplementary Material for: Objective response and progression free survival contribute to prolong overall survival in atezolizumab plus bevacizumab treatment for unresectable hepatocellular carcinoma.

description: Introduction: Atezolizumab plus bevacizumab (Atez/Bev) is a standard treatment for unresectable hepatocellular carcinoma (HCC) due to its good anti-tumor and survival prolongation effects. Post-progression survival (PPS) has been reported to be a great contributor in the treatment with tyrosine kinase inhibitors for unrecetable HCC. This study aimed to clarify the significance of progression-free survival (PFS) or PPS of Atez/Bev treatment for HCC. Methods: We analyzed the correlations of PFS and PPS with overall survival (OS) in studies of HCC patients treated with Atez/Bev and evaluated the contribution to OS in Atez/Bev treatment with patients at our institutions as clinical practice. Results: Analysis of 18 studies involving 2,937 patients treated with Atez/Bev found that PPS had a stronger correlation with OS (R2=0.872, p&lt;0.001) than did PFS (R2=0.605, p=0.001). Analysis of 80 patients with unresectable HCC treated with Atez/Bev found that presence of anti-tumor responses during Atez/Bev was the most significant contributor to OS, and post-progression treatment after Atez/Bev also significantly contribute to OS. Conclusion: The presence of anti-tumor response with tumor shrinkage during Atez/Bev treatment contributes to good OS through its durable response. Atez/Bev treatment could be considered as first-line treatment for unresectable HCC. However, there is a need for optimal biomarkers for good-anti-tumor response.
DOI: 10.6084/m9.figshare.24080478
title: Supplementary Material for: Automatic deep learning-based pipeline for automatic delineation and measurement of fetal brain structures in routine mid-trimester ultrasound images

description: Introduction: The aim of this study was to develop a pipeline using state-of-the-art deep learning methods to automatically delineate and measure several of the most important brain structures in fetal brain ultrasound images. Methods: The dataset was composed of 5,331 images of fetal brain acquired during the routine mid-trimester ultrasound scan. Our proposed pipeline automatically performs the following three steps: brain plane classification (transventricular, transthalamic or transcerebellar plane); brain structures delineation (9 different structures); and automatic measurement (from the structure delineations). The methods were trained on a subset of 4,331 images and each step was evaluated on the remaining 1,000 images. Results: Plane classification reached 98.6% average class accuracy. Brain structure delineation obtained an average pixel accuracy higher than 96% and a Jaccard index higher than 70%. Automatic measurements get an absolute error below 3.5% for the four standard head biometries (head circumference, biparietal diameter, occipitofrontal diameter and cephalic index), 9% for transcerebellar diameter, 12% for cavum septi pellucidi ratio and 26% for Sylvian fissure operculization degree. Conclusions: The proposed pipeline shows the potential of deep learning methods to delineate fetal head and brain structures and obtain automatic measures of each anatomical standard plane acquired during routine fetal ultrasound examination.
DOI: 10.6084/m9.figshare.24083886
title: Supplementary Material for: Weekend effect on clinical outcomes of acute lower gastrointestinal bleeding: A large multicenter cohort study in Japan

description: Introduction Weekend admissions showed increased mortality in several medical conditions. This study aimed to examine the weekend effect on acute lower gastrointestinal bleeding (ALGIB) and its mortality and other outcomes. Methods This retrospective cohort study (CODE BLUE-J Study) was conducted at 49 Japanese hospitals between January 2010 and December 2019. In total, 8120 outpatients with acute hematochezia were enrolled and divided into weekend admissions and weekday admissions groups. Multiple imputation (MI) was used to handle missing values, followed by propensity score matching (PSM) to compare outcomes. The primary outcome was mortality; the secondary outcomes were rebleeding, length of stay (LOS), blood transfusion, thromboembolism, endoscopic treatment, the need for interventional radiology, and the need for surgery. Colonoscopy and computed tomography (CT) management was also evaluated. Results Before PSM, there was no significant difference in mortality (1.3% vs. 0.9%, P=0.133) between weekend and weekday admissions. After PSM with MI, 1,976 cases were matched for each admission. Mortality was not significantly different for weekend admissions compared with weekday admissions (odds ratio [OR] 1.437, 95% confidence interval [CI] 0.785-2.630; P=0.340). No significant difference was found with other secondary outcomes in weekend admissions except for blood transfusion (OR 1.239, 95% CI 1.084-1.417; P=0.006). Weekend admission had a negative effect on early colonoscopy (OR 0.536, 95% CI 0.471-0.609; P&lt;0.001). Meanwhile, urgent CT remained significantly higher in weekend admissions (OR 1.466, 95% CI 1.295-1.660; P&lt;0.001). Discussion/Conclusion Weekend admissions decreases early colonoscopy and increases urgent CT, but do not affect mortality or other outcomes except transfusion.
DOI: 10.6084/m9.figshare.24105426
title: Supplementary Material for: Variations in determining actual orientations of segmented deep brain stimulation leads using the DiODe algorithm: a retrospective study across different lead designs and medical institutions

description: Purpose: Directional deep brain stimulation (DBS) leads have become widely used in the past decade. Understanding the asymmetric stimulation provided by directional leads requires precise knowledge of the exact orientation of the lead in respect to its anatomical target. Recently, the DiODe algorithm was developed to automatically determine the orientation angle of leads from the artifact on postoperative computed tomography (CT) images. However, manual DiODe results are user-dependent. This study analyzed the extent of lead rotation as well as the user agreement of DiODe calculations across the two most common DBS systems, namely Boston Scientific’s Vercise and Abbott’s Infinity, and two independent medical institutions. Methods: Data from 104 patients who underwent an anterior-facing unilateral/bilateral directional DBS implantation at either Northwestern Memorial Hospital (NMH) or Albany Medical Center (AMC) were retrospectively analyzed. Actual orientations of the implanted leads were independently calculated by three individual users using the DiODe algorithm in Lead-DBS and patients’ postoperative CT images. Deviation from the intended orientation and user agreement were assessed. Results: All leads significantly deviated from the intended 0° orientation (p&lt;0.001), regardless of DBS lead design (p&lt;0.05) or institution (p&lt;0.05). However, the Boston Scientific leads showed an implantation bias towards the left at both institutions (p=0.014 at NMH, p=0.029 at AMC). A difference of 10° between at least two users occurred in 28% (NMH) and 39% (AMC) of all Boston Scientific and 76% (NMH) and 53% (AMC) of all Abbott leads. Conclusion: Our results show that there is a significant lead rotation from the intended surgical orientation across both DBS systems and both medical institutions, however, a bias towards a single direction was only seen in Boston Scientific leads. Additionally, these results raise questions into the user error that occurs when manually refining the orientation angles calculated with DiODe.
DOI: 10.6084/m9.figshare.24125301
title: Supplementary Material for: Mismatch repair deficiency in biliary tract cancer: prognostic implications and correlation with histology.

description: Introduction: Mismatch repair (MMR) deficiency represents a biomarker and therapeutic target in various neoplasms, but its role in biliary tract cancers (BTCs) remains misunderstood. Methods: MMR status was retrospectively assessed using immunohistochemistry in 163-BTCs patients. We identified MMR proficiency (pMMR)/deficiency (dMMR) according to the loss of MMR proteins (MLH-1, PMS-2, MSH-2, MSH-6). The primary objective of the study was to assess the incidence of dMMR in BTCs; the secondary purpose was to explore its association with prognosis and clinical features. Results: dMMR was recorded in 9 patients and it was strongly associated with mucinous histology (p&lt;0.01). Regarding the prognostic effect, in 122-radically resected patients, disease-free-survival (DFS) resulted significantly shorter in dMMR-patients compared to pMMR-patients (10.7 vs 31.3 months, p = 0.025) and so did nodal status (48.2 vs 15.3 months in N0 vs N+) (p &lt; 0.01). Moreover, dMMR confirmed its prognostic role in terms of DFS at multivariate analysis (p = 0.03), together with nodal status (p = 0.01) and resection margin (p = 0.03). In 103 M+ patients (encompassing 41 metastatic de novo and 62 recurred after surgery patients) there weren’t differences between dMMR and pMMR regarding survival analyses. Discussion/Conclusions: dMMR status is strongly correlated with mucinous histology and represents an independent prognostic factor in terms of disease-relapse in patients with resected BTC.
DOI: 10.6084/m9.figshare.24131562
title: Supplementary Material for: Effectiveness treatment of a BRAF-ZKSCAN5 fusion gene melanoma case with dabrafenib/trametinib

description: The most important driver gene in malignant melanoma is the BRAF mutation, and molecularly targeted therapies targeting mutations, mainly V600E and V600K, are used in clinical practice. In this report, we treated a patient with malignant melanoma expressing a rare BRAF-ZKSCAN5 fusion gene with dabrafenib/trametinib. The patient was a 71-year-old female. She was diagnosed with malignant melanoma (pT4aN3M0, STAGE IIIC) of the abdomen with axillary lymph node metastasis. She underwent extended resection and axillary lymph node dissection and was treated with adjuvant therapy, but lung and mediastinal lymph node metastases developed. The patient was treated with immune checkpoint inhibitors for metastatic lesions and achieved complete remission, but relapsed and metastatic lesions appeared in the cervical lymph nodes. Next-generation sequencing revealed the BRAF-ZKSCAN5 fusion gene, and treatment with dabrafenib/trametinib was initiated. After one month of treatment, tumor growth stopped and the length of the tumor shrank by 22.2%, but she developed Grade 3 adverse events of nausea, fatigue, and diarrhea and had difficulty exercising, forcing her to discontinue treatment after six weeks. The tumor continued to shrink during drug administration. This case report may provide insight into treatment options for cases that BRAF fusion gene was observed, which are expected to be detected in large numbers by next-generation sequencing in the future.
DOI: 10.6084/m9.figshare.24136452
title: Supplementary Material for: Diversity and evolution of highly repetitive DNA sequences constituting chromosome-site specific heterochromatin in two Gerbillinae species

description: Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the LINE-1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.
DOI: 10.6084/m9.figshare.24137613
title: Supplementary Material for: Renal outcomes in older adults with antineutrophil cytoplasmic autoantibody-associated vasculitis: a new prediction model

description: Introduction: Older patients with antineutrophil cytoplasmic autoantibody-associated vasculitis (AAV) commonly experience renal impairment and poor prognoses. This study aimed to establish a risk-scoring system for predicting composite renal outcomes in older patients with AAV. Methods: This retrospective observational study included all patients with AAV hospitalized in a single-center tertiary hospital in China between January 2013 and April 2022. Patients aged ≥ 65 years were defined as older adults, and short-term composite renal outcomes included a ≥ 25% reduction in eGFR (for AKI), renal replacement therapy, provision of renal replacement therapy (long-term dialysis, kidney transplant, or sustained eGFR &lt; 15 ml/min/1.73m), or all-cause mortality. Patients were randomly divided into development and validation cohorts (2:1). Logistic regression analysis was performed in the development cohort to analyze risk factors. The scoring system was established accordingly and further validated in the validation cohort. Results: 1203 patients were enrolled in the study, among whom the older adult group accounted for 36% with a mean age of 71 years. The older adult group had a worse prognosis, a higher mortality rate, a higher rate of end-stage renal disease, and worsening renal function. Logistic regression showed that age &gt; 75 years, chronic heart disease, and elevated serum creatinine and D-dimer values were risk factors for poor prognosis in patients with AAV. The development and validation cohorts in patients with AAV produced area under the curve values of 0.82 (0.78–0.86) and 0.83 (0.77–0.89), respectively. Conclusion: We established a risk-scoring system based on baseline clinical characteristics to predict composite renal outcomes in patients with AAV. Our results suggest that more attention should be paid to older patients with severe renal impairment and active inflammation.
DOI: 10.6084/m9.figshare.24160719
title: Supplementary Material for: Time of delivery contributes to mortality and morbidity in preterm infants

description: Abstract Introduction Knowledge about the time of birth and its impact on premature infants is essential when planning perinatal and neonatal care and resource allocation. We studied the time of birth and its contribution to early death and morbidity in preterm infants. Methods We explored the time and mode of birth of infants with birthweight of &lt;1500g and gestational age of &lt;32+0/7 weeks. Additionally, we divided the infants into three groups stratified by their time of birth, i.e. during office hours, evening, and nighttime and assessed associations between these groups and mortality and morbidity. Results The study comprised 1610 infants of whom 156 (10%) died during their stay in NICU. The highest number of deliveries occurred on Fridays (21%, n=341/1610), primarily due to high number of cesarean sections. Deliveries peaked on workdays at 10 a.m. and 2 p.m. Mortality was lowest among infants born on Fridays (6%, n=21/341) and highest on Mondays (13%, n=28/218). Intraventricular hemorrhage (IVH) (OR 1.50, 95% Cl 1.10-2.03, p=0.010) and necrotizing enterocolitis (NEC) (OR 2.11, 95%Cl 1.13-3.91, p=0.019) were more common among infants born at nighttime. These associations attenuated after adjustment for covariates. Conclusion Deliveries of premature infants peaked on Fridays. Mortality was lower among those born on Fridays, compared with Mondays. Many low-risk deliveries on Fridays may decrease, and the tendency to postpone high-risk deliveries to Mondays, increase the proportional risk of mortality. Indication of higher risk of IVH and NEC among infants born during nighttime may be due to different patient population.
DOI: 10.6084/m9.figshare.24160920
title: Supplementary Material for: Novel LAGE3 pathogenic variants combined with TRPC6 and NUP160 variants in Galloway-Mowat syndrome: a case report

description: Abstract Galloway-Mowat syndrome (GAMOS) is a rare autosomal recessive disorder characterized by early-onset nephrotic syndrome and microcephaly with brain anomalies in children. Researchers studying GAMOS reported the first pathogenic variant identified was the WDR73 gene, and more recently, four new pathogenic genes, OSGEP, LAGE3, TP53RK, and TPRKB, have been identified. In the present study, we report a new mutation of c.290T&gt;G（p.L97R）LAGE3 in a 4-year-old boy with specific urological and nephrological complications. The patient presented with early-onset proteinuria, brain atrophy, delayed language and motor development, and axial hypotonia. This patient also had mutations in two other genes: TRPC6 and NUP160，make the clinical presentation of this patient more diverse.Our novel findings add to the spectrum of pathogenic variants in the LAGE3 gene. In addition, early genetic diagnosis of GAMOS is essential for genetic counseling and prenatal care.
DOI: 10.6084/m9.figshare.24166692
title: Supplementary Material for: Endobronchial Metastasis of Renal Cancer Presented as Atelectasis

description: The most common primary tumors associated with endobronchial metastasis (EBM) are colorectal, breast and renal. When endobronchial metastasis is present, respiratory symptoms such as shortness of breath or hemoptysis accompanied by coughing usually appear. Herein, we report a case of atelectasis caused by EBM of renal cell carcinoma (RCC) in a 53-year-old man who underwent laparoscopic radical nephrectomy for RCC five years ago. The patient's primary RCC stage was pT1b, and the histological cell type was clear cell RCC with Fuhrman nuclear grade 3/4. At the time of EBM diagnosis, the patient was classified as "favorable" according to IMDC (International mRCC Database Consortium) risk calculator. The patient refused surgical treatment and received targeted therapy with sunitinib. A tumor mass spontaneously detached and came out through the airway during targeted therapy. Subsequently, the patient’s respiratory symptoms were alleviated and his atelectasis disappeared. This case shows that when there is atelectasis due to EBM of RCC, the obstructed bronchus may be reopened with targeted therapy without any interventional treatment.
DOI: 10.6084/m9.figshare.22147886
title: Supplementary Material for: Multiple Small Bowel Gastrointestinal Stromal Tumors Associated with Neurofibromatosis Type 1 That Were Not Detected by Endoscopy: A Case Report

description: We treated a 39-year-old Japanese man who was admitted for an abdominal mass. He had had neurofibroma-like skin lesions since childhood. CT and endoscopic ultrasound results were consistent with a tumor in the small intestine. Although the tumor was undetectable by single-balloon endoscopy, the patient's background and imaging results led us to suspect a gastrointestinal stromal tumor (GIST). He also met the diagnostic criteria for neurofibroma type 1 (NF1). We performed a surgical removal of the tumor, and the biopsy results led to a definitive diagnosis of GIST. Small bowel GISTs should be considered in cases of NF1.