cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23735643.v1
title: Supplementary Material for: Underwater endoscopic mucosal resection for a terminal ileum adenoma

description: Tumors of the terminal ileum are rare, and their diagnosis and treatment standards have not been established. The effectiveness of underwater endoscopic mucosal resection (UEMR) in the duodenum and colon has been reported; however, its effectiveness in the small intestine is rarely reported. We present a case of an ileum adenoma diagnosed using magnifying endoscopy that was completely resected using UEMR. A 56-year-old woman with a lesion in the terminal ileum was referred to our hospital for treatment. Colonoscopy revealed a 10- mm slightly depressed lesion with marginal elevation in the terminal ileum. Magnifying narrow-band imaging (NBI) showed a tubular surface pattern with regular vessels on the slightly elevated marginal area and regular brown vessels on the slightly depressed central area. Magnifying chromoendoscopy using crystal violet staining showed a branch-like or gyrus-like pattern on the marginal area, and a roundish and tubular structure on the central area. The lesion was diagnosed as an adenoma in the terminal ileum, similar to a colonic adenoma; hence, we decided to perform UEMR. The lesion was completely removed using a 10- mm snare. The pathological diagnosis revealed that it was an intestinal-type adenoma with negative margins. At the margins of the lesions, the tumor tended to form a villous structure, while the center appeared tubular with a relatively flat surface. These histopathological findings were consistent with the magnifying endoscopic findings. UEMR for terminal ileum tumors may be effective in their treatment.
DOI: 10.34740/kaggle/dsv/6324008
title: 2021 World Population (updated daily)
DOI: 10.6084/m9.figshare.22874480.v1
title: <strong>Gut flora-derived metabolites mediate protective effect of high fermentable fiber against placental inflammation in gestational diabetes mellitus.</strong>

description: Inflammation-associated insulin resistance is a key trigger of gestational diabetes mellitus (GDM), but the underlying mechanisms and effective interventions remain unclear. Here, we report the association of placental inflammation (tumor necrosis factor-α) and abnormal maternal glucose metabolism in GDM patients, and a high fermentable dietary fiber (HFDF, <em>Konjac</em>) could reduce GDM development through gut microbiota-short-chain fatty acids-placental inflammation axis in GDM mice model. Mechanistically, HFDF increases abundances of <em>Lachnospiraceae</em> and butyrate, reduces placental-derived inflammation by enhancing gut barrier and inhibiting the transfer of bacterial-derived lipopolysaccharide, and ultimately resists high fat diet-induced insulin resistance. Butyrate abundances in placentae of GDM patients and mice are negatively correlated with placental TNF-α. Moreover, <em>Lachnospiraceae</em> and butyrate have similar anti-GDM and anti-placental inflammation effects. These findings demonstrate the involvement of important placental inflammation-related mechanisms in the progression of GDM and the great potential of HFDFs to reduce susceptibility to GDM through gut-microbiota-placenta axis.
DOI: 10.6084/m9.figshare.23641551.v1
title: Supplementary Material for: Preoperative prediction of microvascular invasion with gadoxetic acid-enhanced magnetic resonance imaging in patients with single hepatocellular carcinoma: The implication of surgical decision on the extent of liver resection

description: Introduction: Microvascular invasion (MVI) is one of the most important prognostic factors for hepatocellular carcinoma (HCC) recurrence, but its application in preoperative clinical decisions is limited. This study aimed to identify preoperative predictive factors for MVI in HCC and further evaluate oncologic outcomes of different types and extents of hepatectomy according to stratified risk of MVI. Methods: Patients with surgically resected single HCC (≤5 cm) who underwent preoperative gadoxetic acid-enhanced magnetic resonance imaging (MRI) were included in a single-center retrospective study. Two radiologists reviewed the images with no clinical, pathological, or prognostic information. Significant predictive factors for MVI were identified using logistic regression analysis against pathologic MVI and used to stratify patients. In the subgroup analysis, long-term outcomes of the stratified patients were analyzed using the Kaplan-Meier method with log-rank test and compared between anatomical and non-anatomical or major and minor resection. Results: A total of 408 patients, 318 men and 90 women, with a mean age of 56.7 years were included. Elevated levels of tumor markers (α-FP ≥25 ng/mL and PIVKA-II ≥40 mAU/mL) and three MRI features (tumor size ≥ 3 cm, non-smooth tumor margin, and arterial peritumoral enhancement) were independent predictive factors for MVI. As the MVI risk increased from low (no predictive factor) and intermediate (1–2 factors) to high-risk (3–4 factors), recurrence-free and overall survival of each group significantly decreased (P= 0.001). In the high MVI risk group, 5-year cumulative recurrence rate was significantly lower in patients who underwent major compared to minor hepatectomy (26.6 vs 59.8%, P= 0.027). Conclusion: Tumor markers and MRI features can predict the risk of MVI and prognosis after hepatectomy. Patients with high MVI risk had the worst prognosis among the three groups, and major hepatectomy improved long-term outcomes in these high-risk patients.
DOI: 10.34740/kaggle/dsv/6324016
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.23988099
title: Dataset of "Larval plastic responses to warming and desiccation delay gonadal maturation in post-metamorphic spadefoot toads"

description: Excel document with the dataset of "Larval plastic responses to warming and desiccation delay gonadal maturation in post-metamorphic spadefoot toads". Two sheets can be found, one including the actual dataset, a second one ('Read_me') containing a brief explanation of the dataset.
DOI: 10.5281/zenodo.8262670
title: Altes Land hydrogeology

description: DEM: MERIT DEM based digital elevation model of the Altes land Groundwater measurements: Groundwater tables and salinities in Altes Land region Surface water measurements: Surface water hydraulic heads and salinities in Altes Land region
DOI: 10.6084/m9.figshare.23909847.v1
title: Supplementary Material for: Subperiosteal Orbital Hematoma: a rare clinical manifestation of sickle cell disease - a case report

description: Sickle cell disease (SCD), an inherited vaso-occlusive disorder, results in recurrent painful episodes and a variety of serious systemic complications that can lead to severe disabilities and even death. Here we report a case of a 19-year-old African American patient with homozygous sickle cell trait who presented with right upper lid edema and ptosis, three days after his admission to the hospital following a sickle cell crisis. Initially mistaken as a superinfection in the context of his disease, a diagnosis of orbital abscess was made. Intravenous antibiotics and a proper treatment plan were set accordingly. Only after extensive clinical and radiological examinations, it turned out to be an acute subperiosteal orbital hematoma (SOH), a rare clinical manifestation of SCD. The aim of our case report is to highlight the difference in orbital presentation between osteomyelitis and subperiosteal hematoma, as well as spreading awareness among medical professionals and especially ophthalmologists for this rare presentation of orbital wall infarction, as the initial differential diagnosis of SCD patients with ocular involvement.
DOI: 10.6084/m9.figshare.23675103.v1
title: Supplementary Material for: Objective burden and emotional distress in parents of children with type 1 diabetes

description: Introduction: The management of childhood type 1 diabetes requires the active participation of parents. The aim of the present study was to describe the main characteristics of parents of children with type 1 diabetes, including objective burden regarding time spent on diabetes care, emotional distress (exhaustion, need for respite, quality of life), and symptoms of depression as well as anxiety. Methods: In this observational study, parents of children with type 1 diabetes completed a questionnaire, anonymously. Different questions were asked to the parent about the objective burden of diabetes and its repercussion, their exhaustion and need for respite. Two validated instruments (HADS, WHOQOL-BREF) have been integrated into the questionnaire. Results: Eighty eight parents were included in the study. Among them, 76 (86%) were mothers. All the parents with a child aged 6 years or younger (10/10) reported having to take care of their child’s diabetes twice or more a day, this was the case for 37/39 (94.9%) parents of children aged 7 to 13, and for 16/36 (44.4%) of parents of children aged 14 years or above. In the total population, 33/86 (38.4%) parents declared getting up every night because of their child’s diabetes. The median daily time spent on diabetes management was 40 minutes. There were 54 parents (62.8%) who reported moderate-strong exhaustion, and 27 (30.7%) who expressed a moderate-strong need for respite. Regarding the result of the HADS, 46 parents (55.4%) reported symptoms of anxiety and/or depression. Discussion/Conclusion: Parents of children with type 1 diabetes must carry out multiple daily care, at all times of day and night. Their emotional state can be impacted with, in particular, a risk of exhaustion. Screening for these difficulties should be a part of the overall management of a child with type 1 diabetes and his family to limit various complications.
DOI: 10.6084/m9.figshare.23799366.v1
title: Supplementary Material for: Validation of E/e’ using the index beat method as an estimate of left atrial pressure in patients with atrial fibrillation

description: Introduction: Echocardiographic assessment of diastolic function during atrial fibrillation (AF) remains challenging due to the irregular cardiac cycle length. We sought to assess whether the index-beat method, the beat following two preceding cardiac cycles of equal duration, could provide a more reliable measurement of E/e′ (mitral E wave/diastolic tissue Doppler velocity) than the conventional averaging of consecutive beats and hence facilitate the non-invasive estimation of elevated left atrial pressure (LAP) in patients with AF. Methods: We prospectively studied 35 patients with persistent AF who had preserved left ventricular ejection fraction and underwent radiofrequency ablation. LAP was measured in conjunction with trans-septal puncture during catheter ablation. Echocardiography was performed 24 h before ablation and E/e′ was determined using the recommended averaging of 10 beats and the index-beat method, with the observers blinded to the clinical details and LAP measurements. Results: Correlation analysis showed a strong positive correlation between two methods in terms of both septal E/e′ (r = 0.841, p &lt; 0.001) and lateral E/e′ (r = 0.930, p &lt; 0.001). Bland-Altman analysis also showed a good agreement between the two measurement methods in terms of E/e′. E/e′ determined using both conventional averaging and the index-beat method was significantly correlated with LAP (p &lt; 0.05). After Fisher Z transformation, we found that the index-beat septal E/e′ had a better correlation with LAP than did the conventional averaging E/e′ (r = 0.736 vs. r = 0.392, Zr = -2.110, p = 0.035). Furthermore, the index-beat method took significantly less time to measure E/e′ (mean 33.6 s; 95% confidence intervals (CI): 32.1s to 36.2s), than did conventional averaging method (mean 96.2 s; 95% CI: 90.2s to 102.3s; p &lt; 0.001). Receiver operating characteristic curve analysis revealed that the optimal cut-off for predicting mean LAP &gt; 12mmHg was 11 (sensitivity 100%; specificity 77.3%) for index-beat septal E/e′ and 16 (sensitivity 61.5%; specificity 95.5%) for index-beat lateral E/e′. Conclusions: Good correlations were found between E/e′ and LAP in patients with AF, particularly with the index-beat method. Moreover, the index-beat method can easily measure E/e′ at an accuracy similar to that for the conventional averaging of consecutive beats, which can therefore be applied to assess the diastolic dysfunction and potentially improve the diagnosis of heart failure in patients with AF.
DOI: 10.6084/m9.figshare.23716251.v1
title: Supplementary Material for: Predicting Alzheimer’s Disease with Interpretable Machine Learning

description: Introduction: This study aimed to develop novel machine learning models for predicting Alzheimer's disease (AD) and identify key factors for targeted prevention. Methods: We included 1219, 863, and 482 participants aged 60+ years with only sociodemographic, both sociodemographic and self-reported health, both the former two and blood biomarkers information from Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. Machine learning models were constructed for predicting the risk of AD for the above three populations. Model performance was evaluated by discrimination, calibration, and clinical usefulness. Shapley additive explanations (SHAP) was applied to identify key predictors of optimal models. Results: The mean age was 73.49, 74.52, and 74.29 years for the three populations, respectively. Models with sociodemographic information and models with both sociodemographic and self-reported health information showed modest performance. For models with sociodemographic and self-reported health, and blood biomarker information, their overall performance improved substantially, specifically, LR performed best, with an AUC value of 0.818. Blood biomarkers of ptau protein and plasma neurofilament light, age, blood tau protein and education level were top five significant predictors. In addition, taurine, inosine, xanthine, marital status, and L.Glutamine also showed importance to AD prediction. Conclusion: Interpretable machine learning showed promise in screening high-risk AD individual, and could further identify key predictors for targeted prevention.
DOI: 10.6084/m9.figshare.23764656.v1
title: Supplementary Material for: Interaction between serum cotinine, magnesium intake with childhood asthma: a cross-sectional study

description: Introduction: Serum cotinine and magnesium intake are often associated with childhood asthma. This study evaluated the interaction between serum cotinine, magnesium intake with childhood asthma. Methods: This cross-sectional study included 14,159 subjects from National Health and Nutrition Examination Survey 2005-2018. Serum cotinine levels were classified according to the lower quartile: ≤0.2089 ng/mL as low-level and &gt;0.2089 ng/mL as high-level. Magnesium intake were categorized as high (&gt;98 mg/1000kcal) or low level (≤98 mg/1000kcal) based on the upper quartile. Adopted the weighted logistic regression analyses to analyze the association between cotinine, magnesium intake and childhood asthma. Additionally, the combined effect of cotinine and magnesium intake on childhood asthma risk was examined. The stratified analyses based on gender, body mass index and family history of asthma to further examine the relationship between cotinine, magnesium intake and childhood asthma. Results: The prevalence of asthma was approximately 17.56%. Compared to low-level cotinine, high-level cotinine was associated with asthma [odds ratio (OR) = 1.25, 95% confidence interval (CI): 1.04-1.50]. Low-level magnesium intake was related to asthma compared with high-level magnesium intake (OR=1.21, 95%CI: 1.04-1.40). Using interaction analysis, we also found that the combined effect of cotinine and magnesium intake was associated with childhood asthma risk, and the interaction between high-level cotinine and low-level magnesium intake was associated with the highest risk of childhood asthma (OR=1.35, 95%CI: 1.04-1.74). Additionally, this interaction was also found in male, overweight/non-overweight and those with family history of asthma. Conclusion: There was an interaction between serum cotinine and magnesium intake on childhood asthma. The results suggested that implementing smoking bans in certain settings (e.g., communities, schools) and promoting the consumption of magnesium-rich foods may be effective strategies for preventing childhood asthma.
DOI: 10.5281/zenodo.8262669
title: Altes Land hydrogeology

description: DEM: MERIT DEM based digital elevation model of the Altes land Geology Altes Land: Geological layers of the Altes Land Groundwater measurements: Groundwater tables and salinities in Altes Land region Groundwater recharge: Modelled groundwater recharge of the Altes Land displayed in Figure 1 of the manuscript Surface water measurements: Surface water hydraulic heads and salinities in Altes Land region
DOI: 10.5281/zenodo.8262717
title: Altes Land hydrogeology

description: DEM: MERIT DEM based digital elevation model of the Altes land Geology Altes Land: Geological layers of the Altes Land Groundwater measurements: Groundwater tables and salinities in Altes Land region Groundwater recharge: Modelled groundwater recharge of the Altes Land displayed in Figure 1 of the manuscript Surface water measurements: Surface water hydraulic heads and salinities in Altes Land region
DOI: 10.6084/m9.figshare.23683383
title: Supplementary Material for: Reduced DEFA5 expression and STAT3 activation underlie the submucosal invasion of early gastric cancers

description: Introduction Submucosal invasion is a core hallmark of early gastric cancer (EGC) with poor prognosis. However, the molecular mechanism of the progression from intramucosal gastric cancer (IMGC) to early submucosal-invasive gastric cancer (SMGC) is not fully understood. The objective of this study was to identify genes and pathways involved in the submucosal invasion in EGC using comprehensive gene expression analysis. Methods Gene expression profiling was performed for eight cases of IMGC and eight cases of early SMGC with submucosal invasion ≥ 500 μm. To validate the findings of gene expression analysis and to examine the gene expression pattern in tissues, immunohistochemical (IHC) staining was performed for 50 cases of IMGC and SMGC each. Results Gene expression analysis demonstrated that the expression levels of small intestine-specific genes were significantly decreased in SMGC. Among them, defensin alpha 5 (DEFA5) was the most downregulated gene in SMGC, which was further validated in SMGC tissues by IHC staining. Gene set enrichment analysis showed a strong association between SMGC, the JAK-STAT signaling pathway, and the upregulation of STAT3-activating cytokines. The expression of phosphorylated STAT3 was significant in the nucleus of tumor cells in SMGC tissues but not in areas expressing DEFA5. Conclusion The results of this study strongly suggest that the downregulation of DEFA5 and the activation of STAT3 play a significant role in the submucosal invasion of EGC.
DOI: 10.6084/m9.figshare.23683383.v1
title: Supplementary Material for: Reduced DEFA5 expression and STAT3 activation underlie the submucosal invasion of early gastric cancers

description: Introduction Submucosal invasion is a core hallmark of early gastric cancer (EGC) with poor prognosis. However, the molecular mechanism of the progression from intramucosal gastric cancer (IMGC) to early submucosal-invasive gastric cancer (SMGC) is not fully understood. The objective of this study was to identify genes and pathways involved in the submucosal invasion in EGC using comprehensive gene expression analysis. Methods Gene expression profiling was performed for eight cases of IMGC and eight cases of early SMGC with submucosal invasion ≥ 500 μm. To validate the findings of gene expression analysis and to examine the gene expression pattern in tissues, immunohistochemical (IHC) staining was performed for 50 cases of IMGC and SMGC each. Results Gene expression analysis demonstrated that the expression levels of small intestine-specific genes were significantly decreased in SMGC. Among them, defensin alpha 5 (DEFA5) was the most downregulated gene in SMGC, which was further validated in SMGC tissues by IHC staining. Gene set enrichment analysis showed a strong association between SMGC, the JAK-STAT signaling pathway, and the upregulation of STAT3-activating cytokines. The expression of phosphorylated STAT3 was significant in the nucleus of tumor cells in SMGC tissues but not in areas expressing DEFA5. Conclusion The results of this study strongly suggest that the downregulation of DEFA5 and the activation of STAT3 play a significant role in the submucosal invasion of EGC.
DOI: 10.6084/m9.figshare.23905728.v1
title: Supplementary Material for: Serum Insulin-Like Growth Factor-Binding Protein 7 Deriving from Spleen and Lung Could Be Used for Early Recognition of Cardiac Surgery-Associated Acute Kidney Injury

description: <b><i>Introduction:</i></b> The utility of arithmetic product of urinary tissue metalloproteinase inhibitor 2 (TIMP2) and insulin-like growth factor-binding protein 7 (IGFBP7) concentrations has been widely accepted on early diagnosis of acute kidney injury (AKI). However, which organ is the main source of those two factors and how the concentration of IGFBP7 and TIMP2 changed in serum during AKI still remain to be defined. <b><i>Methods:</i></b> In mice, gene transcription and protein levels of IGFBP7/TIMP2 in the heart, liver, spleen, lung, and kidney were measured in both ischemia-reperfusion injury (IRI)- and cisplatin-induced AKI models. Serum IGFBP7 and TIMP2 levels were measured and compared in patients before cardiac surgery and at inclusion (0 h), 2 h, 6 h, and 12 h after intensive care unit (ICU) admission, and compared with serum creatinine (SCr), blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR), and serum uric acid (UA). <b><i>Results:</i></b> In mouse IRI-AKI model, compared with the sham group, the expression levels of IGFBP7 and TIMP2 did not change in the kidney, but significantly upregulated in the spleen and lung. Compared with patients who did not develop AKI, the concentration of serum IGFBP7 at as early as 2 h after ICU admission (sIGFBP7-2 h) was significantly higher in patients who developed AKI. The relationships between sIGFBP7-2 h in AKI patients and log<sub>2</sub> (SCr), log<sub>2</sub> (BUN), log<sub>2</sub> (eGFR), and log<sub>2</sub> (UA) were statistically significant. The diagnostic performance of sIGFBP7-2 h measured by the macro-averaged area under the receiver operating characteristic curve was 0.948 (95% CI, 0.853–1.000; <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> The spleen and lung might be the main source of serum IGFBP7 and TIMP2 during AKI. The serum IGFBP7 value demonstrated good predictive accuracy for AKI following cardiac surgery within 2 h after ICU admission.
DOI: 10.5281/zenodo.8017327
title: Assembly Theory Explains and Quantifies Selection and Evolution

description: Dataset and code to go with the asccciated paper from the assembly calculations
DOI: 10.5281/zenodo.8017326
title: Assembly Theory Explains and Quantifies Selection and Evolution

description: Dataset and code to go with the asccciated paper from the assembly calculations