bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear Simulations of Gravity Wave Tunneling and Breaking over Auckland Island
Authors: Mixa Tyler , Dörnbrack Andreas , Rapp Markus 
Published: February 2021

AbstractHorizontally dispersing gravity waves with horizontal wavelengths of 30–40 km were observed at mesospheric altitudes over Auckland Island by the airborne advanced mesospheric temperature mapper during a Deep Propagating Gravity Wave Experiment (DEEPWAVE) research flight on 14 July 2014. A 3D nonlinear compressible model is used to determine which propagation conditions enabled gravity wave penetration into the mesosphere and how the resulting instability characteristics led to widespread momentum deposition. Results indicate that linear tunneling through the polar night jet enabled quick gravity wave propagation from the surface up to the mesopause, while subsequent instability processes reveal large rolls that formed in the negative shear above the jet maximum and led to significant momentum deposition as they descended. This study suggests that gravity wave tunneling is a viable source for this case and other deep propagation events reaching the mesosphere and lower thermosphere.
Evaluating Convective Initiation in High-Resolution Numerical Weather Prediction Models Using GOES-16 Infrared Brightness Temperatures
Authors: Henderson David S. , Otkin Jason A. , Mecikalski John R. 
Published: February 2021

AbstractThe evolution of model-based cloud-top brightness temperatures (BT) associated with convective initiation (CI) is assessed for three bulk cloud microphysics schemes in the Weather Research and Forecasting Model. Using a composite-based analysis, cloud objects derived from high-resolution (500 m) model simulations are compared to 5-min GOES-16 imagery for a case study day located near the Alabama–Mississippi border. Observed and simulated cloud characteristics for clouds reaching CI are examined by utilizing infrared BTs commonly used in satellite-based CI nowcasting methods. The results demonstrate the ability of object-based verification methods with satellite observations to evaluate the evolution of model cloud characteristics, and the BT comparison provides insight into a known issue of model simulations producing too many convective cells reaching CI. The timing of CI from the different microphysical schemes is dependent on the production of ice in the upper levels of the cloud, which typically occurs near the time of maximum cloud growth. In particular, large differences in precipitation formation drive differences in the amount of cloud water able to reach upper layers of the cloud, which impacts cloud-top glaciation. Larger cloud mixing ratios are found in clouds with sustained growth leading to more cloud water lofted to the upper levels of the cloud and the formation of ice. Clouds unable to sustain growth lack the necessary cloud water needed to form ice and grow into cumulonimbus. Clouds with slower growth rates display similar BT trends as clouds exhibiting growth, which suggests that forecasting CI using geostationary satellites might require additional information beyond those derived at cloud top.
Outcomes of Cardiac Diffuse Large B-Cell Lymphoma in the Rituximab Era
Authors: Al-Juhaishi Taha , Abu Zeinah Ghaith , Al-Kindi Sadeer 
Published: February 2021

Introduction:
Cardiac lymphomas are very rare with diffuse large B-cell lymphoma (DLBCL) considered to be the most common histology. These lymphomas can be either local "primary cardiac" disease, or part of dissemination by systemic lymphoma. There is limited data regarding outcomes of patients with this disease. We sought to evaluate the outcomes of cardiac DLBCL in both pre- and rituximab eras using a large retrospective database.
Methods:
The public Surveillance, Epidemiology and End Results (SEER) database was used to identify all patients diagnosed with DLBCL and heart as the primary disease site. Data cutoff in the database was in 2016. Patients with missing date of diagnosis or survival data were excluded. Patients were divided into two groups based on diagnosis year, with rituximab cohort included all DLBCLs diagnosed in 2006 and later (2006 was FDA approval year of rituximab in untreated DLBCL). Treatment effect (surgery, radiation, chemotherapy) was analyzed when available. survival was estimated using the Kaplan-Meier method, and compared using Log-Rank test. Cox proportional hazards models were used for adjusted survival analyses.
Results:
Total of 106 patients were included in the final analysis, baseline characteristics are summarized in table 1. Median age at diagnosis was 69.5 years with only about 10% of patients being 50 years or younger. Most patients were white 71 (67%), had local stage I/II disease 68 (64.2%), and belonged to the rituximab era group 71 (67%). Most patients had chemotherapy 82 (77.4%), while only 25 (23.6%) had surgery, and 16 (15.1%) had radiotherapy. Median overall survival (OS) for the entire cohort was 22 months (0-292). Median OS was 16 months (95% CI, 0.55 -31) for the pre-rituximab group, and was 26 months (95% CI, 7.5 - 45) for the rituximab group which were not statistically different (p-value =0.340). Median lymphoma-specific survival (LCS) was 30 months (95% CI, 8.0 -52) for the pre-rituximab group, and was 36 months (95% CI, 16 - 158) for the rituximab group which were not statistically different (p-value =0.295). OS and LCS were also not different between the two era groups when stratified by chemotherapy (figure 1). On univariate analysis, Chemotherapy was associated with better OS [HR = 0.472, 95% CI (0.277-0.806); p-value = 0.006] but not LCS [HR = 0.690, 95% CI (0.341-1.396); p-value = 0.302]. Using a multivariate analysis model, both OS and LCS were associated with lymphoma stage, insurance status and age but not with diagnosis era or chemotherapy (table 2).
Conclusion:
Cardiac DLBCLs are rare and affecting mostly the elderly. No significant improvement in outcomes were noted in the current rituximab era. Age, disease stage, and having health insurance were associated with better outcomes. The role of chemotherapy needs further evaluation in larger studies.

Disclosures
No relevant conflicts of interest to declare.
Prognostic value of right atrial dilation in patients with pulmonary embolism
Authors: Lerchbaumer Markus H. , Ebner Matthias , Ritter Christian O. , Steimke Laura , Rogge Nina I.J. , Sentler Carmen , Thielmann Aaron , Hobohm Lukas , Keller Karsten , Lotz Joachim , Hasenfuß Gerd , Wachter Rolf , Hamm Bernd , Konstantinides Stavros V. , Aviram Galit , Lankeit Mareike 
Published: February 2021

AimsRight atrial (RA) dilation and stretch provide prognostic information in patients with cardiovascular diseases. We investigated the prevalence, confounding factors and prognostic relevance of RA dilation in patients with pulmonary embolism (PE).MethodsOverall, 609 PE patients were consecutively included in a prospective single-centre registry between September 2008 and August 2017. Volumetric measurements of heart chambers were performed on routine non-electrocardiographic-gated computed tomography and plasma concentrations of mid-regional pro-atrial natriuretic peptide (MR-proANP) measured on admission. An in-hospital adverse outcome was defined as PE-related death, cardiopulmonary resuscitation, mechanical ventilation or catecholamine administration.ResultsPatients with an adverse outcome (11.2%) had larger RA volumes (median 120 (interquartile range 84–152)versus102 (78–134) mL; p=0.013), RA/left atrial (LA) volume ratios (1.7 (1.2–2.4)versus1.3 (1.1–1.7); p<0.001) and MR-proANP levels (282 (157–481)versus129 (64–238) pmol·L−1; p<0.001) compared to patients with a favourable outcome. Overall, 499 patients (81.9%) had a RA/LA volume ratio ≥1.0 and a calculated cut-off value of 1.8 (area under the curve 0.64, 95% CI 0.56–0.71) predicted an adverse outcome, both in unselected (OR 3.1, 95% CI 1.9–5.2) and normotensive patients (OR 2.7, 95% CI 1.3–5.6). MR-proANP ≥120 pmol·L−1was identified as an independent predictor of an adverse outcome, both in unselected (OR 4.6, 95% CI 2.3–9.3) and normotensive patients (OR 5.1, 95% CI 1.5–17.6).ConclusionsRA dilation is a frequent finding in patients with PE. However, the prognostic performance of RA dilation appears inferior compared to established risk stratification markers. MR-proANP predicted an in-hospital adverse outcome, both in unselected and normotensive PE patients, integrating different prognostic relevant information from comorbidities.
Microbiological community structure on logs used for groynes in a riverbank system
Authors: Ishiyama Nanako , Horisawa Sakae , Hara Tadashi , Yoshida Makoto , Momohara Ikuo 
Published: February 2021

AbstractIt is important for civil engineering applications to investigate resistance to wood decay in aqueous environments. DNA from microorganisms inhabiting logs (groynes) that had been used for about 15 years as a water control system to prevent riverbank erosion was extracted and the microbial community structure was examined. DNA was extracted from specimens in four sections, above and under the water, under the ground and from the bottom parts of the logs that were pulled out from the river. Then, barcode sequences for the detection of fungi and bacteria were amplified from each DNA sample by polymerase chain reaction. Microbes were identified from the nucleotide sequences, and the relationships between microbes and environmental conditions were discussed. The wood in the section above the water was significantly decayed, while slight decay and strength loss were observed in the other sections. The white-rot basidiomycete Xeromphalina sp. was detected in the section above the water, suggesting that this fungal species was responsible for the significant decay of the logs in this study. Wood in the sections under the water and under the ground including the bottom of the logs was not decayed even though the fungus was detected in all sections of the logs, suggesting that Xeromphalina sp. could not degrade the wood in the water and underground where the oxygen supply was limited.
Hierarchical non-negative matrix factorization using clinical information for microbial communities
Authors: Abe Ko , Hirayama Masaaki , Ohno Kinji , Shimamura Teppei 
Published: February 2021

Abstract
Background
The human microbiome forms very complex communities that consist of hundreds to thousands of different microorganisms that not only affect the host, but also participate in disease processes. Several state-of-the-art methods have been proposed for learning the structure of microbial communities and to investigate the relationship between microorganisms and host environmental factors. However, these methods were mainly designed to model and analyze single microbial communities that do not interact with or depend on other communities. Such methods therefore cannot comprehend the properties between interdependent systems in communities that affect host behavior and disease processes.

Results
We introduce a novel hierarchical Bayesian framework, called BALSAMICO (BAyesian Latent Semantic Analysis of MIcrobial COmmunities), which uses microbial metagenome data to discover the underlying microbial community structures and the associations between microbiota and their environmental factors. BALSAMICO models mixtures of communities in the framework of nonnegative matrix factorization, taking into account environmental factors. We proposes an efficient procedure for estimating parameters. A simulation then evaluates the accuracy of the estimated parameters. Finally, the method is used to analyze clinical data. In this analysis, we successfully detected bacteria related to colorectal cancer.

Conclusions
These results show that the method not only accurately estimates the parameters needed to analyze the connections between communities of microbiota and their environments, but also allows for the effective detection of these communities in real-world circumstances.
Changes in the growth, ileal digestibility, intestinal histology, behavior, fatty acid composition of the breast muscles, and blood biochemical parameters of broiler chickens by dietary inclusion of safflower oil and vitamin C
Authors: Amer Shimaa A. , Mohamed Wafaa A. M. , Gharib Heba S. A. , Al-Gabri Naif A. , Gouda Ahmed , Elabbasy Mohamed Tharwat , Abd El-Rahman Ghada I. , Omar Anaam E. 
Published: February 2021

Abstract
Background
The effects of safflower oil and vitamin C (Vit. C) inclusion in broiler chicken diets on the growth performance, apparent ileal digestibility coefficient “AID%” of amino acids, intestinal histology, behavior, carcass traits, fatty acid composition of the breast muscle, antioxidant and immune status for a 35-day feeding period were evaluated. A total of 300 three-day-old Ross chicks (58.25 g ± 0.19) were randomly allotted in a 2 × 3 factorial design consisting of two levels of vitamin C (0 and 400 mg/kg diet) and three levels of safflower oil (0, 5, and 10 g/kg diet).

Results
An increase in the final body weight, total body weight gain, total feed intake, and the relative growth rate (P <  0.05) were reported by safflower oil and vitamin C inclusion. Dietary supplementation of safflower oil and vitamin C had a positive effect (P <  0.05) on the ingestive, resting, and feather preening behavior. Vitamin C supplementation increased (P <  0.05) the AID% of lysine, threonine, tryptophan, arginine, and valine. Safflower inclusion (10 g/kg) increased (P <  0.05) the AID% of methionine and isoleucine. Safflower oil inclusion increased (P <  0.05) the levels of stearic acid, linoleic acid, saturated fatty acids, and omega-3 fatty acids (ω-3) in the breast muscle. In contrast, the supplementation of only 10 g of safflower oil/kg diet increased (P = 0.01) the omega-3/omega-6 (ω-3/ω-6) fatty acids ratio. Vit. C supplementation increased (P <  0.05) the CAT serum levels, SOD, and GSH enzymes. Dietary supplementation of safflower oil and vitamin C improved the intestinal histology. They increased the villous height and width, crypt depth, villous height/crypt depth ratio, mucosal thickness, goblet cell count, and intra-epithelium lymphocytic lick cell infiltrations. The serum levels of IgA and complement C3 were increased (P <  0.01) by Vit. C supplementation and prominent in the 400 vit. C +  10 safflower Oil group.

Conclusion
A dietary combination of safflower oil and vitamin C resulted in improved growth rate, amino acids AID%, intestinal histology, welfare, immune and antioxidant status of birds, and obtaining ω-3 and linoleic acid-enriched breast muscles. The best inclusion level was 400 vit. C +  10 safflower Oil.
Circulating levels of IL-33 are elevated by obesity and positively correlated with metabolic disorders in Chinese adults
Authors: Tang Haoneng , Liu Ning , Feng Xiaojing , Yang Yanyi , Fang Yiyuan , Zhuang Siqi , Dai Yufeng , Liu Meilian , Tang Lingli 
Published: February 2021

Abstract
Background
Interleukin-33 (IL-33) plays a pivotal role in regulating innate immune response and metabolic homeostasis. However, whether its circulating level is correlated with obesity and metabolic disorders in humans remains largely unknown. We aimed to address this gap by determining IL-33 serum level and its downstream type 2 inflammatory cytokines interleukin-5 (IL-5) and interleukin-13 (IL-13) in overweight/obese population, and analyzing the specific associations between IL-33 and obesity metabolic phenotypes.

Methods
217 subjects were enrolled and divided into three groups: healthy control (HC) subjects, metabolically healthy overweight/obese (MHOO) subjects and metabolically unhealthy overweight/obese (MUOO) subjects. Circulating levels of IL-33, IL-5 and IL-13 were measured using ELISA analyses. Multivariate regression analyses were further performed to determine the independent association between IL-33 and obesity metabolic phenotypes.

Results
Circulating levels of IL-33 were significantly elevated in subjects of MUOO group compared with HC group and MHOO group, while no significant difference was observed between the latter two groups in IL-33 levels. Consistent with this, serum levels of IL-5/13 were higher in the MUOO group compared with HC and MHOO groups. After adjusted for all confounders, MUOO phenotype was significantly associated with increased IL-33 serum levels (OR = 1.70; 95% CI 1.09–2.64; p = 0.019). With the MHOO group as the reference population, higher circulating level of IL-33 was also positively associated with MUOO phenotype after adjusting for confounders (OR = 1.50; 95% CI 1.20–1.88; p = 2.91E−4). However, there was no significant association between MHOO phenotype and IL-33 levels (p = 0.942). Trend analysis further confirmed the positive correlation between MUOO phenotype and IL-33 level (p for trend = 0.019). Additionally, IL-33 was significantly and positively correlated with diastolic blood pressure (DBP), total cholesterol (TC), alanine aminotransferase (ALT), aspartate aminotransferase (AST), white blood cell (WBC), neutrophil and IL-5 only in MUOO group, while inversely correlated with high density lipoprotein cholesterol (HDL-C) in MHOO subjects.

Conclusion
Circulating levels of IL-33 were significantly elevated in overweight/obese Chinese adults with metabolic disorders. Increased levels of IL-33 were positively associated with metabolically unhealthy overweight/obese phenotype and several metabolic syndrome risk factors.
Cranial organs at risk delineation: heterogenous practices in radiotherapy planning
Authors: Vogin Guillaume , Hettal Liza , Bartau Clarisse , Thariat Juliette , Claeys Marie-Virginie , Peyraga Guillaume , Retif Paul , Schick Ulrike , Antoni Delphine , Bodgal Zsuzsa , Dhermain Frederic , Feuvret Loic 
Published: February 2021

Abstract
Background
Segmentation is a crucial step in treatment planning that directly impacts dose distribution and optimization. The aim of this study was to evaluate the inter-individual variability of common cranial organs at risk (OAR) delineation in neurooncology practice.

Methods
Anonymized simulation contrast-enhanced CT and MR scans of one patient with a solitary brain metastasis was used for delineation and analysis. Expert professionals from 16 radiotherapy centers involved in brain structures delineation were asked to segment 9 OAR on their own treatment planning system. As reference, two experts in neurooncology, produced a unique consensual contour set according to guidelines. Overlap ratio, Kappa index (KI), volumetric ratio, Commonly Contoured Volume, Supplementary Contoured Volume were evaluated using Artiview™ v 2.8.2—according to occupation, seniority and level of expertise of all participants.

Results
For the most frequently delineated and largest OAR, the mean KI are often good (0.8 for the parotid and the brainstem); however, for the smaller OAR, KI degrade (0.3 for the optic chiasm, 0.5% for the cochlea), with a significant discrimination (p < 0.01). The radiation oncologists, members of Association des Neuro-Oncologue d’Expression Française society performed better in all indicators compared to non-members (p < 0.01). Our exercise was effective in separating the different participating centers with 3 of the reported indicators (p < 0.01).

Conclusion
Our study illustrates the heterogeneity in normal structures contouring between professionals. We emphasize the need for cerebral OAR delineation harmonization—that is a major determinant of therapeutic ratio and clinical trials evaluation.
Changes in epigenetic profiles throughout early childhood and their relationship to the response to pneumococcal vaccination
Authors: Pischedda Sara , O’Connor Daniel , Fairfax Benjamin P. , Salas Antonio , Martinon-Torres Federico , Pollard Andrew J. , Trück Johannes 
Published: February 2021

AbstractBackgroundPneumococcal infections are a major cause of morbidity and mortality in young children and immaturity of the immune system partly underlies poor vaccine responses seen in the young. Emerging evidence suggests a key role for epigenetics in the maturation and regulation of the immune system in health and disease. The study aimed to investigate epigenetic changes in early life and to understand the relationship between the epigenome and antigen-specific antibody responses to pneumococcal vaccination.MethodsThe epigenetic profiles from 24 healthy children were analyzed at 12 months prior to a booster dose of the 13-valent pneumococcal conjugate vaccine (PCV-13), and at 24 months of age, using the Illumina Methylation 450 K assay and assessed for differences over time and between high and low vaccine responders.ResultsOur analysis revealed 721 significantly differentially methylated positions between 12 and 24 months (FDR < 0.01), with significant enrichment in pathways involved in the regulation of cell–cell adhesion and T cell activation. Comparing high and low vaccine responders, we identified differentially methylated CpG sites (Pvalue < 0.01) associated withHLA-DPB1andIL6.ConclusionThese data imply that epigenetic changes that occur during early childhood may be associated with antigen-specific antibody responses to pneumococcal vaccines.
Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits
Authors:   The VA Million Veteran Program, Bone William P. , Siewert Katherine M. , Jha Anupama , Klarin Derek , Damrauer Scott M. , Chang Kyong-Mi , Tsao Philip S. , Assimes Themistocles L. , Ritchie Marylyn D. , Voight Benjamin F. 
Published: February 2021

Abstract
Background
Identification of genetic risk factors that are shared between Alzheimer’s disease (AD) and other traits, i.e., pleiotropy, can help improve our understanding of the etiology of AD and potentially detect new therapeutic targets. Previous epidemiological correlations observed between cardiometabolic traits and AD led us to assess the pleiotropy between these traits.

Methods
We performed a set of bivariate genome-wide association studies coupled with colocalization analysis to identify loci that are shared between AD and eleven cardiometabolic traits. For each of these loci, we performed colocalization with Genotype-Tissue Expression (GTEx) project expression quantitative trait loci (eQTL) to identify candidate causal genes.

Results
We identified three previously unreported pleiotropic trait associations at known AD loci as well as four novel pleiotropic loci. One associated locus was tagged by a low-frequency coding variant in the gene DOCK4 and is potentially implicated in its alternative splicing. Colocalization with GTEx eQTL data identified additional candidate genes for the loci we detected, including ACE, the target of the hypertensive drug class of ACE inhibitors. We found that the allele associated with decreased ACE expression in brain tissue was also associated with increased risk of AD, providing human genetic evidence of a potential increase in AD risk from use of an established anti-hypertensive therapeutic.

Conclusion
Our results support a complex genetic relationship between AD and these cardiometabolic traits, and the candidate causal genes identified suggest that blood pressure and immune response play a role in the pleiotropy between these traits.