bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genes and Mechanisms Associated With Experimentally Induced Bovine Respiratory Disease Identified With Supervised Machine Learning Methodology on Integrated Transcriptomic Datasets
Authors: Scott Matthew , Woolums Amelia , Swiderski Cyprianna , Perkins Andy , Nanduri Bindu 
Published: August 2021

Abstract
Bovine respiratory disease (BRD) is a multifactorial disease involving complex host immune interactions shaped by pathogenic agents and environmental factors. Advancements in RNA sequencing and associated analytical methods are improving our understanding of host response related to BRD pathophysiology. Supervised machine learning (ML) approaches present one such method for analyzing new and previously published transcriptome data to identify novel genes and mechanisms. Our objective was to apply ML models to lung and immunological tissue datasets acquired from previous clinical BRD experiments to identify genes that classify disease with high accuracy. Raw mRNA sequencing reads from 151 bovine datasets (n=123 BRD, n=28 control) were downloaded from NCBI-GEO. Quality filtered reads were assembled in a HISAT2/Stringtie2 pipeline. Raw gene counts for ML analysis were normalized, transformed, and analyzed with MLSeq, utilizing six ML models. Cross-validation parameters (5-fold, repeated 10 times) were applied in a 70:30 training/testing ratio. Downstream analysis of genes identified by the top sparse classifiers for each etiological association was performed within WebGestalt and Reactome (FDR < 0.05). Support vector machines was routinely the top non-sparse classifier for predicting etiological disease versus sham control. Nearest shrunken centroid and Poisson linear discriminant analysis with power transformation could reliably classify IBR and BRSV with 100% accuracy. Genes identified in IBR and BRSV, but not BVDV, were related to type I interferon production and IL-8 secretion, specifically in lymphoid tissue and not lung. Genes identified in Mannheimia haemolytica infections were involved in activating classical and alternative pathways of complement. Novel findings, including expression of genes related to reduced mitochondrial oxygenation and ATP synthesis in consolidated lung tissue, were discovered. Genes identified in each analysis represent distinct genomic events relevant to understanding and predicting clinical BRD. The few genes shared across analyses may be reliably associated with clinical BRD. Our analysis demonstrates the utility of ML with published datasets for discovering functional information to support prediction and understanding BRD acquisition.
Impact of Lipid Profile, Cardiac Biomarkers, Serum Angiotensin-Converting Enzyme Activity, Oxidative Stress and Antioxidant on Blood Pressure Status
Authors: Mehri Sounira , Rebhi Ikhlass , KHAMLAOUI Wided , Finsterer Josef , Chaaba Raja , zarrouk Sinda , HAMMAMI Sonia , HAMMAMI Mohamed 
Published: August 2021

Abstract
The hemodynamic determinants of myocardial oxygen demand measured were heart rate (HR), systolic blood pressure (BP), and rate pressure product (RPP). This study aimed to evaluate the impact of lipid profile, cardiac biomarkers, and serum angiotensin-converting enzyme (ACE) activity, oxidative stress (plasma malondialdehyde, MDA; conjugated diene, DC), and antioxidant status (glutathione peroxidase, GPx) on BP. Three hundred and six non-ST-elevated myocardial infarction (NSTEMI) patients compared to 410 healthy controls. The diastolic and systolic BP was correlated positively with serum ACE activity. The rate pressure product (RPP) was correlated negatively with Fasting glucose (r= -0.144; p = 0.012), HbA1c (r= -0.117; p = 0.041) and GPx activity (r= -0.148; p = 0.009), and positively with smoking (r = 0,197; p = 0.001), BMI (r = 0,219; p = 0.001), peak cTnI (r = 0.131; p = 0.022), serum ACE activity (r = 0,190; p = 0.001) and DC level (r = 0.189; p = 0.001) in NSTEMI patients. Regarding healthy controls, no correlation was found between the diastolic or systolic BP with serum ACE activity, peak cTnI, MDA, DC level, GPx activity, and lipid parameters. The existence of a specific correlation between the rate pressure product, diastolic and systolic BP and, lipid profile, serum ACE activity and, cardiac biomarkers, oxidative stress, and antioxidant status increase the NSTEMI risk on patients.
A Real-World-Data Retrospective Cohort Study of Low Estrogen Receptor Positive Early Breast Cancer: Natural History and Treatment Outcomes.
Authors: Costa Ricardo , Bari Shahla , Boulware David , Li Jiannong , Loftus Loretta , Soyano Aixa , Jameel Zena , Khong Hung , Czerniecki Brian 
Published: August 2021

Abstract
Purpose
Estrogen receptor–positive (ER+) breast cancer (BC) is a heterogeneous disease with an ongoing debate regarding the optimal cutoff point for clinically relevant ER expression. We used a real-world database to assess prognostic and predictive values of lower ER expression levels on treatment outcomes with endocrine therapy.
Methods
We used a nationwide electronic health record– (EHR-) derived deidentified database. Descriptive statistics were used to evaluate the correlation between ER expression, tumor characteristics, and treatment patterns among patients with early-stage BC. We used Kaplan-Meier survival curves to estimate relapse-free survival (RFS) and overall survival (OS). To assess an optimal ER expression level cut point, correlations between ER+ expression and clinical outcomes were performed.
Results
Among 4697 patients with early-stage BC, 83 (1.76%) had ER+-low BC (ER expression, 1%-9.99%), and 36 (0.8%) had ER+-intermediate BC (10%-19.9%). ER+-low tumors were associated with higher tumor grade, larger size and higher axillary tumor burden than ER+-high tumors (≥ 20% ER expression). African Americans had a higher prevalence of both triple-negative BC (TNBC; 21%) and ER+-low BC (22%) than ER+-high tumors (8%). Patients with ER+-low and ER+-intermediate tumors had survival outcomes similar to patients with TNBC and worse survival outcomes than patients with ER+-high tumors (P < .001). No significant correlations between endocrine therapy and RFS or OS were observed among patients with either ER+-low or ER+-intermediate BCs. Further tumors with < 20% ER expression were associated with worse outcomes.
Conclusions
Patients with ER expression levels < 20% derive minimal benefit from endocrine therapies.
Wireless Power Transfer System with Enhanced Efficiency by Using Frequency Reconfigurable Metamaterial
Authors: Shan Dongyong , Wang Haiyue , Cao Ke , Zhang Junhua 
Published: August 2021

Abstract
The wireless power transfer (WPT) system has been widely used in various fields such as household appliances, electric vehicle charging and sensor applications. A frequency reconfigurable magnetic resonant coupling wireless power transfer (MRCWPT) system with dynamically enhanced efficiency by using the frequency reconfigurable metamaterial is proposed in this paper. The reconfigurability is achieved by adjusting the capacitance value of the variable capacitor connected in the coil of the system. Finite element simulation results have shown that the frequency reconfigurable electromagnetic metamaterial can manipulate the direction of the electromagnetic field of the system due to its abnormal effective permeability. The ultra-thin frequency reconfigurable metamaterial is designed at the different working frequency of 14.1 MHz, 15 MHz, 16.2 MHz, 17.5 MHz, 19.3 MHz, 21.7 MHz and 25 MHz to enhance the magnetic field and power transfer efficiency (PTE) of the system. Frequency reconfigurable mechanism of the system with the frequency reconfigurable metamaterial is derived by the equivalent circuit theory. Finally, further measurement which verifies the simulation by reasonable agreement is carried out. PTE of the system by adding the metamaterial are 59%, 73%, 67%, 66%, 65%, 60% and 58% at different working frequencies. PTE of the system without and with the metamaterial is 72% and 49% at the distance of 120 mm and the frequency of 15 MHz, respectively.
Biomechanical Effects of Polyetheretherketone and Titanium Rods in Transforaminal Lumbar Interbody Fusion: A Finite Element Analysis
Authors: Li Jie , Cao Shuai , Wang Jie , Zong Gaoyang , Qiao Hao , Liu Weidong , Li Haopeng , Lu Teng 
Published: August 2021

Abstract
Background: Currently, the comprehensive biomechanical evaluation of polyetheretherketone (PEEK) rods in transforaminal lumbar interbody fusion (TLIF) is limited. The purpose of this study was to compare the biomechanical differences between titanium alloy (Ti) rods and PEEK rods in TLIF. Methods: L3-5 lumbar models were developed using the finite element method. Four surgical models of TLIF were constructed by simulating different fusion methods and rods: cage fusion with Ti rods, cage fusion with PEEK rods, bone graft alone with Ti rods, and bone graft alone with PEEK rods. The range of motion (ROM) and stress distribution of the surgical and adjacent segments were then compared. Results: Compared to the Ti rods, the PEEK rods increased the ROM by 0.7–20% at the L4/5 segment and decreased the ROM by 0.8–15.1% at the L3/4 segment. The disc stresses at the L3/4 level were similar among the surgical models (0.79–1.80 MPa). The peak stresses of the screws, rods, and bone-screw interfaces in the PEEK rod models were 0–1.2 times, 1.6–4.4 times, and 0–1.4 times lower than those of the Ti rod models, respectively. PEEK rods increased the average strain of the bone graft by 0.5–61.6% and the stresses of the cage by 0.9–44.1% and endplates by 2.1–52.9%. Conclusion: In TLIF, PEEK rods played a positive role in restoring the ROM. They also increased the strain of the bone graft, stresses of the endplates and cages, and the risk of rod fracture and reduced the stress of the screw-rod system. Bone grafts alone combined with PEEK rods had acceptable biomechanical behavior in TLIF.
Real-World Effectiveness of Liraglutide Versus Dulaglutide In Japanese Patients With Type 2 Diabetes: A Retrospective Study
Authors: Tanaka Kenichi , Okada Yosuke , Tokutsu Akemi , Tanaka Yoshiya 
Published: August 2021

Abstract
Real-world data comparing the effectiveness of various glucagon-like peptide 1 receptor agonists (GLP-1 RAs) in type 2 diabetes mellitus (T2DM) are limited. We investigated the clinical effectiveness of liraglutide and dulaglutide in Japanese T2DM in a real-world setting. This retrospective study included 179 patients with T2DM who were treated with GLP-1 RA for at least 12 months (liraglutide, n=97; dulaglutide, n=82). Changes in glycated hemoglobin (HbA1c) at the end of 12-month treatment were evaluated. Compared with the liraglutide group, the dulaglutide group included significantly older patients with longer disease duration, lower body mass index, and higher proportion of dementia cases. HbA1c was significantly lower at 12 months in both groups (liraglutide, 8.9 to 7.6%; dulaglutide, 8.8 to 7.5%). Hierarchical regression analysis showed no differences in the extent of changes in HbA1c at 12 months between the two agents, after adjustment for differences in patient characteristics and drug adjustments during the 12-month period. High baseline HbA1c, the addition of GLP-1 RA treatment, and in-hospital initiation of GLP-1 RA treatment were identified as significant contributing factors to HbA1c reduction. Although patient characteristics were different between the two treatment groups, comparable HbA1c-lowering effects were noted in real-world settings.
Gaucher disease: clinical phenotypes and refining GBA mutational spectrum in Thai patients
Authors: Phetthong Tim , Tim-Aroon Thipwimol , Khongkraparn Arthaporn , Noojarern Saisuda , Kuptanon Chulaluck , Wichajarn Khunton , Sathienkijkanchai Achara , Suphapeetiporn Kanya , Charoenkwan Pimlak , Tantiworawit Adisak , Noentong Naruwan , Wattanasirichaigoon Duangrurdee 
Published: August 2021

Abstract
Background
Gaucher disease (GD is a rare lysosomal storage disorder, characterized by hepatosplenomegaly and pancytopenia, with or without neurologic involvement. The disorder is categorized into three phenotypes: GD type 1 or nonneuronopathic GD; GD type 2 or acute neuronopathic GD; and GD type 3 or chronic neuronopathic GD. The purposes of this study were to describe clinical characteristics of Thai GD in patients diagnosed and/or followed up during 2010–2018 and to perform re-genotyping including analysis of GBA recombinant alleles which had not been investigated in Thai patients before.
Results
There were 27 patients from seven medical centers, enrolled in the study. All the cases had pediatric onset. GD3 (44.5%) was the most common phenotype, followed by GD2 (40.7%) and GD1 (14.8%), with one case of neonatal GD. The median age of onset for GD1, GD2, and GD3 was 72, 4 and 12 months, respectively, suggesting relatively earlier onset of GD1 and GD3 in Thai patients. All patients with GD1 and most patients with GD3 received ERT. Four patients with GD3 had ERT followed by HSCT. Patients with GD3 who received no or late ERT showed unfavorable outcomes. We identified 14 mutations including two novel (p.S384F and p.W533*) and 12 reported pathogenic variants: p.L483P, p.N409S, p.R159W, p.P305A, p.A175G, p.D448H, p.V414L, IVS2 + 1G > A, IVS6-1G > C, IVS7 + 1G > C, IVS9-3C > G, and Rec1a. The p.L483P was the most prevalent allele found in this study, at 66% (33/50 alleles), followed by IVS2 + 1G > A, Rec1a, and IVS6-1G > C. Twenty-four percent of patients were reassigned with validated genotypes, most of whom (4 of 6) were patients with GD2. The [p.S384F + p.W533*] being compounded with p.L483P, was found in the patient with neonatal GD, suggesting that the p.S384F could potentiate the deleterious effect of the p.W533*, and/or vice versa.
Conclusions
Neuronopathic GD was strikingly prevalent among Thai affected population. Homozygous p.L483P was the most common genotype identified in Thai patients. Recombinant allele Rec1a and splicing mutations were associated with GD2 and severe cases of GD3. Mutation spectrum could be useful for designing stepwise molecular analysis, genetic screenings in population, and new therapeutic research for neuronopathic GD.
Influence of Surface Passivation on Perovskite CsPbBr1.2I1.8 Quantum Dots and Application of High Purity Red Light-Emitting Diodes
Authors: Chen Lung-Chien , Tien Yen-Hung , Tian Jianjun 
Published: August 2021

Abstract
In this work, trioctylphosphine oxide (TOPO) ligand is employed to improve the quality of CsPbBr1.2I1.8 quantum dots (QDs) films. Lead nitrate (Pb(NO3)2) is also used to passivate the surface of the films. The study of ligand and surface passivation on the luminous efficiency of red light-emitting diode (LED) is discussed. The CsPbBr1.2I1.8 QDs films co-doped with TOPO and Pb(NO3)2 can effectively improve the performance of the CsPbBr1.2I1.8 QDs LEDs due to reduction of non-radiation recombination of the carriers and smooth morphology in the active layer, thus improving the injection and transportation capabilities of carriers. As a result, the highest luminosity and current efficiency are 502.7 cd/m2 and 0.175 cd/A, respectively.
Increasing Autophagy ameliorate all-trans-retinal-activated NLRP3 Inflammasome 2 in human THP-1 macrophage cells
Authors: Xia Qingqing , Huang Lvxing , Chen Hengyi , Zhou Yingying , Zhang Lingmin , Xie Jing , Wang Junjuan , Li Jie 
Published: August 2021

Abstract
BackgroundProfound inflammation that mediated by innate immune sensors can be observed in retina, and is considered to play an important role in the pathogenesis of all-trans-retinal (atRAL)-caused retinal degeneration. However, the underlying mechanism remains elusive. MethodsCell viability was detected with Cell Counting Kit-8 (CCK-8). The concentration of IL-1β was evaluated using IL-1β ELISA Kits. The levels of autophagy-related proteins were measured by Western blotting. The measurement of autophagic flux was performed with virus vectors packing tandem monomeric mCherry-eGFP-tagged LC3B. ResultsWe focused on studying the effects of atRAL on macrophage cell line THP-1 and determining the underlying signal pathway through pharmacological and genetical manipulation. We first found the maturation and release of IL-1β was regulated by the activation of NLRP3 inflammasome. We secondly found that mitochondria-associated reactive oxygen species (ROS) were involved in the regulation of NLRP3 inflammasome activation and caspase 1 cleavage. Finally, we found that atRAL functionally activated autophagy in THP-1 cells, and atRAL-caused NLRP3 inflammasome activation is suppressed by autophagy. Overall, our results show atRAL simultaneously activates NLRP3 inflammasome and autophagy in THP-1 cells, and increasing autophagy leads to the inhibition of the excessive activation of NLRP3 inflammasome. Our study provides new insight into the pathogenesis of aging related retina degeneration.
Systematic comparison of incomplete-supervision approaches for biomedical imaging classification
Authors: Boushehri Sayedali Shetab , Qasim Ahmad , Waibel Dominik , Schmich Fabian , Marr Carsten 
Published: August 2021

Abstract
Deep learning based classification of biomedical images requires manual annotation by experts, which is time-consuming and expensive. Incomplete-supervision approaches including active learning, pre-training and semi-supervised learning address this issue and aim to increase classification performance with a limited number of annotated images. Up to now, these approaches have been mostly benchmarked on natural image datasets, where image complexity and class balance typically differ considerably from biomedical classification tasks. In addition, it is not clear how to combine them to improve classification performance on biomedical image data. We thus performed an extensive grid search combining seven active learning algorithms, three pre-training methods and two training strategies as well as respective baselines (random sampling, random initialization, and supervised learning). For four biomedical datasets, we started training with 1% of labeled data and increased it by 5% iteratively, using 4-fold cross-validation in each cycle. We found that the contribution of pre-training and semi-supervised learning can reach up to 20% macro F1-score in each cycle. In contrast, the state-of-the-art active learning algorithms contribute less than 5% to macro F1-score in each cycle. Based on performance, implementation ease and computation requirements, we recommend the combination of BADGE active learning, ImageNet-weights pre-training, and pseudo-labeling as training strategy, which reached over 90% of fully supervised results with only 25% of annotated data for three out of four datasets. We believe that our study is an important step towards annotation and resource efficient model training for biomedical classification challenges.
Inter-Basin Water Governance by Transfer Rules Based on System Dynamics
Authors: Abdi-Dehkordi Mehri , Bozorg-Haddad Omid , Salavitabar Abdolrahim , Loáiciga Hugo A. 
Published: August 2021

Abstract
Inter-basin water transfers are widely implemented to counter the uneven geographical distribution of natural water sources. The Big Karun Basin, Iran, has long been of interest to water managers due to its discharge potential, and where several water transfer projects are operated or are under study. This study implements system dynamics modeling (SDM) to the Big Karun Basin consisting of 6 dams, 12 drinking and industrial consumers, 7 fish farmers, 31 agricultural consumers, 5 operational inter-basin water transfer projects, and 7 under-study inter-basin water transfer projects. SDM was applied considering existing inter-basin water transfers. The results show an average annual 8 to 10 billion cubic meters of water is transfered from the Karun River to the Persian Gulf. Part of this flow can be used to meet some of the water demands in the central and eastern basins of Iran subject to accurate social and environmental assessment of impacts. SDM modeling was also implemented accounting for all existing water transfers plus under-study water transfers. The results indicate the firm energy from hydropower produced by the Big Karun Basin system would decrease by 28% relative to existing water transfer conditions. This issue raises concerns given the Big Karun Basin contribution to electricity production Iran. The water supply to several sectors would be marginally impacted by future water tranfers, yet water quality would be compromised in some instances. Therefore, the Big Karun Basin water system was simulated considering inter-basin water governance based on hedging rules for the under-study water transfers. Results indicate the minimum demands of destination basins and source basin (drinking and industrial consumers) couldbe met, the hydropower energy could be generated with a high reliability when implementing inter-basin water governance. The results also indicate the firm energy from hydropower produced by the Big Karun Basin system would decrease by 12% relative to existing water transfer conditions and the vulnerability of the water system would decrease in terms of required quality for downstream demands and water users relative to the full-transfer water condition.
Expression and Function of Tumor Necrosis Factor- α-Induced Protein 8-Like (TIPE) Family in Glioma
Authors: Chen Qiong , Wang Haitao , Li Jing , Chen Yisi , Liu Tiancai , Deng Hao , Lin Li , Xu Jiangping 
Published: August 2021

Abstract
Although novel strategies of glioma are emerging sequentially, the effectiveness of novel treatment remains suboptimal at present. Therefore, profiles of molecular are needed for improving diagnosis, survival prediction and identification of therapeutic targets for glioma. Tumor necrosis factor-α-induced protein 8-like (TNFAIP8/TIPE) family members are involved in tumorigenesis and inflammatory responses but have been poorly studied in glioma. In this study, we aimed to investigate the expression and functions of TIPE family in glioma. The expression data of the TIPE family from the Chinese Glioma Genome Atlas(CGGA), the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were conducted to analyze TIPEs expression and functional networks in gliomas. Kaplan-Meier analysis and Cox regression were performed to access the overall survival of these genes. The related functional networks were identified using Gene Set Enrichment Analysis and LinkedOmics. The relationship between TNFAIP8 and tumor immune system were analyzed by TISIDB. The results shown that TIPEs were generally expression in gliomas. Glioma patients with high TNFAIP8 levels tend to be more malignant than those with low expression and are associated with reduced survival. GSEA identified a variety of oncogenic and immune pathway that were tightly linked with TNFAIP8. TISIDB data found that TINAIP8 expression was significantly positively correlated with immune infiltrates cells and immune-related factors.TNFAIP8 exhibit crucial role in reduced survival in glioma and could serve as a potential prognostic biomarker. The present study revealed the expression patterns and potential functional networks of TNFAIP8 in glioma, providing insights for future research of the role of TNFAIP8 in carcinogenesis.
Experimental Demonstrations of Coherence de Broglie Waves Using Sub-Poisson Distributed Coherent Photon Pairs
Authors: Kim S. , Ham Byoung S. 
Published: August 2021

Abstract
Recently, a new interpretation of quantum mechanics has been developed for the wave nature of a photon, where determinacy in quantum correlations becomes an inherent property without the violation of quantum mechanics. Here, we experimentally demonstrate a direct proof of the wave natures of quantum correlation for the so-called coherence de Broglie waves (CBWs) using sub-Poisson distributed coherent photon pairs obtained from an attenuated laser. The observed experimental data coincides with the analytic solutions and the numerical calculations. Thus, the CBWs pave a road toward deterministic and macroscopic quantum technologies for such as quantum metrology, quantum sensing, and even quantum communications, that are otherwise heavily limited due to the microscopic non-determinacy of the particle nature-based quantum mechanics.