bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence research and training in computational bioengineering: a case study on AI/ML driven biofilm-material interaction discovery
Authors: Zylla Jessica LS , Z. Etienne Gnimpieba , Bomgni Alain B , Sani Rajesh K , Subramaniam Mahadevan , Lushbough Carol , Winter Robb , Gadhamshetty Venkataramana R , Chundi Parvathi 
Published: September 2023

Abstract

Initially, research disciplines operated independently, but the emergence of trans-
disciplinary sciences led to convergence research, impacting graduate programs and research laboratories, especially in bioengineering and material engineering as presented here. Current graduate curriculum fails to efficiently prepare students for multidisciplinary and convergence research, thus creating a gap between the students and research laboratory expectations. We present a convergence training framework for graduate students, incorporating problem-based learning under the guidance of senior scientists and collaboration with postdoctoral researchers. This case study serves as a template for transdisciplinary convergent training projects - bridging the expertise gap and fostering successful convergence learning experiences in computational biointerface (material-biology interface). The 18-month Advanced Data Science Workshop, initiated in 2019, involves project-based learning, online training modules, and data collection. A pilot solution utilized Jupyter notebook on Google collaborator and culminated in a face-to-face workshop where project presentations and finalization occurred. The program started with 9 experts in the four diverse fields creating 14 curated projects in data science (Artificial Intelligence/Machine Learning), material science, biofilm engineering, and biointerface. These were integrated into convergence research through webinars by the experts. The experts chose 8 of the 14 projects to be part of an all-day in-person workshop, where over 20 learners formed eight teams that tackled complex problems at the interface of digital image processing, gene expression analysis, and material prediction. Each team was comprised of students and postdoctoral researchers or research scientists from diverse domains including computer science, materials science, and biofilm research. Some projects were selected for presentation at the international IEEE Bioinformatics conference in 2022, with three resulting Machine Learning (ML) models submitted as a journal paper. Students engaged in problem discussions, collaborated with experts from different disciplines, and received guidance in decomposing learning objectives. Based on learner feedback, this successful experience allows for consolidation and integration of convergence research via problem-based learning into the curriculum. Three bioengineering participants, who received training in data science and engineering, have received bioinformatics jobs in biotechnology industries.
A stable and low loss oxide layer on α-Ta (110) film for superconducting qubits
Authors: Ding Zengqian , zhou Boyi , Wang Tao , Yang Lina , Wu Yanfu , Cai Xiao , Xiong Kanglin , Feng Jiagui 
Published: September 2023

Abstract
The dielectric loss of amorphous oxide layers is a major limiting factor for the coherent time of superconducting qubits. Usually, the surface oxides of superconductor film are lossy and unstable in air. To increase the coherence time, it is essential for qubits to have stable and low dielectric loss oxides, either as barrier or passivation layers. Here, we demonstrate that a kind of amorphous tantalum oxide on α-Ta (110) film is robust and stable by means of chemical and structural analysis. Such kind of oxide layer forms in a self-limiting process on the surface of α-Ta (110) film in piranha solution, yielding stable thickness and steady chemical composition. Quarter-wavelength coplanar waveguide resonators are made to study the loss of this oxide. One fresh resonator have a Qi of 3.0×106 in the single photon region. The Qi of most devices are higher than 2.0×106. And most of them are still over one million even after exposed to air for months. Based on these findings, we propose an all-tantalum superconducting qubit utilizing such oxide as passivation layers, which possess low dielectric loss and improved stability.
Interpretation of Thermoluminescence Dosimetry System from the Information Theory Perspective
Authors: Moslehi A. , Ataeinia V. , Payervand F. , Semsarha F. 
Published: September 2023

Abstract
Shannon’s information theory expresses that reduction in entropy of a communication system quantifies the increase in information one receives about the system. In this work, the thermoluminescence (TL) dosimetry system is investigated from this perspective. It is supposed that the quantum energy of radiation is transmitted by the TLD chip and is converted to the TL light(s) by the TLD reader. Hence, we get some information about the TL system. To examine this concept, the TL responses of GR-200 chips (irradiated with 90Sr beta rays, 60Co gamma rays) and TLD-600 chips (irradiated with thermal neutrons) before and after irradiation with different dose-equivalents are determined. Shannon’s entropy is calculated using the measured glow curves (GCs). The results show that while the TL response increases after irradiation, the entropy decreases and then remains stable with the increase in dose-equivalent. Furthermore, the maximum transmission rate of TL lights increases by the dose-equivalent.
Reactive Oxygen Species (ROS) related signature acted as the immunotherapy clinical response index in melanoma
Authors: Yue Chao , Lian Wenqin , Duan Mengying , Xia Die , Cao Xianbin , Peng Jianzhong 
Published: September 2023

Abstract
Background: At present, melanoma has become an important factor that seriously threatens people's life, property and health. Oxidative stress is currently believed to affect the prognosis of melanoma patients by affecting the progression of melanoma cells.
Method: In this study, the TCGA-SKCM dataset was used to obtain the HTSeq-FPKM RNA-seq transcriptome and clinical data of 471 cutaneous melanoma patients. Subsequently, the GEO database was used to obtain the GSE65904 dataset and GSE120575 single-cell sequencing data, and EMBL-EBI database was used to obtain the transcriptome data of PRJEB23709 as the validation group. In the analysis of single-cell sequencing data, logarithmic normalization was performed on the combined data, and the
FindVariableFeatures function was used to identify the first 2000 highly variable genes. All genes were then normalized using the ScaleData function and the dimensions of the data were reduced to 50 principal components by the RunPCA function. Cluster analysis using the "FindNeighbors" and "FindClusters" functions to identify cell clusters at a resolution of 0.1. Next, reduce the dimensions further by selecting the first 50 principal components and applying the UMAP method. CIBERSORT analysis was used to estimate changes in immune cell subpopulations in different groups, and Spearman correlation analysis was used to assess the association between risk scores and immune infiltrating cells. Predictors were selected using LASSO analysis, and prognostic models were constructed by Cox regression analysis. The TIDE approach was used to evaluate the effectiveness of immunotherapy in melanoma patients, and statistical methods were used to analyze the data.
Result: In the study, immune cells from melanoma patients were analyzed using the GSE120575 single-cell RNA sequencing dataset and genes associated with ROS were identified. Further studies found that most cell types in the non-responding group had higher ROS marker scores than those in the responding group, and multiple up-regulated gene pathways were present in cells with high ROS markers. By Lasso-Cox regression analysis, a prognostic model based on five ROS-related genes was constructed, and the reliability and validity of the model in the TCGA-SKCM and GSE65904 datasets were verified. In addition, the study found a negative correlation between risk scores and immune-related genes and immune-infiltrating cells, and that patients in the low-risk group responded better to immunotherapy.
Thymoquinone Modifies CD4+:CD8+ Ratio without Affecting Tumor Necrosis Factor-α and Interleukin-1β Levels in Wallerian Degeneration Crush Injury Rat Model
Authors: Besin Valentinus , Bajamal Abdul Hafid , Nugraha Jusak , Notopuro Paulus Budiono , Naesilla Naesilla , Humardani Farizky Martriano 
Published: September 2023

Abstract
Background Wallerian degeneration following nerve injury not only suppresses CD4 + T-cell responses but also promotes pro-inflammatory immunological responses through TNF-α and IL-1β. Recent research suggests that thymoquinone might enhance nerve recovery by exerting anti-inflammatory effects on both the innate and adaptive immune systems. This study aims to evaluate the effect of thymoquinone on neuroinflammation in a sciatic nerve crush injury, as represented by TNF-α, IL-1β, and the CD4+:CD8 + ratio.Methods In this study, 126 Wistar rats were divided into three main groups: placebo, thymoquinone 100 mg/kg, and thymoquinone 250 mg/kg administered daily. Rats were euthanised at six distinct time points: 12, 18, and 24 hours, as well as on day-5, day-6, and day-7. TNF-α and IL-1β levels were assessed using the Enzyme-Linked Immunosorbent Assay (ELISA). The CD4+:CD8 + ratio in peripheral blood was determined via flow cytometry. Data analysis was conducted using MANOVA, Kruskal-Wallis, and Mann-Whitney U tests.Results No significant difference was noted in TNF-α levels between the treatment and placebo groups across all observation times. However, on day-6, the IL-1β level in the TQ 250mg/kg group was statistically lower than in the placebo group (p = 0.008). Furthermore, both the TQ 100mg/kg and 250mg/kg groups exhibited a higher CD4+:CD8 + ratio compared to the placebo group on day-5 (p = 0.007).Conclusion Daily TQ administration did not consistently reduce TNF-α and IL-1ß levels. However, both doses elevated the CD4+:CD8 + ratio during the early stages of Wallerian degeneration, suggesting a potential benefit of TQ on nerve regeneration.
Long Non-Coding RNAs Related to N6-Methyladenosine and Immune Cell Infiltration in Cervical Carcinoma: A Comprehensive Analysis
Authors: Lu Lidan , Bao Neng , Wei Qingxue , Cai Ximei , Ji Hongjian , Ni Haiyan , Wang Peijuan 
Published: September 2023

Abstract
Objective: The aim of this study was to explore the effect of N6-methyladenoxin (m6A-lncRNAs) on the prognosis of cervical cancer (CC).
Method: The Cancer Genome Atlas dataset was used to comprehensively analyze the prognostic value of m6A-lncRNAs in cervical carcinoma (CC) and their relationship to tumor microenvironment. These data were then used to generate a prognostic model by LASSO regression. Finally, all prognosis-related m6A-lncRNAs were validated in HeLa cells.
Results: A total of 87 m6A-lncRNAs were found to be significantly associated with the overall survival of patients with CC. Two subtypes were isolated by clustering the 87 prognostic m6A-lncRNAs. Cluster 1 performed better in terms of patient survival than cluster 2. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of CC using gene set enrichment analysis revealed that the ADHESION_JUNCTION pathway was the most active in Cluster 1, while the OXIDATIVE_PHOSPHORYLATION pathway showed higher activity in Cluster 2. The clinical correlation heatmap and boxplot showed differences in age, tumor grade, immune characteristics, and clustering. Thirteen prognosis-related m6A-lncRNAs were identified by LASSO regression, and of these, LINC006 and NNT-AS1 were finally validated through in vitro studies.
Conclusion: Prognostic m6A-lncRNA markers could be an important mediator of the immune microenvironment of CC and a potential target for immunotherapy.
K.F Mini- Implant Placement Guide: A Simplified Template for Mini-Implant Placement in Orthodontics.
Authors: Agrawal Amol Rajendra 
Published: September 2023

Abstract
Background
Orthodontic mini‑implants (MI) have gained popularity among orthodontists mainly because they provide an effective tool in orthodontic cases with high anchorage demands.
The main objective of this study is to avoid a risk of injury to dental roots during placement of orthodontic mini-implants, especially when they are inserted between teeth and design a placement guide which is simple in design, easy to fabricate, inexpensive, supportive and can be used with a variety of mini-screws.
Findings
The mini-implant placement guide was fabricated using rectangular 0.017 x 0.025/0.019 × 0.025 stainless steel (SS) archwire, the wire was bent vertically distal to second premolar along the long axis. The vertical length of the wire is according to the desired length for micro-implant insertion, which is generally 5-6 mm apical to the alveolar crest. After the vertical bend 2-3 mm (which is an interradicular space between two roots) [8] horizontal bend is given pointing posteriorly towards the first molar region. A periapical radiograph is taken to confirm the correct position of template guide, radiograph is repeated until the desired position is achieved. The point of mini-implant insertion site is just at the middle of the horizontal bend, which can be readily marked using a marker or a burr.
Conclusion
K.A. micro-implant placement guide is simple in design, easy to fabricate, inexpensive, supportive and can be used with a variety of mini-screws.
Disparities in Healthcare Access Experienced by Hispanic Chronic Kidney Disease Patients: A Cross Sectional Analysis
Authors: Ashrafi Sadia Anjum , Alam Rifat Binte , Kraay Alicia , Ogunjesa Babatope Ayokunle , Schwingel Andiara 
Published: September 2023

Abstract
Background: Chronic kidney disease (CKD) is a public health concern, and the disease disproportionately affects Hispanics. Improved healthcare access for Hispanic CKD patients can reduce the disease burden. This study assesses the healthcare access disparities experienced by Hispanic CKD patients compared to Whites.
Methods: We analyzed three National Health and Nutrition Examination Survey (NHANES) datasets for 2013-2014, 2015-2016, and 2017-2018. The primary predictor variable was race, and the outcome variable was three domains of healthcare access: insurance status, having any routine place for healthcare, and having any health visits in the past year. Chi-square tests and unadjusted and adjusted multivariate logistic regressions were conducted. The models were adjusted for age, education, income, and CKD stages and were weighted to account for the sampling strategy.
Results: The sample size was 1864 CKD patients from three two years cycles of NHANES datasets (2013-2014, 2015-2016, and 2017-2018). The final adjusted model found that Hispanic CKD patients were more likely to be uninsured (OR: 2.52, CI: 1.66-3.83) and have no routine place for healthcare (OR: 1.68, CI: 1.03-2.75) than White CKD patients but did not have differences in healthcare visits in the past year.
Conclusions: Hispanic CKD patients have limited healthcare access compared to White populations showing existing care access disparities experienced by them. Policy-level attention is required to resolve the disparities and improve Hispanic’s kidney health.
PSR versus TSR Relaying Protocols: Leveraging Full-DuplexDF and Energy Harvesting for SWIPT in NOMA Systems
Authors: Q. Tran Huu 
Published: September 2023

Abstract
In this study, we introduce a cooperative non-orthogonal multiple access(NOMA) system model for simultaneous wireless information and power transfer(SWIPT)withtheassistanceofarelaynode,allwithinthecontextoffull-duplex(FD)communication mode. Within this framework, we consider the utilization of two dis-tinct protocols: the power splitting protocol (PSR) and the time switching protocol (T-SR). These protocols are designed to accommodate both delay-limited-transmission(DLT) and delay-tolerant-transmission (DTT) modes, enabling efficient energy har-vesting and information processing at the relay user. The paper also presents compre-hensive closed-form expressions for various performance metrics, including outageprobability, throughput, ergodic rate, and energy efficiency (EE). Furthermore, weexplore the impact of key parameters such as energy harvesting time, power splittingratio, energy harvesting efficiency, source data rate, and inter-node distance acrossnormal and high signal-to-noise ratio (SNR) regimes. Our findings demonstrate thatenhanced energy harvesting efficiency leads to improved overall system performance.Notably, our results underscore the superiority of NOMA over conventional orthog-onal multiple access schemes, particularly in terms of energy efficiency.
A measure for multiple bends and shear damage of RC rigid-frame bridge tall piers: application to seismic fragility analysis
Authors: MEI Zhu , Liu Yang , WU Bin , BURSI Oreste S. , LU Da-gang , PAOLACCI Fabrizio 
Published: September 2023

Abstract
The reinforced-concrete (RC) rigid-frame bridges with tall hollow piers were widely constructed in Southwestern China with many seismic activities. For such bridges, the seismic damages would be underestimated because of the tall piers’ multiple bends caused by their high-mode shapes that can be activated under earthquakes. Moreover, the seismic damage assessment can be incorrect if we ignore the tall piers’ shear damages caused by their vastly weakened sectional areas and multiple bends. With this respect, this paper presents a fragility analysis for such bridges. A novel seismic damage measure (piecewise drift ratio, PDR) involving shear effects and multiple bends is proposed and experimentally validated. Damage states congruent to the PDR are provided by statistically acquiring from the 40 existing tests of hollow piers. A finite element (FE) model of an RC rigid-frame bridge with two tall piers was established and adequately calibrated based on the model-updating hybrid tests. To provide more comprehensive assessments of the damage measures and the seismic fragility, the ground motions were selected and divided into four categories by identifying their first two frequencies and their amplitude ratio. Both the 5% damped spectral acceleration of the fundamental period (Sa(T1, 5%)) and the peak ground acceleration (PGA) are adopted as the demand parameter to develop the seismic demand models (PSDMs). Results show the effectiveness of the proposed PDR, provide the more adverse types of ground motions, and reveal the high exceedance probability of the complete damage state of tall piers.
Evolution of Microbial Community Structure and Diversity Analysis during Acclimation for High-oil Food Waste Anaerobic Digestion
Authors: HU Yangqing , ZHOU Zhaozhi , SHEN Ce , SUN Guiling , TANG Yuanjun 
Published: September 2023

Abstract
Anaerobic digestion is one of the most promising options for dealing with biodegradable food waste. However, the relatively high content of oil in food waste inhibits the conversion efficiency of anaerobic digestion because of the accumulation of long-chain fatty acids (LCFA). In this study, the activated anaerobic sludge was acclimated to accommodate the high-oil condition. The shift of the microbial communities during the acclimation period was represented by high-throughput sequencing based on the 16S rRNA gene. The results indicated that Bacteroidetes, Firmicutes, Chloroflexi and Proteobacteria were the dominant bacteria at the phylum level. The relative abundances of Anaerolinea, Clostridium and Longilinea at the genus level improved during the acclimation period, likely triggered by the degradation of LCFA. Among the archaea communities, the hydrogenotrophic methanogen Methanobacterium nearly supplanted the acetotrophic methanogen Methanosaeta. The fluctuations of pH and volatile fatty acids during the period provide extra evidence for the effectiveness of the acclimation. The methane yield of high-oil food waste digested by the acclimated sludge was 24.9% higher than with the raw sludge.
Organic water features of three adjacent Eastern Mediterranean urbanized watersheds
Authors: Abboud Nour , Maatouk Elias , Matar Zeinab , Wazne Mahmoud , Kazpard Veronique 
Published: September 2023

Abstract
Landscape urbanization broadly affects watersheds ecosystems, but until now the influence of nonpoint source urban inputs on dissolved organic matter (DOM) amount, composition and source is poorly understood. To understand how DOM composition varied with urbanization, fluorescence excitation emission matrices (EEMs) was collected from two types of waters: urban and non-urban waters from upstream to downstream sites along three adjacent watersheds that pour into the Mediterranean Sea. Two humic-like DOM fluorescent components (C1 and C4), two protein-like components (C5 and C7) and two microbial components (C2 and C3) were identified by parallel factor analysis (PARAFAC). The results indicated that urbanization had an important influence on DOM concentration and composition, with urban waters having a high degree of DOM variation due to different land use surrounding each body of water. Urban waters presented higher DOM fluorescence index (FI), a greater proportion of protein-like manifested by BIX values, and less proportion of humic-like (demonstrated by HIX values) than non-urban waters which were dominated by allochthonous inputs. In addition, the EEM was compared in dry and wet season where higher DOM amount and FI appeared in summer due to autochthonous production coming from algae growth compared to allochthonous input from rainfall dominated in wet season.
Comparing survival rates and mortality in operative vs. non-operative treatment for femoral neck fractures in Alzheimer’s disease patients: a retrospective cohort study
Authors: Yang Yijiong , Drake Stacy , Wang Jing , Shen Gordon , Miao Hongyu , Morgan Robert , Du Xianglin , Lairson David 
Published: September 2023

Abstract

Background.This study aims to assess the differences in survival rates and mortality outcomes between operative surgery and non-operative treatment approaches for patients diagnosed with Alzheimer's disease (AD) who have sustained femoral neck fractures. Given the complexities of treating patients with AD who experience ground level falls, understanding the variations in post-fracture survival rates, mortality, and hazard ratios within this population remains limited.Methods.This retrospective cohort study compared the mortality, hazard ratio and survival rate between operative treatment and non-operative treatment, controlling for patients’ demographic information and baseline health status. The study population consisted of Optum beneficiaries diagnosed with AD, who experienced an initial femoral neck fracture claim between January 1, 2012, and December 31, 2017. Claims records with diagnosis and procedure codes corresponding to AD and femoral neck fracture were included; combination of hip fracture sections and pathological hip fractures were excluded. Kaplan-Meier survival curve and log-rank test were applied to compare post fracture survival rates and mortality between the treatment groups. Cox regression was applied to examine the survival period by controlling the covariates.Results.Out of the 4,157 AD patients with femoral neck fractures, 59.8% were female (n = 2,487). The median age was 81 years. The one-year survival rate for non-operative treatment (70.19%) was significantly lower than that for internal fixation (75.27%) and arthroplasty treatment (82.32%). The arthroplasty surgical group exhibited the lowest mortality rate compared to the internal fixation and non-operative groups (mortality rate: 0.0215 vs 0.0243 vs 0.0246).Conclusions.The findings suggest that the operative treatment group experiences higher survival rates and lower mortality rates when compared to the non-operative group. Treating femoral neck fractures presents a substantial mortality risk for patients and places an economic burden on the healthcare system. This study offers valuable insights for healthcare providers, administrators, and policymakers in assessing optimal approaches to femoral neck fracture treatment.