bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Advantages of Searching Infeasible Regions in Constrained Evolutionary-Based Multi-Objective Engineering Optimization
Authors: Bimo Dwianto Yohanes , Satria Palar Pramudita , Rizki Zuhal Lavi , Oyama Akira 
Published: October 2023

Abstract
Solving a multiple-criteria optimization problem with severe constraints remains a significant issue in multi-objective evolutionary algorithms. The problem primarily stems from the need for a suitable constraint handling technique. One potential approach is balancing the search in feasible and infeasible regions to find the Pareto front efficiently. The justification for such a strategy is that the infeasible region also provides valuable information, especially in problems with a small percentage of feasibility areas. To that end, this paper investigates the potential of the infeasibility-driven principle based on multiple constraint ranking-based techniques to solve a multi-objective problem with a small feasibility ratio. By analyzing the results from intensive experiments on a set of test problems, including the realistic multi-objective car structure design and actuator design problem, it is shown that there is a significant improvement gained in terms of convergence by utilizing the generalized version of the multiple constraint ranking techniques.
Bronchopulmonary penetration of isavuconazole in lung transplant recipients
Authors: Caballero-Bermejo Antonio F. , Darnaude-Ximénez Ignacio , Aguilar-Pérez Myriam , Gomez-Lopez Alicia , Sancho-López Aránzazu , López García-Gallo Cristina , Díaz Nuevo Gema , Diago-Sempere Elena , Ruiz-Antorán Belén , Avendaño-Solá Cristina , Ussetti-Gil Piedad ,   PBISA01‐Study Group
Published: October 2023

ABSTRACT
Isavuconazole’s (ISA) pharmacokinetics was studied among lung transplant recipients to evaluate its bronchopulmonary penetration. This study included 13 patients and showed mean serum concentrations of 3.30 (standard deviation [SD] 0.45), 5.12 (SD 1.36), and 6.31 (SD 0.95) at 2 h, 4 h, and 24 h respectively. Mean concentrations in the epithelial lining fluid were 0.969 (SD 0.895), 2.141 (SD 1.265), and 2.812 (SD 0.693) at the same time points. ISA is a drug with a tolerable safety profile that achieves adequate concentrations in the lung.
Axial Ratio Improvement of Circularly Polarized Antenna Using Parasitic Elements for 5G Applications
Authors: Mohammadkhani Samira , Mallahzadeh Alireza 
Published: October 2023

A circular polarization (CP) antenna that can switch between right-handed circular polarization (RHCP) and left-handed circular polarization (LHCP) modes has been designed and introduced for 5G applications in the 3.5 GHz frequency band in this work. The proposed antenna comprises a crossed dipole fed by a 90° hybrid coupler. The axial ratio (AR) enhancement of 190 MHz is achieved by vertically stacking a substrate with a distance of

λ
/
4

from the ground plane, including an annular ring-shaped parasitic element above a circular-shaped disc. Consequently, by creating surface current rotation on the parasitic elements, the CP performance of the antenna is improved. According to the experiments, a wide impedance bandwidth of 930 MHz (3.19-4.12 GHz) and an overlapped AR bandwidth of 23.5% for both modes are achieved. The overall size of the antenna is

100
×
92.5
×
24

m

m

3

, and the gain is stable across the operating frequency band with a peak value of 6.78 dBic.
Safety of Intravenous Cangrelor Versus Dual Oral Antiplatelet Loading Therapy in Endovascular Treatment of Tandem Lesions: An Observational Cohort Study
Authors: Rodriguez‐Calienes Aaron , Oliver Marion , Hassan Ameer E. , Vivanco‐Suarez Juan , Divani Afshin A. , Ribo Marc , Petersen Nils , Abraham Michael , Fifi Johanna , Guerrero Waldo R. , Malik Amer M. , Siegler James E. , Nguyen Thanh , Sheth Sunil , Yoo Albert , Linares Guillermo , Janjua Nazli , Quispe‐Orozco Darko , Galecio‐Castillo Milagros , Alhajala Hisham , Malaga Marco , Farooqui Mudassir , Jovin Tudor , Jumaa Mouhammad , Ortega‐Gutierrez Santiago 
Published: October 2023

Background
Procedural intravenous cangrelor has been proposed as an effective platelet inhibition strategy for stenting in acute ischemic stroke. We aimed to compare the safety profile of low‐dose intravenous cangrelor versus dual oral antiplatelet therapy (DAPT) loading in patients with acute cervical tandem lesions.

Methods
We retrospectively identified cases from an international multicenter cohort who underwent intraprocedural administration of intravenous cangrelor (15 μg/kg followed by an infusion of 2 μg/kg per min) or DAPT loading during acute tandem lesions intervention. Safety outcomes included rates of symptomatic intracranial hemorrhage, parenchymal hematoma type 2, petechial hemorrhage, and in‐stent thrombosis. Inverse probability of treatment weighting matching was used to reduce confounding.

Results

From 691 patients, we included 195 patients, 30 of whom received intravenous cangrelor and 165 DAPT. The DAPT regimens were aspirin+clopidogrel (93.3%) or aspirin+ticagrelor (6.6%). After inverse probability of treatment weighting, the patients treated with cangrelor were not at greater odds of symptomatic intracranial hemorrhage (odds ratio [OR], 1.30 [95% CI, 0.09–17.3];
P
=0.837), symptomatic intracranial hemorrhage–parenchymal hematoma type 2 (OR, 0.54 [95% CI, 0.05–4.98];
P
=0.589), or petechial hemorrhage (OR, 1.11 [95% CI, 0.38–3.28];
P
=0.836). Similarly, the rate of in‐stent thrombosis was not significantly different between the 2 groups (1.8% versus 0%;
P
=0.911).

Conclusion
Cangrelor at the half dose of the myocardial infarction protocol showed a similar safety profile compared with the commonly used DAPT loading protocols in patients with acute tandem lesions. Further studies with larger samples are warranted to elucidate the safety of antiplatelet therapy in tandem lesions.
Graph regularized non-negative matrix factorization with $$L_{2,1}$$ norm regularization terms for drug–target interactions prediction
Authors: Zhang Junjun , Xie Minzhu 
Published: October 2023

Abstract
Background
Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are costly and time consuming. Effective computational methods to predict DTIs are useful to speed up the process of drug discovery. A variety of non-negativity matrix factorization based methods are proposed to predict DTIs, but most of them overlooked the sparsity of feature matrices and the convergence of adopted matrix factorization algorithms, therefore their performances can be further improved.

Results
In order to predict DTIs more accurately, we propose a novel method iPALM-DLMF. iPALM-DLMF models DTIs prediction as a problem of non-negative matrix factorization with graph dual regularization terms and $$L_{2,1}$$

L

2
,
1

norm regularization terms. The graph dual regularization terms are used to integrate the information from the drug similarity matrix and the target similarity matrix, and $$L_{2,1}$$

L

2
,
1

norm regularization terms are used to ensure the sparsity of the feature matrices obtained by non-negative matrix factorization. To solve the model, iPALM-DLMF adopts non-negative double singular value decomposition to initialize the nonnegative matrix factorization, and an inertial Proximal Alternating Linearized Minimization iterating process, which has been proved to converge to a KKT point, to obtain the final result of the matrix factorization. Extensive experimental results show that iPALM-DLMF has better performance than other state-of-the-art methods. In case studies, in 50 highest-scoring proteins targeted by the drug gabapentin predicted by iPALM-DLMF, 46 have been validated, and in 50 highest-scoring drugs targeting prostaglandin-endoperoxide synthase 2 predicted by iPALM-DLMF, 47 have been validated.
plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
Authors: Cao Tianze , Li Qian , Huang Yuexia , Li Anshui 
Published: October 2023

Abstract
Background
The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The programming language used by bioinformaticians began to shift to Python. Providing APIs in Python that are similar to those in R can reduce the learning cost of relearning a programming language. And compared to ggplot2 in R, drawing framework is not as easy to use in Python. The appearance of plotnine (ggplot2 in Python version) makes it possible to unify the programming methods of bioinformatics visualization tools between R and Python.

Results
Here, we introduce plotnineSeqSuite, a new plotnine-based Python package provides a ggseqlogo-like API for programmatic drawing of sequence logos, sequence alignment diagrams and sequence histograms. To be more precise, it supports custom letters, color themes, and fonts. Moreover, the class for drawing layers is based on object-oriented design so that users can easily encapsulate and extend it.

Conclusions
plotnineSeqSuite is the first ggplot2-style package to implement visualization of sequence -related graphs in Python. It enhances the uniformity of programmatic plotting between R and Python. Compared with tools appeared already, the categories supported by plotnineSeqSuite are much more complete. The source code of plotnineSeqSuite can be obtained on GitHub (https://github.com/caotianze/plotnineseqsuite) and PyPI (https://pypi.org/project/plotnineseqsuite), and the documentation homepage is freely available on GitHub at (https://caotianze.github.io/plotnineseqsuite/).
Angelica polysaccharides relieve blood glucose levels in diabetic KKAy mice possibly by modulating gut microbiota: an integrated gut microbiota and metabolism analysis
Authors: Tang Xiaolong , Yang Lixia , Miao Yandong , Ha Wuhua , Li Zheng , Mi Denghai 
Published: October 2023

Abstract
Background
Angelica polysaccharides (AP) have numerous benefits in relieving type 2 diabetes (T2D). However, the underlying mechanisms have yet to be fully understood. Recent many reports have suggested that altering gut microbiota can have adverse effects on the host metabolism and contribute to the development of T2D. Here, we successfully established the T2D model using the male KKAy mice with high-fat and high-sugar feed. Meanwhile, the male C57BL/6 mice were fed with a normal feed. T2D KKAy mice were fed either with or without AP supplementation. In each group, we measured the mice's fasting blood glucose, weight, and fasting serum insulin levels. We collected the cecum content of mice, the gut microbiota was analyzed by targeted full-length 16S rRNA metagenomic sequencing and metabolites were analyzed by untargeted-metabolomics.

Results
We found AP effectively alleviated glycemic disorders of T2D KKAy mice, with the changes in gut microbiota composition and function. Many bacteria species and metabolites were markedly changed in T2D KKAy mice and reversed by AP. Additionally, 16 altered metabolic pathways affected by AP were figured out by combining metagenomic pathway enrichment analysis and metabolic pathway enrichment analysis. The key metabolites in 16 metabolic pathways were significantly associated with the gut microbial alteration. Together, our findings showed that AP supplementation could attenuate the diabetic phenotype. Significant gut microbiota and gut metabolite changes were observed in the T2D KKAy mice and AP intervention.

Conclusions
Administration of AP has been shown to improve the composition of intestinal microbiota in T2D KKAy mice, thus providing further evidence for the potential therapeutic application of AP in the treatment of T2D.
Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis
Authors: Shi Hai , Ernst Evan , Heinzel Nicolas , McCorkle Sean , Rolletschek Hardy , Borisjuk Ljudmilla , Ortleb Stefan , Martienssen Robert , Shanklin John , Schwender Jorg 
Published: October 2023

Abstract
Background
Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions.

Results
To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts.

Conclusions
Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.
Risk factors for the mortality of hepatitis B virus-associated acute-on-chronic liver failure: a systematic review and meta-analysis
Authors: Tu Hanyun , Liu Rong , Zhang Anni , Yang Sufei , Liu Chengjiang 
Published: October 2023

Abstract
Background
Hepatitis B virus-associated acute-on-chronic liver failure (HBV-ACLF) has been confirmed as a prevalent form of end-stage liver disease in people subjected to chronic HBV infection. However, there has been rare in-depth research on the risk factors for the mortality of HBV-ACLF. This study aimed at determining the risk factors for the mortality of HBV-ACLF.

Methods
The relevant research was selected from four electronic databases that have been published as of August 2023. The existing research was reviewed in accordance with the inclusion and exclusion criteria. The level of quality of previous research was evaluated using the Newcastle–Ottawa scale. Moreover, a pooled estimate of the odds ratios (ORs) with their associated 95% confidence intervals (CIs) was provided through a meta-analysis. The data were combined, and the risk variables that at least two studies had considered were analyzed. The publication bias was examined through Egger's test and Begg's test.

Results
Twenty two studies that conformed to the inclusion criteria were selected from 560 trials. Eight risk variables in terms of HBV-ACLF mortality were determined, which covered INR (OR = 1.923, 95% CI = 1.664–2.221, P < 0.001), Monocytes (OR = 1.201, 95% CI = 1.113–1.296, P < 0.001), Cirrhosis (OR = 1.432, 95% CI = 1.210–1.696, P < 0.001), HE (OR = 2.553, 95% CI = 1.968–3.312, P < 0.001), HE grade (OR = 2.059, 95% CI = 1.561–2.717, P < 0.001), SBP (OR = 1.383, 95% CI = 1.080–1.769, P = 0.010), Hyponatremia (OR = 1.941, 95% CI = 1.614–2.334, P < 0.001), as well as HRS (OR = 2.610, 95% CI = 1.669–4.080, P < 0.001).

Conclusion
The most significant risk factors for HBV-ACLF mortality comprise HRS, HE, and HE grade, followed by INR and hyponatremia. The Monocytes, cirrhosis, and SBP have been confirmed as the additional key risk factors for HBV-ACLF mortality.
Identification of the potential association between SARS-CoV-2 infection and acute kidney injury based on the shared gene signatures and regulatory network
Authors: Zhou Xue , Wang Ning , Liu Wenjing , Chen Ruixue , Yang Guoyue , Yu Hongzhi 
Published: October 2023

Abstract
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is identified as the cause of coronavirus disease 2019 (COVID-19) pandemic. Acute kidney injury (AKI), one of serious complications of COVID-19 infection, is the leading contributor to renal failure, associating with high mortality of the patients. This study aimed to identify the shared gene signatures and construct the gene regulatory network between COVID-19 and AKI, contributing to exploring the potential pathogenesis.

Methods
Utilizing the machine learning approach, the candidate gene signatures were derived from the common differentially expressed genes (DEGs) obtained from COVID-19 and AKI. Subsequently, receiver operating characteristic (ROC), consensus clustering and functional enrichment analyses were performed. Finally, protein-protein interaction (PPI) network, transcription factor (TF)-gene interaction, gene-miRNA interaction, and TF-miRNA coregulatory network were systematically undertaken.

Results
We successfully identified the shared 6 candidate gene signatures (RRM2, EGF, TMEM252, RARRES1, COL6A3, CUBN) between COVID-19 and AKI. ROC analysis showed that the model constructed by 6 gene signatures had a high predictive efficacy in COVID-19 (AUC = 0.965) and AKI (AUC = 0.962) cohorts, which had the potential to be the shared diagnostic biomarkers for COVID-19 and AKI. Additionally, the comprehensive gene regulatory networks, including PPI, TF-gene interaction, gene-miRNA interaction, and TF-miRNA coregulatory networks were displayed utilizing NetworkAnalyst platform.

Conclusions
This study successfully identified the shared gene signatures and constructed the comprehensive gene regulatory network between COVID-19 and AKI, which contributed to predicting patients’ prognosis and providing new ideas for developing therapeutic targets for COVID-19 and AKI.
Using complaints from obstetric care for improving women’s birth experiences – a cross sectional study
Authors: Walløe Sisse , Bogh Søren Bie , Birkeland Søren Fryd , Pedersen Lone Kjeld , Lykkebo Annemette Wildfang , Andersen Lise Lotte Torvin , Frederiksen-Møller Britta , Morsø Lars 
Published: October 2023

Abstract
Introduction
Staff shortages and quality in obstetric care is a concern in most healthcare systems and a hot topic in the public debate that has centred on complaints about deficient care. However there has been a lack of empirical data to back the debate. The aim of this study was to analyse and describe complaints in obstetric care. Further, to compare the obstetric complaint pattern to complaints from women about other hospital services.

Materials and methods
We used the Healthcare Complaints Analysis Tool to code, analyse and extract contents of obstetric complaint cases in a region of Denmark between 2016 and 2021. We compared the obstetric complaint pattern to all other hospital complaint cases in the same period regarding female patients at a large University Hospital in a cross-sectional study.

Results
Complaints regarding obstetric care differed from women’s complaints regarding other healthcare services. Women from obstetric care raised more problems per complaint, and tended to complain more about relational issues indicated by odds for complaints about staff shortage four times higher in the obstetric care group. Women from obstetric care had a lower proportion of compensation claims.

Conclusion
Systematic complaint analysis acknowledged women’s experience in obstetric care and may point to areas that potentially need further attention. Complaints from obstetric care show that women experience deficiencies related to relational problems like recognition and individualized support compared to complaints from women receiving other hospital healthcare services.
Histone regulator KAT2A acts as a potential biomarker related to tumor microenvironment and prognosis of diffuse large B cell lymphoma
Authors: Yu Zhuoya , Ding Mengfei , Cai Yiqing , Lu Tiange , Chen Xiaomin , Zhou Xiangxiang , Wang Xin 
Published: October 2023

Abstract
Background
Recent studies have indicated that epigenetic alterations contribute significantly to lymphoma pathogenesis. A type of epigenetic regulation known as histone acetylation plays a crucial role in transcriptional regulation in eukaryotic cells. Specifically, a significant effect of histone acetylation modifications on the abnormal progression and microenvironment of diffuse large B-cell lymphoma (DLBCL) has been observed.

Methods
To provide insight into the significance of histone acetylation-related genes, we developed a HAscore model for analyzing histone acetylation patterns in DLBCL samples. Furthermore, KAT2A, a regulator of histone acetylation, was knocked down in DLBCL cell lines to investigate its role in proliferation, cell cycle, and apoptosis.

Results
The HAscore model has been demonstrated to provide insight into the significance of these patterns, showing that patients with a low HAscore have distinct tumor immune microenvironments and poorer prognoses. Besides, KAT2A was identified as a potential biomarker related to immune infiltration and malignant pathways in DLBCL.

Conclusion
According to these findings, it is evident that the histone acetylation pattern score model is helpful in describing the immune status of DLBCL and that KAT2A may be used as a biomarker for its treatment.