bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of chloroplast genome sequences of four camellia species
Authors: Bingqing Hao , Yingying Xia , Zhaoyuan Zhang , Dongxue Wang , hang Ye , Jinlin Ma 
Published: May 2023

Abstract
Researching the photosynthetic characteristics based on the whole chloroplast genome sequence of Camellia osmantha cv ‘yidan’. is important for improving production. We sequenced and analyzed the chloroplast (cp) genomes of C. osmantha cv‘yidan’. The total cp genome length was 156,981 bp. The cp genomes included 134 genes encoding 81 proteins, 39 transfer RNAs, 8 ribosomal RNAs, and 6 genes with unknown functions. In total, 50 repeat sequences were identified in C. osmantha cv‘yidan’ cp genomes. Phylogenetic analysis showed that C. osmantha cv‘yidan’ is more closely related to Camellia vietnamensis cv ‘hongguo’ and Camellia oleifera cv ‘cenruan 3’ than to Camellia semiserrata cv ‘hongyu 1’. Our complete assembly of four Camelliacp genomes may contribute to breeding for high oil content and further biological discoveries. The results of this study provide a basis for the assembly of the entire chloroplast genome of C. osmantha cv‘yidan’.
Comparing chromatin contact maps at scale: methods and insights
Authors: Gunsalus Laura , McArthur Evonne , Gjoni Ketrin , Kuang Shuzhen , Pittman Maureen , Capra John , Pollard Katherine 
Published: May 2023

Abstract
Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome.
Integrated management of eucalyptus bacterial wilt in Sumatra, Indonesia.
Authors: Oliveira Leonardo Sarno soares , Sirait Betty Andriani , Saha Muhammad Agni , Sipayung Jaliaman , Maretha Maggie Vency , Tarigan Marthin , Duran Alvaro 
Published: May 2023

Abstract
Bacterial wilt is one the most destructive plant diseases and responsible for great losses in eucalyptus plantations worldwide. Since the use of highly productive monoclonal stands became a common practice in forest companies, the industry have experienced severe bacterial wilt outbreaks. Thus, the present study aimed to provide alternative methods that can be incorporated in the management of bacterial wilt of eucalyptus in Sumatra, Indonesia. Pathogen identification with molecular markers, effect of plant propagation on the disease incidence, chemical sterilization of sand beds, antibacterial activity, and genetic resistance of eucalyptus clones were evaluated. Colonies obtained from diseased plants were morphologically indistinguishable, but specific primers 759F/760R and sequencing of 16S ribosomal RNA gene confirmed the pathogen identity as Ralstonia pseudosolanacearum. In-field evaluation showed that plants propagated via mini-cuttings had the highest disease incidence, 16.5%, while the tissue culture plants rooted in-vitro had the lowest disease incidence, 3%. Chemical sterilization of sand beds with NaOCl and H2O2 was effective on reducing bacterial cells by 97 and 42%, respectively. In-vitro assays confirmed the antibacterial activity of oxolinic acid and streptomycin by promoting a clear zone of 1.3 and 1.4 cm in diameter, respectively. The susceptibility to bacterial wilt varied among eucalyptus genotypes, and of the 21 clones tested eight were resistant, nine were moderate and four were susceptible. Therefore, an effective management of eucalyptus bacterial wilt can be achieved by combining all methods used in this study with best practices used in commercial nurseries and plantations.
The Identification of Hub Genes in Diagnosing Blunt Trauma with Venous Thromboembolism Using Integrated Bioinformatic Analysis
Authors: Sun Qian , Tan Fei , Zheng Hui , Wei Shilin , Zhang Lirong , Zhang Hongwei , Qi Wei 
Published: May 2023

Abstract
Background
Whether blunt trauma patient will get venous thromboembolism (VTE) is still a huge challenge to forecast. The objective of our study is to investigate and identify the potential biomarker genes for blunt trauma patients with VTE based on the method of bioinformatics analysis.
Methods
To investigate differentially expressed genes (DEGs) of blunt trauma and VTE, firstly we used the data obtained from the gene expression omnibus (GEO) database, and DEGs were respectively obtained via LIMMA. Next Weighted gene co-expression network analysis (WGCNA) was used to investigate the co-expression network of blunt trauma DEGs and two modules were found. We chose the most significant module as the key one in correlation with blunt trauma. We got intersection of DEGs in blunt trauma and VTE, which were analyzed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Then we used STRING to create a protein-protein interaction (PPI) network, and hub genes were screened by Cytoscape software and analyzed of functional enrichment. We chose another GEO database to evaluate the value of hub genes, and receiver operating characteristic (ROC) curves were done at last.
Results
There are a total of 546 DEGs of VTE and 4266 DEGs of blunt trauma were screened out from GSE19151 and GSE36809 respectively. Then 1568 DEGs of blunt trauma were identified in the most significant module. And 101 intersections of DEGs were found to be enriched for various functions and pathways. Among these DEGs, 6 overlapped hub genes with high degrees of stress method were selected. These hub genes include MRPL3, RPLP0, MRPL15, TP53, MYC, CD3D.And the six hub genes were tested to have high diagnostic values.
Impact of first health care provider on Acanthamoeba keratitis course.
How to overcome poor prognosis in AK treatment?
Single tertiary center, observational study
Authors: Walkden Andrew , Brahma Arun , Chidambaram Jaya , Carley Fiona , Przybek-Skrzypecka Joanna 
Published: May 2023

Abstract
Background
To assess the difference in course and final visual outcome of Acanthamoeba keratitis (AK) patients based on the first health care provider (HCP) seen.
Methods
Retrospective observational cohort study of AK patients admitted to the Manchester Royal Eye Hospital between 2003 and 2017. HCPs were grouped (Group 1: Optometrists, Opticians; Group 2: General Practitioners (GPs); Group 3: Ophthalmologists) and the data analyzed on demographics, risk factors, clinical history, clinical features, and Acanthamoeba subspecies.
Results
41 patients with unilateral culture-proven AK were included. Median time to consultation with first HCP was 7 days (IQR 4–14 days) while mean time to the correct diagnosis of AK was 15 days (IQR 7–29 days). Patients saw an optician/optometrist significantly earlier than GPs or ophthalmologists (median 4 days, vs 15 or 5 days respectively, p = 0.04). Bacterial keratitis was the most common initial clinical diagnosis (43%). The shortest time to making the AK diagnosis (median 11 days) and the highest rate of initiating AK treatment started at the first visit (38%) were both in the Ophthalmologists’ group. No significant differences were observed in initial and final visual acuity between HCP groups (p = 0.36).
Conclusions
AK patients often seek help earlier from optometrists and opticians than medical doctors. Final clinical outcomes did not significantly differ based on the first HCP, but ophthalmologists were more likely to make the diagnosis of AK and initiate anti-amoebal therapy faster than other HCPs. Greater education and collaboration between ophthalmologists and other HCPs to increase awareness of AK are needed.
Corchorus olitorius leaves affect nutrient utilization and improve biochemical indices of alloxan induced diabetic Wistar rats.
Authors: Oganezi Nuria , OJIMELUKWE PHILIPPA 
Published: May 2023

Abstract
BACKGROUND/ OBJECTIVES. The effective management of type 2 diabetes depends on the ability to maintain or improve insulin utilization, regulation of blood glucose, and the control of hyperlipidaemia. The effectiveness of Corchorus olitorius leaves in these three domains were evaluated in the present research. The objective of this research was to evaluate the ameliorative effects of Corchorus olitorius leaves on alloxan induced diabetes in Wistar rats
METHODS. Nutrient composition of shade dried C. olitorius leaves was determined using standard AOAC methods.; alpha-amylase inhibition potentials of C. olitorius leaves were determined using four solvent systems. Bioactive compounds in C. olitorius were determined using GC-MS. Diets were formulated to contain 0–20% C. olitorius and fed to alloxan-induced diabetic rats alongside positive and negative standards for 70 days. Indices of nutritional quality and biochemical indices were compared in diabetic, diabetic/nutritionally managed and normoglycaemic Wistar rats. Histopathology of the pancreas of the three groups of animals were also compared.
RESULTS. Water and 99% ethanol were the best solvents for extracting alpha amylase inhibitor from C. olitorius leaves. 9-octadecanoic acid (Z), benzoic acid,2 phenyl ester, 9-octadeceneZ-methylester and hexadecenoic acids were bioactive compounds identified in C. olitorius leaves. Formulated diets containing C. olitorius decreased feed intake, body mass gain, HBA1c, fasting blood glucose (FBG), total cholesterol (TC), triglycerides (TGs) in a concentration dependent manner. HDL-C (good cholesterol) increased. C. olitorius caused the regeneration of the islets of Langerhans of the alloxan -induced diabetic rats.
CONCLUSION. Corchorus olitorius leaves is effective for the control of hyperglycaemia and hyperlipidaemia. Its water and ethanol extracts contain significant quantities of alpha amylase inhibitor that slows down carbohydrate breakdown into sugars thereby controlling the blood glucose level.
Airway management during unusual tracheal stenosis: A Clinical Feasibility Trial
Authors: Altun Demet , Canbaz Mert , Altun Dilek , Sen Cömert , Çamcı Emre 
Published: May 2023

AbstractBackgroundWhile actual figures are still lacking, this incidence of laryngotracheal stenosis (LTS) is expected to increase because of the high COVID-19 patient numbers requiring (prolonged) invasive mechanical ventilation. While prolonged intubation is a known risk factor of LTS, LTS related to COVID-19 may be result in a different phenotype: pronation affects the location of stenosis and COVID-19 pneumonia can decline lung mechanics. Therefore, airway management in patients with COVID-19 related LTS has unique challenges for both anesthesiologists and surgeons for its location and severity. This prospective observational feasibility trial aims to evaluate the use of a novel thin, cuffed, endotracheal tube (Tritube) in combination with flow_controlled ventilation (FCV) in the management of patients with LTS secondary to COVID-19 related LTS undergoing laryngeal surgery.Methods20 patients suffering from COVID-19 related LTS, as diagnosed by CT, requiring endolaryngeal surgery were included. Ultrathin endotracheal tube Tritube, together with FCV was used for airway management and ventilation. Feasibility, ventilation efficiency and surgical exposure were evaluated.ResultsMedian duration of mechanical ventilation during their ICU stay was 17 days, [range (7-27] and the prone position was used in all patients. In 18/20 patients endoscopic diagnosis, confirmed the initial CT diagnosis: posterior subglottic stenosis. Visual Analogue Scale (VAS) score was 9 out of 10 (range 7-10). FCV ventilation was performed with or without CO2laser. All hemodynamic and respiratory variables were within the normal clinical range. In 1 patient a respiratory complication occurred, meaning that the SpO2temporarily dropped to 89 %. Note that this patient had SpO2of 90 % before induction of anesthesia.ConclusionThis study shows that it is feasible to use Tritube with FCV in patients with unusual location of tracheal stenosis, namely a subglottic posterior location, undergoing laryngotracheal surgery. Tritube provides a good surgical field and FCV provided highly adequate ventilation especially in patients with compromised lung mechanics.Trial registrationClinical trial registration was done prospectively (NCT05317923) on 08/04/2022.
A Cooperative optimization method for the layout of shared bicycle parking areas and delivery quantity
Authors: Chen Hao , Wang Wenxian , Cheng Ligang , Li Ping 
Published: May 2023

Abstract
With the popularity of shared bicycles in urban areas, more and more residents choose this fast and convenient mode of transportation for short-distance travel. By optimizing the layout of shared bicycle parking areas and delivery quantity, the investment cost of shared bicycle enterprises can be effectively reduced, and the convenience of residents' travel can be improved at the same time. In this paper, we develop a collaborative optimization model for the layout of the shared bicycle parking area and delivery quantity, aiming at minimizing the walking distance of residents and the investment cost of enterprises, while considering the constraints of the parking area's attractive range and the number of bicycles placed. Aiming at the characteristics of this mixed integer nonlinear problem, an improved genetic algorithm incorporating symmetric individual precision control mechanism is designed. Finally, taking the planned area between the Second Ring Road and the Third Ring Road in the northern part of Jin-niu District, Chengdu as the background, the proposed collaborative optimization model for the layout of shared bicycle parking areas and delivery quantity is applied to a real scene. The results show that after optimization, the number of parking areas is reduced by 2, and the total investment cost is reduced by about 12.2%.
Predicting the likelihood of cardiovascular disease in patients with rheumatoid arthritis: development and Validation of a Novel Model
Authors: Feng Min , Meng Fanxing , Yu Jiali , Wang Yanlin , Qin Yan , Jia Yuhan , Ji Guozhen , Liang Zhaojun , Gao Chong , Guo Hui , Luo Jing 
Published: May 2023

Abstract

BackgroundPatients with rheumatoid arthritis (RA) have increased mortality and morbidity due to cardiovascular disease (CVD). Distinguishing RA with CVD, RA with CVD risk factors and patients with RA only (pure RA), is still a challenge. The study aimed to develop a better model to predict the likelihood of CVD in RA.MethodsPure RA (n = 402), RA with CVD risk factors (n = 394), and RA with CVD (n = 201) were ultimately recruited into the study and their peripheral bloods were collected to measure the levels of routine examination indicators, vascular endothelial growth factor (VEGF) and immune cells. Univariate analysis, the least absolute shrinkage and selection operator (LASSO), the random forest (RF) and the logistic regression models (LR) were employed to screen characteristic variables between each two groups, and individualized nomograms were further established to more conveniently predict the likelihood of CVD in RA.ResultsUnivariate analysis showed that the levels of WBC, BUN, creatinine, CK, LDH and VEGF were significantly elevated in RA with CVD, as well as serum TC, TG, LDL, ApoB100 and ApoE, while ApoA1 and HDL/CHOL were decreased. Furthermore, the ratio of Treg cells, exhibiting excellent separation performance, in RA with CVD was significantly lower than that in other groups, while the ratio of Th1/Th2/NK and Treg were significantly elevated. LASSO, RF and LR models were also used to find the risk factors for CVD in RA. Through the final selected indicators screened by three machine learning models and univariate analysis, a convenient nomogram was established for predicting CVD risk in RA.ConclusionsSerum lipids, lipoproteins, and Treg cells have been identified as risk factors for CVD in patients with RA, and three nomograms combining various risk factors were constructed and were used for individualized prediction of CVD in patients with RA (pure RA and/or with CVD risk factors).
Identification of diagnostic genes for acute appendicitis and appendiceal cancer based on bioinformatics and machine learning
Authors: Zhang Xiali , Liu Zhihan , Wu Lidong , Feng Qian , Zhou Jinchuang , Luo Zhiqiang , Wang Yibing 
Published: May 2023

Abstract
Background
Appendiceal cancer is a rare malignancy that is often discovered incidentally in acute appendicitis patients. The diagnosis and treatment of this disease are challenging due to its low incidence and nonspecific symptoms. In this study, we used bioinformatics and machine learning to identify novel diagnostic genes for appendiceal cancer in acute appendicitis.
Methods
To identify differentially expressed genes (DEGs) between acute appendicitis and appendiceal cancer, we analyzed two GEO datasets (GSE9575 and GSE7535). Then, to select the most important differential expressed genes for diagnosis, we used three machine learning methods (LASSO logistic regression, SVM-RFE, and RandomForest). We also performed functional enrichment analysis and CIBERSORT analysis to explore the biological functions and immune cell infiltration of the feature genes.
Results
We identified 45 DEGs between appendiceal cancer and acute appendicitis, of which 23 were upregulated and 22 were downregulated in appendiceal cancer. The ROC curve analysis showed that the feature genes had an AUC of 1.000 for discriminating appendiceal cancer from acute appendicitis. The functional enrichment analysis revealed that the feature genes were mainly involved in cell cycle regulation, DNA replication, and DNA repair pathways. The CIBERSORT analysis showed that the feature genes were associated with different immune cell types, such as B cells, T cells, macrophages, and dendritic cells.
Conclusion
We identified novel critical genes involved in the progression of appendiceal cancer and provided potential biomarkers for its diagnosis. Our findings also suggested that the feature genes might play a role in modulating the immune response in appendiceal cancer.
Determinants of cognitive fatigue: Evaluating the effects of brain injury, disease and tasks
Authors: Wylie Glenn R , Genova Helen M , Yao Bing , Chiaravalloti Nancy , AF Román Cristina , Sandroff Brian M , DeLuca John 
Published: May 2023

Abstract

Because cognitive fatigue (CF) is common and debilitating following brain injury or disease we investigated the relationships among CF, behavioral performance, and cerebral activation within and across populations by combining the data from two cross-sectional studies. Individuals with multiple sclerosis (MS) were included to model CF resulting from neurological disease; individuals who had sustained a traumatic brain injury (TBI) were included to model CF resulting from neurological insult; both groups were compared with a control group (Controls). CF was induced while neuroimaging data was acquired using two different tasks. CF significantly differed between the groups, with the clinical groups reporting more CF than Controls. The accrual of CF did not differ across the three groups; and CF ratings were consistent across tasks. Increasing CF was associated with longer response time for all groups. The brain activation in the caudate nucleus and the thalamus was consistently correlated with CF in all three groups, while more dorsally in the caudate, activation differed across the groups. These results suggest the caudate and thalamus to be central to CF while more dorsal aspects of the caudate may be sensitive to damage associated with particular types of insult.
Magnetic poles enabled kirigami meta-structure for stable mechanical memory storage with high information density and structural robustness
Authors: Li Yanbin , Wang Baolong , Li Z.Q. , Xin Libiao 
Published: May 2023

Abstract
Some bi/multi-stable mechanical meta-structures have been implemented as mechanical memory devices which however are with limits such as complex structural forms, low information storage capability and/or fragile structural stability to maintain the stored information bits robustly under external interferences. To address these issues, we refer to the structural intelligence by constructing a simple 3D-printable multi-layered cylindrical kirigami module with gradient structural parameters and propose a mechanical memory device that can robustly store information bits exponentially larger than previous designs. We demonstrate the promising enhancement of information storage capability of our proposed mechanical memory device relies on two mechanisms: (1) the deformation sequences of the kirigami module enabled by the gradient structural parameter, which brings the extra dimensional degree of freedom to break the traditional mechanical memory unit with only planar form and merits information bits with spatially combinatorical programmability, and (2) the combinatorics of the deformation independences among the cylindrical kiriagmi unit arrays in the constructed mechanical memory device. Particularly, we achieve both the structural stabilities and the desired structural robustness in the mechanical memory devices by additively introducing magnetic “N-S” poles in units, which can protect the stored information from interferences like mechanical crushing, impacting and/or shaking.
Reversible Modulation of Interlayer Stacking in 2D Copper-Organic Frameworks for Tailoring Porosity and Photocatalytic Activity
Authors: You Pei-Ye , Wang Yu-Mei , Lin Xiao-Chun , Mo Kai-Ming , Lin Jia-Tong , Xie Mo , Wei Rong-Jia , Ning Guo-Hong , Li Dan 
Published: May 2023

Abstract
The properties of two-dimensional covalent organic frameworks (2D COFs) including porosity, catalytic activity as well as electronic and optical properties are greatly affected by their interlayer stacking structures. The precise control of their interlayer stacking mode, especially in a reversible fashion, is a long-standing pursuit, but still remains challenging. Herein, we prepared three 2D copper-organic frameworks, namely JNM-n (n = 7, 8, and 9). Interestingly, the reversible interlayer sliding between eclipsed AA stacking (i.e., JNM-7-AA and JNM-8-AA) and staggered ABC stacking (i.e., JNM-7-ABC and JNM-8-ABC) can be achieved through environmental stimulation, which endows reversible encapsulation and release of lipase. Importantly, JNM-7-AA and JNM-8-AA exhibited a broader light absorption range, higher charge-separation efficiency and higher photocatalytic activity for sensitizing O2 to 1O2 and O2•− than their ABC stacking isostructures. Consequently, JNM-8-AA exhibited much higher photocatalytic activities for oxidative cross-coupling reaction than those for JNM-8-ABC and other reported homogeneous and heterogeneous catalysts.