bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt
Authors: Shaaban Mohamed T. , Abdel-Raouf Mohamed , Zayed Muhammad , Emara Mahmoud A. 
Published: May 2024

Abstract
Background
Pseudomonas aeruginosa is an opportunistic pathogen responsible for complicated UTIs and exhibits high antibiotic resistance, leading to increased mortality rates, especially in cases of multidrug-resistant strains. This study aimed to investigate the antibiotic susceptibility patterns and genomic characterization of XDR strains identified in end-stage liver disease patients who underwent liver transplants.

Methods
In this study, a number of 30 individuals who underwent liver transplants were registered. Ninety urine and 60 wound site swab samples were collected and processed for culturing, identification, and antimicrobial sensitivity. Extensively drug-resistant strain EMARA01 was confirmed through Sanger sequencing and was then processed for whole genome sequencing to characterize the genomic pattern. Sequencing data were processed for de novo assembly using various tools and databases, including genome annotation, serotype identification, virulence factor genes, and antimicrobial resistance gene. Pangenome analysis of randomly selected 147 reference strains and EMAR01 sequenced strain was performed using the Bacterial Pan Genome Analysis (BPGA) software.

Results
Of these total examined samples, nosocomial infection due to P. aeruginosa was detected in twelve patients’ samples. AST analysis showed that P. aeruginosa strains exhibit resistance to tobramycin, erythromycin, and gentamicin, followed by piperacillin and ofloxacin, and no strains exhibit resistance to meropenem and imipenem. The CARD database identified 59 AMR genes similar to the EMAR01 strain genome and mostly belong to the family involved in the resistance-nodulation-cell division (RND) antibiotic efflux pump. Five genes; nalC, nalD, MexR, MexA, and MexB, exhibit resistance to 14 classes of antibiotics, while two AMR; CpxR, and OprM, exhibit resistance to 15 classes of drugs. Pangenome analysis revealed that the pan-genome remained open, suggesting the potential for acquiring accessory and unique genes. Notably, the genes predominantly involved in amino acid transport metabolism were identified using the KEGG database.

Conclusions
This study provides valuable insights into the antimicrobial resistance profile, genetic features, and genomic evolution of P. aeruginosa strains causing UTIs in liver transplant patients. The findings emphasize the significance of comprehending AMR mechanisms and genetic diversity in P. aeruginosa for developing effective treatment strategies and infection control measures.
Phytochemical profile and antifungal activity of essential oils obtained from different Mentha longifolia L. accessions growing wild in Iran and Iraq
Authors: Mustafa Kosrat Hama , Khorshidi Jalal , Vafaee Yavar , Rastegar Azad , Morshedloo Mohammad Reza , Hossaini Somaieh 
Published: May 2024

Abstract
Background
Mentha longifolia L. is a perennial plant belonging to the Lamiaceae family that has a wide distribution in the world. M. longifolia has many applications in the food and pharmaceutical industries due to its terpenoid and phenolic compounds. The phytochemical profile and biological activity of plants are affected by their genetics and habitat conditions. In the present study, the content, constituents and antifungal activity of the essential oil extracted from 20 accessions of M. longifolia collected from different regions of Iran and Iraq countries were evaluated.

Results
The essential oil content of the accessions varied between 1.54 ± 0.09% (in the Divandarreh accession) to 5.49 ± 0.12% (in the Khabat accession). Twenty-seven compounds were identified in the essential oils of the studied accessions, which accounted for 85.5-99.61% of the essential oil. The type and amount of dominant compounds in the essential oil were different depending on the accession. Cluster analysis of accessions based on essential oil compounds grouped them into three clusters. The first cluster included Baziyan, Boukan, Sarouchavah, Taghtagh, Darbandikhan, Isiveh and Harir. The second cluster included Khabat, Kounamasi, Soni and Mahabad, and other accessions were included in the third cluster. Significant correlations were observed between the essential oil content and components with the climatic and soil conditions of the habitats. The M. longifolia essential oil indicated antifungal activity against Fusarium solani in both methods used. In all studied accessions, the fumigation method compared to the contact method was more able to control mycelia growth. In both methods, the inhibition percentage of essential oil on mycelia growth increased with an increase in essential oil concentration. Significant correlations were found between the essential oil components and the inhibition percentage of mycelium growth.

Conclusion
The studied M. longifolia accessions showed significant differences in terms of the essential oil content and components. Differences in phytochemical profile of accessions can be due to their genetic or habitat conditions. The distance of the accessions in the cluster was not in accordance with their geographical distance, which indicates the more important role of genetic factors compared to habitat conditions in separating accessions. The antifungal activity of essential oils was strongly influenced by the essential oil quality and concentration, as well as the application method. Determining and introducing the elite accession in this study can be different depending on the breeder’s aims, such as essential oil content, desired chemical composition, or antifungal activity.
Transcriptome analysis of Gossypium hirsutum cultivar Zhongzhimian No.2 uncovers the gene regulatory networks involved in defense against Verticillium dahliae
Authors: Ma Xi-Yue , Zhou Xiao-Han , Liu Bin-Bin , Zhang Ye-Jing , Zhu He , Li Yue , Wang Zi-Sheng , Dai Xiao-Feng , Chen Jie-Yin , Su Zhen-Qi , Li Ran 
Published: May 2024

Abstract
Background
Cotton is globally important crop. Verticillium wilt (VW), caused by Verticillium dahliae, is the most destructive disease in cotton, reducing yield and fiber quality by over 50% of cotton acreage. Breeding resistant cotton cultivars has proven to be an efficient strategy for improving the resistance of cotton to V. dahliae. However, the lack of understanding of the genetic basis of VW resistance may hinder the progress in deploying elite cultivars with proven resistance.

Results
We planted the VW-resistant Gossypium hirsutum cultivar Zhongzhimian No.2 (ZZM2) in an artificial greenhouse and disease nursery. ZZM2 cotton was subsequently subjected to transcriptome sequencing after Vd991 inoculation (6, 12, 24, 48, and 72 h post-inoculation). Several differentially expressed genes (DEGs) were identified in response to V. dahliae infection, mainly involved in resistance processes, such as flavonoid and terpenoid quinone biosynthesis, plant hormone signaling, MAPK signaling, phenylpropanoid biosynthesis, and pyruvate metabolism. Compared to the susceptible cultivar Junmian No.1 (J1), oxidoreductase activity and reactive oxygen species (ROS) production were significantly increased in ZZM2. Furthermore, gene silencing of cytochrome c oxidase subunit 1 (COX1), which is involved in the oxidation-reduction process in ZZM2, compromised its resistance to V. dahliae, suggesting that COX1 contributes to VW resistance in ZZM2.

Conclusions
Our data demonstrate that the G. hirsutum cultivar ZZM2 responds to V. dahliae inoculation through resistance-related processes, especially the oxidation-reduction process. This enhances our understanding of the mechanisms regulating the ZZM2 defense against VW.
Swedish consensus regarding difficult pre-hospital airway management: a Delphi study
Authors: Borgström Anton Modée , Bäckström Denise 
Published: May 2024

Abstract
Background
The aim of this study was to establish a consensus among experts in prehospital work regarding the management of difficult airways in prehospital care in Sweden. The results were subsequently used to develop an algorithm for handling difficult airway in prehospital care, as there was none available in Sweden prior to this study.

Methods
This two-round Delphi study was conducted by forming an expert panel comprising anesthesiologists and anesthesia nurses working in prehospital setting in Sweden. The expert panel responded digital forms with questions and statements related to airway management. The study continued until consensus was reached, defined as more than 70% agreement. The study took place from December 4, 2021, to May 15, 2022.

Results
In the first round, 74 participants took part, while the second round involved 37 participants. Consensus was reached in 16 out of 17 statements. 92% of the participants agreed that an airway algorithm adapted for prehospital use is necessary.

Conclusions
The capacity to adapt the approach to airway management based on specific pre-hospital circumstances is crucial. It holds significance to establish a uniform framework that is applicable across various airway management scenarios. Consequently, the airway management algorithm that has been devised should be regarded as a recommendation, allowing for flexibility rather than being interpreted as a rigid course of action.
This represents the inaugural nationwide algorithm for airway management designed exclusively for pre-hospital operations in Sweden. The algorithm is the result of a consensus reached by experts in pre-hospital care.
Sports-related fractures in the geriatric population at a level I trauma center
Authors: Jeon Young Dae , Park Ki-Bong , Ko Sang-Hun , Oh Jae-Min , Kim Sang-Gon 
Published: May 2024

Abstract
Background
The population is rapidly aging and remains active over the age of 65 years. An increasing number of sports-related fractures (SRFs) in individuals 65 and older are thus anticipated. Despite the increase in SRFs among the geriatric population, there are limited studies regarding the epidemiological data regarding SRFs in geriatric patients. This study examined the epidemiology of SRFs in a geriatric population who visited a level I trauma center.

Methods
Data from geriatric patients who visited a level I trauma center were collected between June 2020 and July 2023. Overall, 1,109 geriatric patients with fractures were included in the study. Among them, 144 (13.0%) had fractures during sports activities (SRF group) and 965 (87.0%) had fractures during non-sports activities (non-SRF group). We investigated the type of sport in the SRFs and compared SRFs and NSRFs to describe the differences in patient, fracture, and treatment characteristics.

Results
The mean age of SRFs was significantly lower (73.6 vs. 78.7 years; P < .001). The proportion of men was significantly higher in the SRF group than in the non-SRF group (51.4 vs. 29.6%; P < .001). We identified 13 types of sports associated with fractures, and the four most common were outdoor walking (36.1%), outdoor biking (27.8%), mountain hiking (19.4%), and gym (8.3%). There were no significant differences in the rate of hospitalization, operative treatment, or length of hospital stay between the two groups. However, compared to the non-SRF group, patients in the SRF group tended to return home after hospitalization (P = .002).

Conclusion
This epidemiological study describes geriatric population that continues to be involved in sports and is thus susceptible to fractures. The identification of the type and distribution of SRFs in geriatric patients provides useful information for determining risk factors and appropriate preventive measures that may reduce their incidence.
A complex case study: coexistence of multi-drug-resistant pulmonary tuberculosis, HBV-related liver failure, and disseminated cryptococcal infection in an AIDS patient
Authors: Fu Wei , Deng Zi Wei , Wang Pei , Zhu Zhen Wang , Pu Ye , Xie Zhi Bing , Li Yong Zhong , Yu Hong Ying 
Published: May 2024

Abstract
Background
Hepatitis B virus (HBV) infection can cause liver failure, while individuals with Acquired Immunodeficiency Virus Disease (AIDS) are highly susceptible to various opportunistic infections, which can occur concurrently. The treatment process is further complicated by the potential occurrence of immune reconstitution inflammatory syndrome (IRIS), which presents significant challenges and contributes to elevated mortality rates.

Case presentation
The 50-year-old male with a history of chronic hepatitis B and untreated human immunodeficiency virus (HIV) infection presented to the hospital with a mild cough and expectoration, revealing multi-drug resistant pulmonary tuberculosis (MDR-PTB), which was confirmed by XpertMTB/RIF PCR testing and tuberculosis culture of bronchoalveolar lavage fluid (BALF). The patient was treated with a regimen consisting of linezolid, moxifloxacin, cycloserine, pyrazinamide, and ethambutol for tuberculosis, as well as a combination of bictegravir/tenofovir alafenamide/emtricitabine (BIC/TAF/FTC) for HBV and HIV viral suppression. After three months of treatment, the patient discontinued all medications, leading to hepatitis B virus reactivation and subsequent liver failure. During the subsequent treatment for AIDS, HBV, and drug-resistant tuberculosis, the patient developed disseminated cryptococcal disease. The patient’s condition worsened during treatment with liposomal amphotericin B and fluconazole, which was ultimately attributed to IRIS. Fortunately, the patient achieved successful recovery after appropriate management.

Conclusion
Enhancing medical compliance is crucial for AIDS patients, particularly those co-infected with HBV, to prevent HBV reactivation and subsequent liver failure. Furthermore, conducting a comprehensive assessment of potential infections in patients before resuming antiviral therapy is essential to prevent the occurrence of IRIS. Early intervention plays a pivotal role in improving survival rates.
Tumour growth rate predicts overall survival in patients with recurrent WHO grade 4 glioma
Authors: Pang Jeffer Hann Wei , Saffari Seyed Ehsan , Lee Guan Rong , Yu Wai-Yung , Lim Choie Cheio Tchoyoson , Lim Kheng Choon , Lee Chia Ching , Koh Wee Yao , Chia Wei Tsau, David , Chua Kevin Lee Min , Tham Chee Kian , Low Yin Yee Sharon , Ng Wai Hoe , Low Chyi Yeu David , Lin Xuling 
Published: May 2024

Abstract
Purpose
Accurate prognostication may aid in the selection of patients who will benefit from surgery at recurrent WHO grade 4 glioma. This study aimed to evaluate the role of serial tumour volumetric measurements for prognostication at first tumour recurrence.

Methods
We retrospectively analyzed patients with histologically-diagnosed WHO grade 4 glioma at initial and at first tumour recurrence at a tertiary hospital between May 2000 and September 2018. We performed auto-segmentation using ITK-SNAP software, followed by manual adjustment to measure serial contrast-enhanced T1W (CE-T1W) and T2W lesional volume changes on all MRI images performed between initial resection and repeat surgery.

Results
Thirty patients met inclusion criteria; the median overall survival using Kaplan-Meier analysis from second surgery was 10.5 months. Seventeen (56.7%) patients received treatment post second surgery. Univariate cox regression analysis showed that greater rate of increase in lesional volume on CE-T1W (HR = 2.57; 95% CI [1.18, 5.57]; p = 0.02) in the last 2 MRI scans leading up to the second surgery was associated with a higher mortality likelihood. Patients with higher Karnofsky Performance Score (KPS) (HR = 0.97; 95% CI [0.95, 0.99]; p = 0.01) and who received further treatment following second surgery (HR = 0.43; 95% CI [0.19, 0.98]; p = 0.04) were shown to have a better survival.

Conclusion
Higher rate of CE-T1W lesional growth on the last 2 MRI images prior to surgery at recurrence was associated with increase mortality risk. A larger prospective study is required to determine and validate the threshold to distinguish rapidly progressive tumour with poor prognosis.
UHPLC-HRMS-based Multiomics to Explore the Potential Mechanisms and Biomarkers for Colorectal Cancer
Authors: Wang Xuancheng , Guan Xuan , Tong Ying , Liang Yunxiao , Huang Zongsheng , Wen Mingsen , Luo Jichu , Chen Hongwei , Yang Shanyi , She Zhiyong , Wei Zhijuan , Zhou Yun , Qi Yali , Zhu Pingchuan , Nong Yanying , Zhang Qisong 
Published: May 2024

Abstract
Background
Understanding the metabolic changes in colorectal cancer (CRC) and exploring potential diagnostic biomarkers is crucial for elucidating its pathogenesis and reducing mortality. Cancer cells are typically derived from cancer tissues and can be easily obtained and cultured. Systematic studies on CRC cells at different stages are still lacking. Additionally, there is a need to validate our previous findings from human serum.

Methods
Ultrahigh-performance liquid chromatography tandem high-resolution mass spectrometry (UHPLC-HRMS)-based metabolomics and lipidomics were employed to comprehensively measure metabolites and lipids in CRC cells at four different stages and serum samples from normal control (NR) and CRC subjects. Univariate and multivariate statistical analyses were applied to select the differential metabolites and lipids between groups. Biomarkers with good diagnostic efficacy for CRC that existed in both cells and serum were screened by the receiver operating characteristic curve (ROC) analysis. Furthermore, potential biomarkers were validated using metabolite standards.

Results
Metabolite and lipid profiles differed significantly among CRC cells at stages A, B, C, and D. Dysregulation of glycerophospholipid (GPL), fatty acid (FA), and amino acid (AA) metabolism played a crucial role in the CRC progression, particularly GPL metabolism dominated by phosphatidylcholine (PC). A total of 46 differential metabolites and 29 differential lipids common to the four stages of CRC cells were discovered. Eight metabolites showed the same trends in CRC cells and serum from CRC patients compared to the control groups. Among them, palmitoylcarnitine and sphingosine could serve as potential biomarkers with the values of area under the curve (AUC) more than 0.80 in the serum and cells. Their panel exhibited excellent performance in discriminating CRC cells at different stages from normal cells (AUC = 1.00).

Conclusions
To our knowledge, this is the first research to attempt to validate the results of metabolism studies of serum from CRC patients using cell models. The metabolic disorders of PC, FA, and AA were closely related to the tumorigenesis of CRC, with PC being the more critical factor. The panel composed of palmitoylcarnitine and sphingosine may act as a potential biomarker for the diagnosis of CRC, aiding in its prevention.
Long-term follow-up of protective effects on salivary and swallowing structures and improvement of late xerostomia and dysphagia by level IIb optimisation in clinical target volume of nasopharyngeal carcinoma
Authors: Zhou Jiawei , Wang Li , Qiu Ting , Gao Han , Wang Lijun , Huang Shengfu , He Xia , Wu Lirong 
Published: May 2024

Abstract
Background
This study aimed to assess the long-term effect of level IIb clinical target volume (CTV) optimisation on survival, xerostomia, and dysphagia in patients with nasopharyngeal carcinoma (NPC).

Methods
Clinical data of 415 patients with NPC treated with intensity-modulated radiotherapy between December 2014 and October 2018 were retrospectively analysed. The patients were categorised into modified and comparison groups. Late xerostomia and dysphagia were evaluated using Radiation Therapy Oncology Group/European Organisation for Research and Treatment of Cancer scoring. Survival analysis was performed using the Kaplan–Meier method. Differences in late toxicity and dose parameters between both groups were compared. Prognostic factors for survival and late toxicity were assessed using regression analyses.

Results
Patients in the modified group developed late xerostomia and dysphagia less frequently than those in the comparison group did (P < 0.001). The mean dose (Dmean) and V26 of parotid glands; Dmean and V39 of submandibular glands; and Dmean of sublingual glands, oral cavity, larynx, and superior, middle, and lower pharyngeal constrictor muscles were lower in the modified group than those in the comparison group (all P < 0.001). Both groups had no significant differences in overall, local recurrence-free, distant metastasis-free, or progression-free survival. The Dmean of the parotid and sublingual glands was a risk factor for xerostomia. The Dmean of the parotid and sublingual glands and middle pharyngeal constrictor muscle was a risk factor for dysphagia.

Conclusions
Level IIb optimisation in NPC patients who meet certain criteria specially the exclusion of positive retropharyngeal nodes treated with intensity-modulated radiotherapy has the potential to better protect the salivary and swallowing structures, decreasing the development of late radiation-induced xerostomia and dysphagia while maintaining long-term survival.
CD276 enhances sunitinib resistance in clear cell renal cell carcinoma by promoting DNA damage repair and activation of FAK-MAPK signaling pathway
Authors: Zhang Zhi-yu , Xu Jian-hao , Zhang Jiang-lei , Lin Yu-xin , Ou-Yang Jun 
Published: May 2024

Abstract
Objective
This study aimed to explore the effect of CD276 expression on the sunitinib sensitivity of clear cell renal cell carcinoma (ccRCC) cell and animal models and the potential mechanisms involved.

Methods
CD276 expression levels of ccRCC and normal samples were analyzed via online databases and real-time quantitative PCR (RT-qPCR). CD276 was knocked down in ccRCC cell models (sunitinib-resistant 786-O/R cells and sunitinib-sensitive 786-O cells) using shRNA transfection, and the cells were exposed to a sunitinib (2 µM) environment. Cells proliferation was then analyzed using MTT assay and colony formation experiment. Alkaline comet assay, immunofluorescent staining, and western blot experiments were conducted to assess the DNA damage repair ability of the cells. Western blot was also used to observe the activation of FAK-MAPK pathway within the cells. Finally, a nude mouse xenograft model was established and the nude mice were orally administered sunitinib (40 mg/kg/d) to evaluate the in vivo effects of CD276 knockdown on the therapeutic efficacy of sunitinib against ccRCC.

Results
CD276 was significantly upregulated in both ccRCC clinical tissue samples and cell models. In vitro experiments showed that knocking down CD276 reduced the survival rate, IC50 value, and colony-forming ability of ccRCC cells. Knocking down CD276 increased the comet tail moment (TM) values and γH2AX foci number, and reduced BRCA1 and RAD51 protein levels. Knocking down CD276 also decreased the levels of p-FAK, p-MEK, and p-ERK proteins.

Conclusion
Knocking down CD276 effectively improved the sensitivity of ccRCC cell and animal models to sunitinib treatment.