bluuebunny/crossref_metadata_2025_split huggingface dataset:
Who’s afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data
Authors: Inkster Amy M. , Wong Martin T. , Matthews Allison M. , Brown Carolyn J. , Robinson Wendy P. 
Published: January 2023

AbstractBackgroundMany human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from large-scale analyses of the human genome and epigenome due to analytical complexity associated with sex chromosome dosage differences between XX and XY individuals, and the impact of X-chromosome inactivation (XCI) on the epigenome. As such, little attention has been given to considering the methods by which sex chromosome data may be included in analyses of DNA methylation (DNAme) array data.ResultsWith Illumina Infinium HumanMethylation450 DNAme array data from 634 placental samples, we investigated the effects of probe filtering, normalization, and batch correction on DNAme data from the X and Y chromosomes. Processing steps were evaluated in both mixed-sex and sex-stratified subsets of the analysis cohort to identify whether including both sexes impacted processing results. We found that identification of probes that have a high detection p-value, or that are non-variable, should be performed in sex-stratified data subsets to avoid over- and under-estimation of the quantity of probes eligible for removal, respectively. All normalization techniques investigated returned X and Y DNAme data that were highly correlated with the raw data from the same samples. We found no difference in batch correction results after application to mixed-sex or sex-stratified cohorts. Additionally, we identify two analytical methods suitable for XY chromosome data, the choice between which should be guided by the research question of interest, and we performed a proof-of-concept analysis studying differential DNAme on the X and Y chromosome in the context of placental acute chorioamnionitis. Finally, we provide an annotation of probe types that may be desirable to filter in X and Y chromosome analyses, including probes in repetitive elements, the X-transposed region, and cancer-testis gene promoters.ConclusionWhile there may be no single “best” approach for analyzing DNAme array data from the X and Y chromosome, analysts must consider key factors during processing and analysis of sex chromosome data to accommodate the underlying biology of these chromosomes, and the technical limitations of DNA methylation arrays.
The acyl-CoA-binding protein 2 exhibited the highest affinity for palmitoyl-CoA and promoted Monascus pigment production
Authors: Cui Jingjing , Liu Mengmeng , Wu Weiwei , Long Chuannan , Zeng Bin 
Published: January 2023

Abstract
Purpose
The present study aimed to explore the binding ability of acyl-CoA binding protein 2 to fatty acid acyl-CoA esters and its effect on Monascus pigment production in M. ruber CICC41233.

Methods
The Mracbp2 gene from M. ruber CICC41233 was cloned with a total DNA and cDNA as the templates through the polymerase chain reaction. The cDNA of the Mracbp2 gene fragment was ligated to expression vector pGEX-6P-1 to construct pGEX-MrACBP2, which was expressed in Escherichia coli BL21 to obtain the fusion protein GST-MrACBP2 and then measure the binding ability of fatty acid acyl-CoA esters. Additionally, the DNA of the Mracbp2 gene fragment was ligated to expression vector pNeo0380 to construct pNeo0380-MrACBP2, which was homologously over-expressed in M. ruber CICC41233 to evaluate Monascus pigment production and fatty acid.

Results
The cloned Mracbp2 gene of the DNA and cDNA sequence was 1525 bp and 1329 bp in length, respectively. The microscale thermophoresis binding assay revealed that the purified GST-MrACBP2 had the highest affinity for palmitoyl-CoA (Kd =70.57 nM). Further, the Mracbp2 gene was homologously overexpressed in M. ruber CICC41233, and a positive transformant M. ruber ACBP-E was isolated. In the Monascus pigments fermentation, the expression level of the Mracbp2 gene was increased by 1.74-fold after 2 days and 2.38-fold after 6 days. The palmitic acid content and biomass in M. ruber ACBP2-E were significantly lower than that in M. ruber CICC41233 on 2 days and 6 days. However, compared with M. ruber CICC41233, the yields of total pigment, ethanol-soluble pigment, and water-soluble pigment in M. ruber ACBP2-E increased by 63.61%, 71.61%, and 29.70%, respectively.

Conclusions
The purified fusion protein GST-MrACBP2 exhibited the highest affinity for palmitoyl-CoA. The Mracbp2 gene was overexpressed in M. ruber CICC41233, which resulted in a decrease in palmitic acid and an increase in Monascus pigments. Overall, the effect of MrACBP2 on the synthesis of fatty acid and Monascus pigment was explored. This paper explored the effect of MrACBP2 on the fatty acid synthesis and the synthesis of Monascus pigment. The results indicated the regulation of fatty acid synthesis could affect Monascus pigment synthesis, providing a novel strategy for improving the yield of Monascus pigment.
Role of nebulized colistin as a substitutive strategy against nosocomial pneumonia caused by CR-GNB in intensive care units: a retrospective cohort study
Authors: Feng Jia-Yih , Huang Jhong-Ru , Lee Chang-Ching , Tseng Yen-Han , Pan Sheng-Wei , Chen Yuh-Min , Yang Kuang-Yao 
Published: January 2023

Abstract
Background
Adverse reactions, especially nephrotoxicity, are great concerns of intravenous colistin treatment. The role of substitutive nebulized colistin in treating nosocomial pneumonia caused by carbapenem-resistant Gram-negative bacterial (CR-GNB) in critically ill patients remains unknown.

Methods
This retrospective study enrolled patients with nosocomial pneumonia caused by colistin-susceptible CRGNB in the intensive care unit (ICU) without intravenous colistin treatment. Patients were categorized based on whether substitutive nebulized colistin was used alongside other intravenous antibiotics. Clinical responses and mortality rates were compared between the two groups in the original and propensity score (PS)-matched cohorts. This study aimed to investigate the clinical effectiveness of substitutive nebulized colistin in treatment outcomes of nosocomial pneumonia caused by CR-GNB. The impact of dosing strategy of nebulized colistin was also explored.

Results
In total, 343 and 214 patients with and without substitutive nebulized colistin, respectively, were enrolled for analysis. In the PS-matched cohort, clinical failure rates on day 7 (22.6 vs. 42.6%, p = 0.001), day 14 (27.0 vs. 42.6%, p = 0.013), and day 28 (27.8 vs. 41.7%, p = 0.027) were significantly lower in patients with nebulized colistin. In multivariate analysis, nebulized colistin was an independent factor associated with lower day 14 clinical failure (Original cohort: adjusted odds ratio (aOR) 0.45, 95% confidence interval (CI) 0.30–0.67; PS-matched cohort: aOR 0.48, 95% CI 0.27–0.87). There were no differences in clinical failure rate and mortality rate between patients receiving high (> 6 MIU/day) and low (≤ 6 MIU/day) dose nebulized colistin in the PS-matched cohort.

Conclusions
In ICU-admitted patients with nosocomial pneumonia caused by colistin-susceptible CRGNB, substitutive nebulized colistin was associated with better clinical outcomes.
Load balancing and service discovery using Docker Swarm for microservice based big data applications
Authors: Singh Neelam , Hamid Yasir , Juneja Sapna , Srivastava Gautam , Dhiman Gaurav , Gadekallu Thippa Reddy , Shah Mohd Asif 
Published: January 2023

AbstractBig Data applications require extensive resources and environments to store, process and analyze this colossal collection of data in a distributed manner. Containerization with cloud computing provides a pertinent remedy to accommodate big data requirements, however requires a precise and appropriate load-balancing mechanism. The load on servers increases exponentially with increased resource usage thus making load balancing an essential requirement. Moreover, the adjustment of containers accurately and rapidly according to load as per services is one of the crucial aspects in big data applications. This study provides a review relating to containerized environments like Docker for big data applications with load balancing. A novel scheduling mechanism of containers for big data applications established on Docker Swarm and Microservice architecture is proposed. The concept of Docker Swarm is utilized to effectively handle big data applications' workload and service discovery. Results shows that increasing workloads with respect to big data applications can be effectively managed by utilizing microservices in containerized environments and load balancing is efficiently achieved using Docker Swarm. The implementation is done using a case study deployed on a single server and then scaled to four instances. Applications developed using containerized microservices reduces average deployment time and continuous integration.
A study on endovascular treatment alone and bridging treatment for acute ischemic stroke
Authors: Ji Xiyang , Song Bo , Zhu Hao , Jiang Zhao , Hua Feng , Wang Sa , Zhou Jianbo , Li Lin , Dai Changfei , Zhang Mijuan , Wei Dong , Zhang Lele , Zhang Xiaojie , Zhang Qun , Chen Ping 
Published: January 2023

Abstract
Objectives
To investigate whether intravenous thrombolysis (IVT) with alteplase (a recombinant tissue plasminogen activator, rt-PA) before endovascular treatment (EVT) is beneficial for acute ischemic stroke (AIS) patients in different periods.

Methods
This study enrolled a total of 140 patients hospitalized between 2019 and 2022 with AIS from large vessel occlusion (LVO) in the anterior circulation. Those patients were divided into the EVT alone group and IVT + EVT group, in which EVT was preceded by intravenous rt-PA. According to the time from onset to femoral artery puncture, the above two groups were divided into the following subgroups: < 4.5 h, between 4.5 and 6 h, between 6 and 8 h, and between 8 and 10 h. There were 78 patients in the EVT alone group and 62 patients in the IVT + EVT group.

Results
There was no statistically significant difference in functional independence, recanalization rate, favorable outcome rate, or mortality between the EVT and IVT + EVT groups (P > 0.05). After adjusting for confounding factors, a lower incidence of intracerebral hemorrhage was observed in the EVT group (P < 0.05). A comparison of time-dependent efficacy between the two groups showed that within 6–8 h, there were statistically significant differences between admission and postoperation in the National Institutes of Health Stroke Scale scores at 24 h (P = 0.01) or 7 days (P = 0.02).

Conclusions
Although there was no difference in clinical efficacy and safety between the abovementioned two groups, treatment with IVT + EVT could increase the risk of bleeding compared to EVT. Moreover, in the 6–8 h subgroup, the efficacy of EVT alone was better than that of IVT + EVT.
The impact of partial and complete lockdown during the COVID-19 pandemic on acute surgical services: a retrospective cohort study
Authors: Al manasra Abdel Rahman A. , Alabdallah Nadeem B. , Mesmar Zaid , Almasarweh Sami A. , Nofal Mohammad , Shattarah Osama , Aljarrah Qusai , Ibrahim Khalid S. , Al-qaoud Doaa 
Published: January 2023

Abstract
Purpose
The burden of the coronavirus disease of 2019 (COVID-19) pandemic on the healthcare sector has been overwhelming, leading to drastic changes in access to healthcare for the public. We aimed to establish the impact of implemented government partial and complete lockdown policies on the volume of surgical patient admissions at a tertiary referral center during the pandemic.

Methods
A database was retrospectively created from records of patients admitted to the surgical ward through the emergency department. Three 6-week periods were examined: The complete lockdown period (CLP), which included a ban on the use of cars with the exception of health service providers and essential sector workers; A pre-COVID period (PCP) 1 year earlier (no lockdown); and a partial lockdown period (PLP) that involved a comprehensive curfew and implementing social distancing regulations and wear of personal protective equipment (e.g., masks) in public places.

Results
The number of patients admitted to the surgery ward was significantly higher in the PCP cohort compared to the CLP and PLP cohorts (p = 0.009), with a 42.1% and 37% decline in patients’ admissions, respectively. Admission rates for patients with biliary pathologies and vascular thrombotic events increased. 30-day mortality rates did not differ significantly between the three periods (p = 0.378).

Conclusions
While COVID-19 lockdown regulations had a significant impact on patient admission rates, surgical outcomes were not affected and the standards of care were maintained. Future protocols should strive to improve access to healthcare to avoid complications caused by delayed diagnosis and treatment.
The association between blood manganese and liver stiffness in participants with chronic obstructive pulmonary disease: a cross-sectional study from NHANES 2017–2018
Authors: Han Kexing , Shen Jiapei , Tan Kexuan , Liu Jiaying , Sun Weijie , Gao Yufeng 
Published: January 2023

Abstract
Background
To explore the relationship between blood manganese and liver stiffness in the United States among participants with chronic obstructive pulmonary disease (COPD).

Methods
All data were obtained from the 2017–2018 National Health and Nutrition Examination Survey database (NHANES). A total of 4690 participants were included in the study. All participants included complete information on COPD, liver stiffness, and blood manganese. Liver stiffness (kPa) was measured from “Examination Date” and blood manganese (ug/L) was obtained from “Laboratory Data”. A multiple linear regression model was used to assess the correlation between blood manganese and liver stiffness.

Results
Among the 4690 participants, blood manganese was lower in the COPD group but liver stiffness was higher (p < 0.05). There was a positive correlation between blood manganese and liver stiffness (β = 0.08, 95% CI 0.03, 0.12). This positive association was more pronounced in COPD participants (β = 0.25, 95% CI 0.08, 0.42) and there was a non-linear relationship, which was more significant when blood manganese exceeded 14.43 ug/L (β = 1.76, 95% CI 1.10, 2.41).

Conclusions
The association between blood manganese and liver stiffness was positive, which was more apparent in COPD patients.
Bipolar disorders in Nigeria: a mixed-methods study of patients, family caregivers, clinicians, and the community members’ perspectives
Authors: Jidong Dung Ezekiel , Husain M. Ishrat , Ike Tarela J. , Husain Nusrat , Taru Maigari Yusufu , Nnaemeka Nwoga Charles , Francis Christopher , Jack David B. , Mwankon Shadrack B. , Xue Siqi , Pwajok Juliet Y. , Nyam Pam P. , Murshed Maisha 
Published: January 2023

Abstract
Background
Bipolar Disorders (BDs) are chronic mental health disorders that often result in functional impairment and contribute significantly to the disability-adjusted life years (DALY). BDs are historically under-researched compared to other mental health disorders, especially in Sub-Saharan Africa and Nigeria.

Design
We adopted a mixed-methods design. Study 1 examined the public knowledge of BDs in relation to sociodemographic outcomes using quantitative data whilst Study 2 qualitatively assessed the lived experiences of patients with BDs, clinicians, and family caregivers.

Methods
In Study 1, a non-clinical sample of n = 575 participants responded to a compact questionnaire that examined their knowledge of BDs and how they relate to certain sociodemographic variables. One-way ANOVA was used to analyse quantitative data. Study 2 interviewed N = 15 participants (n = 5 patients with BDs; n = 7 clinicians; n = 3 family caregivers). These semi-structured interviews were audio-recorded, transcribed, and thematically analysed.

Results
In Study 1, findings showed no statistically significant differences, suggesting low awareness of BDs, especially among vulnerable populations such as young people and older adults. However, there was a trajectory in increased knowledge of BDs among participants between the ages of 25–44 years and part-time workers compared to other ages and employment statuses. In Study 2, qualitative findings showed that BDs are perceived to be genetically and psycho-socially induced by specific lived experiences of patients and their family caregivers. Although psychotropic medications and psychotherapy are available treatment options in Nigeria, cultural and religious beliefs were significant barriers to treatment uptake.

Conclusions
This study provides insight into knowledge and beliefs about BDs, including the lived experiences of patients with BDs, their caregivers and clinicians in Nigeria. It highlights the need for further studies assessing Nigeria's feasibility and acceptability of culturally adapted psychosocial interventions for patients with BDs.
Amide Proton Transfer-weighted MRI combined with serum prostate-specific antigen levels for differentiating malignant prostate lesions from benign prostate lesions: a retrospective cohort study
Authors: Yang Lu , Wang Lei , Tan Yuchuan , Dan Hanli , Xian Peng , Zhang Yipeng , Tan Yong , Lin Meng , Zhang Jiuquan 
Published: January 2023

Abstract
Background
Early diagnosis of prostate cancer improves its prognosis, while it is essential to upgrade screening tools. This study aimed to explore the value of a novel functional magnetic resonance imaging (MRI) technique, namely amide proton transfer (APT)-weighted MRI, combined with serum prostate-specific antigen (PSA) levels to differentiate malignant prostate lesions from benign prostate lesions.

Methods
Data of patients who underwent prostate examinations at Chongqing University Cancer Hospital between July 2019 and March 2022 were retrospectively analyzed. All patients underwent T2-weighted imaging (T2WI), APT, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) MRI. Two radiologists analyzed the images independently. The ability of the quantitative parameters alone or in different combinations in differentiating malignant prostate lesions from benign prostate lesions were compared by using receiver operating characteristic (ROC) curves. According to the DeLong test, the combined parameters were significantly different from the corresponding single parameter (P < 0.05).

Results
A total of 79 patients were finally enrolled, including 52 patients in the malignant group and 27 patients in the benign group. The separate assessment of indexes revealed that APTmax, APTmean, mean apparent diffusion coefficient (ADCmean), ADCmax, ADCmin, tPAD, free prostate-specific antigen (FPSA), FPSA/total prostate-specific antigen (tPSA), and PSA density (PSAD) were significantly different between the two groups (P < 0.05), while APTmin was not significantly different between the two groups (P > 0.05). APTmax and APTmean had the high values of area under the ROC curve (AUC), which were 0.780 and 0.710, respectively. APTmax had a high sensitivity, and APTmean had a high specificity. The combination of APTmax, APTmean, ADCmean, and PSAD had the highest AUC value (AUC: 0.880, sensitivity: 86.540, specificity: 78.260).

Conclusion
APTmax, APTmean, ADCmean, ADCmin, tPAD, FPSA, and PSAD showed to have a high value in differentiating malignant prostate lesions from benign prostate lesions in the separate assessment of indexes. The combination of APTmax, APTmean, ADCmean, and PSAD had the highest diagnostic value.
Perceptions and factors affecting the adoption of digital games for engineering education: a mixed-method research
Authors: Udeozor Chioma , Russo-Abegão Fernando , Glassey Jarka 
Published: January 2023

AbstractDigital games are considered relevant in higher education due to their ability to foster authentic, active and experiential learning opportunities that are of importance in engineering education. However, as a relatively new pedagogical tool, there is the need to understand the perceptions of engineering students as well as to identify factors that influence their adoption of games for learning. So far, only a few studies have investigated the perceptions of higher education students towards learning games and even fewer for engineering students. To bridge this research gap, the current study utilises a mixed-method research design to identify factors that influence the adoption of digital learning games by engineering students as well as their overall perceptions of the use of games for engineering education. Results from the analysed quantitative and qualitative data suggest that engineering students value fun and engagement as well as relevance to the curriculum as factors that would influence their intentions to use digital games for engineering education. Students also showed openness to the use of digital games for learning, but resistance to their use for assessment. These findings have implications for the design of games and classroom deployment of games, as these provide insights to game designers and educators on the factors to consider in the design and classroom deployment of games, respectively.
Gentiana lutea attenuates hepatotoxicity induced by ketoconazole in rats by fortifying the cellular antioxidant defense system
Authors: Hamza Alaaeldin Ahmed , Gamel Mona , Abdalla Ali , Abdalla Youssef , Amin Amr 
Published: January 2023

AbstractBackgroundKetoconazole (KET) is a broad-spectrum antifungal drug that has been reported to induce hepatotoxicity in humans and animals.MethodsThe safe guarding response of Gentiana extract (GEN) against KET-induced hepatotoxicity was investigated in this study using male Wistar rats. GEN ethanol extract was orally administered to rats (1 g/kg b.wt) for 30 days. Beginning on day 26, KET was intraperitoneally administered once daily for 5 days using a dose of 100 mg/kg. The hepatoprotective effects of GEN against liver damage induced by KET were monitored through significant decrements in serum levels of aminotransferase and alpha-fetoprotein as well as recorded hepatic histopathological changes.ResultsThe hepatotoxicity of KET treatment was accompanied with a marked oxidative damage to hepatic proteins, lipids, and DNA, and depletions in natural antioxidants (glutathione and superoxide dismutase). GEN inhibited KET-induced oxidative stress by diminishing lipid peroxidation, protein carbonylation, and oxidative stress in DNA. These free radical mediated effects were greatly decreased with GEN treatment.ConclusionsThis study suggests that GEN’s hepatoprotective effects could be attributed to its antioxidant properties.