bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-infections among COVID-19 Patients in Ugandan Intensive Care Units
Authors: Olowo Samuel , Obwiin John K. , Pido Florence , Alupo Martha , Ssendikadiwa Charles , Nakibuuka Jane , Jjuuko Edrin , Okello Erasmus E. , Ssenyonga Lydia VN. , Iramiot Jacob S. 
Published: October 2022

Abstract
Background: The pandemic of COVID-19 has led to an upsurge of critically ill patients requiring advanced life support. Bacteria and fungi have been isolated as etiological agents for co-infections among COVID-19 patients in the intensive care unit (ICU). Co-infection has been associated with worse outcomes among COVID-19 patients in ICUs. The aim of this study was to determine the prevalence of co-infections and their antimicrobial susceptibility patterns among COVID-19 patients admitted to intensive care units in Uganda.
Materials and Methods: A multi-center cross-sectional retrospective survey was carried out in Intensive Care Units (ICUs) in Mulago national referral hospital, UMC Victoria and TMR international hospital in Uganda. The records of 216 hospitalized ICU COVID-19 patients were purposively sampled using a standardized data abstraction tool. The collected data were double entered in Epi-data version 3.1 and exported to Stata version 17.0 for statistical analysis.
Results: The prevalence of co-infections (bacterial and fungal) was 111(51.39%) with respiratory tract infections 57(51.35%) being the most prevalent. Staphylococcus aureus 23(28.75%), Citrobacter freudii 19(23.75%), Pseudomonas aureginosa 15(18.75%) and Klebsiella pneumoniae 10(12.50%) were the most frequently isolated bacterial species. The prevalence of multidrug resistant bacterial species was 75.95%. About 07/8(8.75%) of the bacterial species were extended spectrum beta lactamase or AmpC beta lactamase producers. Some of ESBL producers demonstrated susceptibility to Augmentin, Amikacin and trimethoprim. Augmentin 33/54(61.11%) and ceftriaxone 4/44(9.09%) had the highest and lowest overall antibiotic susceptibility respectively. About 31/111(27.93%) of the organisms were Candida albicans. The fungal species isolated had good overall susceptibility to most commonly used antifungal agents in the study setting.
Conclusion: This study found a high prevalence of co-infections (bacterial and fungal). Respiratory tract infection was the most prevalent. There was an overwhelming burden of multidrug resistant infections with some extended spectrum drug resistant organisms isolated among COVID-19 patients admitted in the Ugandan ICUs. There is need for establishment of stronger policy measures in regards to antibiotic stewardship, antimicrobial surveillance and infection control to inform empirical antibiotic therapy and mitigate the spread MDR bacteria and antibiotic drug resistance among COVID-19 patients.
Incidence, susceptibility and outcomes of candidemia in adults living in Calgary, Alberta, Canada (2010 – 2018)
Authors: Bourassa-Blanchette Samuel , Biesheuvel Marit M. , Lam John C. , Kipp Alexander , Church Deirdre , Carson Julie , Dalton Bruce , Parkins Michael D. , Barkema Herman W. , Gregson Daniel B. 
Published: October 2022

Abstract
Background
Candidemia is increasing in frequency and is associated with high mortality. We sought to determine the burden of illness, the population it affects and its resistance profile in our region.
Methods
The Calgary Zone (CZ) provides all care for residents of Calgary and surrounding communities (~ 1.69 million) via five tertiary hospitals each served by a common single laboratory for acute care microbiology. All adult patients in the CZ with at least one Candida spp.-positive blood culture between January 1, 2010, and December 31, 2018, were identified using microbiological data from Calgary Lab Services, the laboratory that processes > 95% of all blood culture samples in the CZ, were reviewed for the study.
Results
The overall annual incidence of candidemia among individuals living in the CZ was 3.8 per 100,000 persons (Median age 61 years (IQR 48–72) and 221/455 (47.4%) were female). C. albicans was the most common species (50.6%), followed by C. glabrata, (24.0%). No other species accounted for more than 7% of cases. Overall mortality at 30, 90, and 365 days was 32.2, 40.1, and 48.1% respectively. Mortality rate did not differ by Candida species. Of individuals who developed candidemia, more than 50% died within the next year. No new resistance pattern has emerged in the most common Candida species in Calgary, Alberta.
Conclusions
In Calgary, Alberta, the incidence of candidemia has not increased in the last decade. C. albicans was the most common species and it remains susceptible to fluconazole.
Experimental model of emulsion viscosity during water-based EOR: Effect of water content and pressure
Authors: Shafiei Masoud , Shirazi Ghazal Mohammadzadeh , Kazemzadeh Yousef , Riazi Masoud 
Published: October 2022

Abstract
Emulsion formation during production from oil reservoirs or even on the surface is one of the common phenomena in the oil industry. Viscosity and stability of emulsions are very important parameters that have a significant impact on the transfer, separation and sale of oil. The purposes of this work were to investigate the effect of water content and pressure on the viscosity of emulsions and also to present an experimental mathematical model for predicting viscosity at different pressures and water content. Viscosity was measured by a rolling ball viscometer that made and calibrated by this team. The results show that the viscosity of the emulsions is a strong function of water content and pressure and increases significantly with increasing these two parameters. In the next step, according to the viscosity behavior with pressure, three mathematical models were developed. Examination of errors related to each of the models illustrated that the lowest error between 2–7% was related to the exponential base model and the second-degree polynomial based model and the highest error was related to the linear base model. Among these three models, the polynomial base model showed the best and the linear base model showed the worst performance in prediction of viscosity. The most errors related to linear, exponential and polynomial models were, 11.96, 6.99 and 4.52%, respectively, which occurred at pressures of 12.53, 12.53 and 1000 psi respectively.
Comparing the accuracy of NEORUBIN NEO-2020 jaundice meter, Dräger JM103 jaundice meter and conventional blood testing for estimating total serum bilirubin in infants with jaundice in Malaysia
Authors: Hasim Ruziaton , Harrun Noor Harzana , Baharuddin Faridah Azna , Bahasa Abdul Rahman , Zainudin Muhammad Khairil 
Published: October 2022

Abstract
Objective: To assess the accuracy of NEORUBIN® NEO-2020, a transcutaneous bilirubinometer in the clinical evaluation of bilirubin levels, versus a competitor device (Dräger JM103) and conventional blood testing (gold standard comparator) in infants diagnosed with jaundice in Malaysia.
Study design: Infants who were brought to a public primary care clinic for follow-up due to suspected jaundice were screened using Dräger JM103 to assess the level of total serum bilirubin (TsB). Newborn infants who were at least 1 day old and born after 35–44 weeks of gestation/pregnancy with a TsB between 6–13.4 mg/dL/day (103–229 μmol/L/day) at screening were included in the study. Bilirubin levels of the infants were measured using NEO-2020, Dräger JM103, and conventional blood testing and the readings compared to validate NEO-2020’s accuracy, robustness, and reliability in clinical settings against the competitor device and conventional blood testing.
Results: Compared to Dräger JM103, NEO-2020 showed a sensitivity of 99.4% (95% CI 96.9, 100), specificity of 0% (as all subjects in the study had jaundice symptoms), positive predictive value of 96.7% (95% CI 96.9, 96.7), and negative predictive value of 0%. The NEO-2020 had a 96.2% (95% CI 92.3, 98.5) accuracy rate in clinically evaluating bilirubin levels.
Conclusion(s): Serum bilirubin levels recorded by the non-invasive NEO-2020 bilirubinometer were comparable to the readings from Dräger JM103 and conventional blood testing. Further tweaking and tests may improve the accuracy of NEO-2020.
PSMD8 can serve as potential biomarker and therapeutic target of the PSMD family based on bioinformatics analysis and in vitro validation
Authors: Li Xiao , Li Xinru , Hu Yuexin , Yang Qing , Lin Bei , Liu Ouxuan , Wang Yuxuan , Li Siting 
Published: October 2022

Abstract

Background The ubiquitin-proteasome system is an indispensable mechanism for regulating intracellular protein degradation, thereby affecting human antigen processing, signal transduction, and cell cycle regulation. We used bioinformatics database to predict the expression and related roles of all members of thePSMDfamily in ovarian cancer. Our findings may provide a theoretical basis for early diagnosis, prognostic assessment, and targeted therapy of ovarian cancer. Methods GEPIA, cBioPortal, and Kaplan–Meier Plotter databases were used to analyze the mRNA expression levels, gene variation, and prognostic value ofPSMDfamily members in ovarian cancer.PSMD8was identified as the member with the best prognostic value. The TISIDB database was used to analyze the correlation betweenPSMD8and immunity, and the role of PSMD8 in ovarian cancer tissue was verified by immunohistochemical experiments. The relationship of PSMD8 expression with clinicopathological parameters and survival outcomes of ovarian cancer patients was analyzed. The effects of PSMD8 on malignant biological behaviors of invasion, migration, and proliferation of ovarian cancer cells were studied byin vitroexperiments. Results The expression levels ofPSMD8/14mRNA in ovarian cancer tissues were significantly higher than those in normal ovarian tissues, and the expression levels ofPSMD2/3/4/5/8/11/12/14mRNA were associated with prognosis. Up-regulation ofPSMD4/8/14mRNA expression was associated with poor OS, and the up-regulation ofPSMD2/3/5/8mRNA expression was associated with poor PFS in patients with ovarian serous tumors. Gene function and enrichment analysis showed thatPSMD8is mainly involved in biological processes such as energy metabolism, DNA replication, and protein synthesis. Immunohistochemical experiments showed that PSMD8 was mainly expressed in the cytoplasm and the expression level was correlated with FIGO stage. Patients with high PSMD8 expression had poor prognosis. Overexpression of PSMD8 significantly enhanced the proliferation, migration, and invasion abilities in ovarian cancer cells. Conclusion We observed different degrees of abnormal expression of members ofPSMDfamily in ovarian cancer. Among these, PSMD8 was significantly overexpressed in ovarian malignant tissue, and was associated with poor prognosis.PSMDs, especiallyPSMD8, can sereve as potential diagnostic and prognostic biomarkers and therapeutic targets in ovarian cancer.
Exogenous gibberellic acid shortening after-ripening process and promoting seed germination in a medicinal plant Panax notoginseng
Authors: Ge Na , Yang Ling , Huang Rong-Mei , Jia Jin-Shang , Wang Qing-Yan , Chen Cui , Meng Zhen-Gui , Li Long-Geng , Chen Jun-Wen 
Published: October 2022

Abstract

BackgroundPanax notoginseng(Burk) F.H. Chen is an important medicinal plant in the family of Araliaceae. Its seeds are classified as the type of morphophysiological dormancy (MPD), and are characterized by recalcitrance during the after-ripening process. However, it is not clear about the molecular mechanism on the dormancy in harvested recalcitrant seeds. Results In this study, exogenous supply of gibberellic acid (GA3) with different concentrations shortened after-ripening process and promoted germination ofP. notoginsengseeds. Among the identified plant hormone metabolites, exogenous GA3results in an increased levels of endogenous hormone GA3through permeation. A total of 2971 and 9827 differentially expressed genes (DEGs) were identified in response to 50 mg L− 1GA3(LG) and 500 mg L− 1GA3(HG) treatment, respectively, and the plant hormone signal and related metabolic pathways regulated by GA3was significantly enriched. GA3treatment upregulated the expression ofent-copalyl diphosphate synthase(CPS),GA 20-oxidase(GA20ox) andGIBBERELLIN INSENSITIVE DWARF1(GID1), whereas it downregulatedDELLA,Pyrabactin resistance 1-like(PYL) andABA-INSENSITIVE5(ABI5). This effect was associated with higher expression of crucial seed embryo development and cell wall loosening genes,Leafy Contyledon1(LEC1),Late Embryogenesis Abundant(LEA),expansins(EXP) andPectinesterase(PME). Conclusions Exogenous GA3application promotes the germination ofP. notoginsengseeds by increasing GA3contents through permeation. Furthermore, the altered ratio of GA and ABA contributes to the development of the embryo, breaks the mechanical constraints of the seed coat and promotes the protrusion of the radicle in recalcitrantP. notoginsengseeds. These findings improve our knowledge of the contribution of GA to regulating dormancy of MPD seeds during the after-ripening process, and provide a new theoretical guidance for the application of recalcitrant seeds in agricultural production and storage.
Association of bone mineral density and osteoporosis with trichlorophenol: A national-representative, population-based study
Authors: Yan Zijian , Xiong Xianmei , Tao Jiasheng , Wang Sheng 
Published: October 2022

Abstract
Background: Trichlorophenols (TCPs) are metabolites of several organochlorine chemicals, including chlorobenzene, hexachlorocyclohexane, and chlorophenoxy acid, present in air, surface water, soil, and sediment. However, the relationship between TCP and bone mineral density (BMD) and osteoporosis has not been studied yet.
Methods: We used data from the 2005-2010 National Health and Nutrition Examination Survey (NHANES). TCP were obtained from urine specimens of 3385 participants and bone mineral density was obtained by dual X-ray absorptiometry (DXA) whole-body scanning. Multiple regression analysis, stratified analysis, curve fitting analysis, and trend tests were used to assess the relationship between TCP and BMD and osteoporosis.
Result: After adjusting for confounding factors, the results of multiple regression analysis only showed that ln-2,4,5-TCP was negatively associated with BMD of lumbar spine. In stratified analyses, ln-2,4,5-TCP and ln-2,4,6-TCP was were not statistically associated with BMD in total femur, femoral neck, femoral tuberosity, intertrochanteric femur and lumbar spine, which was also confirmed by curve fitting analyses and trend tests. Multiple regression analysis and stratified analysis showed that ln-2,4,5-TCP and ln-2,4,6-TCP was were not statistically associated with osteopenia/osteoporosis.
Conclusion: 2,4,5-TCP and 2,4,6-TCP were not significantly associated with BMD and osteopenia/osteoporosis in the US population.
WITHDRAWN: Psychometric evaluation of the Chinese version of the Self-awareness in Nursing Scale
Authors: Chen Qing , Yan Xiangru , Wang Liying , Zhang Hui , Yu Haitao , Liang Chunguang , Lu Jing 
Published: October 2022

Abstract

Background There are many studies about awareness, but few studies are specifically focused on the nurses’ self-awareness. Study shows nurse self-awareness helps nurses and patients. The Self-awareness in Nursing Scale is a brief measurement tool used to assess the self-awareness of clinical nurses. Methods This study investigated 549 clinical nurses in Liaoning Province, China. Our study used two methods of construct validity to analyze the factor structure of the Chinese version of this scale. Two weeks later, the 40 relevant hospital nurses previously labeled were measured for test-retest reliability. Results The Chinese version of the self-awareness in Nursing scale reserved 17 items, and the results differed from the original scale in that its Exploratory factor analysis (EFA) supported a three-factor structure, and the confirmatory factor analysis (CFA) results indicated a good model fit. The overall Cronbach’s coefficient for this scale was 0.869, and the reliability of the retest was 0.804. Conclusions The Chinese version of the self-awareness in Nursing scale exhibited suitable psychometric characteristic and it can be used to measure the Chinese nurses’ level of self-awareness.
Network Embedding Framework for Driver Gene Discovery by Combining Functional and Structural Information
Authors: Chu Xin , Li Feng , Shang Junliang , Guan Boxin , Dai Lingyun , Liu Jin-xing 
Published: October 2022

Abstract
Comprehensive analysis of multiple data sets can identify potential driver genes for various cancers. In recent years, driver gene discovery based on massive mutation data and gene interaction networks has attracted increasing attention, but there is still a need to explore combining functional and structural information of genes in protein interaction networks to identify driver genes. There, we propose a network embedding framework combining functional and structural information to identify driver genes. Firstly, we combine the mutation data and gene interaction networks to construct mutation integration network using network propagation algorithm. Secondly, the struc2vec model is used for extracting gene features from the mutation integration network, which contains both genes functional and structural information. Finally, machine learning algorithms are utilized to identify the driver genes. At the same time, we also conduct comparative analysis of three gene interaction networks, three gene standard sets, and five machine learning algorithms. Compared with the previous four excellent methods, our method can find gene pairs that are distant from each other through structural similarities and has better performance in identifying driver genes for 12 cancers in the cancer genome atlas. Our framework provides a new perspective for feature selection to identify novel driver genes.
Velocity and transverse mixing in open channel flow featuring interacting vegetated shear layers
Authors: Rojas-Arques Santiago , Nichols Andy , Shucksmith James D. 
Published: October 2022

Abstract
Pollutants originating sources such as combined sewer overflows and wastewater treatment works are known to have a significant detrimental impact on the quality of water resources. Turbulent shear layers have been previously shown to significantly affect mixing in free surface flows, and therefore may facilitate rapid decreases in peak pollution levels. To date, few studies have considered situations where multiple shear layers interact or the associated effects on flow structure and mixing processes. This paper presents an extensive new high resolution laboratory dataset utilising bank arrays of artificial vegetation within free surface flow to form both single and interacting shear layers systems. The data is used to form and test new analytical relationships between vegetation properties and resulting profiles of primary velocity and mixing characteristics. The results demonstrate that interacting shear layers can significantly enhance transverse mixing processes in open channel flow, and expressions based on vegetated characteristics can give a good approximation of experimentally observed velocities and depth averaged solute concentrations.
Pruning and green manure from Alnus acuminata improve soil health, and potato and wheat productivity in Rwanda
Authors: Cyamweshi Athanase R. , Muthuri Catherine W. , Kuyah Shem , Mukuralinda Athanase , Mbaraka Rumanzi S. , Sileshi Gudeta W. 
Published: October 2022

Abstract
Alnus acuminata Kunth. (alnus) has been widely promoted under climate change mitigation and adaptation programs in the East African highlands. However, information is lacking on the impact of its pruning management and green manure (GM) application on soil health and the productivity of associated crops. Using a large suit of soil quality indicators, crop growth and yield measurements, this study identified appropriate combinations of alnus pruning levels and GM application for sustainable intensification of potato (Solanum tuberosum) and wheat (Triticum aestivum) production. This study compared six treatments, namely, (1) sole crops of potato or wheat (control), (2) sole crop + GM, (3) 75% pruning, (4) 75% pruning + GM, (5) 90% pruning and (6) 90% pruning + GM. The best treatments were the 75% pruning + GM and 90% pruning + GM, which significantly differed from the control in soil pH, soil organic carbon (SOC), total nitrogen (TN), total phosphorus (P), exchangeable calcium (Ca) contents, the N:P and C:P stoichiometric ratios and the soil structural stability index (SSI). These treatments increased soil pH by 5–6%, SOC by 74–82%, TN by 58–68%, exchangeable Ca by 76–81%, total P by 17–21%, the N:P ratio by 40%, C:P ratio by 43–51%, the SSI by 71–79%, potato tuber yields by 17–21% and wheat yields by 21–32% over the control. Therefore, it is concluded that pruning and application of alnus green manure have the potential to significantly improve soil health and crop productivity on degraded soils in the study area.
Terminal Nerve Entry Points Locations to Muscles of the Thigh for Selective Peripheral Neurectomy in the Adult Population: A Cadaveric Study
Authors: Garcia-Rueda Maria Fernanda , Nossa-Almanza Sergio Alejandro , Jimenez-Ramirez Jose , Romero-Barreto Camilo , Mendoza-Pulido Camilo 
Published: October 2022

Abstract
Purpose
spasticity is the result of a variety of lesions to the central nervous system and one of the most common causes of disability worldwide. Selective peripheral neurectomy (SPN) is a surgical procedure that permanently decreases focal spasticity. Authors’ objective is to provide recommendations, in terms of probabilities, for locating terminal motor entry points to muscles of the thigh, as alternatives for proximal incision sites to SPN.
Methods
the femoral, obturator, and sciatic nerves, and its corresponding motor rami, were systematically dissected on cadaveric specimens, and terminal motor entry points to each muscle of the thigh were located and carefully measured, relative to the length of the thigh. Measurement distributions were obtained and normal transformations were used when necessary.
Results
in 23 adult cadaveric specimens, 779 motor rami were dissected. Entry points locations are presented as a percentage of the length of the thigh in means and standard deviations, which roughly corresponds to 64 and 95% probability of finding a motor entry point.
Conclusion
Alternative incisions directly over the motor entry points, for the muscles of the thigh, may be helpful when considering SPN as treatment for focal spasticity. A prior degree of certainty of the location of the nerve to be severed, may simplify surgical approach.
Bayesian spatial optimal network design for non-Gaussian environmental processes
Authors: Samadi Zahra , Talebi Hooshang , Rivaz Firoozeh 
Published: October 2022

Abstract
Most spatial optimal network designs have been developed for Gaussian processes. However, environmental data rarely conform to this assumption and usually reveal non-Gaussian features suchas asymmetry, so there is a need for novel methods that can account for skewness. To overcome this limitation, this article develops an optimal network design based on the closed skew Gaussian process and introduces new optimality criteria for different aims using information measures. In the Bayesian framework, the design that maximizes the average overall observationalinformation is optimal. The effect of skewness on the configuration of points in the optimaldesign is demonstrated through simulation examples. Besides, the proposed approach is implemented to expand the precipitation monitoring network in Khuzestan province, south of Iran.