bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid Assembly of Complete Genomes of <I>Yersinia pestis</I> Strains
Authors: Fedorov A. V. , Krasnov Ya. M. , Naryshkina E. A. , Sosedova E. A. , Katyshev A. D. , Eroshenko G. A. , Kukleva L. M. , Osina N. A. , Kutyrev V. V. 
Published: April 2024

The aim of the study was to assemble full-length nucleotide sequences of the chromosome and plasmids for 13 Yersinia pestis strains from 11 natural plague foci located in the Russian Federation, using data from two sequencing technologies.Materials and methods. Y. pestis strains were grown on Hottinger’s agar (pH 7.2) at 37 °C. DNA was isolated using phenol-chloroform extraction. For the MinIon genetic analyzer (Oxford Nanopore), DNA fragments were prepared by ligation according to a modified protocol. For the Ion S5 genetic analyzer (IonTorrent), sample preparation was carried out according to the standard protocol for obtaining a library with a DNA fragment size of 400 nucleotide pairs (bp). The resulting single reads were filtered by average quality Q30 for IonTorrent and Q7 for Oxford Nanopore.Results and discussion. DNA fragments containing 50 000 or more nucleotide pairs were prepared for subsequent sequencing using nanopore sequencing technology (Oxford Nanopore). The Trycycler algorithm was applied for hybrid assembly of the genome of Y. pestis strains and correction of errors arising during this process, allowing the obtainment of full-length nucleotide sequences of the chromosome and plasmids for each genome of the strain. The nucleotide sequences of the chromosomes of 13 Y. pestis strains from 11 natural foci of plague located in the Russian Federation have been deposited in the international genetic database NCBI GenBank. It has been established that to assemble full-length genomes of Y. pestis strains, a significant number of reads with a size of 50 000 bp or more is required, and the use of the Trycycler algorithm allows one to generate a more accurate assembly of complete bacterial genomes.
An Integrated Framework for Reference Site Selection and Benchmarking Soil Health Studies in the United States
Authors: Das Saurav , Hird Aaron , Maharjan Bijesh , Stephenson Mitchell , Kariyawasam Lithma 
Published: April 2024

Abstract

Comparative soil health studies are critical in soil conservation and gauging the success of different management practices in soil health improvement. A primary challenge in these studies is the selection of a consistent natural reference site. Current choices vary widely, from minimally disturbed areas to pristine prairies. This methodological paper underscores the need for deliberate and thoughtful reference site selection for benchmark soil properties. Utilizing the State &Transition models, the study introduces a framework for this selection, drawing upon the ecological site (ES) and reference plant communities detailed in an ecological site description (ESD) within a respective Major Land Resource Area (MLRA). This study advocates for a localized classification within the framework of the Cropland Reference Ecological Unit (CREU), emphasizing the significance of local precipitation and soil data to ensure unbiased comparisons. Soil samples from eastern (MLRA 106) and western (MLRA 67A) Nebraska were collected, representing distinct pedogenetic and climatic differences. Analysis of soil organic matter between MLRAs displayed substantial variations, suggesting potential biases and complexities in soil health gap calculations when using reference sites and croplands not in the same MLRA, soil types (texture class), or precipitation zones. However, refining the comparisons by delineating the MLRA, soil, and precipitation zones within the framework of CREU yielded more consistent and realistic comparative data. Integrating the MLRA and ES, complemented by granular soil and precipitation data, provides a robust method for establishing soil health benchmark data.
Workplace bullying and turnover intention among male nurses: A cross-sectional study in Bangladesh
Authors: Roy Anjan Kumar , Akter Masuda , Akter Nahida , Hossain Md Ikbal , Akter Shimpi , Akter Sopon , Chowdhury Saifur Rahman , Kabir Humayun 
Published: April 2024

Abstract

Background: Workplace bullying (WPB) and nurses’ turnover intention (TI) are important challenges in the healthcare sector, particularly in developing countries like Bangladesh. Understanding this relationship is crucial for developing targeted interventions to improve retention and well-being among male nurses in Bangladesh. Thus, this study aimed to explore the relationship between WPB and TI among Bangladeshi male nurses.
Method: We conducted a cross-sectional study among 379 Bangladeshi registered male nurses between April 26 and July 10, 2021. The study sites included indoor or outdoor settings where nurses provide healthcare. We used the Short Negative Acts Questionnaire-9 (S-NAQ-9) to measure WPB and the Turnover Intention Scale-6 (TIS-6) to assess TI. We performed a multiple linear regression model to explore the association of WPB and other variables with TI.
Results: The study participants were predominantly young male nurses, with a significant proportion employed in urban settings and holding a Bachelor of Science (B.Sc.) degree. The study found a significant positive association between WPB and TI, suggesting that higher levels of WPB were related to increased TI. Likewise, some other factors such as educational degree, smoking status, job types, professional titles, timely payment, and violence-related training showed significant associations with TI.
Conclusion: This study highlights the need for focused interventions to reduce WPB and enhance working conditions for male nurses in Bangladesh. Addressing WPB, as well as improving work satisfaction through targeted initiatives, is critical for reducing TI among this demographic.
Relationship Between Hypertransmission Defect Size and Progression in Eyes with Intermediate Age-related Macular Degeneration
Authors: Sadda SriniVas , Nanegrungsunk Onnisa , Corradetti Giulia , Phinyo Phichayut , Choovuthayakorn Janejit 
Published: April 2024

Abstract

Objectives To determine the associations between the presence of various-sized hypertransmission defects (hyperTDs) and progression to incomplete retinal pigment epithelial (RPE) and outer retinal atrophy (iRORA) and complete RORA (cRORA) in eyes with intermediate age-related macular degeneration (iAMD).Methods Optical coherence tomography (OCT) data from consecutive iAMD patients, were retrospectively reviewed. All of iAMD eyes with or without iRORA (but not cRORA) at baseline were included. Graders evaluated the presence of hyperTDs at baseline (small: 63–124 µm; medium: 125–249 µm; large: ≥ 250 µm in diameter on choroidal en face OCT) and the progression two years later.Results Of the 145 eyes that not developed neovascular AMD at two years, the eyes that progressed to or developed iRORA or cRORA included 13 eyes (10.7%), 5 eyes (83.3%), 9 eyes (81.8%), and 6 eyes (85.7%) in the groups with no, small, medium, and large hyperTDs at baseline, respectively (P-value < 0.001). The odds ratios (95% CI) for progression were 41.6 (4.5–383.6), 37.4 (7.3–192.0), and 49.9 (5.6–447.1) in the small, medium, and large hyperTDs groups, compared to no hyperTDs (P-value ≤ 0.001). Eyes with ≥ 2 hyperTDs also showed more frequent progression than eyes with one or no hyperTDs (100% vs. 16.4%; P-value < 0.001).Conclusions While most iAMD eyes with no hyperTDs remained stable on OCT over two years, eyes with hyperTDs of any size appeared to be at a higher risk for progression. HyperTDs may provide an important OCT biomarker for identifying high-risk iAMD patients.
Vitamin D has therapeutic effects on obesity and hyperandrogenemia in PCOS mouse model induced by low dose DHEA and high-fat diet
Authors: Xu Huiling , Qiu Shumin , Lin Peiyang , Liao Xiuhua , Lin Yunhong , Sun Yan , Zheng Beihong 
Published: April 2024

Abstract

Polycystic ovary syndrome (PCOS) is the most complex and common reproductive endocrine disease among reproductive age women. This study aimed to investigate the effects of vitamin D (Vit.D) in PCOS mouse model. Prepubertal female mice were divided into 4 groups randomly: control, PCOS, PCOS with low dose Vit.D(LDVD), and PCOS with high dose Vit.D༈HDVD༉ groups(n = 10 per group). PCOS model was induced by high-fat diet, and subcutaneous injection with 6mg/kg/day dehydroepiandrosterone. After 30 days, 1,25(OH)2D3 was intend to be administered by intraperitoneal injection for 40 consecutive days, 1.3µg/kg/week in LDVD group, and 13µg/kg /week in HDVD group. However, all mice in HDVD group died within two weeks following the Vit.D injections. The body weight of mice and the testosterone levels in PCOS group were significantly higher than those in the control and LDVD groups (P < 0.001). The total cholesterol levels in the control group were lower than those in PCOS and LDVD groups (P < 0.001). Further, the ratio of liver to body weight was different among groups (P < 0.001). Our data illustrates that Vit.D has therapeutic effects on obesity and hyperandrogenemia in PCOS, which may occur through regulation of liver metabolism. However, over dose of Vit.D is poisonous.
Detection of circulating tumor cells in patients with lung cancer using a Rare Cell Sorter: a pilot study
Authors: Sugai Kazuto , Mori Tomoko , Bilal Turan , Furukawa Atsuko , Sekine Yasuharu , Kobayashi Naohiro , Kikuchi Shinji , Goto Yukinobu , Ichimura Hideo , Masuda Taisuke , Arai Fumihito , Sato Yukio , Matsusaka Satoshi 
Published: April 2024

Abstract

Background
We developed a Rare Cell Sorter (RCS) for collecting single cell including circulating tumor cells (CTCs). This single-institution pilot study evaluated the ability of this device to detect tumor-like cells in patients with lung cancer and confirmed their genuineness based on the epidermal growth factor receptor (EGFR) mutation concordance with tissue samples.
Methods
This study included patients treated for lung cancer from September 2021 to August 2022 in University of Tsukuba Hospital. Peripheral blood samples were obtained before surgery or during periodic medical checks for patients treated with drugs. We used the RCS to capture cells based on size. The cells were stained, and the Hoechst-positive, CD45-negative, and epithelial celladhesion molecule (EpCAM)- positive cells were defined as CTCs, were collected. The presumptive CTCs were counted and tested using digital droplet polymerase chain reaction for EGFR mutations and compared with the tissue EGFR status to check concordance.
Results
Eighteen patients were included in this study and CTCs were detected in 6 patients (33%). The CTCs from three patients showed EGFR mutation, and the EGFR mutation status of CTCs concorded with that of tissue samples in 83% of the cases (5/6). Only one CTC showed a different status from the tissue, and the concordance rate of EGFR status between CTCs and the tissue was 96% (24/25).
Conclusion
The ability of the RCS to detect CTCs in patients with lung cancer was demonstrated based on the concordance of EGFR status in this pilot study. This novel hybrid method of CTC recovery using the RCS has the potential to recover a wide range of CTCs regardless of EpCAM. Further validation through a large-scale study is needed.
Serotonin, cortisol, and DHEA-S levels in anxious and depressive pregnant women living with HIV
Authors: Meza-Rodríguez María del Pilar , Leff-Gelman Philippe , Medina-Bastidas Diana , Avila-García Miroslava , Damián Ricardo Figueroa , Camacho-Arroyo Ignacio 
Published: April 2024

Abstract

Pregnancy in women living with human immunodeficiency virus (WLWH) represents an important challenge for maternal-fetal health. Various pregnant WLWH present anxiety (Anx) and depression (Dep). Imbalances in serotonin (5-HT), dehydroepiandrosterone sulfate (DHEA-S), and cortisol (CORT) levels can contribute to Anx and Dep manifestations. Currently, there is not enough data about the neuroendocrine and neurochemical changes in pregnant WLWH with affective disorders.
The objective of this study was to characterize 5-HT, DHEA-S, and CORT plasma levels in pregnant WLWH presenting Anx/Dep. A total of 42 adult pregnant women were recruited during the third trimester of gestation. These patients were divided into three groups: 1) pregnant WLWH with Anx/Dep (n=16), 2) pregnant without HIV but with Anx/Dep (n=12), and 3) healthy pregnant women without Anx/Dep (n=14). Infected and non-infected pregnant women with Anx/Dep presented a marked reduction in 5-HT and DHEA-S levels compared with the healthy group. The lowest 5-HT levels were observed in WLWH with Anx/Dep. Anx and Dep symptoms were inversely correlated with 5-HT and DHEA-S levels. Interestingly, no significant differences were observed in CORT levels among the three groups. Our results suggest the presence of a disbalance in 5-HT and DHEA-S levels in pregnant WLWHwith affective symptoms.
Assessment of the knowledge, attitude and practices of the informed consent process in oral healthcare among dental students in Makerere University Dental Hospital, Uganda
Authors: NONO DAVID , Mwebesa Ernest , Bagenda Godfrey , Okullo Isaac , Rwenyonyi Charles Mugisha , Williams Simon , Nono David 
Published: April 2024

Abstract

Introduction:
Informed consent is an ethical and legal component of healthcare. It ensures patient autonomy and allows patients to make decisions regarding their treatment. In dental care, informed consent is particularly important because most dental procedures are invasive. Since dental students are future dentists, they need to learn about their ethical obligations and accountability through the informed consent process as this is critical to the patient’s well-being. The present study aimed to determine dental students’ knowledge, attitudes, and practices of informed consent for oral health care in Makerere University Dental Hospital, Uganda.
Study Methodology:
This was a descriptive cross-sectional quantitative study that was carried out at Makerere University Dental Hospital. Third, fourth, and fifth-year students (n = 102) pursuing a Bachelor of Dental Surgery programme took part in a survey. A self-administered structured questionnaire was used to assess their knowledge, attitudes, and practices of informed consent for oral health care. Collected data were entered into Epi-data version 3.1, where it was cleaned, coded, and imported to STATA version 14 software for statistical analysis.
Results
Of the 102 participants, 65.7% were males. The mean age was 25 (SD = 3.21) years. The majority (90%) of the students had a high level of knowledge of the informed consent process. About 80% had a positive attitude towards informed consent and 85% most often practiced the informed consent process. Based on bi-variate analysis, training on informed consent, year of study, age, and sex were significantly associated with the informed consent process. However, there was no significant risk factor associated with informed consent in multiple logistic regression analysis.
Conclusion
The study findings highlighted high levels of knowledge, positive attitude, and practice of the informed consent process among the clinical dental students. Continuous in-service training for dentists and other oral healthcare workers on the informed consent process is highly recommended.
Adaptive Finite Element Method for Magnetotelluric Forward Modeling with Gradient Recovery
Authors: Zhang Yangyang , Ji Naixuan , Wang Zhishui , Guo Chen , Miao Xuhuang 
Published: April 2024

Abstract

In the frequency domain electromagnetic method such as magnetotelluric method, finite element method is the main numerical simulation method because it can better simulate the complex physical distribution and complex boundary shape of the geoelectric model. In the finite element method, the quality and quantity of mesh generation will directly affect the accuracy and efficiency of the solution. Theoretically, the accuracy of the finite element solution will gradually approach the real solution with the mesh encryption, but the increase of the mesh number will directly affect the speed of the finite element solution and computer memory. In addition, in the frequency domain electromagnetic method, the decay speed of electromagnetic waves is different at different frequencies, and the use of the same grid at different frequencies will also cause errors. The adaptive finite element method based on a posteriori error estimation can overcome the above shortcomings and improve the calculation accuracy and efficiency of forward modeling. In this paper, starting from the principle of superconvergent patch recovery algorithm, the superconvergent patch recovery algorithm is deduced in detail, the processing of the boundary element in the superconvergent patch recovery algorithm is used as the indicator factor of the adaptive finite element posterior error estimation, and a mesh encryption strategy is proposed, the encryption strategy is simple and reliable. Finally, using the characteristics of the superconvergent patch recovery algorithm, it is used in the calculation of auxiliary field of magnetotelluric method. Through the forward modeling of three geoelectric models. It is verified that the adaptive finite element method based on the a posteriori error of the superconvergent patch recovery algorithm combined with the auxiliary field calculation method of the superconvergent patch recovery algorithm can effectively improve the accuracy and feasibility of the finite element forward modeling of the superconvergent patch recovery algorithm.
Single-cell Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue Microenvironment
Authors: Luo Ruihan , Liu Jiajia , Wen Jianguo , Zhou Xiaobo 
Published: April 2024

Abstract

Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells. By characterizing dynamics in stem-cell crosstalk with the microenvironment along the pseudotime axis, we found differential roles of ANXA1 at different stages of tumor development. In precancerous stages, reduced ANXA1 levels promoted monocyte differentiation toward M1 macrophages and inflammatory responses, whereas during malignant progression, upregulated ANXA1 fostered M2 macrophage polarization and cancer-associated fibroblast transformation by increasing TGF-β production. Our spatiotemporal analysis further provided insights into mechanisms responsible for immunosuppression and a potential target to control evolution of precancer and mitigate the risk for cancer development.
Comparative Efficacy and Safety of Generic vs Brand-Name Meropenem for Anti-infective Use in Real-world
Authors: Hu Qi , Long Enwu , Zhu Baoqiang , Hu Jiaqiang , Wei Yuankui , Li Wenyuan , You Qiang 
Published: April 2024

Abstract

There is little information on whether generic meropenem can be as safe and effective as brand-name meropenem. This retrospective study aimed to compare the efficacy and safety of generic vs brand-name meropenem for infection treatment. Patients (aged ≥18 years) prescribed generic or brand-name meropenem between January 1, 2020, and December 31, 2021, were identified from the hospital information system database of Sichuan Provincial People's Hospital and Sichuan Academy of Medical Sciences. The efficacy outcomes included clinical efficacy, changes in laboratory testing indicators related to infection, and bacterial clearance rate. Safety outcomes included incidence of adverse reactions, abnormal liver and kidney function indicators, and abnormal blood system indicators. A total of 2288 patients (1414 [61.8%] males and 874 [38.2%] females, mean [IQR] age 66 [52-77] years) were eligible for analysis, of whom 1234 were prescribed generic meropenem. Both the generic and the brand-name groups included 600 patients (729 [60.8%] female, mean [IQR] age, 63 [51-76] years) after propensity score matching. The generic meropenem was comparable to the brand-name drug about efficacy (447 [74.5%] vs 462 [77.0%]; P = 0.360). The generic meropenem was associated with lower rates of bacterial clearance (83 [13.8%] vs 120 [20.0%]; P = <0.001). The brand-name may have a better elimination effect on Escherichia coli compared with its generic counterpart (6 [20.0%] vs 25 [55.6%]; P = 0.002). The risks of adverse reactions were not significantly different between the two groups (20 [3.3%] vs 25 [4.2%]; P = 0.447). In conclusion, the generic meropenem was as effective and safe as brand-name meropenem in adult hospitalized patients diagnosed with serious bacterial infections.
Elevated Serum and Cerebrospinal Fluid Levels of Interleukin-4 Related to Poor Prognosis of Aneurysmal Subarachnoid Hemorrhage
Authors: Hu Xuemei , Zhao Mingyang , Wang Meixue , Wang Dongsen , Zhu Liangzhen , Su Chunhai , Wu Qingjian 
Published: April 2024

Abstract

Aneurysmal subarachnoid hemorrhage (aSAH) is a hemorrhagic cerebrovascular disease that seriously jeopardizes human life and health. Some studies have shown that although Interleukin-4 (IL-4) acts as an anti-inflammatory factor, IL-4 levels are elevated when the disease occurs. This study focuses on exploring the relationship between IL-4 concentrations in the serum and cerebrospinal fluid (CSF) and poor prognosis in patients with aSAH. 210 aSAH patients who met the inclusion criteria were divided into two groups according to their mRS scores, and 210 healthy people were selected as controls. The IL-4 concentration was quantitatively determined with enzyme-linked adsorption assay (ELISA). We can draw a conclusion that Serum and CSF IL-4 concentrations are generally elevated in patients with poor prognosis(P < 0.05), and the CSF IL-4 concentration decreased gradually over the progress of time(P < 0.05). The IL-4 concentration in the CSF was positively correlated with age, platelet-lymphocyte ratio (PLR), C-reactive protein (CRP), Hunt-Hess grade, mRS score, and World Federation of Neurological Surgeons score (WFNS) (P < 0.0001). Additionally, IL-4 concentrations in the CSF were correlated with complications(P < 0.05). Elevated serum and CSF concentrations of IL-4 may affect the prognosis of patients with aSAH and may be a candidate early biomarkers for a poor prognosis of aSAH.
The relationship between physical exercise and interpersonal adjustment of college students: the chain mediating role of self-control and personal growth initiative
Authors: Guo Feng , Guo Kelei 
Published: April 2024

Abstract

Interpersonal adaptation refers to the positive interaction between individuals and the environment and groups, and the establishment of social relations. Physical exercise plays an important role in promoting interpersonal adaptation of college students, but there are few literatures on the influence of physical exercise on interpersonal adaptation of college students and its relationship mechanism. In this study, 1290 college students completed the physical exercise scale, self-control scale, personal growth initiative scale, interpersonal adjustment scale and questionnaire adjustment. The results show that physical exercise is positively correlated with interpersonal adaptation, and self-control and personal growth initiative have independent mediating and chain mediating effects between physical exercise and interpersonal adaptation. This study discusses the relationship between physical exercise and interpersonal adaptation of college students. The results reveal the relationship mechanism between physical exercise and interpersonal adaptation of college students, and provide a preliminary basis for the study of the causal relationship between the two. The results of this study also provide a theoretical basis for promoting the interpersonal adaptation of college students.