bluuebunny/crossref_metadata_2025_split huggingface dataset:
The swan genome and transcriptome, it is not all black and white
Authors: Karawita Anjana C. , Cheng Yuanyuan , Chew Keng Yih , Challagulla Arjun , Kraus Robert , Mueller Ralf C. , Tong Marcus Z. W. , Hulme Katina D. , Bielefeldt-Ohmann Helle , Steele Lauren E. , Wu Melanie , Sng Julian , Noye Ellesandra , Bruxner Timothy J. , Au Gough G. , Lowther Suzanne , Blommaert Julie , Suh Alexander , McCauley Alexander J. , Kaur Parwinder , Dudchenko Olga , Aiden Erez , Fedrigo Olivier , Formenti Giulio , Mountcastle Jacquelyn , Chow William , Martin Fergal J. , Ogeh Denye N. , Thiaud-Nissen Françoise , Howe Kerstin , Tracey Alan , Smith Jacqueline , Kuo Richard I. , Renfree Marilyn B. , Kimura Takashi , Sakoda Yoshihiro , McDougall Mathew , Spencer Hamish G. , Pyne Michael , Tolf Conny , Waldenström Jonas , Jarvis Erich D. , Baker Michelle L. , Burt David W. , Short Kirsty R. 
Published: January 2023

Abstract
Background
The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.

Results
Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.

Conclusion
Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
Temporal variability of Loa loa microfilaraemia
Authors: Campillo Jérémy T. , Hemilembolo Marlhand C. , Louya Frédéric , Bikita Paul , Pion Sébastien D. S. , Boussinesq Michel , Missamou François , Chesnais Cédric B. 
Published: January 2023

Abstract
Background
The diurnal periodicity of Loa loa microfilaraemia is well known but few studies have documented the short- and long-term stability of microfilarial density. It seems stable over time at the community level, but significant variations have been observed at the individual level.

Methods
We assessed the temporal variability of L. loa microfilaraemia at 5-day, 1-month and 16-month intervals and analyzed the influence of sex, age, level of microfilaraemia, temperatures and time of sampling on this variability.

Results
At the community level, L. loa microfilaraemia is very stable over time at 5-day, 1-month and 16-month intervals (Pearson correlation coefficients of 0.92, 0.91 and 0.78, respectively, all three with P < 0.001). However, some individuals had significant variations of up to ± 50% of their initial microfilaraemia at 5-day (33.0%), 1-month (36.5%) and 16-month (62.6%) intervals, even in individuals with an initial microfilaraemia density > 20,000 mf/ml (7.7, 23.1 and 41.4%, respectively, for 5 days, 1 month and 16 months). We do not highlight any external factors that have a major impact on this variability.

Conclusion
Although at the community level, microfilaria density is very stable, we highlight some individuals with large variations in both the short and long term, which may have an important impact on onchocerciasis control campaigns and longitudinal studies evaluating the impact of an intervention on L. loa microfilaraemia.

Graphical Abstract
Population-level predictors of sexually transmitted infection rate changes in Missouri: an ecological study
Authors: Valleroy Ella , Reed Aaron , Lightner Joseph S. 
Published: January 2023

Abstract
Background
Sexually transmitted infection rates continue to increase across the US, further developing health disparities and economic burdens of disease, especially as migration occurs. In this study, we aim to assess the relationship between STI rates and population-level variables from 2008 to 2017 at the county level in Missouri.

Methods
Two data sources were used: STI rates of chlamydia, gonorrhea, syphilis, HIV reported to Missouri DHSS and ACS 1-year county population estimates. Linear regression models and ANOVA tests were conducted in SPSS for each STI from year-to-year and 2008–2017. Covariates included in the analyzes were county-level income, employment rate, race, ethnicity, age, and percent poverty. Further, Akaike Information Criterion tests were performed to indicate the best predictor models and averaged standardized beta values.

Results
Significant relationships among STI rates and population growth were identified. Chlamydia, syphilis, and HIV were positively associated with population growth from 2008 to 2017 (β = 0.15; β = 0.01; β = 0.05, respectively). Gonorrhea was negatively associated with population growth (β = − 0.02) but positively associated with unemployment rates (β = 0.01) highlighting the need to address population growth, as well as other variables in a population.

Conclusions
There seems to be a positive relationship among population change and rates of STIs. As populations change, rates of STIs change. Moving forward, quantitative work should be conducted in various states and the nation to understand this relationship in different contexts. Future studies should be qualitative word focused on county health departments and community health improvement plans. Lastly, public policy should be implemented to buffer the impact of migration on health outcomes.
Rhizosphere fungal community assembly varied across functional guilds in a temperate forest
Authors: Liang Shuang , Arraiano-Castilho Ricardo , Neuenkamp Lena , Li Hui , Bai Zhen , Zhang Mengxu , Yin Jin , Yuan Zuoqiang , Wang Xugao 
Published: January 2023

Abstract
Background
Rhizosphere fungi play an important role in plant community dynamics and biogeochemical cycling. While the drivers of fungal community assembly have been studied in varied ecosystems, it is still unclear how these processes function for rhizosphere soil fungi in temperate forests. Furthermore, it is unknown whether the relative contributions of important determinants remain consistent or vary across fungal ecological guilds. This study used high-throughput next-generation sequencing to characterize the fungal communities of 247 rhizosphere soil samples from 19 tree species in a temperate forest within Northeast China. We aimed to investigate how three important determinants in temperate forests (host tree species, neighbouring plant communities, and edaphic properties) influence the community assembly of fungal functional guilds in the rhizosphere soil of trees.

Results
We found that host tree species contributed more to plant pathogens’ community composition than ectomycorrhizal fungi, and plant pathogens consistently showed higher host specialization than ectomycorrhizal fungi. Saprotrophs also showed high host specialization, which was mediated by the tree species’ effect on rhizosphere soil pH. Although neighboring plant communities contributed remarkably to richness of all fungal guilds, this effect on fungal composition varied across functional guilds, with stronger effect for biotrophic guilds (plant pathogens and ectomycorrhizal fungi) than for non-biotrophic guild (saprotrophs). Neighboring plant communities shaped the ectomycorrhizal community composition strongly in all samples regardless of host trees’ mycorrhizal type, whereas edaphic properties were the most important drivers for this guild in samples from only ectomycorrhizal-associated trees. Edaphic properties played an important role in shaping ectomycorrhizal and saprotrophic fungal compositions, indicating the importance of edaphic properties on the fungal functional guilds associated with the absorption and decomposition of nutrients.

Conclusions
These results demonstrated that rhizosphere soil fungal community assembly determinants varied across fungal guilds, reflecting their different ecological functions in temperate forest ecosystems.
A retrospective comparison of two protocols for correction of skeletal Class III malocclusion in prepubertal children: hybrid hyrax expander with mandibular miniplates and rapid maxillary expansion with face mask
Authors: Tarraf Nour Eldin , Dalci Oyku , Dalci Kerem , Altug Ayse Tuba , Darendeliler M. Ali 
Published: January 2023

Abstract
Background
This study compared the skeletal and dental effects of a hybrid maxillary expander with mandibular miniplates (HE-MP) and Class III elastics to conventional tooth-borne rapid maxillary expander and face mask (RME–FM) in skeletal Class III treatment.

Methods
This retrospective study included 36 skeletal Class III patients. Eighteen patients (mean age 10.24 ± 1.31 years) were treated with a hybrid expander, two mandibular L-shaped miniplates and full-time Class III elastics (HE-MP group). Their results were compared to a group of patients treated with conventional RME–FM (n = 18; mean age 10.56 ± 1.41 year). Radiographs were taken before (T1) and after treatment (T2). All patients were in cervical maturation stages CS1–CS3 at T1. The measured outcomes were the changes in sagittal and vertical skeletal and dental cephalometric measurements.

Results
Treatment time was approximately 15.5 ± 2.8 months with the HE-MP and 11.85 ± 3.41 months for the RME–FM. The Class III malocclusion was corrected in both groups with significant changes. The maxilla advanced more in the HE-MP group, with an increase in SNA of 4.26° ± 2.15° compared to 1.14 ± 0.93 in the RME–FM group (p < 0.001). The effect on the mandible was similar in both groups, while the overall skeletal change was significantly greater with HE-MP, with an increase in the ANB of 5.25° ± 2.03° and a Wits appraisal increase of 6.03 ± 3.13 mm, as opposed to 2.04° ± 1.07° and 2.94 ± 1.75 mm with the RME–FM (p < 0.001). Dental changes were significantly higher with RME–FM, with an increase in incisor inclination (U1-SN) of 5.02° ± 3.93° (p < 0.001), with no significant changes in the HE-MP group. The mandibular incisors retroclined by 5.29° ± 3.57° at L1-MP with the RME–FM, while they advanced slightly with the HE-MP by 2.87° ± 5.37° (p < 0.001).

Conclusion
The use of skeletal anchorage for maxillary expansion and protraction significantly increases skeletal effects and reduces dental side effects compared to tooth-borne maxillary expansion and protraction. These results need to be investigated in the long term.
Characteristics and time-series monitoring by GOES-17 of volcano flume on 15 January 2022 from Tonga submarine volcanic eruption
Authors: Nam Kounghoon , Wang Fawu , Yan Kongming , Zhu Guolong 
Published: January 2023

Abstract
Background
On 15 January 2022, a submarine volcanic eruption occurred at Hunga Tonga. Time-series monitoring from the Geostationary Operational Environmental Satellite (GOES-17) was analysed to estimate the magnitude, location, start time, and duration of the eruption and to measure the evolving characteristics of Hunga Ha’apai Island.

Results
The eruption starting time was between 04:10 and 04:20 UTC with an eruption intensity that increased drastically and produced a plume that reached a maximum height of about 58 km. The explosive phase lasted 13 h and consisted of multiple steam and tephra explosions with an M 5.8 earthquake. The Airmass RGB, which combines water vapor and infrared imagery from the ABI and was used to monitor the evolution of the volcano, captured a plume of gases from the eruption of Hunga Tonga volcano on 15 January 2022. This type of imagery provides information on the middle and upper levels of the troposphere and distinguishes between high- and mid-level clouds.

Conclusion
A sonic explosion also occurred, possibly when the volcano collapsed underwater and seawater rushed in, causing a huge displacement of seawater. The Hunga Tonga–Hunga Ha’apai eruption is not over and could worsen in the coming days. Future studies are required to assess the potential effects on stratospheric chemistry and radiation for secondary damage analysis.
Water, hygiene and sanitation practices are associated with stunting among children of age 24-59 months in Lemo district, South Ethiopia, in 2021: community based cross sectional study
Authors: Woldesenbet Biruk , Tolcha Alemu , Tsegaye Berhan 
Published: January 2023

Abstract
Background
Stunting among children of ages 24-59 months is a major public health challenge in developing countries. It has been linked with poor water quality, water accessibility, a lack of environmental sanitation, and personal hygiene (WASH) practices, particularly in food-insecure areas. Stunting occurs during certain seasons in food-insecure settings. Therefore, a complete understanding of risk factors is the first step in the development of a preventive strategy. However, information is scarce about the prevalence and factors associated with stunting among children of ages 24-59 months in these settings.

Objective
This study aimed to assess the prevalence of and factors associated with stunting among children aged 24–59 months in Lemo district, south Ethiopia, in 2021.

Methods
A community based cross-sectional study was conducted from January 1-30/2021. Data were collected from a total of 415 randomly selected children and mother /guardian/. Logistic regression analysis was done to identify factors associated with childhood stunting. In binary logistic regression analysis, independent variables with p-value < 0.25 were fitted into multivariable logistic regression analysis to explore final predictors of stunting/ thinness/. Independent variables with AOR and 95% CI and P-value < 0.05 was computed and reported as predictors of stunting among children in this study.

Results
From a total of 450 children, only 415 were included in the final analysis, making a response rate of 92.2%. The prevalence of stunting among children was 33.5% (95% CI: 30.4 and 36.6%) in this study. Children ages 48-59 months (AOR = 2.8, 95% CI: 2.1, 12.1), children ages 36-47 months (AOR = 1.6, 95% CI: 1.1, 7.1), children of uneducated women (AOR = 1.8, 95% CI: 1.5, 4.2), children who lived near unimproved toilets (AOR = 1.7, 95% CI: 1.2, 2.6), children whose feces was disposed of unsafely (AOR = 2.8, 95% CI: 1.57, 5.31), and children whose mothers did not wash their hands before feeding their children (AOR = 6.2, 95% CI: 2.0, 19.1) were factors positively associated with stunting among children aged 24 months to 59 months.

Conclusion
The prevalence of stunting is high compared with the national prevalence of stunting in food insecure areas. Policy makers, local leaders, and community health extension workers should enhance environmental sanitation and create awareness about personal hygiene. Furthermore, improved toilet construction and appropriate utilization should be encouraged. Furthermore, the local government should work to improve the socio-economic status of poor households.
Incidence of pneumococcal disease from 2003 to 2019 in children ≤17 years in England
Authors: Mohanty Salini , Podmore Bélène , Cuñado Moral Ana , Matthews Ian , Sarpong Eric , Lacetera Alessandra , Qizilbash Nawab 
Published: January 2023

Abstract
Background
Pneumococcal disease is a leading cause of communicable disease morbidity and mortality globally. We aimed to estimate invasive pneumococcal disease (IPD), pneumococcal pneumonia (PP) and all-cause pneumonia (ACP) incidence rates (IRs) in children aged 0–17 years in England from 2003 to 2019.

Methods
A retrospective study in children ≤17 years old from 2003 to 2019 using the Clinical Practice Research Datalink (CPRD) Gold and Hospital Episodes Statistics Admitted Patient Care (HES APC) databases. IPD episodes were identified in hospital records (HES APC). PP (caused by Streptococcus pneumoniae only) and ACP episodes (caused by any pathogen) were identified in primary care (CPRD) and in hospital records (HES APC). Annual IRs by age-group were calculated as the number of episodes/person-years (PY) at risk, with 95% confidence intervals (95% CI). Interrupted time series analyses were conducted to assess changes in IRs across the post-PCV7 (2007–2009), early post-PCV13 (2011–2014) and late post-PCV13 (2015–2019) periods compared to the pre-PCV7 period (2003–2005) using generalized linear models.

Results
170 IPD episodes, 769 PP episodes and 12,142 ACP episodes were identified in 1,500,686 children in 2003–2019. The overall IPD, PP and ACP IRs (per 100,000 PY) were 2.29 (95% CI 1.96–2.66), 10.34 (95% CI 9.62–11.10) and 163.37 (95% CI 160.47–166.30), respectively. The highest IPD, PP and ACP IRs were observed in children aged < 2 years compared to older children (2–4 and 5–17 years). IPD IRs decreased between the pre-PCV7 period and the late post-PCV13 period from 3.28 (95% CI 2.42–4.33) to 1.41 (95% CI 0.80–2.29), IRR 0.28 (95% CI 0.09–0.90), p-value 0.033. PP IRs declined between the pre-PCV7 period and the late post-PCV13 period from 14.65 (95% CI 12.77–16.72) to 3.87 (95% CI 2.81–5.20), IRR 0.19 (95% CI 0.09–0.38), p-value < 0.001. ACP IRs declined between the pre-PCV7 period and the late post-PCV13 period from 167.28 (95% CI 160.78–173.96) to 124.96 (95% CI 118.54–131.63), IRR 0.77 (95% CI 0.66–0.88), p-value < 0.001.

Conclusions
The clinical burden of IPD, PP and ACP declined in children in England aged 0–17 years between 2003 and 2019, especially in the late post-PCV13 period. This study highlights the importance of PCV vaccination in reducing the burden of PD and ACP in children in England.
Evaluation of the HOXA9 and MEIS1 genes as a potential biomarker in adult acute myeloid leukemia
Authors: Abdelrahman Amira M. N. , Tolba Fetnat Mahmoud , Kamal Howyda Mohamed , Abdellateif Mona S. , Ahmed Heba Abdelmoneim , Hassan Naglaa M. 
Published: January 2023

Abstract
Background
Acute myeloid leukemia (AML) is a heterogeneous disorder encompassing a set of hematopoietic tumors that develop when the myeloid precursor cells undergo disproportionate clonal proliferation. Homeobox A 9 (HOXA9) is a pioneer transcription factor in AML pathogenesis along with its cofactor myeloid ecotropic integration site 1 (MEIS1). Our work aimed to evaluate the different expression levels of HOXA9 and MEIS1 genes and their diagnostic and prognostic significance in adult Egyptian patients with de novo AML. The study was carried out on 91 de novo AML Egyptian patients and 41 healthy individuals. Bone marrow samples were obtained from both patients and controls and then tested by reverse transcription-quantitative polymerase chain reaction to assess the mRNA expression in the studied genes.

Results
HOXA9 and MEIS1 gene expression levels were significantly elevated in AML patients compared to controls (p < 0.001). There was a statistically significant positive correlation between HOXA9 and MEIS1 gene expression in AML patients. However, there was no association between HOXA9 and MEIS1 gene expression levels and disease-free survival (DFS) and overall survival (OS) (p = 0.264 and 0.351, respectively).

Conclusion
HOXA9 and MEIS1 genes are highly expressed in Egyptian AML patients, suggesting their interesting pathogenic role in AML. They could be used as markers for the diagnosis of AML, but not for the disease prognosis.
Multi-slice coronary computed tomography angiography in assessment of coronary artery disease on the basis of syntax score
Authors: Khedr Amira Abd El-Ghany , Dawoud Mohammed Fathy , Salama Al-Siagy Ali , Allah Taymour Moustafa Abd , El-Deeb Basma Samir 
Published: January 2023

Abstract
Background
The SYNTAX score (SS) was created to aid the Heart Team in assessing the severity and extent of coronary artery disease (CAD) in patients with multi-vessel disease, hence helping in the decision between percutaneous coronary intervention (PCI) and coronary artery bypass graft (CABG). SS is an important tool that assesses the angiographic complexity of the CAD based on Invasive coronary angiography (ICA). The study aims to evaluate the role of coronary Multi-Slice Computed Tomography (MSCT) angiography in the assessment of CAD on the basis of SS.

Results
Our study involved 60 patients with a male to female ratio 78.4% to 21.6%. The mean age of the patients was 57 years. Then, we applicate SYNTAX score II (SS-II) by incorporating a combination of SS-I and clinical variables. MSCT findings were compared with the data collected by cardiac catheterization. SYNTAX scores produced from coronary CT-angiography (CCTA) and those derived from ICA are concordant (P = 0.001). Direct correlation and significant relationship between SS-II for PCI and the mortality rate with the CT-derived SS-I. There was an inverse relationship between the CT-derived SS-I and SS-II for CABG. There was an inverse relationship between the CT-derived-SS with CABG mortality rate.

Conclusions
MSCT is a noninvasive imaging modality that has a significant value and high diagnostic accuracy compared to ICA in the evaluation of the complexity of CAD using SS and can be applied in clinical practice to determine the most convenient treatment procedure and predict long-term prognosis.
Assessment of neonatal intensive care unit nurses’ compliance with standard precautions of infection control and identification of enabling factors
Authors: Abou El Fadl Dina K. , Aly Yasmin A. F. , Darweesh Ebtissam Abdel Ghaffar , Sabri Nagwa A. , Ahmed Marwa Adel 
Published: January 2023

Abstract
Background
Rigorous implementation of infection prevention and control practices by healthcare workers in different healthcare settings is of utmost importance. Neonates, particularly preterm babies in neonatal intensive care units, are a vulnerable population at high risk for developing nosocomial infections. Nurses have the greatest risk of spreading healthcare-associated infections among patients and healthcare workers. This study was conducted to assess the compliance of neonatal intensive care unit nurses with standard precautions of infection control and to identify the potential influencing factors.

Results
This was a cross-sectional study, whereby the compliance of a total of 58 neonatal intensive care unit nurses with standard precautions of infection control was assessed using the Arabic version of the Compliance with Standard Precautions Scale (CSPS-A). Student’s t test, ANOVA test, and post hoc test were used for analysis.
A suboptimal compliance rate (66.7%) was detected, with the highest for disposal of sharp articles into sharps boxes (86.2%) and the lowest for disposal of sharps box not only when full (27.6%). Significant differences were observed when participants were grouped according to their clinical experience and qualifications, where participants with longer clinical experience displayed higher mean scores for the use of protective devices score (P = 0.024), disposal of sharps score (P = 0.003), and total CSPS score (P = 0.006).

Conclusions
Clinical experience and educational qualifications are key factors that impact nurses’ compliance with infection control practices. Nurses should receive up-to-date evidence-based educational and practical sessions that link theory to clinical practice and elucidate the importance of accurate implementation of proper infection prevention and control practices.