bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of continuous positive airway pressure during the second and third waves of the COVID-19 pandemic
Authors: Brusasco Claudia , Corradi Francesco , Dazzi Federico , Isirdi Alessandro , Romei Chiara , Parisini Andrea , Boni Silvia , Santori Gregorio , Brusasco Vito ,   the Galliera CPAP-COVID-19 study group,   the Galliera CPAP-COVID-19 study group, Brusasco C. , Corradi F. , Brusasco C. , Isirdi A. , Dazzi F. , Brusasco V. , Parisini A. , Boni S. , Santori G. , Parisini A. , Boni S. , Corradi F. , Brusasco C. , Romei C. , Corradi F. , Brusasco C. , Brusasco V. , Corradi F. , Brusasco C. , Santori G. , Dazzi F. 
Published: November 2022

BackgroundIn a preliminary study during the first COVID-19 pandemic wave, we reported a high rate of success with continuous positive airway pressure (CPAP) in preventing death and invasive mechanical ventilation (IMV). That study, however, was too small to identify risk factors for mortality, barotrauma and impact on subsequent IMV. Thus, we re-evaluated the efficacy of the same CPAP protocol in a larger series of patients during second and third pandemic waves.Methods281 COVID-19 patients with moderate-to-severe acute hypoxaemic respiratory failure (158 full-code and 123 do-not-intubate (DNI)), were managed with high-flow CPAP early in their hospitalisation. IMV was considered after 4 days of unsuccessful CPAP.ResultsThe overall recovery rate from respiratory failure was 50% in the DNI and 89% in the full-code group. Among the latter, 71% recovered with CPAP-only, 3% died under CPAP and 26% were intubated after a median CPAP time of 7 days (IQR: 5–12 days). Of the patients who were intubated, 68% recovered and were discharged from the hospital within 28 days. Barotrauma occurred during CPAP in <4% of patients. Age (OR 1.128; p <0.001) and tomographic severity score (OR 1.139; p=0.006) were the only independent predictors of mortality.ConclusionsEarly treatment with CPAP is a safe option for patients with acute hypoxaemic respiratory failure due to COVID-19.
Land use and soil characteristics affect soil organisms differently from above-ground assemblages
Authors: Burton Victoria J. , Contu Sara , De Palma Adriana , Hill Samantha L. L. , Albrecht Harald , Bone James S. , Carpenter Daniel , Corstanje Ronald , De Smedt Pallieter , Farrell Mark , Ford Helen V. , Hudson Lawrence N. , Inward Kelly , Jones David T. , Kosewska Agnieszka , Lo-Man-Hung Nancy F. , Magura Tibor , Mulder Christian , Murvanidze Maka , Newbold Tim , Smith Jo , Suarez Andrew V. , Suryometaram Sasha , Tóthmérész Béla , Uehara-Prado Marcio , Vanbergen Adam J. , Verheyen Kris , Wuyts Karen , Scharlemann Jörn P. W. , Eggleton Paul , Purvis Andy 
Published: November 2022

Abstract
Background
Land-use is a major driver of changes in biodiversity worldwide, but studies have overwhelmingly focused on above-ground taxa: the effects on soil biodiversity are less well known, despite the importance of soil organisms in ecosystem functioning. We modelled data from a global biodiversity database to compare how the abundance of soil-dwelling and above-ground organisms responded to land use and soil properties.

Results
We found that land use affects overall abundance differently in soil and above-ground assemblages. The abundance of soil organisms was markedly lower in cropland and plantation habitats than in primary vegetation and pasture. Soil properties influenced the abundance of soil biota in ways that differed among land uses, suggesting they shape both abundance and its response to land use.

Conclusions
Our results caution against assuming models or indicators derived from above-ground data can apply to soil assemblages and highlight the potential value of incorporating soil properties into biodiversity models.
Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties
Authors: Ngumbi Esther , Dady Erinn , Calla Bernarda 
Published: November 2022

Abstract
Background
In nature and in cultivated fields, plants encounter multiple stress factors. Nonetheless, our understanding of how plants actively respond to combinatorial stress remains limited. Among the least studied stress combination is that of flooding and herbivory, despite the growing importance of these stressors in the context of climate change. We investigated plant chemistry and gene expression changes in two heirloom tomato varieties: Cherokee Purple (CP) and Striped German (SG) in response to flooding, herbivory by Spodoptera exigua, and their combination.

Results
Volatile organic compounds (VOCs) identified in tomato plants subjected to flooding and/or herbivory included several mono- and sesquiterpenes. Flooding was the main factor altering VOCs emission rates, and impacting plant biomass accumulation, while different varieties had quantitative differences in their VOC emissions. At the gene expression levels, there were 335 differentially expressed genes between the two tomato plant varieties, these included genes encoding for phenylalanine ammonia-lyase (PAL), cinnamoyl-CoA-reductase-like, and phytoene synthase (Psy1). Flooding and variety effects together influenced abscisic acid (ABA) signaling genes with the SG variety showing higher levels of ABA production and ABA-dependent signaling upon flooding. Flooding downregulated genes associated with cytokinin catabolism and general defense response and upregulated genes associated with ethylene biosynthesis, anthocyanin biosynthesis, and gibberellin biosynthesis. Combining flooding and herbivory induced the upregulation of genes including chalcone synthase (CHS), PAL, and genes encoding BAHD acyltransferase and UDP-glucose iridoid glucosyltransferase-like genes in one of the tomato varieties (CP) and a disproportionate number of heat-shock proteins in SG. Only the SG variety had measurable changes in gene expression due to herbivory alone, upregulating zeatin, and O-glucosyltransferase and thioredoxin among others.

Conclusion
Our results suggest that both heirloom tomato plant varieties differ in their production of secondary metabolites including phenylpropanoids and terpenoids and their regulation and activation of ABA signaling upon stress associated with flooding. Herbivory and flooding together had interacting effects that were evident at the level of plant chemistry (VOCs production), gene expression and biomass markers. Results from our study highlight the complex nature of plant responses to combinatorial stresses and point at specific genes and pathways that are affected by flooding and herbivory combined.
Comparison of analysis methods and design choices for treatment-by-period interaction in unidirectional switch designs: a simulation study
Authors: Zhan Zhuozhao , de Bock Geertruida H. , van den Heuvel Edwin R. 
Published: November 2022

Abstract
Background
Due to identifiability problems, statistical inference about treatment-by-period interactions has not been discussed for stepped wedge designs in the literature thus far. Unidirectional switch designs (USDs) generalize the stepped wedge designs and allow for estimation and testing of treatment-by-period interaction in its many flexible design forms.

Methods
Under different forms of the USDs, we simulated binary data at both aggregated and individual levels and studied the performances of the generalized linear mixed model (GLMM) and the marginal model with generalized estimation equations (GEE) for estimating and testing treatment-by-period interactions.

Results
The parallel group design had the highest power for detecting the treatment-by-period interactions. While there was no substantial difference between aggregated-level and individual-level analysis, the GLMM had better point estimates than the marginal model with GEE. Furthermore, the optimal USD for estimating the average treatment effect was not efficient for treatment-by-period interaction and the marginal model with GEE required a substantial number of clusters to yield unbiased estimates of the interaction parameters when the correlation structure is autoregressive of order 1 (AR1). On the other hand, marginal model with GEE had better coverages than GLMM under the AR1 correlation structure.

Conclusion
From the designs and methods evaluated, in general, parallel group design with a GLMM is, preferred for estimation and testing of treatment-by-period interaction in a clustered randomized controlled trial for a binary outcome.
Bacterial colonization of the upper airways of children positive and negative for SARS-CoV-2 during the COVID-19 pandemic
Authors: Ciptaningtyas Vincentia Rizke , Hapsari Rebriarina , Lestari Endang Sri , Farida Helmia , de Mast Quirijn , de Jonge Marinus Isaäk 
Published: November 2022

Abstract
Background
Our understanding of the influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bacterial colonization in the children’s upper nasopharyngeal tract during the coronavirus infectious disease (COVID-19) pandemic is limited. This study aimed to determine whether there were any differences in bacterial colonization between asymptomatic children with or without a positive SARS-CoV-2 quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) results in the community setting.

Methods
A cross-sectional community-based exploratory study was conducted from March to May 2021 in Semarang, Central Java Province, Indonesia. Using stored nasopharyngeal swabs collected from children under 18 years as a contact tracing program, we performed a real-time quantitative (qPCR) for the most important bacterial colonizing pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Klebsiella pneumoniae.

Results
Swabs from a total of 440 children were included in this study, of which 228 (51.8%) were RT-qPCR-confirmed SARS-CoV-2 positive. In the 440 children, colonization rates were highest for H. influenzae (61.4%), followed by S. pneumoniae (17.5%), S. aureus (12.0%), and K. pneumoniae (1.8%). The co-occurrence of both S. pneumoniae and H. influenzae in the upper respiratory tract was significantly associated with a SARS-CoV-2 negative RT-qPCR. In contrast, colonization with only S. aureus was more common in SARS-CoV-2-positive children.

Conclusion
Overall, this exploratory study concludes that there is a significant difference in the bacterial nasopharyngeal colonization pattern between SARS-CoV-2 positive and negative in asymptomatic children in the community in Indonesia.
The indicators for early blood transfusion in patients with placental abruption with intrauterine fetal death: a retrospective review
Authors: Sano Yasuko , Kasai Michi , Shinoda Satoru , Miyagi Etsuko , Aoki Shigeru 
Published: November 2022

Abstract
Background
Placental abruption (PA) with intrauterine fetal death (IUFD) is associated with a high risk of postpartum hemorrhage (PPH) resulting from severe disseminated intravascular coagulation (DIC). Therefore, blood products that are sufficient for coagulation factor replacement must be prepared, and delivery should occur at referral medical institutions that are equipped with sufficient blood products and emergency transfusion protocols. We retrospectively reviewed the records of patients with PA and IUFD (PA-IUFD) to identify possible factors that may indicate the need for early blood transfusion and investigated whether the Japanese scoring system for PPH can be applied in such cases.

Methods
We used a database of 16,058 pregnant patients who delivered at Yokohama City University Medical Center between January 2000 and February 2016. Thirty-three patients were diagnosed with PA-IUFD before delivery and categorized into two groups–blood transfusion and non-transfusion–to compare the maternal characteristics and pregnancy outcomes.

Results
In patients with PA-IUFD, the transfusion group exhibited significantly more blood loss; lower fibrinogen levels and platelet counts; higher levels of fibrin degradation products (FDP), D-dimer, and prothrombin time; and a tendency for tachycardia on admission, compared to the non-transfusion group. Many patients in the transfusion group had normal fibrinogen levels on admission but later displayed markedly decreased fibrinogen levels. The Japan Society of Obstetrics and Gynecology (JSOG) DIC score was significantly higher in the transfusion than in the non-transfusion group.

Conclusions
In PA-IUFD, the fibrinogen level, platelet count, D-dimer, FDP, heart rate, and JSOG DIC score on admission may indicate the need for blood transfusion. However, even with normal fibrinogen levels on admission, continuous monitoring is indispensable for identifying progressive fibrinogen reductions in patients with PA-IUFD.
The prognostic role of tumor mutation burden on survival of breast cancer: a systematic review and meta-analysis
Authors: Ke Liyuan , Li Su , Cui Hongxia 
Published: November 2022

Abstract
Background
As a potential genetic biomarker, tumor mutation burden (TMB) has made progress in numerous tumors. There are limited data regarding TMB and its prognostic role is controversial in breast cancer. This systematic review and meta-analysis were conducted to assess the prognostic value of TMB on survival of breast cancer.

Methods
The databases PubMed, Embase, Web of Science, and Cochrane Library were searched for articles published through May 31, 2022. Moreover, effective data were extracted from included studies and calculated pooled effects of hazard ratio (HR) for overall survival (OS) and progression-free survival (PFS) by STATA 16.0. Heterogeneity was conducted by the I2 statistic and p-value. Using publication bias evaluation, sensitivity analysis, and subgroup analysis, the origin of heterogeneity was further investigated.

Results
They were up to 1,722 patients collected from sixteen cohorts for this analysis. The pooled effects of HR for both OS (HR: 1.14, 95% CI: 0.83,1.58, p > 0.01) and PFS (HR: 0.96, 95% CI: 0.53,1.71, p > 0.01) indicated no statistically significant difference in the high TMB and low TMB group. In immune checkpoint inhibitors (ICIs) subgroup, high TMB patients demonstrated benefit of OS (HR: 0.72, 95% CI: 0.59,0.87, p = 0.001) and PFS (HR: 0.52, 95% CI: 0.35,0.77, p < 0.001), whereas difference was not statistically significant in the non-ICIs subgroup (OS, HR:1.76, 95% CI: 0.97,3.20, p = 0.062; PFS, HR:2.31, 95% CI: 0.89,5.97, p = 0.086). In addition, sensitivity analysis revealed that the pooled effects were stable. The funnel plot and Begg's test suggested the absence of publication bias.

Conclusion
Meta-analysis revealed that the prognostic relevance of TMB in breast cancer is limited in scope. High TMB may be associated with longer survival only in ICIs-based treatment, but the association is not evident in non-ICIs-based treatment.

Trial registration
[https://www.crd.york.ac.uk/PROSPERO], Prospective Register of Systematic Reviews (PROSPERO), identifier: CRD42022342488.
Retinochoroidal microvascular changes in newly developed obese children: an optical coherence tomography angiography study
Authors: Han Shu , Leng Zhenhua , Li Xiaoxiao , Yan Wen , Shen Shiya , Liu Lei , Zhu Hui , Huang Dan , Liu Hu 
Published: November 2022

Abstract
Background
Childhood obesity was associated with retinochoroidal microvascular changes using optical coherence tomography angiography (OCTA), but obesity duration was neglected. Obesity is chronic and progressive and obesity duration is related to microvascular function. Thus, it is important to identify microvascular changes in obese children timely to allow possible interventions with the increase in the number of obese children. This pilot study aimed to characterize retinochoroidal microvascular changes in newly developed obese children compared to age- and sex-matched controls.

Methods
Forty newly developed obese children and 40 age- and sex-matched controls were recruited. All subjects completed comprehensive eye examinations, including axial length, cycloplegic refraction, optical coherence tomography angiography scans (AngioVue; Optovue Inc), etc.

Results
There were no statistically significant differences between groups in terms of month age (P = 0.927), spherical equivalent refraction (P = 0.753) and axial length (P = 0.196). Newly developed obese children had lower vessel density (VD) in the inferior parafovea (P = 0.026), nasal parafovea (P = 0.038) and temporal perifovea (P = 0.026) of deep vascular complex (DVC), higher VD in the fovea of superficial vascular complex (P = 0.021) and the fovea of DVC (P = 0.016), and smaller foveal avascular zone (P = 0.003) when compared to controls. Also, no apparent differences in any quadrant of total retinal thickness, subfoveal choroidal thickness (SFCT), and choriocapillaries fow voids were detected (all P > 0.05).

Conclusion
Retinochoroidal microvascular changes had already occurred in newly developed obese children, so early screening and close follow-up eye examinations were recommended; Retinal microvascular insult may precede its structural change and that retina may be a better candidate to predict the onset of retinochoroidal microvascular changes than choroid in obese children.
Growth and Nutritional Status of Phenylketonuric Children and Adolescents
Authors: Ahmadzadeh Mina , Sohrab Golbon , Alaei Mohammadreza , Eini-Zinab Hassan , mohammadpour-Ahranjani Behzad , Rastgoo Samira , Namkhah Zahra 
Published: November 2022

Abstract
Background
The goal of this study was to assess the anthropometric and biochemical parameters of children and adolescents with phenylketonuria (PKU).

Methods
The participants in this cross-sectional study ranged in age from four to 18 years old. Biochemical markers such as vitamin B12, folic acid, iron, ferritin, calcium, 25-hydroxy vitamin D3, zinc, plasma phenylalanine (Phe) and tyrosine (Tyr) levels in blood were evaluated, as well as demographics and anthropometric measurements. A three-day dietary recall questionnaire was completed by all individuals.

Results
80% (64) of the 80 patients (42 females, 52.5%) had typical PKU. Consanguineous marriages were found in 57.5% (46) of the patients’ parents. According to the height for age index, 17.5% of the study group (n = 14) were short or very short. According to age-related weight and body mass index (BMI), 37.5% (n = 30) and 43.8% (n = 35) of people are obese or overweight, respectively. Biochemical tests revealed increased vitamin B12 levels and 25-hydroxy vitamin D3 deficiency in 35% (n = 28) of the patients, insufficient folic acid in 12.5% (n = 10), and elevated phenylalanine levels in 70.3% (n = 45) of children under 12 years old, and adolescents 62.5% (n = 10). A high Phe intake (OR = 4.44, CI %95 = 1.27–15.57) is a risk factor for obesity and overweight.

Conclusion
Patients with PKU had a high rate of overweight and obesity. PKU patients who are overweight or obese do not differ from normal-weight patients in terms of dietary intake or laboratory findings (except for serum iron levels). One-third of patients with phenylketonuria were vitamin D deficient and had a BMI/A index of overweight/obese. It is recommended to use special medical food to help solve energy and nutrient deficiencies.
Mothers’ knowledge and self-reported performance regarding the management of traumatic dental injuries and associated factors: a cross-sectional study
Authors: Momeni Zahra , Afzalsoltani Sanaz , Moslemzadehasl Mahmoudreza 
Published: November 2022

AbstractBackgroundDental trauma is common among children. It has negative effects on a child’s quality of life. Parental knowledge, especially among mothers is an important factor for the long-term success of this emergency. This study aimed to investigate mothers’ knowledge and self-reported performance regarding the management of traumatic dental injuries and associated socio-demographic factors.MethodsIn this cross-sectional study, 277 mothers of children (8–12 years) attending the pediatrics department of Alborz dental school were studied by convenience sampling. The participants completed a valid reliable questionnaire about the management of traumatic dental injuries. The predictor variables were the child’s gender, maternal education and employment status, economic status, and accommodation status. The outcome variables were the mothers’ knowledge about the management of traumatic dental injuries (Eight statements with 10 scores) and self-reported performance including four case scenarios of traumatic dental injury (Five questions with 7 scores). Data were analyzed by T-test or One-way ANOVA to test the within-group changes, Pearson’s correlation coefficient and Linear multiple regression to examine the effect of predictor variables on maternal knowledge and self-reported performance.ResultsThe mean score of mothers’ knowledge was 3.43; SD = 1.58 (total score ranged from 0 to 10). The mean score of mothers’ performance was 3.38; SD = 1.2 (total score ranged from 0 to 7). Mothers who work (p < 0.001) and mothers with high qualifications (p < 0.001) had higher knowledge. Furthermore, mothers who work (p = 0.011), mothers with high qualifications (p < 0.001), and those who have had previous experience with traumatic dental injuries (p < 0.001) had higher self-reported performance. The results of multiple linear regression analysis demonstrated the association between mothers’ knowledge with mothers’ education (β = 0.22,p = 0.001) and mothers’ employment status (β = 0.15,p = 0.017), while there is a relationship between mothers’ self-reported performance and mothers’ education (β = 0.27,p < 0.001).ConclusionSince the means of mothers’ knowledge and performance scores regarding dental trauma management, were less than half of the obtainable scores as well as mothers have a crucial role in the children’s oral health, it is important to increase the mothers’ knowledge and improve their performance in this context. Therefore, running educational programs is necessary for this respect.
Model-informed COVID-19 exit strategy with projections of SARS-CoV-2 infections generated by variants in the Republic of Korea
Authors: Jung Sung-mok , Huh Kyungmin , Radnaabaatar Munkhzul , Jung Jaehun 
Published: November 2022

Abstract
Background
With the prompt administration of coronavirus disease 2019 (COVID-19) vaccines, highly vaccinated countries have begun to lift their stringent control measures. However, considering the spread of highly transmissible new variants, resuming socio-economic activities may lead to the resurgence of incidence, particularly in nations with a low proportion of individuals who have natural immunity. Here, we aimed to quantitatively assess an optimal COVID-19 exit strategy in the Republic of Korea, where only a small number of cumulative incidences have been recorded as of September 2021, comparing epidemiological outcomes via scenario analysis.

Methods
A discrete-time deterministic compartmental model structured by age group was used, accounting for the variant-specific transmission dynamics and the currently planned nationwide vaccination. All parameters were calibrated using comprehensive empirical data obtained from the Korea Disease Control and Prevention Agency.

Results
Our projection suggests that tapering the level of social distancing countermeasures to the minimum level from November 2021 can efficiently suppress a resurgence of incidence given the currently planned nationwide vaccine roll-out. In addition, considering the spread of the Delta variant, our model suggested that gradual easing of countermeasures for more than 4 months can efficiently withstand the prevalence of severe COVID-19 cases until the end of 2022.

Conclusions
Our model-based projections provide evidence-based guidance for an exit strategy that allows society to resume normal life while sustaining the suppression of the COVID-19 epidemic in countries where the spread of COVID-19 has been well controlled.