bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a yellow fever vaccine model using data from primary vaccination in children and adults, re-vaccination and dose-response in adults and studies with immunocompromised individuals
Authors:   Collaborative Group for Studies of Yellow Fever Vaccine, Bonin Carla Rezende Barbosa , Fernandes Guilherme Côrtes , de Menezes Martins Reinaldo , Camacho Luiz Antonio Bastos , Teixeira-Carvalho Andréa , da Mota Licia Maria Henrique , de Lima Sheila Maria Barbosa , Campi-Azevedo Ana Carolina , Martins-Filho Olindo Assis , dos Santos Rodrigo Weber , Lobosco Marcelo 
Published: December 2020

Abstract
Background
An effective yellow fever (YF) vaccine has been available since 1937. Nevertheless, questions regarding its use remain poorly understood, such as the ideal dose to confer immunity against the disease, the need for a booster dose, the optimal immunisation schedule for immunocompetent, immunosuppressed, and pediatric populations, among other issues. This work aims to demonstrate that computational tools can be used to simulate different scenarios regarding YF vaccination and the immune response of individuals to this vaccine, thus assisting the response of some of these open questions.

Results
This work presents the computational results obtained by a mathematical model of the human immune response to vaccination against YF. Five scenarios were simulated: primovaccination in adults and children, booster dose in adult individuals, vaccination of individuals with autoimmune diseases under immunomodulatory therapy, and the immune response to different vaccine doses. Where data were available, the model was able to quantitatively replicate the levels of antibodies obtained experimentally. In addition, for those scenarios where data were not available, it was possible to qualitatively reproduce the immune response behaviours described in the literature.

Conclusions
Our simulations show that the minimum dose to confer immunity against YF is half of the reference dose. The results also suggest that immunological immaturity in children limits the induction and persistence of long-lived plasma cells are related to the antibody decay observed experimentally. Finally, the decay observed in the antibody level after ten years suggests that a booster dose is necessary to keep immunity against YF.
In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform
Authors: Russo Giulia , Pennisi Marzio , Fichera Epifanio , Motta Santo , Raciti Giuseppina , Viceconti Marco , Pappalardo Francesco 
Published: December 2020

Abstract
Background
SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects.

Results
We present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.

Conclusions
In silico trials are showing to be powerful weapons in predicting immune responses of potential candidate vaccines. Here, UISS has been extended to be used as an in silico trial platform to speed-up and drive the discovery pipeline of vaccine against SARS-CoV-2.
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Authors: Gaonkar Krutika S. , Marini Federico , Rathi Komal S. , Jain Payal , Zhu Yuankun , Chimicles Nicholas A. , Brown Miguel A. , Naqvi Ammar S. , Zhang Bo , Storm Phillip B. , Maris John M. , Raman Pichai , Resnick Adam C. , Strauch Konstantin , Taroni Jaclyn N. , Rokita Jo Lynne 
Published: December 2020

Abstract
Background
Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy.

Results
We developed annoFuse, an R package, and shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated annoFuse using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). annoFuse uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied annoFuse to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. annoFuse annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, reportFuse enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created shinyFuse for algorithm-agnostic interactive exploration and plotting of gene fusions.

Conclusions
annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect annoFuse to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.
Comparative proteomic analysis reveals novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae
Authors: Zhang Fan , Zhang Fan , Huang Liyu , Zeng Dan , Cruz Casiana Vera , Li Zhikang , Zhou Yongli 
Published: December 2020

Abstract
Background
Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Rice introgression line H471, derived from the recurrent parent Huang-Hua-Zhan (HHZ) and the donor parent PSBRC28, exhibits broad-spectrum resistance to Xoo, including to the highly virulent Xoo strain PXO99A, whereas its parents are susceptible to PXO99A. To characterize the responses to Xoo, we compared the proteome profiles of the host and pathogen in the incompatible interaction (H471 inoculated with PXO99A) and the compatible interaction (HHZ inoculated with PXO99A).

Results
In this study, a total of 374 rice differentially abundant proteins (DAPs) and 117 Xoo DAPs were detected in the comparison between H471 + PXO99A and HHZ + PXO99A. Most of the Xoo DAPs related to pathogen virulence, including the outer member proteins, type III secretion system proteins, TonB-dependent receptors, and transcription activator-like effectors, were less abundant in the incompatible interaction than in the compatible interaction. The rice DAPs were mainly involved in secondary metabolic processes, including phenylalanine metabolism and the biosynthesis of flavonoids and phenylpropanoids. Additionally, some DAPs involved in the phenolic phytoalexin and salicylic acid (SA) biosynthetic pathways accumulated much more in H471 than in HHZ after the inoculation with PXO99A, suggesting that phytoalexin and SA productions were induced faster in H471 than in HHZ. Further analyses revealed that the SA content increased much more rapidly in H471 than in HHZ after the inoculation, suggesting that the SA signaling pathway was activated faster in the incompatible interaction than in the compatible interaction.

Conclusions
Overall, our results indicate that during an incompatible interaction between H471 and PXO99A, rice plants prevent pathogen invasion and also initiate multi-component defense responses that inhibit disease development.
Assessment of patient safety challenges and electronic occurrence variance reporting (e-OVR) barriers facing physicians and nurses in the emergency department: a cross sectional study
Authors: Albarrak Ahmed I. , Almansour Ammar S. , Alzahrani Ali A. , Almalki Abdulaziz H. , Alshehri Abdulrahman A. , Mohammed Rafiuddin 
Published: December 2020

AbstractBackgroundThe purpose of patient safety is to prevent harm occurring in the healthcare system. Patient safety is improved by the use of a reporting system in which healthcare workers can document and learn from incidents, and thus prevent potential medical errors. The present study aimed to determine patient safety challenges facing clinicians (physicians and nurses) in emergency medicine and to assess barriers to using e-OVR (electronic occurrence variance reporting).MethodsThis cross-sectional study involved physicians and nurses in the emergency department (ED) at King Khalid University Hospital (KKUH) in Riyadh, Saudi Arabia. Using convenience sampling, a self-administered questionnaire was distributed to 294 clinicians working in the ED. The questionnaire consisted of items pertaining to patient safety and e-OVR usability. Data were analyzed using frequencies, means, and percentages, and the chi-square test was used for comparison.ResultsA total of 197 participants completed the questionnaire (67% response rate) of which 48 were physicians (24%) and 149 nurses (76%). Only 39% of participants thought that there was enough staff to handle work in the ED. Roughly half (48%) of participants spoke up when something negatively affected patient safety, and 61% admitted that they sometimes missed important patient care information during shift changes. Two-thirds (66%) of the participants reported experiencing violence. Regarding e-OVR, 31% of participants found reporting to be time consuming. Most (85%) participants agreed that e-OVR training regarding knowledge and skills was sufficient. Physicians reported lower knowledge levels regarding how to access (46%) and how to use (44%) e-OVR compared to nurses (98 and 95%, respectively;p < 0.01). Less than a quarter of the staff did not receive timely feedback after reporting. Regarding overall satisfaction with e-OVR, only 25% of physicians were generally satisfied compared to nearly half (52%) of nurses.ConclusionAlthough patient safety is well emphasized in clinical practice, especially in the ED, many factors hinder patient safety. More awareness is needed to eliminate violence and to emphasize the needs of additional staff in the ED. Electronic reporting and documentation of incidents should be well supported by continuous staff training, help, and feedback.
Use of out-of-hospital cardiac arrest registries to assess COVID-19 home mortality
Authors: Hubert Hervé , Baert Valentine , Beuscart Jean-Baptiste , Chazard Emmanuel 
Published: December 2020

Abstract
Background
In most countries, the official statistics for the coronavirus disease 2019 (COVID-19) take account of in-hospital deaths but not those that occur at home. The study’s objective was to introduce a methodology to assess COVID-19 home deaths by analysing the French national out-of-hospital cardiac arrest (OHCA) registry (RéAC).

Methods
We performed a retrospective multicentre cohort study based on data recorded in the RéAC by 20 mobile medical teams (MMTs) between March 1st and April 15th, 2020. The participating MMTs covered 10.1% of the French population. OHCA patients were classified as probable or confirmed COVID-19 cases or as non-COVID-19 cases. To achieve our primary objective, we computed the incidence and survival at hospital admission of cases of COVID-19 OHCA occurring at home. Cardiac arrests that occurred in retirement homes or public places were excluded. Hence, we estimated the number of at-home COVID-19-related deaths that were not accounted for in the French national statistics.

Results
We included 670 patients with OHCA. The extrapolated annual incidence of OHCA per 100,000 inhabitants was 91.9 overall and 17.6 for COVID-19 OHCA occurring at home. In the latter group, the survival rate after being taken to the hospital after an OHCA was 10.9%. We estimated that 1322 deaths were not accounted in the French national statistics on April 15, 2020.

Conclusions
The ratio of COVID-19 out-of-hospital deaths to in-hospital deaths was 12.4%, and so the national statistics underestimated the death rate.
Changes and prognostic impact of inflammatory nutritional factors during neoadjuvant chemoradiotherapy for patients with resectable and borderline resectable pancreatic cancer
Authors: Oshima Minoru , Okano Keiichi , Suto Hironobu , Ando Yasuhisa , Kamada Hideki , Masaki Tsutomu , Takahashi Shigeo , Shibata Toru , Suzuki Yasuyuki 
Published: December 2020

Abstract
Background
Inflammatory nutritional factors, such as the neutrophil/lymphocyte ratio (NLR), Glasgow Prognostic Score (GPS), modified GPS (mGPS), and C-reactive protein/albumin (CRP/Alb) ratio, have prognostic values in many types of cancer. In this study, the prognostic values of inflammatory nutritional scores were evaluated in the patients with resectable or borderline resectable pancreatic ductal adenocarcinoma (PDAC) after neoadjuvant chemoradiotherapy (NACRT).

Methods
A total of 49 patients who underwent pancreatectomy after NACRT from September 2009 to May 2016 were enrolled. The NACRT consisted of hypofractionated external-beam radiotherapy (30 Gy in 10 fractions) with concurrent S-1 (60 mg/m2) delivered 5 days/week for 2 weeks before pancreatectomy. Inflammatory nutritional scores were determined before and after NACRT in this series.

Results
The median NLR increased after NACRT (from 2.067 to 3.302), with statistical difference (p < 0.001). In multivariate analysis, high pre-NACRT mGPS (2 or 1; p = 0.0478) and significant increase in CRP/Alb ratio after NACRT (≧ 0.077; p = 0.0036) were associated with shorter overall survival. All patients were divided into two groups according to the ΔCRP/Alb ratio after NACRT: the group with high ΔCRP/Alb ratio (≧ 0.077) and the group with low ΔCRP/Alb ratio (< 0.077). The group with high ΔCRP/Alb ratio after NACRT (n = 13) not only had higher post-NACRT CRP levels (p < 0.001) but also had lower post-NACRT Alb levels (p = 0.002). Patients in the group with high ΔCRP/Alb ratio lost more body weight during NACRT (p = 0.03).

Conclusion
In addition to pre-NACRT mGPS, ΔCRP/Alb after NACRT could provide prognostic value in the patients with PDAC treated by NACRT.
New cut-off values for screening of trisomy 21, 18 and open neural tube defects (ONTD) during the second trimester in pregnant women with advanced maternal age
Authors: Chen Yiming , Wang Xue , Li Liyao , Lu Sha , Zhang Zhifen 
Published: December 2020

AbstractBackgroundTo determine whether advanced maternal age (AMA) causes changes in the maternal serum markers of Trisomy 21, 18 and open neural tube defects (ONTD) during the second trimester of pregnancy. Our research aims to develop new cut-off values for AMA in order to reduce the need for further invasive testing.MethodsThis retrospective cohort study involved 12,739 pregnant women with AMA and 197,101 pregnant women with non-AMA. We then compared the two groups with respect to the positive rate and positive predictive value (PPV) of Trisomy 21, 18 and ONTD. Pregnant women with Trisomy 21, 18 and ONTD were diagnosed by karyotyping the amniotic fluid and by ultrasound diagnosis.ResultsCompared to the non-AMA group, the multiple of the median (MOM) of free beta- human chorionic gonadotropin (free β-hCG), alpha-fetoprotein (AFP), and the risk value forTrisomy 21, were significantly higher in the AMA group (allP < 0.001). The positive rates of Trisomy 21, 18, and ONTD in the AMA group were significantly higher than those in the control group (allP < 0.001). In the AMA group, the PPVs for Trisomy 21 and other deformities were significantly higher (allP < 0.001), although the PPVs for Trisomy 18 and ONTD were similar to those of the non-AMA group. The area under the curve (AUC) values for the AMA group were higher than the non-AMA group, based on free β-hCG MoM, AFP MoM, and the risk value of Trisomy 21. The cut-off value for the risk value of Trisomy 21 was 1/172 for the AMA, group and 1/780 for the non-AMA group.ConclusionsThe positive rates for Trisomy 21, 18 and ONTD, and the PPV for Trisomy 21 and other deformities were significantly higher in the AMA group. It is essential for pregnant women with AMA to be tested using appropriate cut-off values of serum markers screening for Trisomy 21 during the second trimester of pregnancy to improve the efficacy of prenatal screening and reduce the need for further invasive testing.
Developing a complex intervention to support pregnant women with mild to moderate anxiety: application of the Medical Research Council framework
Authors: Evans Kerry , Spiby Helen , Morrell C. Jane 
Published: December 2020

Abstract
Background
To design and develop an intervention to support women with symptoms of mild to moderate anxiety in pregnancy.

Methods
The development followed the MRC framework for complex interventions, utilising psychological theory, review level evidence and professional and public involvement. Two systematic reviews were completed which helped identify potentially beneficial intervention components. The theory underpinning the components was explored to consider the potential benefit for women with mild to moderate anxiety symptoms in pregnancy. Methods of delivering the intervention within maternity services were explored. The intervention comprised: group discussions, one to one support and assisted self-help resources. Midwives were identified as ideally placed to facilitate the intervention supported by midwifery support workers. A bespoke training package was provided by subject experts to prepare the facilitators.

Results
The absence of established interventions and a paucity of evidence based approaches for pregnant women with symptoms of mild to moderate anxiety indicated the need for a rigorous and systematic approach to the intervention design. This approach led to the development of an intervention feasible for implementation in maternity care systems tailored to the needs of pregnant women. The involvement of a multi-professional advisory team and active engagement of service users helped to consider the acceptability of the intervention for women and the feasibility of delivering the intervention in the context of maternity care.

Conclusion
The MRC Framework provided useful overarching guidance to develop a midwife facilitated intervention for women with symptoms of anxiety in pregnancy. The framework assisted the development of a robust rationale for each intervention component and considered the processes of evaluation and implementation into maternity care systems.
Drivers of desire for more children among childbearing women in sub-Saharan Africa: implications for fertility control
Authors: Ahinkorah Bright Opoku , Seidu Abdul-Aziz , Armah-Ansah Ebenezer Kwesi , Budu Eugene , Ameyaw Edward Kwabena , Agbaglo Ebenezer , Yaya Sanni 
Published: December 2020

AbstractBackgroundDespite the extensive research on fertility desires among women the world over, there is a relative dearth of literature on the desire for more children in sub-Saharan Africa (SSA). This study, therefore, examined the desire for more children and its predictors among childbearing women in SSA.MethodsWe pooled data from 32 sub-Saharan African countries’ Demographic and Health Surveys. A total of 232,784 married and cohabiting women with birth history, who had complete information on desire for more children made up the sample for the study. The outcome variable for the study was desire for more children. Multilevel logistic regression analysis was conducted. Results were presented using adjusted odds ratios (aOR), with their corresponding 95% confidence intervals (CI).ResultsThe overall prevalence of the desire for more children was 64.95%, ranging from 34.9% in South Africa to 89.43% in Niger. Results of the individual level predictors showed that women aged 45–49 [AOR = 0.04, CI = 0.03–0.05], those with higher education [AOR = 0.80, CI = 0.74–0.87], those whose partners had higher education [AOR = 0.88; CI = 0.83–0.94], women with four or more births [AOR = 0.10, CI = 0.09–0.11], those who were using contraceptives [AOR = 0.68, CI = 0.66–0.70] and those who had four or more living children [AOR = 0.09 CI = 0.07–0.12] were less likely to desire for more children. On the other hand, the odds of desire for more children was high among women who considered six or more children as the ideal number of children [AOR = 16.74, CI = 16.06–17.45] and women who did not take decisions alone [AOR = 1.58, CI = 1.51–1.65]. With the contextual factors, the odds of desire for more children was high among women who lived in rural areas compared to urban areas [AOR = 1.07, CI = 1.04–1.13].ConclusionsThis study found relatively high prevalence of women desiring more children. The factors associated with desire for more children are age, educational level, partners’ education, parity, current contraceptive use, ideal number of children, decision-making capacity, number of living children and place of residence. Specific public health interventions on fertility control and those aiming to design and/or strengthen existing fertility programs in SSA ought to critically consider these factors.