bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of Telephone Consultation in Primary Health Care During COVID-19 Pandemic, Oman: Perceptions from Physicians
Authors: Hasani Said Al , Ghafri Thamra Al , Al Lawati Hussain , Mohammed Jamshid , Al Mukhainai Ameena , Al Ajmi Fatma , Anwar Huda
Published: December 2020

Introduction:

To enforce physical distancing measures during COVID-19, Telephone Consultation (TC), a form of telemedicine, was initiated as an alternative technology to face to face consultation in primary health care (PHC) in Muscat, Oman. This study aims to explore the perceptions of physicians about the use of TC with respect to process of implementation; challenges and limitations; lessons learned and the way forward.

Method:

This was a qualitative study using interpretive phenomenological analysis. Physicians who were actively conducting TC in PHC were purposively selected and individually interviewed until no new responses were obtained. All interviews were audio-recorded, transcribed verbatim, and analysed using thematic analysis.

Results:

Twenty-two participants were interviewed. Participants were predominantly females (98%) and qualified family physicians (77.3%). Overall, all participants accepted this initiative as a possible method to continue health services during COVID-19. Perceptions about the process of implementing TC in PHC were themed to; inconsistent implementation of the guideline, variability in roles and responsibilities, and Semi-supportive infrastructure. Five themes were identified as challenges and limitations: limited staff training on TC, suboptimal patient-physician interaction, insufficient technical support, ensuring privacy, and confidentiality of the communication, and different ways to document the TC. Physicians expressed that TC worked better in following COVID-19 cases, chronic conditions, and, in general, simple cases. They also expressed a reduction in the crowdedness in PHC facilities and the risk of acquiring COVID-19 and other types of infections. Tailoring the existing structural clinical setting, capacity building activities on the use of TC, and improving the quality of the TC are viewed as essential steps for the future sustainability of TC in PHC.

Conclusion:

Given the exceptional situation of COVID-19, the current evidence suggests that the use of TC in PHC, especially in chronic cases, is promising. However, measures including training of staff, improving the structural setting, and selecting suitable cases for TC are the main elements for high quality and sustainable TC services in PHC from physician’s perspective.
Intranasal delivery of Paclitaxel encapsulated nanoparticles for brain injury due to Glioblastoma
Authors: Zhang Ying , Sun Chao , Zhang Qingtao , Deng Yongbing , Hu Xi , Chen Peng
Published: December 2020

Brain injury is a common cause for physical and emotional effects to the large number of populations. Moreover, glioblastoma is the tumor in brain with no possible treatment leading to death. The blood–brain barrier’s makes the treatment more difficult by preventing the drugs to reach central nervous system. Paclitaxel (PTX) encapsulated Poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs), PTX-PLGA-NPs were developed using emulsification method. The PTX-PLGA-NPs were characterized using Malvern Zetasizer and Scanning Electron Microscopy and were evaluated for their cytotoxicity in U87MG cells. PTX-PLGA-NPs were prepared using single emulsion method having size of 154 ± 22.19 nm with zeta potential of –23.7 mV. The PTX-PLGA-NPs were spherical in shape and have dose dependent cytotoxicity on U87MG cells. The PTX was released from the particles with initial burst release followed by sustained release pattern. The biodistribution was studied in mice with glioblastoma model using 125I radiolabeled PTX-PLGA-NPs and anti-glioblastoma was studied with PTX-PLGA-NPs. The biodistribution studies revealed PTX-PLGA-NPs after intranasal administration resulted in higher in vivo uptake with high anti-glioblastoma efficacy. The results suggest that PTX-PLGA-NPs administered through intranasal route have potential in the treatment of glioblastoma.
Leader Communication and Follower Identity: How Leader Motivating Language Shapes Organizational Identification through Cultural Knowledge and Fit
Authors: Mayfield Milton , Mayfield Jacqueline , Walker Robyn
Published: December 2020

This study examines the links between leader communication (as conceptualized through motivating language) and follower organizational identification as mediated by follower cultural knowledge and fit. Results show that motivating language has a positive and strong effect on follower organizational identification with a one standard deviation increase in motivating language corresponding to over a half of a standard deviation increase in follower organizational identification. This influence comes partly through growth in a follower’s cultural knowledge and fit, but also through a direct influence. Model testing occurred with subjects from the USA and India with the model fitting equally well in both nations. These findings have important implications for research and practice which are explained in the paper’s discussion and conclusion section.
Creating Order Out of Chaos? Development of a Measure of Perceived Effects of Communication on the Crisis Organizing Process
Authors: Fuller Ryan Patrick , Pyle Andrew , Riolli Laura , Mickel Amy
Published: December 2020

Organizations are important sources of communication during natural-hazard crises. How members of an organization perceive these communications (e.g., creating confusion, causing disorder, providing clarity, and restoring order) influences response and recovery from such a crisis. Using Chaos Theory as a guiding framework, the authors developed a new instrument measuring the perceived effects of an organization’s communication on crisis-organizing processes. Three distinct studies were conducted to assess the reliability and validity of this new instrument: the “Perceived Effects of Communication on the Crisis-organizing Process (PEC-COP)” scale. This one-factor scale can be used by both scholars and practitioners to assess the effects of an organization’s communication on how people organize (i.e., react and respond) during a crisis. By gaining greater insight into how an organization’s communication is perceived, the organization can better prepare to communicate in ways that promote efficient and effective crisis-organizing processes throughout a natural-hazard crisis. Effective communication can create order out of chaos.
Evidence-Based Educational Practices for Public Health: How We Teach Matters
Authors: Godley Sophie , Aumiller Betsy , Horigian Viviana , Khalil Naila , Kruger Jessica , Pennel Cara , Youatt Emily , Kiviniemi Marc T.
Published: December 2020

An eight-member team of the Teaching Working Group of the Association of Schools and Programs of Public Health Scholarship of Teaching and Learning Task Force created a call to action advancing the use of evidence-based strategies for public health education. The goal of this article is threefold, to assess briefly the current status of evidence-based teaching in public health, strengthen the case for using evidence-based teaching practices in public health courses, and propose strategies for educators in public health to engage along a continuum of evidence-based teaching. In this article, we define evidence-based teaching (EBT) proposes that EBT is demonstrated by: student mastery of specific short-term learner outcomes (e.g., enhanced effectiveness such as represented by improved knowledge, skills, and/or attitudes); increases the likelihood of successfully completion of a particular public health degree or program, which represents an intermediate- or long-term outcome; and ultimately posits that effective teaching in public health aims to produce well-prepared graduates who contribute to a ready workforce (Impact 1) who are able to improve the health of the public (Impact 2), highlights effective evidence-based teaching practices that improve student learning outcomes, encourages both seasoned faculty and newcomers to the field to incorporate EBT into existing public health curricula and to begin by making small changes, and concludes with a call to action for EBT that improves student learning.
Luteolin abates reproductive toxicity mediated by the oxido-inflammatory response in Doxorubicin-treated rats
Authors: Owumi Solomon E , Ijadele Abigail O , Arunsi Uche O , Odunola Oyeronke A
Published: December 2020

The anti-neoplastic use of Doxorubicin (DOX) is hampered by several limitations, including reproductive toxicity. Luteolin (LUT)–a phytochemical-biological benefits include antioxidative and anti-inflammatory actions. Here we examined the protective effect of LUT against DOX-induced reproductive toxicity in an in vivo model—male albino Wistar rats—randomly assigned to five groups and treated as follows: Control (corn oil 2 mL/kg; per os), LUT (100 mg/kg; per os), DOX (2 mg/kg) by intraperitoneal injections, co-treated groups received LUT (50 and 100 mg/kg) with DOX. Treatment with DOX alone, significantly (p > 0.05), reduced biomarkers of testicular function, reproductive hormone levels, testicular and epididymal antioxidant, and anti-inflammatory cytokine. DOX increased (p > 0.05) sperm morphological abnormalities, as well as reactive oxygen and nitrogen species, lipid peroxidation, xanthine oxidase, a pro-inflammatory cytokine, and apoptotic biomarkers. Furthermore, testicular and epididymal histological lesion complemented the observed biochemical changes in treated rats. LUT co-treatment resulted in a dosage-dependent improvement in rats’ survivability, antioxidants capacity, reduction in biomarkers of oxidative stress, pro-inflammatory cytokines, and apoptosis in rat’s testis and epididymis. Also, LUT treatment resulted in improved histological features in the testis and epididymis, relative to DOX alone treated rats. LUT co-treatment abated DOX-mediated reproductive organ injuries associated with pro-oxidative, inflammatory, and apoptotic mechanisms. LUT supplementation may serve as a phyto-protective agent in alleviating male reproductive organ toxic injuries associated with Doxorubicin therapy.
Screening for toxicological and anti-diabetic potential of n-hexane extract of Tapinanthus bangwensis leaves
Authors: Ihegboro Godwin O , Ononamadu Chimaobi James , Owolarafe Tajudeen Alowonle , Shekwolo Iko
Published: December 2020

Health forecasters predict that cases of diabetes will double in 2030; hence proactive action is required to salvage this problem. Thus, this study was undertaken to evaluate the toxicological and anti-diabetic potential of n-hexane extract of T. bangwensis leaves on α-amylase and α-glucosidase activity. The phytochemical screening, antioxidant activity as well as the inhibitory effect of the plant extract was determined by UV-spectrophotometry method while brine shrimp and Allium cepa methods were used for the toxicity study. Preliminary phytochemical screening detected the presence of flavonoid, phenol, tannin, alkaloid and cardiac glycoside whereas phlobatanin, steroid, terpenoid and saponin were absent. The result also showed that flavonoid concentration was the highest compared to others. The 2,2-diphenyl-1-picrylhydrazine (DPPH) and nitric oxide (NO) results showed that the plant extract exhibited significant antioxidant activity particularly at the highest concentration (100 µg/ml). Brine shrimp lethality result showed that the highest mortality rate of nauplii and median inhibition concentration (IC50) are 97% and 7.46 ± 0.33 µg/ml respectively. Furthermore, the results also revealed that mitotic index, root growth length and mitotic division (cytotoxicity indicators) decreased as concentration increases. Finally, the results showed that the plant extract exhibited significant inhibitory effect on α-amylase and α-glucosidase activities at 100 µg/ml; nevertheless, the effect was higher on α-amylase than α-glucosidase activity. In summary, the significant antioxidant and inhibitory effects may be attributed to the presence of the phytochemicals mentioned above. It can therefore be concluded that T. bangwensis leaves may demonstrate potent anti-diabetic effect.
Improving drug safety predictions by reducing poor analytical practices
Authors: Lazic Stanley E , Williams Dominic P
Published: December 2020

Predicting the safety of a drug from preclinical data is a major challenge in drug discovery, and progressing an unsafe compound into the clinic puts patients at risk and wastes resources. In drug safety pharmacology and related fields, methods and analytical decisions known to provide poor predictions are common and include creating arbitrary thresholds, binning continuous values, giving all assays equal weight, and multiple reuse of information. In addition, the metrics used to evaluate models often omit important criteria and models’ performance on new data are often not assessed rigorously. Prediction models with these problems are unlikely to perform well, and published models suffer from many of these issues. We describe these problems in detail, demonstrate their negative consequences, and propose simple solutions that are standard in other disciplines where predictive modelling is used.
A Guide for Understanding, Publishing, and Building a Career in Entrepreneurship Education
Authors: Weaver K. Mark , Edwards Chase J. , Solomon Shelby J. , Bendickson Joshua S.
Published: December 2020

The following manuscript is a helpful overview for current and aspiring academics that seek to better understand academic research, the publishing process, and building a career in entrepreneurship education. We draw from management literature given the theoretical and practical similarities, and we provide suggestions to entrepreneurship educators as a means of starting a dialogue as opposed to presenting fact. While this guide is not directed toward experienced scholars, it may serve as a helpful review. Publishing in entrepreneurship journals is a worthwhile scholarly endeavor for researchers in a variety of fields and we hope our efforts are helpful to scholars, authors, and entrepreneurship educators.
Contribution of Sonoelastographic Scoring to B-Mode Sonography in the Evaluation of Breast Masses
Authors: Dinç Elibol Funda , Yeniçeri Önder
Published: December 2020

Objectives:

The study aims were to evaluate the contribution of sonoelastography to Breast Imaging Reporting, and Data System (BI-RADS) scoring of breast images.

Materials and Methods:

Two observers evaluated the BI-RADS category, Tsukuba score, and the strain index of 83 lesions of 73 consecutive patients. A new scoring system was established to evaluate the lesions by using the BI-RADS score, Tsukuba score, and strain index ratio.

Results:

There was a statistically significant difference between the strain index value of benign (3.08 ± 2.71) and malignant group (4.62 ± 2.70) ( P < .05). The sensitivity and specificity were 59.1% and 65.1% for the 3.12 cut-off value for the strain index. In the receiver operating characteristic (ROC) analysis, the area under the curve (AUC) of the only BI-RADS score was 0.834, both BT (BI-RADS + revised Tsukuba score) score and the total score (BI-RADS + revised Tsukuba score + strain index score) was 0.843. The interclass correlation coefficient for the two observers’ measurements of the strain index was weak, with .266 ( P < .05).

Conclusion:

The potential contribution of sonoelastography on lesion characterization is still controversial. In this study, the agreement among the observers was inadequate, and the contribution of sonoelastography on BI-RADS classification was limited. In addition, in the daily practice of sonoelastograpic evaluation, the Tsukuba score, was easier to apply and should be used rather than strain index measurements.
Expansion of senescent megakaryocyte-lineage cells maintains CML cell leukemogenesis
Authors: Tanabe Yamato , Kawamoto Shimpei , Takaku Tomoiku , Morishita Soji , Hirao Atsushi , Komatsu Norio , Hara Eiji , Mukaida Naofumi , Baba Tomohisa
Published: December 2020

BCR-ABL, an oncogenic fusion gene, plays a central role in the pathogenesis of chronic myeloid leukemia (CML). Oncogenic signaling induces oncogene-induced senescence and senescence-associated secretory phenotype (SASP), which is characterized by enhanced production of various cytokines. BCR-ABL gene transduction confers senescent phenotype in vitro; however, the in vivo relevance of senescence has not been explored in this context. Transplantation of BCR-ABL–expressing hematopoietic stem/progenitor cells caused CML in mice with an increase in bone marrow BCR-ABL+CD41+CD150+ leukemic megakaryocyte-lineage (MgkL) cells, which exhibited enhanced senescence-associated β-galactosidase staining and increased expression of p16 and p21, key molecules that are crucially involved in senescence. Moreover, knockout of p16 and p21 genes reduced both BCR-ABL–induced abnormal megakaryopoiesis and the maintenance of CML cell leukemogenic capacity, as evidenced by attenuated leukemogenic capacity at secondary transplantation. The expression of transforming growth factor-β1 (TGF-β1), a representative SASP molecule, was enhanced in the leukemic MgkL cells, and TGF-β1 inhibition attenuated CML cell leukemogenic capacity both in vitro and in vivo. Furthermore, BCR-ABL–expressing MgkL cells displayed enhanced autophagic activity, and autophagy inhibition reduced bone marrow MgkL cell number and prolonged the survival of CML mice, which had transiently received the tyrosine kinase inhibitor, imatinib, earlier. Thus, BCR-ABL induced the expansion of senescent leukemic MgkL cells, which supported CML leukemogenesis by providing TGF-β1.
Crisis challenges of small firms in Macao during the COVID-19 pandemic
Authors: Alves Jose C. , Lok Tan Cheng , Luo Yubo , Hao Wei
Published: December 2020

This research develops a framework that combines crisis stages, stakeholder engagement, and crisis challenges. The framework is applied to small firms in Macao during the 2019 novel coronavirus disease (COVID-19) pandemic crisis. We conduct a qualitative study based on semi-structured interviews with the leaders of six small firms in Macao. The findings suggest that the COVID-19 pandemic has turned into a “normal” context, which blurs the traditional crisis termination stage. We also find that participating firms engage more with internal stakeholders than external ones. The strategies adopted by small firms include flexible human resource (HR) practices, cost reduction, enhancing customer relations, and using government support schemes. These strategies are effective in the short term; firms need to pay attention to diversity and learning for the long term.
Overactive bladder symptoms recurrence after sudden versus gradual weaning of Solifenacin
Authors: Abdelbary Ahmed , Al-Dessoukey Ahmad Aref , Moussa Ayman Salah , El-nasr Mohamed Saif , Elmarakbi Akrm Ahmed , Ragheb Ahmed Medhat , Elbatanouny Ahmed Mohamed , Abdellateef Ahmed , Sayed Osama , Lotfy Amr , Mohyelden Khaled , Abdelhamid Amr Mohamad , Galal Ehab Mohamad , Massoud Amr , Ibrahim Rabie M.
Published: December 2020

Background

To evaluate and compare the recurrence rate of overactive bladder (OAB) symptoms after solifenacin treatment in patients who stop the drug suddenly versus those who gradually wean the drug after improvement of their condition.

Methods

Our study included 60 patients with idiopathic OAB and treated with solifenacin 5 mg twice daily for one month. After improvement of their condition, we divided the responders into two groups, group I stopped the drug suddenly, while group II underwent gradual weaning of the drug.

Results

The recurrence rate of symptoms of OAB was 33.3% and 60% after 1 and 3 months in patients who stopped the solifenacin suddenly after improvement of their symptoms, while it was 6.7% and 23.3% after 1 and 3 months in patients who gradually weaned solifenacin.

Conclusion

After the improvement of OAB symptoms, gradual weaning of solifenacin can help in decreasing the recurrence rate of symptoms.
Nanomedicine-mediated induction of immunogenic cell death and prevention of PD-L1 overexpression for enhanced hepatocellular carcinoma therapy
Authors: Zhu Hanzhang , Zhou Weijiang , Wan Yafeng , Ge Ke , Lu Jun , Jia Changku
Published: December 2020

Background

The present study aims to develop a nanoparticle encapsulating doxorubicin (DOX) and programmed death-ligand 1 (PD-L1) siRNA and evaluate its anti-tumor effects on hepatoma carcinoma (HCC).

Methods

Nanoparticle encapsulating DOX and PD-L1 siRNA (NPDOX/siPD-L1) was characterized by dynamic light scattering and transmission electron microscopy. Flow cytometry was applied to analyze cell populations, NPDOX/siPD-L1 internalization, and cell apoptosis. Real-Time (RT)-quantitative reverse transcription (qPCR) and western blotting were used to determine the mRNA and protein levels, respectively. Released ATP was determined using ATP determination kit and cytokines were determined using specific ELISAs. A tumor-bearing animal model was established to evaluate the anti-tumor effects of NPDOX/siPD-L1.

Results

Treatment of NPDOX/siPD-L1 induced immunogenic cell death (ICD) and PD-L1 overexpression in HCC. In vivo study demonstrated that intravenously injection of NPDOX/siPD-L1 significantly inhibited the tumor volume and PD-L1 expressions of tumor tissue in the H22 tumor-bearing animal model. Besides, the treatment of NPDOX/siPD-L1 also regulated the populations of matured dendritic cells and cytotoxic T cells and the productions of cytokines in the tumor tissues.

Conclusion

Taken together, NPDOX/siPD-L1 showed significant anti-tumor effects on HCC by the induction of ICD and inhibition of PD-L1 overexpression.
Generation of digital patients for the simulation of tuberculosis with UISS-TB
Authors: Juárez Miguel A. , Pennisi Marzio , Russo Giulia , Kiagias Dimitrios , Curreli Cristina , Viceconti Marco , Pappalardo Francesco
Published: December 2020

Background

The STriTuVaD project, funded by Horizon 2020, aims to test through a Phase IIb clinical trial one of the most advanced therapeutic vaccines against tuberculosis. As part of this initiative, we have developed a strategy for generating in silico patients consistent with target population characteristics, which can then be used in combination with in vivo data on an augmented clinical trial.

Results

One of the most challenging tasks for using virtual patients is developing a methodology to reproduce biological diversity of the target population, ie, providing an appropriate strategy for generating libraries of digital patients. This has been achieved through the creation of the initial immune system repertoire in a stochastic way, and through the identification of a vector of features that combines both biological and pathophysiological parameters that personalise the digital patient to reproduce the physiology and the pathophysiology of the subject.

Conclusions

We propose a sequential approach to sampling from the joint features population distribution in order to create a cohort of virtual patients with some specific characteristics, resembling the recruitment process for the target clinical trial, which then can be used for augmenting the information from the physical the trial to help reduce its size and duration.
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

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

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

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

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

Background

The 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).

Methods

This 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.

Results

A 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.

Conclusion

Although 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

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

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.
Correction to: Risk factors for mortality in hospitalized patients with COVID-19 at the start of the pandemic in Belgium: a retrospective cohort study
Authors: van Halem Karlijn , Bruyndonckx Robin , van der Hilst Jeroen , Cox Janneke , Driesen Paulien , Opsomer Matthias , Van Steenkiste Eveline , Stessel Björn , Dubois Jasperina , Messiaen Peter
Published: December 2020

An amendment to this paper has been published and can be accessed via the original article.
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

Background

To 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.

Methods

This 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.

Results

Compared 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.

Conclusions

The 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

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

Background

Despite 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.

Methods

We 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).

Results

The 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].

Conclusions

This 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.