bluuebunny/crossref_metadata_2025_split huggingface dataset:
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data
Authors: Lee Sunmyoung , Ono Tamiko , Aoki-Kinoshita Kiyoko 
Published: November 2021

Abstract
Background
The abundance of glycomics data that have accumulated has led to the development of many useful databases to aid in the understanding of the function of the glycans and their impact on cellular activity. At the same time, the endeavor for data sharing between glycomics databases with other biological databases have contributed to the creation of new knowledgebases. However, different data types in data description have impeded the data sharing for knowledge integration. To solve this matter, Semantic Web techniques including Resource Description Framework (RDF) and ontology development have been adopted by various groups to standardize the format for data exchange. These semantic data have contributed to the expansion of knowledgebases and hold promises of providing data that can be intelligently processed. On the other hand, bench biologists who are experts in experimental finding are end users and data producers. Therefore, it is indispensable to reduce the technical barrier required for bench biologists to manipulate their experimental data to be compatible with standard formats for data sharing.

Results
There are many essential concepts and practical techniques for data integration but there is no method to enable researchers to easily apply Semantic Web techniques to their experimental data. We implemented our procedure on unformatted information of E.coli O-antigen structures collected from the web and show how this information can be expressed as formatted data applicable to Semantic Web standards. In particular, we described the E-coli O-antigen biosynthesis pathway using the BioPAX ontology developed to support data exchange between pathway databases.

Conclusions
The method we implemented to semantically describe O-antigen biosynthesis should be helpful for biologists to understand how glycan information, including relevant pathway reaction data, can be easily shared. We hope this method can contribute to lower the technical barrier that is required when experimental findings are formulated into formal representations and can lead bench scientists to readily participate in the construction of new knowledgebases that are integrated with existing ones. Such integration over the Semantic Web will enable future work in artificial intelligence and machine learning to enable computers to infer new relationships and hypotheses in the life sciences.
A new strain of Volutella citrinella with nematode predation and nematicidal activity, isolated from the cysts of potato cyst nematodes in China
Authors: Zhang Xinyue , Zhang Hui , Jiang Zhaochun , Bai Qing , Wu Shishi , Wang Yong , Li Cheng , Zeng Xiangyu , Gan Xiuhai , Xie Xin , Li Zhong , Yang Zaifu 
Published: November 2021

Abstract
Background
Plant parasitic nematodes (PPNs) are responsible for causing many plant diseases and are extremely difficult to control at present. Currently, due to the negative effects of chemical agents on the environment and human health, the development of new biological pesticides has become an important part of plant nematode control. Nematophagous fungi refers to a class of fungi that kill plant nematodes. Notably, a large number of nematophagous fungi resources remain to be studied. The objective of our study was to use in vitro screening to identify nematophagous fungi and select strains that were highly active against nematodes, providing a primary research for the development and utilization of new nematophagous fungi.

Results
A new nematophagous fungal strain (GUCC2219) was isolated from cysts of possibly Globodera spp. and Heterodera spp., identified as Volutella citrinella. The hyphae of V. citrinella produced ring structures of variable size and exhibited predatory and nematicidal activity. The hyphal predation rates (in vitro) against three species of nematodes, Aphelenchoides besseyi, Bursaphelenchus xylophilus, and Ditylenchus destructor, averaged 59.45, 33.35, and 50.95%, respectively, while the fermentation broth produced by the fungus exhibited mortality rates of 100, 100, and 55.63%, respectively, after 72 h.

Conclusion
V. citrinella is a new strain with nematophagous properties, which are a novel discovery. At the same time, this is the first report of nematicidal and nematode predation activity in the genus Volutella.
California TRV-based VIGS vectors mediate gene silencing at elevated temperatures but with greater growth stunting
Authors: Rahman Jamilur , Baldwin Ian T. , Gase Klaus 
Published: November 2021

Abstract
Background
Tobacco rattle virus (TRV) based virus-induced gene silencing (VIGS), a widely used functional genomics tool, requires growth temperatures typically lower than those of the plant’s native environment. Enabling VIGS under native conditions in the field according to applicable safety regulations could be a revolutionary advance for ecological research.

Results
Here, we report the development of an enhanced thermal tolerant VIGS vector system based on a TRV California isolate. cDNA clones representing the whole viral genome were sequenced and used to construct separate binary plant transformation vectors for functional elements of RNA1 (6765 nt) and RNA2 (3682 nt). VIGS of target genes was induced by transient transformation of the host plant with both vectors or by treating the host plant with sap from already VIGS induced plants. In Nicotiana attenuata the silencing efficiency of the PDS (phytoene desaturase) gene was 90% at 28 °C and 78% at 30 °C. Silencing at these temperatures was more prominent and durable than silencing induced by the widely used TRV PpK20-based pBINTRA6/pTV00 system, but was associated with a viral phenotype. Differences in the suppressor protein and RNA dependent RNA polymerase sequences between the TRV California isolate and PpK20 may be the reason for their different thermal tolerance.

Conclusions
The new TRV California-based VIGS vectors induce gene silencing in Nicotiana attenuata at higher temperatures than the existing pBINTRA6/pTV00 vector system, but cause greater growth defects. The new vector system opens up an avenue to study genes functions in planta under field conditions.
Intubation using VieScope vs. Video laryngoscopy in full personal protective equipment – a randomized, controlled simulation trial
Authors: Ecker Hannes , Kolvenbach Simone , Herff Holger , Wetsch Wolfgang A. 
Published: November 2021

Abstract
Background
VieScope is a new type of laryngoscope, with a straight, transparent and illuminated blade, allowing for direct line of sight towards the larynx. In addition, VieScope is disposed of after single patient use, which can avoid cross-contaminations of contagious material. This has gained importance especially when treating patients with highly contagious infectious diseases, such as during the SARS-CoV2 pandemic. In this context, VieScope has not been evaluated yet in a clinical study.

Material and methods
This study compared intubation with VieScope to video-laryngoscopy (GlideScope) in normal and difficult airway in a standardized airway manikin in a randomized controlled simulation trial. Thirty-five medical specialists were asked to perform endotracheal intubation in full personal protective equipment (PPE). Primary endpoint was correct tube position. First-pass rate (i.e., success rate at the first attempt), time until intubation and time until first correct ventilation were registered as secondary endpoints.

Results
For correct tracheal tube placement, there was no significant difference between VieScope and GlideScope in normal and difficult airway conditions. VieScope had over 91% fist-pass success rate in normal airway setting. VieScope had a comparable success rate to GlideScope in difficult airway, but had a significantly longer time until intubation and time until ventilation.

Conclusion
VieScope and GlideScope had high success rates in normal as well as in difficult airway. There was no unrecognized esophageal intubation in either group. Overall time for intubation was longer in the VieScope group, though in an acceptable range given in literature.
Results from this simulation study suggest that VieScope may be an acceptable alternative for tracheal intubation in full PPE.

Trial Registration
The study was registered at the German Clinical Trials Register www.drks.de (Registration date: 09/11/2020; TrialID:
DRKS00023406).
Organisational determinants and consequences of diagnostic discrepancy in two large patient groups in the emergency departments: a national study of consecutive episodes between 2008 and 2016
Authors: Tipsmark Line Stjernholm , Obel Børge , Andersson Tommy , Søgaard Rikke 
Published: November 2021

Abstract
Background
Diagnostic discrepancy (DD) is a common phenomenon in healthcare, but little is known about its organisational determinants and consequences. Thus, the aim of the study was to evaluate this among selected emergency department (ED) patients.

Method
We conducted an observational study including all consecutive ED patients (hip fracture or erysipelas) in the Danish healthcare sector admitted between 2008 and 2016. DD was defined as a discrepancy between discharge and admission diagnoses. Episode and department statistics were retrieved from Danish registers. We conducted a survey among all 21 Danish EDs to gather information about organisational determinants. To estimate the results while adjusting for episode- and department-level heterogeneity, we used mixed effect models of ED organisational determinants and 30-day readmission, 30-day mortality and episode costs (2018-DKK) of DDs.

Results
DD was observed in 2308 (3.3%) of 69,928 hip fracture episodes and 3206 (8.5%) of 37,558 erysipelas episodes. The main organisational determinant of DD was senior physicians (nonspecific medical specialty) being employed at the ED (hip fracture: odds ratio (OR) 2.74, 95% confidence interval (CI) 2.15–3.51; erysipelas: OR 3.29, 95% CI 2.65–4.07). However, 24-h presence of senior physicians (nonspecific medical specialty) (hip fracture) and availability of external senior physicians (specific medical specialty) (both groups) were negatively associated with DD. DD was associated with increased 30-day readmission (hip fracture, mean 9.45% vs 13.76%, OR 1.46, 95% CI 1.28–1.66, p < 0.001) and episode costs (hip fracture, 61,681 DKK vs 109,860 DKK, log cost 0.58, 95% CI 0.53–0.63, p < 0.001; erysipelas, mean 20,818 DKK vs 56,329 DKK, log cost 0.97, 95% CI 0.92–1.02, p < 0.001) compared with episodes without DD.

Conclusion
DD was found to have a negative impact on two out of three study outcomes, and particular organisational characteristics seem to be associated with DD. Yet, the complexity of organisations and settings warrant further studies into these associations.
Exploring relationships between drought and epidemic cholera in Africa using generalised linear models
Authors: Charnley Gina E. C. , Kelman Ilan , Green Nathan , Hinsley Wes , Gaythorpe Katy A. M. , Murray Kris A. 
Published: November 2021

Abstract
Background
Temperature and precipitation are known to affect Vibrio cholerae outbreaks. Despite this, the impact of drought on outbreaks has been largely understudied. Africa is both drought and cholera prone and more research is needed in Africa to understand cholera dynamics in relation to drought.

Methods
Here, we analyse a range of environmental and socioeconomic covariates and fit generalised linear models to publicly available national data, to test for associations with several indices of drought and make cholera outbreak projections to 2070 under three scenarios of global change, reflecting varying trajectories of CO2 emissions, socio-economic development, and population growth.

Results
The best-fit model implies that drought is a significant risk factor for African cholera outbreaks, alongside positive effects of population, temperature and poverty and a negative effect of freshwater withdrawal. The projections show that following stringent emissions pathways and expanding sustainable development may reduce cholera outbreak occurrence in Africa, although these changes were spatially heterogeneous.

Conclusions
Despite an effect of drought in explaining recent cholera outbreaks, future projections highlighted the potential for sustainable development gains to offset drought-related impacts on cholera risk. Future work should build on this research investigating the impacts of drought on cholera on a finer spatial scale and potential non-linear relationships, especially in high-burden countries which saw little cholera change in the scenario analysis.
Environmental factors and spatiotemporal distribution of Japanese encephalitis after vaccination campaign in Guizhou Province, China (2004–2016)
Authors: Zhao Suye , Li Yidan , Fu Shihong , Liu Ming , Li Fan , Liu Chunting , Yu Jing , Rui Liping , Wang Dingming , Wang Huanyu 
Published: November 2021

Abstract
Background
Although a vaccination campaign has been conducted since 2004, Japanese encephalitis (JE) is still a public health problem in Guizhou, one of the provinces with the highest incidence of JE in China. The aim of this study was to understand the spatiotemporal distribution of JE and its relationship with environmental factors in Guizhou Province in the post-vaccination era, 2004–2016.

Methods
We collected data on human JE cases in Guizhou Province from 2004 to 2016 from the national infectious disease reporting system. A Poisson regression model was used to analyze the relationship between JE occurrence and environmental factors amongst counties.

Results
Our results showed that the incidence and mortality of JE decreased after the initiation of vaccination. JE cases were mainly concentrated in preschool and school-age children and the number of cases in children over age 15 years was significantly decreased compared with the previous 10 years; the seasonality of JE before and after the use of vaccines was unchanged. JE incidence was positively associated with cultivated land and negatively associated with gross domestic product (GDP) per capita, vegetation coverage, and developed land. In areas with cultivated land coverage < 25%, vegetation coverage > 55%, and urban area coverage > 25%, the JE risk was lower. The highest JE incidence was among mid-level GDP areas and in moderately urbanized areas.

Conclusions
This study assessed the relationship between incidence of JE and environmental factors in Guizhou Province. Our results highlight that the highest risk of JE transmission in the post-vaccination era is in mid-level developed areas.
Evaluation and enhancement of standard equations for renal function estimation in individuals with components of metabolic disease
Authors: Brunetti Luigi , Back Hyunmoon , Yu Sijia , Jalil Urma , Kagan Leonid 
Published: November 2021

Abstract
Background
The primary objective of this study aims to test patient factors, with a focus on cardiometabolic disease, influencing the performance of the Cockcroft-Gault equation in estimating glomerular filtration rate.

Methods
A cohort study was performed using data from adult patients with both a 24-h urine creatinine collection and a serum creatinine available. Creatinine clearance was calculated for each patient using the Cockcroft-Gault, Modified Diet in Renal Disease, and Chronic Kidney Disease Epidemiology Collaboration equations and estimates were compared to the measured 24-h urine creatinine clearance. In addition, new prediction equations were developed.

Results
In the overall study population (n = 484), 44.2% of patients were obese, 44.0% had diabetes, and 30.8% had dyslipidemia. A multivariable model which incorporating patient characteristics performed the best in terms of correlation to measured 24-h urine creatinine clearance, accuracy, and error. The modified Cockcroft-Gault equation using lean body weight performed best in the overall population, the obese subgroup, and the dyslipidemia subgroup in terms of strength of correlation, mean bias, and accuracy.

Conclusions
Regardless of strategy used to calculate creatinine clearance, residual error was present suggesting novel methods for estimating glomerular filtration rate are urgently needed.
Chlamydia pneumoniae-associated pleuropericarditis: a case report and systematic review of the literature
Authors: Kyriakoulis Konstantinos G. , Kollias Anastasios , Diakos George E. , Trontzas Ioannis P. , Fyta Eleni , Syrigos Nikolaos K. , Poulakou Garyphallia 
Published: November 2021

Abstract
Background
Chlamydia pneumoniae is a common cause of atypical community acquired pneumonia (CAP). The diagnostic approach of chlamydial infections remains a challenge. Diagnosis of delayed chlamydial-associated complications, involving complex autoimmune pathophysiological mechanisms, is still more challenging. C. pneumoniae-related cardiac complications have been rarely reported, including cases of endocarditis, myocarditis and pericarditis.

Case presentation
A 40-year old female was hospitalized for pleuropericarditis following lower respiratory tract infection. The patient had been hospitalized for CAP (fever, dyspnea, chest X-ray positive for consolidation on the left upper lobe) 5 weeks ago and had received ceftriaxone and moxifloxacin. Four weeks after her discharge, the patient presented with fever, shortness of breath and pleuritic chest pain and was readmitted because of pericardial and bilateral pleural effusions (mainly left). The patient did not improve on antibiotics and sequential introduction of colchicine and methylprednisolone was performed. The patient presented impressive clinical and laboratory response. Several laboratory and clinical assessments failed to demonstrate any etiological factor for serositis. Chlamydial IgM and IgG antibodies were positive and serial measurements showed increasing kinetics for IgG. Gold standard polymerase chain reaction of respiratory tract samples was not feasible but possibly would not have provided any additional information since CAP occurred 5 weeks ago. The patient was discharged under colchicine and tapered methylprednisolone course. During regular clinic visits, she remained in good clinical condition without pericardial and pleural effusions relapse.

Conclusions
C. pneumoniae should be considered as possible pathogen in case of pleuritis and/or pericarditis during or after a lower respiratory tract infection. In a systematic review of the literature only five cases of C. pneumoniae associated pericarditis were identified. Exact mechanisms of cardiovascular damage have not yet been defined, yet autoimmune pathways might be implicated.
Using the ‘huddle’ to enhance interprofessional teamwork among nursing students through a podcast: a qualitative and exploratory pilot study
Authors: Aase Ingunn , Tjoflåt Ingrid , Hjorthaug Urstad Kristin 
Published: November 2021

Abstract
Background
Interprofessional teamwork is crucial for fostering healthcare performance and for minimizing adverse events. The daily huddle is an important arena for interprofessional interaction and communication between nurses and physicians in hospitals.
Although prevalence strongly rooted in clinical practice, the huddle does not seem to be a prioritized area in nursing education programs. Taking part in a huddle is traditionally something nursing students learn in their clinical studies.
Therefore, there is need for learning tools that can provide nursing students with quality assured training that can improve their preparation for interprofessional teamwork and strengthen the link between the educational institution and the field of practice. In this study, we have developed and tested a podcast to increase nursing students’ competence in interprofessional teamwork when participating in huddles.
The aim of the pilot study was to explore nursing students’ experiences with utilizing a huddle-focused podcast as a learning tool during their clinical practice studies in the hospital.

Method
This qualitative and exploratory pilot study used focus group interviews.
Eleven third-year nursing students who had listened to the podcast during their practical studies at a medical hospital ward were included. The interviews were subjected to content analysis.

Result
The analysis identified four categories that resonated across all participants in the focus group interviews: 1. understanding one’s own role in the huddle; 2. being encouraged to speak up; 3. using the huddle as a flexible learning tool; and 4. being authentic but not always realistic.

Conclusion
Findings indicate that the huddle-focused podcast seems to be valuable for nursing students learning about interprofessional teamwork. The podcast seemed especially useful in helping the students to understand their own role and to speak up in the huddle meetings. The positive experiences with the flexibility of the podcast learning tool are promising for use in other educational settings.
Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine
Authors: Webster Rebecca , Sekuloski Silvana , Odedra Anand , Woolley Stephen , Jennings Helen , Amante Fiona , Trenholme Katharine R. , Healer Julie , Cowman Alan F. , Eriksson Emily M. , Sathe Priyanka , Penington Jocelyn , Blanch Adam J. , Dixon Matthew W. A. , Tilley Leann , Duffy Michael F. , Craig Alister , Storm Janet , Chan Jo-Anne , Evans Krystal , Papenfuss Anthony T. , Schofield Louis , Griffin Paul , Barber Bridget E. , Andrew Dean , Boyle Michelle J. , de Labastida Rivera Fabian , Engwerda Christian , McCarthy James S. 
Published: November 2021

Abstract
Background
There is a clear need for novel approaches to malaria vaccine development. We aimed to develop a genetically attenuated blood-stage vaccine and test its safety, infectivity, and immunogenicity in healthy volunteers. Our approach was to target the gene encoding the knob-associated histidine-rich protein (KAHRP), which is responsible for the assembly of knob structures at the infected erythrocyte surface. Knobs are required for correct display of the polymorphic adhesion ligand P. falciparum erythrocyte membrane protein 1 (PfEMP1), a key virulence determinant encoded by a repertoire of var genes.

Methods
The gene encoding KAHRP was deleted from P. falciparum 3D7 and a master cell bank was produced in accordance with Good Manufacturing Practice. Eight malaria naïve males were intravenously inoculated (day 0) with 1800 (2 subjects), 1.8 × 105 (2 subjects), or 3 × 106 viable parasites (4 subjects). Parasitemia was measured using qPCR; immunogenicity was determined using standard assays. Parasites were rescued into culture for in vitro analyses (genome sequencing, cytoadhesion assays, scanning electron microscopy, var gene expression).

Results
None of the subjects who were administered with 1800 or 1.8 × 105 parasites developed parasitemia; 3/4 subjects administered 3× 106 parasites developed significant parasitemia, first detected on days 13, 18, and 22. One of these three subjects developed symptoms of malaria simultaneously with influenza B (day 17; 14,022 parasites/mL); one subject developed mild symptoms on day 28 (19,956 parasites/mL); and one subject remained asymptomatic up to day 35 (5046 parasites/mL). Parasitemia rapidly cleared with artemether/lumefantrine. Parasitemia induced a parasite-specific antibody and cell-mediated immune response. Parasites cultured ex vivo exhibited genotypic and phenotypic properties similar to inoculated parasites, although the var gene expression profile changed during growth in vivo.

Conclusions
This study represents the first clinical investigation of a genetically attenuated blood-stage human malaria vaccine. A P. falciparum 3D7 kahrp– strain was tested in vivo and found to be immunogenic but can lead to patent parasitemia at high doses.

Trial registration
Australian New Zealand Clinical Trials Registry (number: ACTRN12617000824369; date: 06 June 2017).