bluuebunny/crossref_metadata_2025 huggingface dataset:
CorDiffViz: an R package for visualizing multi-omics differential correlation networks
Authors: Yu Shiqing , Drton Mathias , Promislow Daniel E. L. , Shojaie Ali
Published: October 2021

Background

Differential correlation networks are increasingly used to delineate changes in interactions among biomolecules. They characterize differences between omics networks under two different conditions, and can be used to delineate mechanisms of disease initiation and progression.

Results

We present a new R package, , that facilitates the estimation and visualization of differential correlation networks using multiple correlation measures and inference methods. The software is implemented in , and , and is available athttps://github.com/sqyu/CorDiffViz. Visualization has been tested for the Chrome and Firefox web browsers. A demo is available athttps://diffcornet.github.io/CorDiffViz/demo.html.

Conclusions

Our software offers considerable flexibility by allowing the user to interact with the visualization and choose from different estimation methods and visualizations. It also allows the user to easily toggle between correlation networks for samples under one condition and differential correlations between samples under two conditions. Moreover, the software facilitates integrative analysis of cross-correlation networks between two omics data sets.
Comparison of sequencing data processing pipelines and application to underrepresented African human populations
Authors: Breton Gwenna , Johansson Anna C. V. , Sjödin Per , Schlebusch Carina M. , Jakobsson Mattias
Published: October 2021

Background

Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.

Results

We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK “Best Practices” are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.

Conclusions

We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.
Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Authors: Gan Mingyu , Wu Bingbing , Yan Gangfeng , Li Gang , Sun Li , Lu Guoping , Zhou Wenhao
Published: October 2021

Background

Enzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing machine, which enabled effective enrichment of microbial sequences. However, few studies have compared the enzyme-based host depletion and nanopore adaptive sequencing for microbial enrichment efficiency.

Results

To compare the host depletion and microbial enrichment efficiency of enzyme-based and adaptive sequencing methods, the present study collected clinical samples from eight children with respiratory tract infections. The same respiratory samples were subjected to standard methods, adaptive sequencing methods, enzyme-based host depletion methods, and the combination of adaptive sequencing and enzyme-based host depletion methods. We compared the host depletion efficiency, microbial enrichment efficiency, and pathogenic microorganisms detected between the four methods. We found that adaptive sequencing, enzyme-based host depletion and the combined methods significantly enriched the microbial sequences and significantly increased the diversity of microorganisms (p value < 0.001 for each method compared to standard). The highest microbial enrichment efficiency was achieved using the combined method. Compared to the standard method, the combined method increased the microbial reads by a median of 113.41-fold (interquartile range 23.32–327.72, maximum 1812), and the number of genera by a median of 70-fold (interquartile range 56.75–86.75, maximum 164). The combined method detected 6 pathogens in 4 samples with a median read of 547, compared to 5 pathogens in 4 samples with a median read of 4 using the standard method.

Conclusion

The combined method is an effective, easy-to-run method for enriching microbial sequences in clinical metagenomics from sputum and bronchoalveolar lavage fluid samples and may improve the sensitivity of clinical metagenomics for other host-derived clinical samples.
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes
Authors: Lueder Matthew R. , Cer Regina Z. , Patrick Miles , Voegtly Logan J. , Long Kyle A. , Rice Gregory K. , Bishop-Lilly Kimberly A.
Published: October 2021

Background

Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Manual annotation efforts are time-consuming and complex; however, software can help reduce these drawbacks.

Results

We created Manual Annotation Studio (MAS) to improve the efficiency of the process of manual functional annotation prokaryotic and viral genomes. MAS allows users to upload unannotated genomes, provides an interface to edit and upload annotations, tracks annotation history and progress, and saves data to a relational database. MAS provides users with pertinent information through a simple point and click interface to execute and visualize results for multiple homology search tools (blastp, rpsblast, and HHsearch) against multiple databases (Swiss-Prot, nr, CDD, PDB, and an internally generated database). MAS was designed to accept connections over the local area network (LAN) of a lab or organization so multiple users can access it simultaneously. MAS can take advantage of high-performance computing (HPC) clusters by interfacing with SGE or SLURM and data can be exported from MAS in a variety of formats (FASTA, GenBank, GFF, and excel).

Conclusions

MAS streamlines and provides structure to manual functional annotation projects. MAS enhances the ability of users to generate, interpret, and compare results from multiple tools. The structure that MAS provides can improve project organization and reduce annotation errors. MAS is ideal for team-based annotation projects because it facilitates collaboration.
Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles
Authors: Achari Saidi R. , Edwards Jacqueline , Mann Ross C. , Kaur Jatinder K. , Sawbridge Tim , Summerell Brett A.
Published: October 2021

Background

The fungal pathogen Fusarium oxysporum f.sp. pisi (Fop) causes Fusarium wilt in peas. There are four races globally: 1, 2, 5 and 6 and all of these races are present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales; however, there has been no transcriptomic Fop-pea pathosystem study.

Results

A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcriptome analysis at 20 days post-inoculation revealed differences in the differentially expressed genes (DEGs) in the Fop races potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes, CAZymes and effector-like proteins were expressed in race 2. Race 6 expressed the least number of genes at this time point.

Conclusion

Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during the necrotrophic stage of infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.
Impact of human gene annotations on RNA-seq differential expression analysis
Authors: Hamaguchi Yu , Zeng Chao , Hamada Michiaki
Published: October 2021

Background

Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are available for the human genome and are continually updated–a process complicated with the development and application of high-throughput sequencing technologies. However, the impact of the complexity of gene annotations on DE analysis remains unclear.

Results

Using “mappability”, a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. We found that mappability was significantly different among the human gene annotations. We also found that increasing mappability improved the performance of DE analysis, and the impact of mappability mainly evident in the quantification step and propagated downstream of DE analysis systematically.

Conclusions

We assessed how the complexity of gene annotations affects DE analysis using mappability. Our findings indicate that the growth and complexity of gene annotations negatively impact the performance of DE analysis, suggesting that an approach that excludes unnecessary gene models from gene annotations improves the performance of DE analysis.
Detection of viable and total fungal community in zaopei of Chinese strong-flavor baijiu using PMA combined with qPCR and HTS based on ITS2 region
Authors: Liu Huanming , Tan Guangxun , Chen Qitong , Dong Weiwei , Chen Ping , Cai Kaiyun , Hu Yuanliang , Zhang Weiyan , Peng Nan , Liang Yunxiang , Zhao Shumiao
Published: October 2021

Background

Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce ethanol and flavor substances during fermentation, which fundamentally determined the quality of baijiu. It is of great importance to study microbial community of fermented grains (zaopei) during baijiu brewing process for improving its quality. In this study, we firstly used propidium monoazide (PMA) to treat zaopei samples from 5-year pit and 20-year pit for removing the interference of non-viable fungi, and analyzed the diversity of total fungi and viable fungi by quantitative PCR (qPCR) and high-throughput sequencing (HTS) based on ITS2 gene.

Results

The results showed that total fungi and viable fungi displayed no significant differences at OTU, phylum, or genus levels during fermentation within two kinds of pits. A total of 6 phyla, 19 classes, and 118 genera in fungi were found based on OTUs annotation in zaopei samples from 5-year pit and 20-year pit. Besides, non-viable fungi had little effect on the fungal community diversity during the fermentation cycle. It was found that the most dominant viable fungi belonged to Saccharomyces, Kazachstania, Naumovozyma, and Trichosporon, and Naumovozyma was firstly detected in zaopei samples of CSFB. Moreover, based on the variation of flavor substances in zaopei samples, the quality of CSFB produced from older pit was better than that produced from younger pit.

Conclusion

The non-viable fungi had little effect on the fungal diversity, structure, and relative abundance in zaopei samples of CSFB, and Naumovozyma was firstly detected in zaopei samples of CSFB. Our findings can be applied as guidance for improving the quality and stability of CSFB.
Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation
Authors: Wu Kunjing , Duan Xiaojing , Zhu Zhonglong , Sang Ziyang , Duan Jie , Jia Zhongkui , Ma Luyi
Published: October 2021

Background

Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 °C, 4 °C and 0 °C, was compared by RNA sequencing.

Results

Over 426 million clean reads were produced from three libraries (22 °C, 4 °C and 0 °C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation.

Conclusion

M. denudata exhibits responses to non-freezing cold temperature (4 °C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 °C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.
Comparative physiological and transcriptomic analyses reveal ascorbate and glutathione coregulation of cadmium toxicity resistance in wheat genotypes
Authors: Zhang Tao , Xiao Jingui , Zhao Yongsheng , Zhang Yifan , Jie Yaqi , Shen Dandan , Yue Caipeng , Huang Jinyong , Hua Yingpeng , Zhou Ting
Published: October 2021

Background

Cadmium (Cd) is a heavy metal with high toxicity that severely inhibits wheat growth and development. Cd easily accumulates in wheat kernels and enters the human food chain. Genetic variation in the resistance to Cd toxicity found in wheat genotypes emphasizes the complex response architecture. Understanding the Cd resistance mechanisms is crucial for combating Cd phytotoxicity and meeting the increasing daily food demand.

Results

Using two wheat genotypes (Cd resistant and sensitive genotypes T207 and S276, respectively) with differing root growth responses to Cd, we conducted comparative physiological and transcriptomic analyses and exogenous application tests to evaluate Cd detoxification mechanisms. S276 accumulated more H2O2, O2−, and MDA than T207 under Cd toxicity. Catalase activity and levels of ascorbic acid (AsA) and glutathione (GSH) were greater, whereas superoxide dismutase (SOD) and peroxidase (POD) activities were lower in T207 than in S276. Transcriptomic analysis showed that the expression ofRBOHA,RBOHC, andRBOHEwas significantly increased under Cd toxicity, and two-thirds (22 genes) of the differentially expressedRBOHgenes had higher expression levels in S276 than inT207. Cd toxicity reshaped the transcriptional profiling of the genes involving the AsA-GSH cycle, and a larger proportion (74.25%) of the corresponding differentially expressed genes showed higher expression in T207 than S276. The combined exogenous application of AsA and GSH alleviated Cd toxicity by scavenging excess ROS and coordinately promoting root length and branching, especially in S276.

Conclusions

The results indicated that the ROS homeostasis plays a key role in differential Cd resistance in wheat genotypes, and the AsA-GSH cycle fundamentally and vigorously influences wheat defense against Cd toxicity, providing insight into the physiological and transcriptional mechanisms underlying Cd detoxification.
Significance of day-to-day glucose variability in patients after acute coronary syndrome
Authors: Miyoshi Machiko , Uzui Hiroyasu , Shimizu Tomohiro , Aiki Takayoshi , Shiomi Yuichiro , Nodera Minoru , Ikeda Hiroyuki , Tama Naoto , Hasegawa Kanae , Morishita Tetsuji , Ishida Kentaro , Miyazaki Shinsuke , Tada Hiroshi
Published: October 2021

Background

Several studies have recently addressed the importance of glycemic variability (GV) in patients with acute coronary syndrome (ACS). Although daily GV measures, such as mean amplitude of glycemic excursions, are established predictors of poor prognosis in patients with ACS, the clinical significance of day-to-day GV remains to be fully elucidated. We therefore monitored day-to-day GV in patients with ACS to examine its significance.

Methods

In 25 patients with ACS, glucose levels were monitored for 14 days using a flash continuous glucose monitoring system. Mean of daily differences (MODD) was calculated as a marker of day-to-day GV. N-terminal pro-brain natriuretic peptide (NT-proBNP) was evaluated within 4 days after hospitalization. Cardiac function (left ventricular end-diastolic volume, left ventricular ejection fraction, stroke volume) was assessed by echocardiography at 3–5 days after admission and at 10–12 months after the disease onset.

Results

Of the 25 patients, 8 (32%) were diagnosed with diabetes, and continuous glucose monitoring (CGM)-based MODD was high (16.6 to 42.3) in 17 patients (68%). Although MODD did not correlate with max creatine kinase (CK), there was a positive correlation between J-index, high blood glucose index, and NT-proBNP (r = 0.83, p < 0.001; r = 0.85, p < 0.001; r = 0.41, p = 0.042, respectively).

Conclusions

In patients with ACS, MODD was associated with elevated NT-proBNP. Future studies should investigate whether day-to-day GV in ACS patients can predict adverse clinical events such as heart failure.
EMS non-conveyance: A safe practice to decrease ED crowding or a threat to patient safety?
Authors: Paulin Jani , Kurola Jouni , Koivisto Mari , Iirola Timo
Published: October 2021

Background

The safety of the Emergency Medical Service’s (EMS’s) non-conveyance decision was evaluated by EMS re-contacts, primary health care or emergency department (ED) visits, and hospitalization within 48 h. The secondary outcome was 28-day mortality.

Methods

This cohort study used prospectively collected data on non-conveyed EMS patients from three different regions in Finland between June 1 and November 30, 2018. The Adjusted International Classification of Primary Care (ICPC2) as the reason for care was compared to hospital discharge diagnoses (ICD10). Multivariable logistic regressions were used to determine factors that were independently associated with adverse outcomes. Results are presented with adjusted odds ratios (aORs) together with 95% confidence intervals (CIs). Data regarding deceased patients were reviewed by the study group.

Results

Of the non-conveyed EMS patients (n = 11,861), 6.3% re-contacted the EMS, 8.3% attended a primary health care facility, 4.2% went to the ED, 1.6% were hospitalized, and 0.1% died 0–24 h after the EMS mission. The 0–24 h adverse event rate was higher than 24–48 h. After non-conveyance, 32 (0.3%) patients were admitted to an intensive care unit within 24 h. Primary non-urgent EMS mission (aOR 1.49; 95% CI 1.25 to 1.77), EMS arrival at night (aOR 1.82; 95% CI 1.58 to 2.09), ALS unit type vs BLS (aOR 1.43; 95% CI 1.16 to 1.77), rural area (aOR 1.74; 95% CI 1.51 to 1.99), and older patient age (aOR 1.41; 95% CI 1.20 to 1.66) were associated with subsequent primary health care visits (0–24 h).

Conclusions

Four in five non-conveyed patients did not have any re-contact in follow-up period. EMS non-conveyance seems to be a relatively safe method of focusing ED resources and avoiding ED crowding.
Joint modelling of multivariate longitudinal clinical laboratory safety outcomes, concomitant medication and clinical adverse events: application to artemisinin-based treatment during pregnancy clinical trial
Authors: Patson Noel , Mukaka Mavuto , D’Alessandro Umberto , Chapotera Gertrude , Mwapasa Victor , Mathanga Don , Kazembe Lawrence , Laufer Miriam K. , Chirwa Tobias
Published: October 2021

Background

In drug trials, clinical adverse events (AEs), concomitant medication and laboratory safety outcomes are repeatedly collected to support drug safety evidence. Despite the potential correlation of these outcomes, they are typically analysed separately, potentially leading to misinformation and inefficient estimates due to partial assessment of safety data. Using joint modelling, we investigated whether clinical AEs vary by treatment and how laboratory outcomes (alanine amino-transferase, total bilirubin) and concomitant medication are associated with clinical AEs over time following artemisinin-based antimalarial therapy.

Methods

We used data from a trial of artemisinin-based treatments for malaria during pregnancy that randomized 870 women to receive artemether–lumefantrine (AL), amodiaquine–artesunate (ASAQ) and dihydroartemisinin–piperaquine (DHAPQ). We fitted a joint model containing four sub-models from four outcomes: longitudinal sub-model for alanine aminotransferase, longitudinal sub-model for total bilirubin, Poisson sub-model for concomitant medication and Poisson sub-model for clinical AEs. Since the clinical AEs was our primary outcome, the longitudinal sub-models and concomitant medication sub-model were linked to the clinical AEs sub-model via current value and random effects association structures respectively. We fitted a conventional Poisson model for clinical AEs to assess if the effect of treatment on clinical AEs (i.e. incidence rate ratio (IRR)) estimates differed between the conventional Poisson and the joint models, where AL was reference treatment.

Results

Out of the 870 women, 564 (65%) experienced at least one AE. Using joint model, AEs were associated with the concomitant medication (log IRR 1.7487; 95% CI: 1.5471, 1.9503; p < 0.001) but not the total bilirubin (log IRR: -0.0288; 95% CI: − 0.5045, 0.4469; p = 0.906) and alanine aminotransferase (log IRR: 0.1153; 95% CI: − 0.0889, 0.3194; p = 0.269). The Poisson model underestimated the effects of treatment on AE incidence such that log IRR for ASAQ was 0.2118 (95% CI: 0.0082, 0.4154; p = 0.041) for joint model compared to 0.1838 (95% CI: 0.0574, 0.3102; p = 0.004) for Poisson model.

Conclusion

We demonstrated that although the AEs did not vary across the treatments, the joint model yielded efficient AE incidence estimates compared to the Poisson model. The joint model showed a positive relationship between the AEs and concomitant medication but not with laboratory outcomes.

Trial registration

ClinicalTrials.gov: NCT00852423
Consensus for a primary care clinical decision-making tool for assessing, diagnosing, and managing shoulder pain in Alberta, Canada
Authors: Eubank Breda H. F. , Lackey Sebastian W. , Slomp Mel , Werle Jason R. , Kuntze Colleen , Sheps David M.
Published: October 2021

Background

Shoulder pain is a highly prevalent condition and a significant cause of morbidity and functional disability. Current data suggests that many patients presenting with shoulder pain at the primary care level are not receiving high quality care. Primary care decision-making is complex and has the potential to influence the quality of care provided and patient outcomes. The aim of this study was to develop a clinical decision-making tool that standardizes care and minimizes uncertainty in assessment, diagnosis, and management.

Methods

First a rapid review was conducted to identify existing tools and evidence that could support a comprehensive clinical decision-making tool for shoulder pain. Secondly, provincial consensus was established for the assessment, diagnosis, and management of patients presenting to primary care with shoulder pain in Alberta, Canada using a three-step modified Delphi approach. This project was a highly collaborative effort between Alberta Health Services’ Bone and Joint Health Strategic Clinical Network (BJH SCN) and the Alberta Bone and Joint Health Institute (ABJHI).

Results

A clinical decision-making tool for shoulder pain was developed and reached consensus by a province-wide expert panel representing various health disciplines and geographical regions. This tool consists of a clinical examination algorithm for assessing, diagnosis, and managing shoulder pain; recommendations for history-taking and identification of red flags or additional concerns; recommendations for physical examination and neurological screening; recommendations for the differential diagnosis; and care pathways for managing patients presenting with rotator cuff disease, biceps pathology, superior labral tear, adhesive capsulitis, osteoarthritis, and instability.

Conclusions

This clinical decision-making tool will help to standardize care, provide guidance on the diagnosis and management of shoulder pain, and assist in clinical decision-making for primary care providers in both public and private sectors.
The influence of a MOBile-based video Instruction for Low back pain (MOBIL) on initial care decisions made by primary care providers: a randomized controlled trial
Authors: Rhon Daniel I. , Mayhew Rachel J. , Greenlee Tina A. , Fritz Julie M.
Published: October 2021

Background

Adherence to guidelines for back pain continues to be a challenge, prompting strategies focused on improving education around biopsychosocial frameworks.

Objective

Assess the influence of an interactive educational mobile app for patients on initial care decisions made for low back pain by the primary care provider. The secondary aim was to compare changes in self-reported pain and function between groups.

Methods

This was a randomized controlled trial involving patients consulting for an initial episode of low back pain. The intervention was a mobile video-based education session (Truth About Low Back Pain) compared to usual care. The app focused on addressing maladaptive beliefs typically associated with higher risk of receiving low-value care options. The primary outcome was initial medical utilization decisions made by primary care practitioners (x-rays, MRIs, opioid prescriptions, injections, procedures) and secondary outcomes included PROMIS pain interference and physical function subscales at 1 and 6 months, and total medical costs.

Results

Of 208 participants (71.2% male; mean age 35.4 years), rates of opioid prescriptions, advanced imaging, analgesic patches, spine injections, and physical therapy use were lower in the education group, but the differences were not significant. Total back-related medical costs for 1 year (mean diff = $132; P = 0.63) and none of the 6-month PROMIS subscales were significantly different between groups. Results were no different in opioid-naïve subjects. Instead, prior opioid use and high-risk of poor prognosis on the STarT Back Screening Tool predicted 1-year back pain-related costs and healthcare utilization, regardless of intervention.

Conclusion

Factors that influence medical treatment decisions and guideline-concordant care are complex. This particular patient education approach directed at patients did not appear to influence healthcare decisions made by primary care providers. Future studies should focus on high-risk populations and/or the impact of including the medical provider as an active part of the educational process.

Trial Registration

clinicaltrials.gov NCT02777983.
Hospitalization for urinary tract infections in Japan, 2010–2015: a retrospective study using a national inpatient database
Authors: Sako Akahito , Yasunaga Hideo , Matsui Hiroki , Fushimi Kiyohide , Yanai Hidekatsu , Gu Yoshiaki , Ohmagari Norio
Published: October 2021

Background

Urinary tract infections (UTI) are common and can have severe consequences. However, there are few recent large-scale studies about them. We aimed to determine the incidence of hospitalization for UTI and to elucidate patient characteristics, clinical practice, and clinical outcomes by drawing on a Japanese nationwide database.

Methods

This was a retrospective observational study using a national database that covers half the acute care inpatients in Japan. Patients aged ≥ 15 years who were hospitalized for UTI were eligible. We did not include patients with lower UTI such as cystitis. We investigated the annual number of patients hospitalized in Japan, those patients’ characteristics, and risk factors for in-hospital mortality.

Results

We identified 232,396 eligible patients from 31 million records of discharge between April 2010 and March 2015. The average age was 73.5 years and 64.9% of patients were female. The estimated annual number of hospitalizations because of UTI was 106,508. The incidence was 6.8 per 10,000 for men and 12.4 for women. The median medical care cost was 4250 USD. In-hospital mortality was 4.5%. Risk factors of poor survival included male sex, older age, lower bed capacity, non-academic hospital, admission in winter, higher Charlson Comorbidity Index score, low body mass index, coma on admission, ambulance use, disseminated intravascular coagulation, sepsis, renal failure, heart failure, cerebrovascular diseases, pneumonia, malignancies, use of anti-diabetic drugs, and use of corticosteroid or immunosuppressive drugs.

Conclusions

We found that older patients of both sexes accounted for a significant proportion of those hospitalized for UTI. The clinical and economic burden of UTI is considerable.
A Schizophyllum commune fungus ball in a lung cancer cavity: a case report
Authors: Itoh Naoya , Akazawa Nana , Murakami Hiromi , Ishibana Yuichi , Takahashi Yusuke , Hosoda Waki , Yaguchi Takashi , Kamei Katsuhiko
Published: October 2021

Background

Schizophyllum commune is a basidiomycete that lives in the environment and can cause infections, mainly those of the respiratory system. Although S. commune is increasingly reported as a cause of allergic bronchopulmonary mycosis and sinusitis, cases of fungal ball formation are extremely uncommon. Identification of S. commune is difficult using routine mycological diagnostic methods, and in clinically suspicious cases, internal transcribed spacer sequencing should be used for diagnosis. Here, we report a first case of lung cancer with a fungal ball formation of S. commune, confirmed by analyzing the internal transcribed spacer.

Case presentation

A 76-year-old man with diabetes and hypertension was admitted to the hospital with a chief complaint of hemosputum, which he had for about 19 months. A computed tomography image of the patient’s chest showed a cavity and internal nodule in the left upper lobe of his lung. A left upper lobectomy was performed, and histopathological examination revealed squamous cell carcinoma of the lung and a fungal ball. The isolate from the surgical specimen was identified as S. commune by analyzing the internal transcribed spacer. The patient had no recurrence of the infection during 5 months of follow-up.

Conclusions

Only three cases of lung fungal balls caused by S. commune have been previously reported, and this is the first case of lung cancer cavity with a fungal ball formation. In cases of fungal ball formation in the lung, S. commune should be considered a possible causative microorganism.
Epidemiological characteristics, clinical characteristics, and prognostic factors of children with atopy hospitalised with adenovirus pneumonia
Authors: Li Miao , Han Xiao-Hua , Liu Li-Yun , Yao Hui-Sheng , Yi Li-Li
Published: October 2021

Background

Atopy may be associated with disease severity and a poor prognosis of human adenovirus (HAdV) pneumonia in children. Our aim was to observe the clinical characteristics and pulmonary radiological changes in children with atopy and HAdV pneumonia in China.

Methods

Children hospitalised with HAdV pneumonia from June 2018 to December 2019 were analysed. All children were divided into atopic with HAdV, non-atopic with HAdV, and atopic without HAdV infection group. Each group was further divided into the mild and severe pneumonia groups according to disease severity. Standard treatment was initiated after admission, and regular follow-up evaluations were conducted at 1 month after discharge. Baseline and clinical characteristics and pulmonary radiological changes in children with and without atopy were evaluated. Risk factors associated with small airway lesions in patients with HAdV pneumonia were analysed.

Results

The eosinophil count in the atopic group was significantly higher than that in the non-atopic group (P < 0.05). Severe coughing, wheezing, and small airway lesions on chest high-resolution computed tomography (HRCT) upon admission, after discharge and 1 month after discharge were significantly higher in the atopic group (with or without HAdV infection) than in the non-atopic group (P < 0.05). There were significant differences in the number of patients with wheezing and small airway lesions during hospitalisation and after discharge among the three groups (P < 0.05). The risks of small airway lesions in children with a family or personal history of asthma, severe infection, atopy, and HAdV infection were 2.1-, 2.7-, 1.9-, 2.1-, and 1.4-times higher than those in children without these characteristics, respectively.

Conclusions

Children with atopy and HAdV pneumonia may experience severe coughing in mild cases and wheezing in mild and severe cases. Children with atopy are more susceptible to the development of small airway lesions, recurrent wheezing after discharge and slower recovery of small airway lesions as observed on pulmonary imaging than non-atopic children after HAdV infection. A family or personal history of asthma, atopy, severe infection, and HAdV infection are independent risk factors associated with the development of small airway lesion as observed on chest HRCT.
Associations between YKL-40 and markers of disease severity and death in patients with necrotizing soft-tissue infection
Authors: Hedetoft Morten , Hansen Marco Bo , Madsen Martin Bruun , Johansen Julia Sidenius , Hyldegaard Ole
Published: October 2021

Background

Necrotizing soft-tissue infection (NSTI) is a severe and fast-progressing bacterial infection. Prognostic biomarkers may provide valuable information in treatment guidance and decision-making, but none have provided sufficient robustness to have a clinical impact. YKL-40 may reflect the ongoing pathological inflammatory processes more accurately than traditional biomarkers as it is secreted by the activated immune cells, but its prognostic yields in NSTI remains unknown. For this purpose, we investigated the association between plasma YKL-40 and 30-day mortality in patients with NSTI, and assessed its value as a marker of disease severity.

Methods

We determined plasma YKL-40 levels in patients with NSTI (n = 161) and age-sex matched controls (n = 65) upon admission and at day 1, 2 and 3.

Results

Baseline plasma YKL-40 was 1191 ng/mL in patients with NSTI compared with 40 ng/mL in controls (p < 0.001). YKL-40 was found to be significantly higher in patients with septic shock (1942 vs. 720 ng/mL, p < 0.001), and in patients receiving renal-replacement therapy (2382 vs. 1041 ng/mL, p < 0.001). YKL-40 correlated with Simplified Acute Physiology Score II (Rho 0.33, p < 0.001). Baseline YKL-40 above 1840 ng/mL was associated with increased risk of 30-day mortality in age-sex-comorbidity adjusted analysis (OR 3.77, 95% CI; 1.59–9.24, p = 0.003), but after further adjustment for Simplified Acute Physiology Score II no association was found between YKL-40 and early mortality.

Conclusion

High plasma YKL-40 to be associated with disease severity, renal-replacement therapy and risk of death in patients with NSTI. However, YKL-40 is not an independent predictor of 30-day mortality.
Reversible cerebral vasoconstriction syndrome with cerebral infarction caused by acute high-level vapor exposure of ethylene oxide: a case report
Authors: Lin Bin , Wang Chao , Lu Nan , Zhang Le , Jiang Biao
Published: October 2021

Background

With the increasing production and use of ethylene oxide (EO) worldwide, its explicit bio-toxicity has drawn more and more attention. At present, most studies focus on chronic EO exposure. Studies on acute EO exposure are rare, especially with imaging studies. To our knowledge, this work is the first documented case of reversible cerebral vasoconstriction syndrome (RCVS) with cerebral infarction caused by EO.

Case presentation

A 58-year-old woman who worked in a capsule production factory got an unprotected acute EO inhalation due to accidental exposure to sterilization gas. She suffered from nausea, vomiting, and severe paroxysmal headaches, but the first brain MRI scan of the patient showed no significant abnormality. Nine days after inhalation, she developed recurrent thunderclap headaches and gradual complete blindness. The follow-up brain MRI, 12 days after inhalation, demonstrated extensive cytotoxic edema. Fifteen days and 21 days after EO (ethylene oxide) inhalation, head MRA and CTA respectively showed diffuse vasoconstriction of cerebral arteries. Fifty-nine days after EO inhalation, head MRA assessed reversibility of the vasoconstriction. According to clinical features and imaging findings, RCVS with cerebral infarction can be diagnosed. The patient was sensitive to light and light reflection but still blind after symptomatic and rehabilitation therapy.

Conclusions

We report an acute EO exposure case in which the patient suffered from RCVS with cerebral infarction, which previous literature has not reported. This article aimed to raise awareness of encephalopathy after EO acute exposure.
Accessing and engaging with antenatal care: an interview study of teenage women
Authors: Wong Shee Anna , Frawley Natasha , Robertson Carolyn , McKenzie AnneMarie , Lodge Julie , Versace Vincent , Nagle Cate
Published: October 2021

Background

Pregnant teenagers in rural and regional areas experience distinct disadvantages, that are not simply a function of their age, and these have a substantial impact on their health and that of their baby. Studies demonstrate that antenatal care improves pregnancy outcomes amongst pregnant women, especially adolescents. Understanding teenager’s views and experiences of pregnancy and motherhood is important to ensure antenatal care meets young women’s needs. This study explored teenage women’s experiences and perceptions of barriers and facilitators to engaging in pregnancy care in rural and regional Victoria, Australia.

Methods

Between February–October 2017, pregnant women aged ≤19 years were purposively recruited from one regional and two rural health services in Victoria. Semi-structured, face-to-face interviews guided by naturalistic inquiry were conducted and an inductive approach to analysis was applied.

Results

Four key themes emerged from the analysis of the transcripts of 16 interviews: Valuing pregnancy care, Interactions with Maternity Service, Woman-centred care, and Support systems. Teenage women primary motivation to attend care was to ensure their baby’s wellbeing and lack of engagement occurred when the relevance of antenatal care was not understood. Appointment flexibility and an accessible location was important; most participants were reliant on others for transport. Continuity of carer and respectful, non-judgement communication by staff was highly valued. Many young women had fractured families with pregnancy diminishing their social world, yet having a baby gave them purpose in their lives.

Conclusion

Maternity services and health professionals that provide flexible, adaptable women-centred care and support through pregnancy and early motherhood will assist young women’s engagement in antenatal care.
Conjoined twins in dichorionic diamniotic triplet pregnancy: a report of three cases and literature review
Authors: Liu Hongyan , Deng Chunyan , Hu Qing , Liao Hua , Wang Xiaodong , Yu Haiyan
Published: October 2021

Background

Conjoined twins are a rare and serious complication of monochorionic twins. The total incidence is 1.5 per 100,000 births, and about 50% are liveborn. Prenatal screening and diagnosis of conjoined twins is usually performed by ultrasonography. Magnetic resonance imaging can be used to assist in the diagnosis if necessary. Conjoined twins in dichorionic diamniotic triplet pregnancy are extremely rare.

Case presentation

We reported three cases of dichorionic diamniotic triplet pregnancy with conjoined twins. Due to the poor prognosis of conjoined twins evaluated by multidisciplinary teams, selective termination of conjoined twins was performed in three cases. In case 1, selective reduction of the conjoined twins was performed at 16 gestational weeks, and a healthy female baby weighing 3270 g was delivered at 37 weeks. In case 2, the conjoined twins were selectively terminated at 17 weeks of gestation, and a healthy female baby weighing 2760 g was delivered at 37 weeks and 4 days. In case 3, the conjoined twins were selectively terminated at 15 weeks and 2 days, and a healthy female baby weighing 2450 g was delivered at 33 weeks and 6 days. The babies of all three cases were followed up and are in good health.

Conclusion(s)

Surgical separation is the only treatment for conjoined twins after birth. Early determination of chorionicity and antenatal diagnosis of conjoined twins in triplet gestations are critical for individualized management options and the prognosis of normal triplets. Expecting parents should be extensively counseled by multidisciplinary teams. If there are limitations in successful separation after birth, early selective termination of the conjoined twins by intrathoracic injection of potassium chloride may be a procedure in dichorionic diamniotic triplet pregnancy to improve perinatal outcomes of the normal triplet.
Uterine artery pseudoaneurysm after treatment of cesarean scar pregnancy: a case report
Authors: Wang Jiao , Yang Qing , Zhang Ningning , Wang Dandan
Published: October 2021

Background

Pseudoaneurysms are formed when a local arterial wall ruptures, leading to hemorrhage and hematoma adjacent to the artery. Continuous perfusion of the injured artery increases the pressure in the lumen of the pseudoaneurysm. It may rupture and lead to massive hemorrhage that could be life-threatening. Cesarean scar pregnancy (CSP) is an ectopic pregnancy where the gestational sac is implanted in the cesarean scar. Uterine artery pseudoaneurysm (UAP) after CSP treatment is rare.

Case presentation

We report the case of a 36-year-old Chinese woman who presented with acute massive vaginal bleeding 53 days after transabdominal scar pregnancy excision. Doppler ultrasound confirmed UAP. Selective uterine artery embolization (UAE) failed because of the thin and curved blood vessels. The lesion decreased in size after transvaginal ultrasound-guided direct thrombin injection (UGTI); however, massive vaginal bleeding recurred and endangered the patient’s life. The uterus was removed thereafter.

Conclusions

UAP is a rare complication after CSP treatment that can lead to fatal massive hemorrhage. Ultrasound should be reexamined regularly after treatment of CSP. In case of unexplained vaginal bleeding, we should be alert to the existence of UAP and the possibility of rupture and take effective diagnosis and treatment measures promptly.
Results of the observational prospective RealFLOT study
Authors: Giommoni Elisa , Lavacchi Daniele , Tirino Giuseppe , Fornaro Lorenzo , Iachetta Francesco , Pozzo Carmelo , Satolli Maria Antonietta , Spallanzani Andrea , Puzzoni Marco , Stragliotto Silvia , Sisani Michele , Formica Vincenzo , Giovanardi Filippo , Strippoli Antonia , Prisciandaro Michele , Di Donato Samantha , Pompella Luca , Pecora Irene , Romagnani Alessandra , Fancelli Sara , Brugia Marco , Pillozzi Serena , De Vita Ferdinando , Antonuzzo Lorenzo
Published: October 2021

Background

Perioperative FLOT (5-fluorouracil, oxaliplatin and docetaxel) has recently become the gold standard treatment for fit patients with operable gastric (GC) or gastroesophageal (GEJ) adenocarcinoma, getting a 5-year overall survival (OS) of 45%, over 23% with surgery alone.

Methods

RealFLOT is an Italian, multicentric, observational trial, collecting data from patients with resectable GC or GEJ adenocarcinoma treated with perioperative FLOT. Aim of the study was to describe feasibility and safety of FLOT, pathological complete response rate (pCR), surgical outcomes and overall response rate (ORR) in an unselected real-world population. Additional analyses evaluated the correlation between pCR and survival and the prognostic role of microsatellite instability (MSI) status.

Results

Of 206 patients enrolled that received perioperative FLOT at 15 Italian centers, 124 (60.2%) received at least 4 full-dose cycles, 190 (92.2%) underwent surgery, and 142 (68.9%) started the postoperative phase. Among patients who started the postoperative phase, 105 (51.0%) received FLOT, while 37 (18%) received de-intensified regimens, depending on clinical condition or previous toxicities. pCR was achieved in 7.3% of cases. Safety profile was consistent with literature. Neutropenia was the most common G 3–4 adverse event (AE): 19.9% in the preoperative phase and 16.9% in the postoperative phase. No toxic death was observed and 30-day postoperative mortality rate was 1.0%. ORR was 45.6% and disease control rate (DCR) was 94.2%. Disease-free survival (DFS) and OS were significantly longer in case of pCR (p = 0.009 and p = 0.023, respectively). A trend towards better DFS was observed among MSI-H patients.

Conclusions

These real-world data confirm the feasibility of FLOT in an unselected population, representative of the clinical practice. pCR rate was lower than expected, nevertheless we confirm pCR as a predictive parameter of survival. In addition, MSI-H status seems to be a positive prognostic marker also in patients treated with taxane-containing triplets.