bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying the impacts of climate variation, damming, and flow regulation on river thermal dynamics: a case study of the Włocławek Reservoir in the Vistula River, Poland
Authors: Yang Rui , Wu Shiqiang , Wu Xiufeng , Ptak Mariusz , Li Xudong , Sojka Mariusz , Graf Renata , Dai Jiangyu , Zhu Senlin
Published: January 2022

Background

River damming inevitably reshapes water thermal conditions that are important to the general health of river ecosystems. Although a lot of studies have addressed the damming’s thermal impacts, most of them just assess the overall effects of climate variation and human activities on river thermal dynamics. Less attention has been given to quantifying the impact of climate variation, damming and flow regulation, respectively. In addition, for rivers that have already faced an erosion problem in downstream channels, an adjustment of the hydroelectric power plant operation manner is expected, which reinforces the need for understanding of flow regulation’s thermal impact. To fill this gap, an air2stream-based approach is proposed and applied at the Włocławek Reservoir in the Vistula River in Poland.

Results

In the years of 1952–1983, downstream river water temperature rose by 0.31 ℃ after damming. Meanwhile, the construction of dam increased the average annual water temperature by 0.55 ℃, while climate change oppositely made it decreased by 0.26 ℃. In addition, for the seasonal impact of damming, autumn was the most affected season with the warming reached 1.14 ℃, and the least affected season was winter when water temperature experienced a warming of 0.1 ℃. The absolute values of seasonal average temperature changes due to flow regulation were less than 0.1 ℃ for all the seasons.

Conclusions

The impacts of climate variation, damming, and flow regulation on river water temperatures can be evaluated reasonably on the strength of the proposed methodology. Climate variation and damming led to general opposite impacts on the downstream water temperature at the Włocławek Reservoir before 1980s. It is noted that the climate variation impact showed an opposite trend compared to that after 1980s. Besides, flow regulation below dam hardly affected downstream river water temperature variation. This study extends the current knowledge about impacts of climate variation and hydromorphological conditions on river water temperature, with a study area where river water temperature is higher than air temperature throughout a year.
scDIOR: single cell RNA-seq data IO software
Authors: Feng Huijian , Lin Lihui , Chen Jiekai
Published: January 2022

Background

Single-cell RNA sequencing is becoming a powerful tool to identify cell states, reconstruct developmental trajectories, and deconvolute spatial expression. The rapid development of computational methods promotes the insight of heterogeneous single-cell data. An increasing number of tools have been provided for biological analysts, of which two programming languages- R and Python are widely used among researchers. R and Python are complementary, as many methods are implemented specifically in R or Python. However, the different platforms immediately caused the data sharing and transformation problem, especially for Scanpy, Seurat, and SingleCellExperiemnt. Currently, there is no efficient and user-friendly software to perform data transformation of single-cell omics between platforms, which makes users spend unbearable time on data Input and Output (IO), significantly reducing the efficiency of data analysis.

Results

We developed scDIOR for single-cell data transformation between platforms of R and Python based on Hierarchical Data Format Version 5 (HDF5). We have created a data IO ecosystem between three R packages (Seurat, SingleCellExperiment, Monocle) and a Python package (Scanpy). Importantly, scDIOR accommodates a variety of data types across programming languages and platforms in an ultrafast way, including single-cell RNA-seq and spatial resolved transcriptomics data, using only a few codes in IDE or command line interface. For large scale datasets, users can partially load the needed information, e.g., cell annotation without the gene expression matrices. scDIOR connects the analytical tasks of different platforms, which makes it easy to compare the performance of algorithms between them.

Conclusions

scDIOR contains two modules, dior in R and diopy in Python. scDIOR is a versatile and user-friendly tool that implements single-cell data transformation between R and Python rapidly and stably. The software is freely accessible at https://github.com/JiekaiLab/scDIOR.
Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing
Authors: Sharma Atul , Jain Pranjal , Mahgoub Ashraf , Zhou Zihan , Mahadik Kanak , Chaterji Somali
Published: January 2022

Background

Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g.,k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Alignment-rate or Gain) of a given tool usually relies on a reference genome, but quality reference genomes are not always available. We introduceLernafor the automated configuration ofk-mer-based EC tools.Lernafirst creates a language model (LM) of the uncorrected genomic reads, and then, based on this LM, calculates a metric called theperplexity metricto evaluate the corrected reads for different parameter choices. Next, it finds the one that produces the highest alignment ratewithoutusing a reference genome. The fundamental intuition of our approach is that the perplexity metric is inversely correlated with the quality of the assembly after error correction. Therefore,Lernaleverages the perplexity metric for automated tuning ofk-mer sizes without needing a reference genome.

Results

First, we show that the bestk-mer value can vary for different datasets, even for the same EC tool. This motivates our design that automatesk-mer size selection without using a reference genome. Second, we show the gains of our LM using its component attention-based transformers. We show the model’s estimation of the perplexity metric before and after error correction. The lower the perplexity after correction, the better thek-mer size. We also show that the alignment rate and assembly quality computed for the corrected reads are stronglynegativelycorrelated with the perplexity, enabling the automated selection ofk-mer values for better error correction, and hence, improved assembly quality. We validate our approach on both short and long reads. Additionally, we show that our attention-based models have significant runtime improvement for the entire pipeline—18$$\times$$×faster than previous works, due to parallelizing the attention mechanism and the use of JIT compilation for GPU inferencing.

Conclusion

Lerna improvesde novogenome assembly by optimizing EC tools. Our code is made available in a public repository at:https://github.com/icanforce/lerna-genomics.
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms
Authors: Dong Xuemin , Dong Shanshan , Pan Shengkai , Zhan Xiangjiang
Published: January 2022

Background

Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results.

Results

We present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub:https://github.com/dongxuemin666/RNA-combine.

Conclusion

Our results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.
Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711
Authors: Shrestha Prasansah , Kim Min-Su , Elbasani Ermal , Kim Jeong-Dong , Oh Tae-Jin
Published: January 2022

Background

Metabolism including anabolism and catabolism is a prerequisite phenomenon for all living organisms. Anabolism refers to the synthesis of the entire compound needed by a species. Catabolism refers to the breakdown of molecules to obtain energy. Many metabolic pathways are undisclosed and many organism-specific enzymes involved in metabolism are misplaced. When predicting a specific metabolic pathway of a microorganism, the first and foremost steps is to explore available online databases. Among many online databases, KEGG and MetaCyc pathway databases were used to deduce trehalose metabolic network for bacteria Variovorax sp. PAMC28711. Trehalose, a disaccharide, is used by the microorganism as an alternative carbon source.

Results

While using KEGG and MetaCyc databases, we found that the KEGG pathway database had one missing enzyme (maltooligosyl-trehalose synthase, EC 5.4.99.15). The MetaCyc pathway database also had some enzymes. However, when we used RAST to annotate the entire genome of Variovorax sp. PAMC28711, we found that all enzymes that were missing in KEGG and MetaCyc databases were involved in the trehalose metabolic pathway.

Conclusions

Findings of this study shed light on bioinformatics tools and raise awareness among researchers about the importance of conducting detailed investigation before proceeding with any further work. While such comparison for databases such as KEGG and MetaCyc has been done before, it has never been done with a specific microbial pathway. Such studies are useful for future improvement of bioinformatics tools to reduce limitations.
Evaluation of CRISPR gene-editing tools in zebrafish
Authors: Uribe-Salazar José M. , Kaya Gulhan , Sekar Aadithya , Weyenberg KaeChandra , Ingamells Cole , Dennis Megan Y.
Published: January 2022

Background

Zebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create ‘knockout’ models. In particular, the use of G0mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies.

Methods

To systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G0-based CRISPR screens by assaying control embryos for spurious mutations and altered gene expression.

Results

We compared our experimental in vivo editing efficiencies in mosaic G0embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (< 1%). To characterize if commonly used ‘mock’ CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G0mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the ‘mock’ injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation.

Conclusion

Overall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.
Admission pattern, treatment outcomes, and associated factors for children admitted to pediatric intensive care unit of Tikur Anbessa specialized hospital, 2021: a retrospective cross-sectional study
Authors: Seifu Ashenafi , Eshetu Oliyad , Tafesse Dawit , Hailu Seyoum
Published: January 2022

Background

Assessement of the pattern of admission and treatment outcomes of critically ill pediatrics admitted to pediatric intensive care units (PICU) in developing countries is crucial. In these countries with resource limitations, it may help to identify priorities for resource mobilization that may improve patient service quality. The PICU mortality rate varies globally, depending on the facilities of the intensive care unit, availability of experties, and admission patterns. This study assessed the admission pattern, treatment outcomes, and associated factors for children admitted to the PICU.

Methods

A retrospective cross-sectional study was implemented on 406 randomly selected pediatrics patients admitted to the PICU of Tikur Anbessa Specialized Hospital from 1-Oct-2018 to 30-Sept-2020. The data were collected with a pretested questionnaire. A normality curve was used to check for data the distribution. Both bivariable and multivariable analyses were used to see association of variables. A variable with a p-value of < 0.2 in the bivariable model was a candidate for multivariate analysis. The strength of association was shown by an adjusted odds ratio (AOR) with a 95% Confidence interval (CI), and a p-value of < 0.05 was considered statistically significant. Frequency, percentage,and tables were used to present the data.

Results

A total of 361 (89% response rate) patient charts were studied, 197 (54.6%) were male, and 164(45.4%) were female. The most common pattern for admission was a septic shock (27.14%), whereas the least common pattern was Asthma 9(2.50%). The mortality rate at the pediatric intensive care unit was 43.8%. Moreover, mechanical ventilation need (AOR = 11.2, 95%CI (4.3–28.9), P < 0.001), need for inotropic agents (AOR = 10.7, 95%CI (4.1–27.8), P < 0.001), comorbidity (AOR =8.4, 95%CI (3.5–20.5), P < 0.001), length of PICU stay from 2 to 7 days (AOR = 7.3, 95%CI (1.7–30.6), P = 0.007) and severe GCS (< 8) (AOR = 10.5, 95%CI (3.8–29.1), P < 0.001) were independent clinical outcome predictors (mortality).

Conclusion

The mortality rate at the PICU was 43.8%. Septic shock, and meningitis were the common cause of death and the largest death has happened in less than 7 days of admission.
Study on clinical characteristics and related factors of schizophrenic patients with intestinal obstruction
Authors: Li Mingchao , Guo Ping , Zeng Jihua , Li Chi , Ji Qiuming , Zhao Yunqing , Chen Haiying , Wang Ying , Hu Yunjiao , Liu Lianzhong
Published: January 2022

Background

There are still few studies on the clinical characteristics and related risk factors of schizophrenia patients with intestinal obstruction. Our aim is to explore the clinical characteristics and related risk factors of schizophrenia patients with intestinal obstruction.

Methods

This study focused on schizophrenia patients with intestinal obstruction who were hospitalized in the psychiatric department of a hospital in Wuhan from January 2007 to December 2020 as the main research object. We intend to retrospectively analyze the clinical characteristics and related risk factors of schizophrenia patients with intestinal obstruction.

Results

In the 1937 persons with schizophrenia included in this study, 97 patients were complicated with intestinal obstruction, and the incidence was 5.01%.The results of the study showed that patients with age ≥ 60 years old, visiting time ≥ 24 h, hospital stay ≥ 90 days, history of abdominal surgery, course of disease ≥ 5 years, male, and patients with cardiovascular and cerebrovascular diseases are prone to intestinal obstruction; Logistic multiple regression analysis showed that the related risk factors of schizophrenia patients with intestinal obstruction mainly included the patient's age, visiting time, length of hospital stay, history of abdominal surgery, course of disease and gender.

Conclusion

The older the age, the longer the hospital stay, the longer the course of the disease, the history of previous surgery, and the male schizophrenia who do not see a doctor within 24 h of the onset, the risk of intestinal obstruction is higher, and it is easy to be misdiagnosed and even life-threatening.
The dynamics of frailty development and progression in older adults in primary care in England (2006–2017): a retrospective cohort profile
Authors: Fogg Carole , Fraser Simon D. S. , Roderick Paul , de Lusignan Simon , Clegg Andrew , Brailsford Sally , Barkham Abigail , Patel Harnish P. , Windle Vivienne , Harris Scott , Zhu Shihua , England Tracey , Evenden Dave , Lambert Francesca , Walsh Bronagh ,   The Frailty Dynamics study team
Published: January 2022

Background

Frailty is a common condition in older adults and has a major impact on patient outcomes and service use. Information on the prevalence in middle-aged adults and the patterns of progression of frailty at an individual and population level is scarce. To address this, a cohort was defined from a large primary care database in England to describe the epidemiology of frailty and understand the dynamics of frailty within individuals and across the population. This article describes the structure of the dataset, cohort characteristics and planned analyses.

Methods

Retrospective cohort study using electronic health records. Participants were aged ≥50 years registered in practices contributing to the Oxford Royal College of General Practitioners Research and Surveillance Centre between 2006 to 2017. Data include GP practice details, patient sociodemographic and clinical characteristics, twice-yearly electronic Frailty Index (eFI), deaths, medication use and primary and secondary care health service use. Participants in each cohort year by age group, GP and patient characteristics at cohort entry are described.

Results

The cohort includes 2,177,656 patients, contributing 15,552,946 person-years, registered at 419 primary care practices in England. The mean age was 61 years, 52.1% of the cohort was female, and 77.6% lived in urban environments. Frailty increased with age, affecting 10% of adults aged 50–64 and 43.7% of adults aged ≥65. The prevalence of long-term conditions and specific frailty deficits increased with age, as did the eFI and the severity of frailty categories.

Conclusion

A comprehensive understanding of frailty dynamics will inform predictions of current and future care needs to facilitate timely planning of appropriate interventions, service configurations and workforce requirements. Analysis of this large, nationally representative cohort including participants aged ≥50 will capture earlier transitions to frailty and enable a detailed understanding of progression and impact. These results will inform novel simulation models which predict future health and service needs of older people living with frailty.

Study registration

Registered on www.clinicaltrials.gov October 25th 2019, NCT04139278.
Adherence and barriers to the vitamin D and calcium supplement recommendation at Danish nursing homes: a cross-sectional study
Authors: Mortensen Charlotte , Tetens Inge , Kristensen Michael , Snitkjaer Pia , Beck Anne Marie
Published: January 2022

Background

Nursing home residents are in high risk of vitamin D deficiency, which negatively affects bone health. Vitamin D and calcium supplements haves shown to increase bone density and reduce fracture risk. Therefore, The Danish Health Authority recommends all nursing home residents a daily supplement of 20 μg vitamin D and 800–1000 mg calcium. However, adherence to the recommendation and knowledge of it is unknown. The aims of this study were to investigate adherence, knowledge, and potential barriers to this recommendation in Denmark.

Methods

A cross-sectional electronic survey was conducted in May–June 2020 among 50 randomly selected nursing homes widely distributed in Denmark. Questions included degree of adherence to the recommendation at each nursing home as well as respondent’s knowledge and attitudes towards it, and experienced barriers in relation to adherence.

Results

Respondents from 41 nursing homes answered the questionnaire, and these were mainly nurses (63%) or nursing home leaders (20%). Low adherence (≤ 40% of residents receiving both supplements) was reported at 35% of nursing homes, and only 8% of the nursing homes had a high adherence (> 80% of residents receiving both supplements). Most respondents (88%) had knowledge of the recommendation and 62% rated importance of increased implementation as high. Common explanations of low implementation were a lack of prescription by the general practitioner in the central electronic database (60%), resident-refusal to eat tablets (43%), chewing-swallowing difficulties (40%), and a high number of tablets given to the residents daily (34%).

Conclusions

The recommendation of daily vitamin D and calcium supplements to Danish nursing home residents is poorly implemented even though knowledge of the recommendation is relatively high. Barriers relate to an ambiguity of responsibility between the general practitioners and the nursing home staff, as well as the high number of tablets to be consumed in total by the residents. These barriers must be targeted to improve adherence in this vulnerable group of institutionalized older adults.
Clinical sign and biomarker-based algorithm to identify bacterial pneumonia among outpatients with lower respiratory tract infection in Tanzania
Authors: Hogendoorn Sarika K. L. , Lhopitallier Loïc , Richard-Greenblatt Melissa , Tenisch Estelle , Mbarack Zainab , Samaka Josephine , Mlaganile Tarsis , Mamin Aline , Genton Blaise , Kaiser Laurent , D’Acremont Valérie , Kain Kevin C. , Boillat-Blanco Noémie
Published: January 2022

Background

Inappropriate antibiotics use in lower respiratory tract infections (LRTI) is a major contributor to resistance. We aimed to design an algorithm based on clinical signs and host biomarkers to identify bacterial community-acquired pneumonia (CAP) among patients with LRTI.

Methods

Participants with LRTI were selected in a prospective cohort of febrile (≥ 38 °C) adults presenting to outpatient clinics in Dar es Salaam. Participants underwent chest X-ray, multiplex PCR for respiratory pathogens, and measurements of 13 biomarkers. We evaluated the predictive accuracy of clinical signs and biomarkers using logistic regression and classification and regression tree analysis.

Results

Of 110 patients with LRTI, 17 had bacterial CAP. Procalcitonin (PCT), interleukin-6 (IL-6) and soluble triggering receptor expressed by myeloid cells-1 (sTREM-1) showed an excellent predictive accuracy to identify bacterial CAP (AUROC 0.88, 95%CI 0.78–0.98; 0.84, 0.72–0.99; 0.83, 0.74–0.92, respectively). Combining respiratory rate with PCT or IL-6 significantly improved the model compared to respiratory rate alone (p = 0.006, p = 0.033, respectively). An algorithm with respiratory rate (≥ 32/min) and PCT (≥ 0.25 μg/L) had 94% sensitivity and 82% specificity.

Conclusions

PCT, IL-6 and sTREM-1 had an excellent predictive accuracy in differentiating bacterial CAP from other LRTIs. An algorithm combining respiratory rate and PCT displayed even better performance in this sub-Sahara African setting.
Sentinel surveillance for influenza A viruses in Lahore District Pakistan in flu season 2015–2016
Authors: Hasan Saima , Webby Richard J. , Iqbal Muhammad , Rashid Hamad Bin , Ahmad Mansur-ud-Din , Nazir Jawad , DeBeauchamp Jennifer , Sadiq Shakera , Chaudhry Mamoona
Published: January 2022

Background

Influenza A virus (IAV) remains an important global public health threat with limited epidemiological information available from low-and-middle-income countries. The major objective of this study was to describe the proportions, temporal and spatial distribution, and demographic and clinical characteristics of IAV positive patients with influenza like illness (ILI) and severe acute respiratory illness (SARI) in Lahore, Pakistan.

Methods

Prospective surveillance was established in a sentinel hospital from October 2015 to May 2016. All eligible outpatients and inpatients with ILI or SARI were enrolled in the study. Nasal and/or throat swabs were collected along with clinico-epidemiological data. Samples were tested by real-time RT-PCR (rRT-PCR) to identify IAV and subtype. The descriptive analysis of data was done in R software.

Results

Out of 311 enrolled patients, 284 (91.3%) were ILI and 27 (8.7%) were SARI cases. A distinct peak of ILI and SARI activity was observed in February. Fifty individuals (16%) were positive for IAV with peak positivity observed in December. Of 50 IAV, 15 were seasonal H3N2, 14 were H1N1pdm09 and 21 were unable to be typed. The majority of IAV positive cases (98%) presented with current or history of fever, 88% reported cough and 82% reported sore throat. The most common comorbidities in IAV positive cases were hepatitis C (4%), obesity (4%) and tuberculosis (6%). The highest incidence of patients reporting to the hospital was seen three days post symptoms onset (66/311) with 14 of these (14/66) positive for IAV.

Conclusion

Distinct trends of ILI, SARI and IAV positive cases were observed which can be used to inform public health interventions (vaccinations, hand and respiratory hygiene) at appropriate times among high-risk groups. We suggest sampling from both ILI and SARI patients in routine surveillance as recommended by WHO.
Burden of illness in carbapenem-resistant Acinetobacter baumannii infections in US hospitals between 2014 and 2019
Authors: Pogue Jason M. , Zhou Yun , Kanakamedala Hemanth , Cai Bin
Published: January 2022

Background

Carbapenem-resistant (CR) Acinetobacter baumannii is a concerning pathogen in the USA and worldwide.

Methods

To assess the comparative burden of CR vs carbapenem-susceptible (CS) A. baumannii, this retrospective cohort study analyzed data from adult patients in 250 US hospitals from the Premier HealthCare Database (2014–2019). The outcomes analyzed included hospital length of stay (LOS), intensive care unit (ICU) utilization, discharge status, in-hospital mortality, readmission rates and hospital charges. Logistic regression was used for univariate and multivariable assessment of the independent relationship between relevant covariates, with a focus on CR status, and in-hospital mortality.

Results

2047 Patients with CR and 3476 patients with CS A. baumannii infections were included. CR A. baumannii was more commonly isolated in respiratory tract infections (CR 40.7% and CS 27.0%, P < 0.01), whereas CS A. baumannii was more frequently associated with bloodstream infections (CS 16.7% and CR 8.6%, P < 0.01). Patients with CR A. baumannii infections had higher in-hospital (CR 16.4% vs CS 10.0%; P < 0.01) and 30-day (CR 32.2% vs CS 21.6%; P < 0.01) mortality compared to those with CS infections. After adjusting for age, sex, admission source, infection site, comorbidities, and treatment with in vitro active antibiotics within 72 h, carbapenem resistance was independently associated with increased mortality (adjusted odds ratio 1.42 [95% confidence interval 1.15; 1.75], P < 0.01). CR infections were also associated with increases in hospital length of stay (CR 11 days vs CS 9 days; P < 0.01), rate of intensive care unit utilization (CR 62.3% vs CS 45.1%; P < 0.01), rate of readmission with A. baumannii infections (CR 17.8% vs CS 4.0%; P < 0.01) and hospital charges.

Conclusions

These data suggest that the burden of illness is significantly greater for patients with CR A. baumannii infections and are at higher risk of mortality compared with CS infections in US hospitals.
Chlorhexidine – a commonly used but often neglected culprit of dialysis associated anaphylactic reactions (case report)
Authors: TAN Jia Neng , DA Yi , HAROON Sabrina , LAU Titus
Published: January 2022

Background

Hemodialysis-associated anaphylactic reactions are rare and frequently complex in nature due to the sheer number of possible culprit agents. Unfortunately, dialysis is often unavoidable or strictly essential for life-saving solute clearance or fluid removal in patients with end stage kidney failure and those with severe acute kidney injury. It is of utmost importance that the culprit agent is identified and avoided to allow continuation of dialysis treatment as needed.

Case presentation

We present 2 cases of hemodialysis-associated anaphylactic reactions. These patients developed anaphylactic reactions peri-dialysis and were initially suspected to have dialyser reactions. They were investigated in a controlled healthcare setting and possible culprit agents were systemically identified and eliminated. They both underwent allergy testing and were diagnosed with chlorhexidine allergy. Of note, Case 1 was an incident dialysis patient at the time of presentation and Case 2 was a prevalent dialysis patient. This suggests that the time from initial sensitization to reaction may not always be helpful in determining if a particular agent is the culprit of an anaphylactic reaction.

In both cases, the patients were dialysed through a tunnelled dialysis catheter. We postulate that the presence of an exit site, which represents a compromise to the integrity of the skin’s epidermal barrier, may have a significant role in the development of these reactions.

As chlorhexidine is a widely used disinfectant in hemodialysis, it is imperative that we consider it as a possible culprit agent when these reactions arise. To our knowledge, there are no other reported cases of anaphylaxis secondary to chlorhexidine use in dialysis patients other than a previous report in 2017.

Our report also highlights the possibility of these reactions occurring more frequently in patients with damaged epidermal barriers and in patients exposed to higher environmental concentrations of chlorhexidine. These are novel concepts that can be explored with further research.

Conclusion

Chlorhexidine associated anaphylactic reactions can occur in the peri-dialysis setting and a high index of suspicion is paramount to diagnosis.
Spontaneous Intracerebral Hemorrhage (ICH) associated with pregnancy and SARS-CoV-2 infection: a case report
Authors: Dini Parisa , Aminimoghaddam Soheila , Mirzaasgari Zahra , Rahimian Neda , Khotbehsara Samaneh Tanhapour , Abolmaali Meysam
Published: January 2022

Background

Coronavirus Disease 2019 (COVID-19) is predominately known as a respiratory disease associated with pneumonia, acute respiratory distress syndrome and multiorgan failure. However, extra-pulmonary complications of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are increasingly being recognized. In this regard, some studies implied the hemostatic and vascular involvements in patients with SARS-CoV-2 infection.

Case presentation

We describe a case of spontaneous Intracerebral Hemorrhage (ICH) in a pregnant patient with COVID-19 and history of cesarean section a week before the occurrence of ICH. The patient underwent emergent craniotomy with acceptable outcome. Hemorrhagic events, including ICH, may happen during COVID-19 infection with several possible mechanisms.

Conclusion

COVID-19 patients, especially high-risk groups, are at a risk of intracranial hemorrhage. Therefore, close follow-up must be maintained and hemorrhagic events must be kept in mind in these cases.
Roles of extended human papillomavirus genotyping and multiple infections in early detection of cervical precancer and cancer and HPV vaccination
Authors: Song Fangbin , Yan Peisha , Huang Xia , Wang Chun , Du Hui , Qu Xinfeng , Wu Ruifang
Published: January 2022

Background

The aim of the study was to investigate the risk of human papillomavirus (HPV) genotyping particularly vaccine genotypes and multiple infections for cervical precancer and cancer, which might contribute to developing genotype-specific screening strategy and assessing potential effects of HPV vaccine.

Methods

The HPV genotypes were identified using the Seq HPV assay on self-collected samples. Hierarchical ranking of each genotype was performed according to positive predictive value (PPV) for cervical intraepithelial neoplasia 2/3 or worse (CIN2+/CIN3+). Multivariate logistic regression model was used to estimate the odds ratios (ORs) with 95% confidence interval (CI) of CIN2+ according to multiplicity of types and vaccine types.

Results

A total of 2811 HPV-positive women were analyzed. The five dominant HPV genotypes in high-grade lesions were 16/58/52/33/18. The overall ranking orders were HPV16/33/35/58/31/68/18/ 56/52/66/51/59/45/39 for CIN2+ and HPV16/33/31/58/45/66/52/18/35/56/51/68/59/39 for CIN3+. The risks of single infection versus co-infections with other types lower in the hierarchy having CIN2+ were not statistically significant for HPV16 (multiple infection vs. single infection: OR = 0.8, 95%CI = 0.6-1.1, P = 0.144) or other genotypes (P > 0.0036) after conservative Bonferroni correction. Whether HPV16 was present or not, the risks of single infection versus multiple infection with any number (2, ≥2, or ≥ 3) of types for CIN2+ were not significantly different. In addition, HPV31/33/45/52/58 covered by nonavalent vaccine added 27.5% of CIN2, 23.0% of CIN3, and 12.5% of cancer to the HPV16/18 genotyping. These genotype-groups were at significantly higher risks than genotypes not covered by nonavalent vaccine. Moreover, genotypes covered by nonavalent vaccine contributed to 85.2% of CIN2 lesions, 97.9% of CIN3 and 93.8% of cancers.

Conclusions

Partial extended genotyping such as HPV33/31/58 but not multiplicity of HPV infections could serve as a promising triage for HPV-positive self-samples. Moreover, incidence rates of cervical cancer and precancer were substantial attributable to HPV genotypes covered by current nonavalent vaccination.
Validation of the efficacy of the NUTRISCORE for the nutritional screening of cancer patients in China
Authors: Kang Junren , Li Hailong , Shi Xiaodong , Ma Enling , Chen Wei
Published: January 2022

Background

Malnutrition is common in cancer patients. The NUTRISCORE is a newly developed cancer-specific nutritional screening tool and was validated by comparison with the Patient-Generated Subjective Global Assessment (PG-SGA) and Malnutrition Screening Tool (MST) in Spain. We aimed to evaluate the performance of the NUTRISCORE, MST, and PG-SGA in estimating the risk of malnutrition in Chinese cancer patients.

Methods

Data from an open parallel and multicenter cross-sectional study in 29 clinical teaching hospitals in 14 Chinese cities were used. Cancer patients were assessed for malnutrition using the PG-SGA, NUTRISCORE, and MST. The sensitivity, specificity, and areas under the receiver operating characteristic curve were estimated for the NUTRISCORE and MST using the PG-SGA as a reference.

Results

A total of 1000 cancer patients were included. The mean age was 55.9 (19 to 92 years), and 47.5% were male. Of these patients, 450 (45.0%) had PG-SGA B and C, 29 (2.9%) had a NUTRISCORE ≥5, and 367 (36.7%) had an MST ≥ 2. Using the PG-SGA as a reference, the sensitivity, specificity, and area under the curve values of the NUTRISCORE were found to be 6.2, 99.8%, and 0.53, respectively. The sensitivity, specificity, and area under the curve values of the MST were 50.9, 74.9%, and 0.63, respectively. The kappa index between the NUTRISCORE and PG-SGA was 0.066, and that between the MST and PG-SGA was 0.262 (P < 0.05).

Conclusions

The NUTRISCORE had an extremely low sensitivity in cancer patients in China compared with the MST when the PG-SGA was used as a reference.
Cue-based feeding and short-term health outcomes of premature infants in newborn intensive care units: a non-randomized trial
Authors: Samane Sefatbaqa , Yadollah Zahed Pasha , Marzieh Hasanpour , Karimollah Hajian - Tilaki , Reza Zarkesh Mohammad , Afsaneh Arzani , Als Heidelise
Published: January 2022

Background

Feedings based on behavioral cues is a method relying on infants’ behavioral expressions of readiness to feed. The objective of this interventional study was to determine the effect of cue-based feeding on the short-term health outcomes of preterm infants.

Methods

This quasi-experimental study utilized a historical or phase lag design. It involved 60 preterm infants admitted to an Iranian referral hospital’s Level III-Newborn Intensive Care Unit (NICU) from April 2017 until January 2018. The experimental group (n = 30) received a three-step intervention of offering behavioral-cue-based oral (BCBO) feedings: Step 1 – One BCBO feeding every 12 hours for 3 days; Step 2 - Two BCBO feedings every 12 h for 3 days; and Step 3 – All feedings as BCBO feedings for 3 days. The control group received standard care feedings. Group difference data were analyzed with SPSS version 16 using descriptive and inferential statistics.

Results

The infants’ mean weight at time of discharge for the intervention and control groups were 1492.79 ± 21.65 g and 1395.71 ± 17.61 g (P = .003) respectively. The mean durations of achieving full oral feedings in the intervention and control groups were 17 ± 6 and 20 ± 11 days, respectively (P = .19). The mean frequencies of hypoxia were 1 ± 1.54 and 5 ± 9.31 respectively (P = .03) and of gavage feedings 725 ± 584 and 1846 ± 2097 respectively (P = .009). No apnea events were reported for the intervention group; the frequency of apnea in the control group was 1 ± 2.11 (P = .16).

Conclusion

The findings indicate that cue-based feeding is beneficial for preterm infants. Therefore, it is recommended that nurses employ cue-based feeding in the NICU.

Trial registration

IRCTID: IRCT20170828035962N2. Registered 27 may 2018 – Retrospectively registered, https://en.irct.ir/trial/27024.
Transnasal endoscopic resection of nasal chondromesenchymal hamartoma in infancy: an analysis of 5 cases
Authors: Zhu Zheng Jie , Huang Qi , Cheng Lan , Yang Jun
Published: January 2022

Background

Nasal chondromesenchymal hamartomas (NCMHs) are extremely rare benign tumors that most commonly affect children in the first year of life. The purpose of this study was to investigate and summarize the characteristics of NCMH cases and the efficacy of transnasal endoscopic resection of NCMHs.

Methods

This is a retrospective study including 5 cases of infant diagnosed as NCMH between April 2016 and April 2020. Diagnostic techniques include nasoendoscopy, computerized tomography (CT) scan, magnetic resonance imaging (MRI) with contrast and microscopic and immunohistologic studies. Data collected included patient demographics, patient symptoms, radiographic findings, characteristics of tumor growth, follow-up time, recurrence, and postoperative complications.

Results

In 5 cases, 3 were males and 2 were females who aged 1, 2, 3, 6 months and 1 year, respectively. The size of the mass measured 1.6 cm*1.9 cm*1.8 cm at its smallest and largest was 4.0 cm*3.5 cm*3.0 cm. All five patients underwent tumor resection via transnasal endoscopic approach. Four tumors were completely removed, and one underwent partial resection, which was completely resected by midfacial degloving operation 13 months after the first surgery. There was no postoperative complication. The current postoperative follow-up period was 1 to 4 years, and no recurrence has been observed.

Conclusions

Complete surgical resection of NCHM is necessary to resolve the symptoms and prevent recurrence. Transnasal endoscopic approach is a safe and effective choice for pediatric NCMH patients.
The association between entrapment and depression among migrant workers in China: a social rank theory based study
Authors: Long Rusi , Chen Hui , Hu Tian , Chen Yaqi , Cao Bolin , Wang Rongxi , Hu Fan , Xu Chen , Yu Xiaoyue , Liu Yujie , Liu Shangbin , Zhang Kechun , Zou Huachun , Wang Zixin , Xue Wenjie , Cai Yong
Published: January 2022

Background

Migrant workers are a group susceptible for depression evolution due to occupational maladaptive triggers. The social rank theory illustrates the pathology process from defensive adaptation to depression, pointing out the early prevention of depression by discovering entrapment. This study aims to reveal the relationship between migrant workers’ entrapment and depressive symptoms.

Methods

A total of 1805 migrant workers in Shenzhen were recruited by stratified multi-stage sampling. Sample’s demographic, behavioral and psychosocial characteristics were described and analyzed to reveal the relationship between entrapment and depressive symptoms. The Receiver Operator Characteristic was performed to find the optimal cut-off point of Entrapment Scale for predicting depressive symptoms.

Results

In the binary logistic regression of sociodemographic variables, migrant workers who were married (univariate odds ratio (ORu) = 0.69, 95% Confidence Interval (CI) = 0.56–0.84), owned 1 or 2 children (ORu = 0.71, 95% CI = 0.58–0.86), had been working over 10 years (ORu = 0.71, 95% CI = 0.54–0.95), earned > 4999 yuan per month (ORu = 0.68, 95% CI = 0.47–0.99; multivariate odds ratio (ORm) = 0.57, 95% CI = 0.38–0.87) or with low risks of alcohol use disorders (ORu = 0.51, 95% CI = 0.34–0.75) had lower risks of depressive symptoms. After adjusted the aforementioned significant sociodemographic variables, migrant workers with severer entrapment were more likely to have depressive symptoms (adjusted odds ratio (ORa) = 1.13, 95% CI = 1.12–1.15). Besides, the study proved the reliability and validity of the Chinese version Entrapment Scale, preferring a two-dimensional structure, and 11 was the optimal cut-off value of this scale for predicting depressive symptoms among migrant workers.

Conclusions

This result indicates the potential value of entrapment according to the social rank theory on facilitating early prevention of migrant works’ depression and the application value of Entrapment Scale for effectively measuring mental status among migrant workers.
Relation of corona-specific health literacy to use of and trust in information sources during the COVID-19 pandemic
Authors: De Gani Saskia Maria , Berger Fabian Marc Pascal , Guggiari Elena , Jaks Rebecca
Published: January 2022

Background

COVID-19 has developed into a worldwide pandemic which was accompanied by an «infodemic» consisting of much false and misleading information. To cope with these new challenges, health literacy plays an essential role. The aim of this paper is to present the findings of a trend study in Switzerland on corona-specific health literacy, the use of and trust in information sources during the COVID-19 pandemic, and their relationships.

Methods

Three online surveys each with approximately 1′020 individuals living in the German-speaking part of Switzerland (age ≥ 18 years) were conducted at different timepoints during the COVID-19 pandemic, namely spring, fall and winter 2020. For the assessment of corona-specific health literacy, a specifically developed instrument (HLS-COVID-Q22) was used. Descriptive, bivariate, and multivariate data analyses have been conducted.

Results

In general, a majority of the Swiss-German population reported sufficient corona-specific health literacy levels which increased during the pandemic: 54.6% participants in spring, 62.4% in fall and 63.3% in winter 2020 had sufficient corona-specific health literacy. Greatest difficulties concerned the appraisal of health information on the coronavirus. The most used information sources were television (used by 73.3% in spring, 70% in fall and 72.3% in winter) and the internet (used by 64.1, 64.8 and 66.5%). Although health professionals, health authorities and the info-hotline were rarely mentioned as sources for information on the coronavirus, respondents had greatest trust in them. On the other hand, social media were considered as the least trustworthy information sources. Respondents generally reporting more trust in the various information sources, tended to have higher corona-specific health literacy levels.

Conclusions

Sufficient health literacy is an essential prerequisite for finding, understanding, appraising, and applying health recommendations, particularly in a situation where there is a rapid spread of a huge amount of information. The population should be supported in their capability in appraising the received information and in assessing the trustworthiness of different information sources.
Predicting human papillomavirus vaccine uptake in men who have sex with men the influence of vaccine price and receiving an HPV diagnosis
Authors: Yao Po-Yi , Lin Chung-Ying , Ko Nai-Ying , Zou Huachun , Lee Chia-Wen , Strong Carol
Published: January 2022

Background

To understand how human papillomavirus (HPV) screening results, HPV-related knowledge and attitudes are related to vaccination intention in three cost ranges and the actual vaccination behavior in a community sample of men who have sex with men (MSM).

Methods

MSM aged 20 years of age or older were recruited between October 2015 and May 2016 from community health centers that provide HIV testing and consultation services in Southern Taiwan and on social media. MSM were seen at baseline and again at 6 months after baseline in a cohort study. The baseline study included 253 individuals; 182 of them returned for the 6th-month follow-up. At each visit, MSM were asked to receive HPV screening and filled out a questionnaire. Structural equation modeling was used to test whether attitudinal factors and HPV screening results from the baseline affect their self-reported actual vaccine uptake at the in 6th-month follow-up.

Results

Our research included 171 participants from the cohort because they had full information of the study variables (mean ± SD age = 29.21 ± 6.18). Our model showed good model fit using indices such as the comparative fit index (value = 0.998) and root mean square error of approximation (value = 0.013). HPV knowledge can predict those who have intention to take up HPV vaccine no matter what the price (p = .02), and then predict vaccine uptake at the follow-up (p < .001). A positive HPV screening result can predict vaccine uptake at the follow-up (p = .004).

Conclusion

Our findings highlight the impact of vaccine price and HPV screening results on the intention and uptake of HPV vaccine. It is important to raise awareness of HPV in male populations. Clinicians and health educators should establish a safe and private environment for male patients for inquiring about HPV vaccine and HPV-related cancers.