bluuebunny/crossref_metadata_2025 huggingface dataset:
2-kupl: mapping-free variant detection from DNA-seq data of matched samples
Authors: Wang Yunfeng , Xue Haoliang , Pourcel Christine , Du Yang , Gautheret Daniel
Published: June 2021

Background

The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats.

Results

We introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves higher accuracy than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome sequencing data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease.

Conclusions

We developed a mapping-free protocol for variant calling between matched DNA-seq samples. Our protocol is suitable for variant detection in unmappable genome regions or in the absence of a reference genome.
A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients
Authors: Dessie Eskezeia Y. , Tsai Jeffrey J. P. , Chang Jan-Gowth , Ng Ka-Lok
Published: June 2021

Background

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival rate. Despite microRNAs (miRNAs) are used as potential biomarkers in many cancers, miRNA biomarkers for predicting the tumor stage of ccRCC are still limitedly identified. Therefore, we proposed a new integrated machine learning (ML) strategy to identify a novel miRNA signature related to tumor stage and prognosis of ccRCC patients using miRNA expression profiles. A multivariate Cox regression model with three hybrid penalties including Least absolute shrinkage and selection operator (Lasso), Adaptive lasso and Elastic net algorithms was used to screen relevant prognostic related miRNAs. The best subset regression (BSR) model was used to identify optimal prognostic model. Five ML algorithms were used to develop stage classification models. The biological significance of the miRNA signature was analyzed by utilizing DIANA-mirPath.

Results

A four-miRNA signature associated with survival was identified and the expression of this signature was strongly correlated with high risk patients. The high risk patients had unfavorable overall survival compared with the low risk group (HR = 4.523, P-value = 2.86e−08). Univariate and multivariate analyses confirmed independent and translational value of this predictive model. A combined ML algorithm identified six miRNA signatures for cancer staging prediction. After using the data balancing algorithm SMOTE, the Support Vector Machine (SVM) algorithm achieved the best classification performance (accuracy = 0.923, sensitivity = 0.927, specificity = 0.919, MCC = 0.843) when compared with other classifiers. Furthermore, enrichment analysis indicated that the identified miRNA signature involved in cancer-associated pathways.

Conclusions

A novel miRNA classification model using the identified prognostic and tumor stage associated miRNA signature will be useful for risk and stage stratification for clinical practice, and the identified miRNA signature can provide promising insight to understand the progression mechanism of ccRCC.
Exploring the functional composition of the human microbiome using a hand-curated microbial trait database
Authors: Weissman J L , Dogra Sonia , Javadi Keyan , Bolten Samantha , Flint Rachel , Davati Cyrus , Beattie Jess , Dixit Keshav , Peesay Tejasvi , Awan Shehar , Thielen Peter , Breitwieser Florian , Johnson Philip L. F. , Karig David , Fagan William F. , Bewick Sharon
Published: June 2021

Background

Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates.

Results

We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth.

Conclusions

Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.
WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates
Authors: Heikema Astrid P. , Jansen Rick , Hiltemann Saskia D. , Hays John P. , Stubbs Andrew P.
Published: June 2021

Background

Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing. Bioinformatics pipelines have been developed for ONT-generated sequencing but require computational skills that frequently are beyond the abilities of scientific researchers. To overcome this challenge, the authors developed ‘WeFaceNano’, a user-friendly Web interFace for rapid assembly and analysis of plasmid DNA sequences generated using the ONT platform. WeFaceNano includes: a read statistics report; two assemblers (Miniasm and Flye); BLAST searching; the detection of antibiotic resistance- and replicon genes and several plasmid visualizations. A user-friendly interface displays the main features of WeFaceNano and gives access to the analysis tools.

Results

Publicly available ONT sequence data of 21 plasmids were used to validate WeFaceNano, with plasmid assemblages and anti-microbial resistance gene detection being concordant with the published results. Interestingly, the “Flye” assembler with “meta” settings generated the most complete plasmids.

Conclusions

WeFaceNano is a user-friendly open-source software pipeline suitable for accurate plasmid assembly and the detection of anti-microbial resistance genes in (clinical) samples where multiple plasmids can be present.
Infection related catheter complications in patients undergoing prone positioning for acute respiratory distress syndrome: an exposed/unexposed study
Authors: Louis Guillaume , Belveyre Thibaut , Jacquot Audrey , Hochard Hélène , Aissa Nejla , Kimmoun Antoine , Goetz Christophe , Levy Bruno , Novy Emmanuel
Published: June 2021

Background

Prone positioning (PP) is a standard of care for patients with moderate–severe acute respiratory distress syndrome (ARDS). While adverse events associated with PP are well-documented in the literature, research examining the effect of PP on the risk of infectious complications of intravascular catheters is lacking.

Method

All consecutive ARDS patients treated with PP were recruited retrospectively over a two-year period and formed the exposed group. Intensive care unit (ICU) patients during the same period without ARDS for whom PP was not conducted but who had an equivalent disease severity were matched 1:1 to the exposed group based on age, sex, centre, length of ICU stay and SAPS II (unexposed group). Infection-related catheter complications were defined by a composite criterion, including catheter tip colonization or intravascular catheter-related infection.

Results

A total of 101 exposed patients were included in the study. Most had direct ARDS (pneumonia). The median [Q1–Q3] PP session number was 2 [1–4]. These patients were matched with 101 unexposed patients. The mortality rates of the exposed and unexposed groups were 31 and 30%, respectively. The incidence of the composite criterion was 14.2/1000 in the exposed group compared with 8.2/1000 days in the control group (p = 0.09). Multivariate analysis identified PP as a factor related to catheter colonization or infection (p = 0.04).

Conclusion

Our data suggest that PP is associated with a higher risk of CVC infectious complications.
Klebsiella spp. cause severe and fatal disease in Mozambican children: antimicrobial resistance profile and molecular characterization
Authors: Massinga Arsénia J. , Garrine Marcelino , Messa Augusto , Nobela Nélio A. , Boisen Nadia , Massora Sergio , Cossa Anélsio , Varo Rosauro , Sitoe António , Hurtado Juan Carlos , Ordi Jaume , Mucavele Hélio , Nhampossa Tacilta , Breiman Robert F. , Whitney Cynthia G. , Blau Dianna M. , Bassat Quique , Mandomando Inácio
Published: June 2021

Background

Klebsiella spp. are important pathogens associated with bacteremia among admitted children and is among the leading cause of death in children < 5 years in postmortem studies, supporting a larger role than previously considered in childhood mortality. Herein, we compared the antimicrobial susceptibility, mechanisms of resistance, and the virulence profile of Klebsiella spp. from admitted and postmortem children.

Methods

Antimicrobial susceptibility and virulence factors of Klebsiella spp. recovered from blood samples collected upon admission to the hospital (n = 88) and postmortem blood (n = 23) from children < 5 years were assessed by disk diffusion and multiplex PCR.

Results

Klebsiella isolates from postmortem blood were likely to be ceftriaxone resistant (69.6%, 16/23 vs. 48.9%, 43/88, p = 0.045) or extended-spectrum β-lactamase (ESBL) producers (60.9%, 14/23 vs. 25%, 22/88, p = 0.001) compared to those from admitted children. blaCTX-M-15 was the most frequent ESBL gene: 65.3%, 9/14 in postmortem isolates and 22.7% (5/22) from admitted children. We found higher frequency of genes associated with hypermucoviscosity phenotype and invasin in postmortem isolates than those from admitted children: rmpA (30.4%; 7/23 vs. 9.1%, 8/88, p = 0.011), wzi-K1 (34.7%; 8/23 vs. 8%; 7/88, p = 0.002) and traT (60.8%; 14/23 vs. 10.2%; 9/88, p < 0.0001), respectively. Additionally, serine protease auto-transporters of Enterobacteriaceae were detected from 1.8% (pic) to 12.6% (pet) among all isolates. Klebsiella case fatality rate was 30.7% (23/75).

Conclusion

Multidrug resistant Klebsiella spp. harboring genes associated with hypermucoviscosity phenotype has emerged in Mozambique causing invasive fatal disease in children; highlighting the urgent need for prompt diagnosis, appropriate treatment and effective preventive measures for infection control.
Neonatal hypoxic-ischemic encephalopathy diagnosis and treatment: a National Survey in China
Authors: Wang Zheng , Zhang Peng , Zhou Wenhao , Xia Shiwen , Zhou Wei , Zhou Xiaoyu , Cheng Xiuyong , Shi Yuan , Lin Zhenlang , Song Dongli , Cheng Guoqiang
Published: June 2021

Background

Neonatal hypoxic-ischemic encephalopathy (HIE) affects as many as 100,000 infants each year in China. Therapeutic hypothermia reduces HIE related mortality and long-term neurodevelopmental disabilities. National guidelines for HIE management were published a decade ago. This study aimed to investigate the current status of HIE diagnosis and treatment in China.

Method

This prospective cross-sectional national survey used a questionnaire evaluating practices related to HIE management. Descriptive statistics and Chi-square or Fisher’s exact test were used, and a p-value of < 0.05 was considered significant.

Results

The 273 hospitals that completed the survey were located in 31 of the 34 provincial districts in China. Eighty-eight percent of the hospitals were Level III hospitals, and 74% treated 10 or more HIE cases annually. Awareness rates of the national guidelines for HIE diagnosis, HIE treatment, and therapeutic hypothermia protocol were 85, 63, and 78%, respectively. Neurological manifestations and blood gas were used as HIE diagnostic criteria by 96% (263/273) and 68% (186/273) of the hospitals, respectively. Therapeutic hypothermia was used in 54% (147/273) of hospitals. The percentage of general hospitals that implemented therapeutic hypothermia (43%, 71/165) was significantly lower than that in maternity and infant hospitals (67%, 49/73) (χ2 = 11.752, p = 0.001) and children’s hospitals (77%, 27/35) (χ2 = 13.446, p < 0.001). Reasons for not providing therapeutic hypothermia included reduction of HIE cases in recent years (39%), high cost of cooling devices and treatment (31%), lack of training (26%), and safety concerns (4%). Among the hospitals that provided therapeutic hypothermia, 27% (39/147) were in full compliance with the recommended protocol. Eighty-one percent (222/273) of the hospitals treated HIE infants with putative neuroprotective agents alone or in combination with cooling. Ninety-one percent of the hospitals had long-term neurodevelopmental follow-up programs for infants with HIE.

Conclusions

There is significant heterogeneity in HIE diagnosis and treatment in China. Therapeutic hypothermia has not become a standard of care for neonatal HIE nationwide. Unproven agents are widely used for HIE treatment. Nationwide standardization of HIE management and dissemination of therapeutic hypothermia represent the opportunities to reduce mortality and improve long-term neurodevelopmental outcomes of children affected by HIE.
Prevalence of symptoms of body dysmorphic disorder (BDD) and associated features in Swiss military recruits: a self-report survey
Authors: Drüge Marie , Rafique Gabriela , Jäger Anne , Watzke Birgit
Published: June 2021

Background

Body dysmorphic disorder (BDD), defined as the obsessive idea that some aspect of one’s own body or appearance is severely flawed/deformed, is relatively common in the general population and has been shown to have strong associations with mood and anxiety disorders and substance abuse disorders. Furthermore, a previous study on symptoms of BDD among people in the military showed that muscles are an important area of preoccupation. Hence, this study aimed to 1. assess the prevalence of BDD symptoms in Swiss military recruits, 2. specify the areas of preoccupation, and 3. analyze associated features (depression and alcohol/drug abuse).

Method

A total of 126 Swiss male military recruits (age: M = 20.12, SD = 1.09, range: 18–24) were examined using self-report measurements to assess symptoms of BDD, depression, alcohol/drug abuse.

Results

The results showed that symptoms of BDD were relatively common (9.5% reached the cutoff value for probable BDD, 84% reported some symptoms), with the muscles as the most common area of preoccupation. A positive correlation (r = .38, p < .001) between depressive symptoms and symptoms of BDD was found, thus no correlation between alcohol/drug abuse and symptoms of BDD.

Conclusion

The results indicate a need to develop and implement measures for prevention (e.g. raising awareness among the military) and intervention in this specific population.
Determinants of adverse birth outcome in Sub-Saharan Africa: analysis of recent demographic and health surveys
Authors: Tamirat Koku Sisay , Sisay Malede Mequanent , Tesema Getayeneh Antehunegn , Tessema Zemenu Tadesse
Published: June 2021

Background

More than 75% of neonatal deaths occurred in the first weeks of life as a result of adverse birth outcomes. Low birth weight, preterm births are associated with a variety of acute and long-term complications. In Sub-Saharan Africa, there is insufficient evidence of adverse birth outcomes. Hence, this study aimed to determine the pooled prevalence and determinants of adverse birth outcomes in Sub-Saharan Africa.

Method

Data of this study were obtained from a cross-sectional survey of the most recent Demographic and Health Surveys (DHS) of ten Sub-African (SSA) countries. A total of 76,853 children born five years preceding the survey were included in the final analysis. A Generalized Linear Mixed Models (GLMM) were fitted and an adjusted odds ratio (AOR) with a 95% Confidence Interval (CI) was computed to declare statistically significant determinants of adverse birth outcomes.

Result

The pooled prevalence of adverse birth outcomes were 29.7% (95% CI: 29.4 to 30.03). Female child (AOR = 0.94, 95%CI: 0.91 0.97), women attended secondary level of education (AOR = 0.87, 95%CI: 0.82 0.92), middle (AOR = 0.94,95%CI: 0.90 0.98) and rich socioeconomic status (AOR = 0.94, 95%CI: 0.90 0.99), intimate-partner physical violence (beating) (AOR = 1.18, 95%CI: 1.14 1.22), big problems of long-distance travel (AOR = 1.08, 95%CI: 1.04 1.11), antenatal care follow-ups (AOR = 0.86, 95%CI: 0.83 0.86), multiparty (AOR = 0.88, 95%CI: 0.84 0.91), twin births (AOR = 2.89, 95%CI: 2.67 3.14), and lack of women involvement in healthcare decision-making process (AOR = 1.10, 95%CI: 1.06 1.13) were determinants of adverse birth outcomes.

Conclusion

This study showed that the magnitude of adverse birth outcomes was high, abnormal baby size and preterm births were the most common adverse birth outcomes. This finding suggests that encouraging antenatal care follow-ups and socio-economic conditions of women are essential. Moreover, special attention should be given to multiple pregnancies, improving healthcare accessibilities to rural areas, and women’s involvement in healthcare decision-making.
Spatio-temporal epidemiology of the tuberculosis incidence rate in Iran 2008 to 2018
Authors: Kiani Behzad , Raouf Rahmati Amene , Bergquist Robert , Hashtarkhani Soheil , Firouraghi Neda , Bagheri Nasser , Moghaddas Elham , Mohammadi Alireza
Published: June 2021

Background

Effective reduction of tuberculosis (TB) requires information on the distribution of TB incidence rate across time and location. This study aims to identify the spatio-temporal pattern of TB incidence rate in Iran between 2008 and 2018.

Methods

This cross-sectional study was conducted on aggregated TB data (50,500 patients) at the provincial level provided by the Ministry of Health in Iran between 2008 and 2018. The Anselin Local Moran’s I and Getis-Ord Gi* were performed to identify the spatial variations of the disease. Furthermore, spatial scan statistic was employed for purely temporal and spatio-temporal analyses. In all instances, the null hypothesis of no clusters was rejected at p ≤ 0.05.

Results

The overall incidence rate of TB decreased from 13.46 per 100,000 (95% CI: 13.19–13.73) in 2008 to 10.88 per 100,000 (95% CI: 10.65–11.11) in 2018. The highest incidence rate of TB was observed in southeast and northeast of Iran for the whole study period. Additionally, spatial cluster analysis discovered Khuzestan Province, in the West of the country, having significantly higher rates than neighbouring provinces in terms of both total TB and smear-positive pulmonary TB (SPPTB). Purely temporal analysis showed that high-rate and low-rate clusters were predominantly distributed in the time periods 2010–2014 and 2017–2018. Spatio-temporal results showed that the statistically significant clusters were mainly distributed from centre to the east during the study period. Some high-trend TB and SPPTB statistically significant clusters were found.

Conclusion

The results provided an overview of the latest TB spatio-temporal status In Iran and identified decreasing trends of TB in the 2008–2018 period. Despite the decreasing incidence rate, there is still need for screening, and targeting of preventive interventions, especially in high-risk areas. Knowledge of the spatio-temporal pattern of TB can be useful for policy development as the information regarding the high-risk areas would contribute to the selection of areas needed to be targeted for the expansion of health facilities.
Association between body mass index and patient-reported-outcome questionnaire scores (CAT™, ACT™, mMRC dyspnoea scale, IPAQ) in Ukraine, Kazakhstan and Azerbaijan: results of the CORE study
Authors: Nugmanova D. , Feshchenko Y. , Iashyna L. , Polianska M. , Malynovska K. , Stafeyeva I. , Makarova J. , Vasylyev A.
Published: June 2021

Background

The overweight/obese population (evaluated by a body mass index, BMI) represents a global health problem and contributes to the development of various chronic diseases. In this epidemiological study we evaluated this relationship by analyzing patient-reported questionnaires related to respiratory function, physical activity and BMI.

Methods

In 2013–2015, adult residents of selected cities were enrolled to this study in: Ukraine (M/F: 403/561), Kazakhstan (M/F = 348/597) and Azerbaijan (M/F: 389/544). Height was measured using a vertical measuring board, and body weight was measured by using portable digital scales. All participants were interviewed using CAT™, mMRC scale and IPAQ; respondents who also reported wheezing or whistling chest sounds during the previous 12 months additionally ACT™.

Results

45.4% of respondents in Ukraine, 47.6% in Kazakhstan and 54.9% of respondents in Azerbaijan were found to be overweight/obese (BMI ≥ 25 kg/m2). The mean CAT™ total score among this population versus those respondents with a normal weight was 5.2 versus 3.6 (Ukraine, p < 0.001), 4.2 versus 2.9 (Kazakhstan, p < 0.001) and 5.9 versus 4.3 (Azerbaijan, p < 0.001). The number of respondents without airflow limitations (mMRC score 0) among overweight/obese respondents versus normal weight respondents was 298 (68.2%) versus 456 (86.7%) in Ukraine, 261 (58.1%) versus 387 (78.2%) in Kazakhstan and 343 (67.1%) versus 345 (82.3%) in Azerbaijan. The ACT™ total score between overweight/obese respondents and normal weight respondents was not statistically different. IPAQ showed a tendency towards a higher proportion of “low activity” results (compared to “moderate” and “high”) in the overweight/obese subgroup (24.7% vs. 23.8% in Kazakhstan, 18.5% vs. 14.6% in Azerbaijan), and in Ukraine this difference was significant (12.4% vs. 5.2%, p < 0.001).

Conclusion

CAT™ and mMRC are widely used tools for respiratory function assessment. Despite CAT™ scores being close to a normal value (< 5), the relationship of both CAT™ and mMRC scores with being overweight/obese was demonstrated in the general adult population of three CIS countries. IPAQ may also be a useful instrument for measuring activity level however, more objective studies are required to evaluate the relationship between BMI and physical activity.
Orthotic treatment of idiopathic toe walking with a lower leg orthosis with circular subtalar blocking
Authors: Berger N. , Bauer M. , Hapfelmeier A. , Salzmann M. , Prodinger P. M.
Published: June 2021

Background

There is no universally accepted treatment standard for idiopathic toe walking patients (ITW) in the current literature. None of the established methods provide homogenous satisfying results. In our department we treat ITW patients with lower leg orthoses with a circular foot unit for a total of 16 weeks. In this study we reviewed our database to evaluate the success of our treatment protocol for a 24 months follow up period.

Results

Twenty-two patients were included in this study. Age at the beginning of treatment was 7.0 years +/− 2.9 (range 2.5-13.1). Percentage of ITW at the beginning of treatment according to the perception of the parents was 89% +/− 22.2 (range 50-100). Immediately after the treatment with our device, percentage of ITW dropped to 11% +/− 13.2 (range 0-50). After 12 months, 73% of the patients (16/22) walked completely normal or showed ITW less than 10% of the day. After 24 months, 64% of the patients kept a normal gait (14/22).

Conclusion

This study provides evidence that the treatment of idiopathic toe walking with lower leg orthoses with a circular foot unit results in satisfying long-term results in two thirds of the patients.
Bias estimation in study design: a meta-epidemiological analysis of transcatheter versus surgical aortic valve replacement
Authors: Youn Saerom , Wong Shannon Avery , Chrystoja Caitlin , Tomlinson George , Wijeysundera Harindra C. , Bell Chaim M. , Gagliardi Anna R. , Baxter Nancy N. , Takata Julie , Sandhu Lakhbir , Urbach David Robert
Published: June 2021

Background

Paucity of RCTs of non-drug technologies lead to widespread dependence on non-randomized studies. Relationship between nonrandomized study design attributes and biased estimates of treatment effects are poorly understood. Our purpose was to estimate the bias associated with specific nonrandomized study attributes among studies comparing transcatheter aortic valve implantation with surgical aortic valve replacement for the treatment of severe aortic stenosis.

Results

We included 6 RCTs and 87 nonrandomized studies. Surgical risk scores were similar for comparison groups in RCTs, but were higher for patients having transcatheter aortic valve implantation in nonrandomized studies. Nonrandomized studies underestimated the benefit of transcatheter aortic valve implantation compared with RCTs. For example, nonrandomized studies without adjustment estimated a higher risk of postoperative mortality for transcatheter aortic valve implantation compared with surgical aortic valve replacement (OR 1.43 [95% CI 1.26 to 1.62]) than high quality RCTs (OR 0.78 [95% CI 0.54 to 1.11). Nonrandomized studies using propensity score matching (OR 1.13 [95% CI 0.85 to 1.52]) and regression modelling (OR 0.68 [95% CI 0.57 to 0.81]) to adjust results estimated treatment effects closer to high quality RCTs. Nonrandomized studies describing losses to follow-up estimated treatment effects that were significantly closer to high quality RCT than nonrandomized studies that did not.

Conclusion

Studies with different attributes produce different estimates of treatment effects. Study design attributes related to the completeness of follow-up may explain biased treatment estimates in nonrandomized studies, as in the case of aortic valve replacement where high-risk patients were preferentially selected for the newer (transcatheter) procedure.
Oral health and caries/gingivitis-associated factors of adolescents aged 12–15 in Shandong province, China: a cross-sectional Oral Health Survey
Authors: Zhang Meng , Lan Jing , Zhang Tiantian , Sun Wenshuang , Liu Panpan , Wang Zhifeng
Published: June 2021

Background

We aimed to analyse the oral health status of adolescents in Shandong province, including dental caries and gingivitis, and their associated factors.

Methods

Adolescents aged 12–15-years in Shandong province were recruited. Caries and gingival status were assessed following the World Health Organisation diagnostic criteria. Information including the sociodemographic, oral hygiene knowledge, attitudes and practices were collected through the questionnaire. Chi-square test and multivariate logistic regression analysis were used to investigate the oral diseases associated factors.

Results

In total, 3868 students (50.2% males) were enrolled. Of these, 39.9% of the participants experienced caries, and 81.7% and 31.3% had calculus and bleeding gingival, respectively. Multivariate logistic regression analysis revealed that there was an association between dental caries and toothaches, dental visits and sleeping troubles caused by oral problems (P < 0.024). A low-frequency of brushing, high sugar consumption and no flossing were more associated with calculus formation and gingival bleeding (P < 0.008).

Conclusion

Compared to caries, worse gingival condition was more prevalent among adolescents in Shandong province. Brushing behaviour is associated with gingivitis, while dental visits and toothaches are associated with caries. Hence, prevention-oriented dental visits and oral hygiene training are strongly recommended to improve oral health status.
Is trigeminal neuralgia the only definitive diagnosis for pain in a tooth extraction site?
Authors: Taheri Arman , Sepehrmand Shahram
Published: June 2021

Knowing the International Classification of Orofacial Pain helps pain specialists to differentiate types of orofacial pain. It is important to select the best treatment or intervention for the patients based on the diagnosis. As part of our study, we reviewed the article published in BMC Oral Health, titled “Clinical characteristics and associated factors of trigeminal neuralgia: Experience from Addis Ababa, Ethiopia” by Ayele et al. (Ethiopia BMC Oral Health 20(1):7, 2020). For patients suffering from Classical Trigeminal Neuralgia taking a suitable dose of Carbamazepine or Gasser Ganglion radiofrequency could be helpful. Patients complaining Trigeminal neuralgia who had a history of a dental extraction in the painful region should be categorized in other group as Complex Regional Pain Syndrome type 1, who need larger dose of carbamazepine with anticonvulsant or tricyclic agent drugs (e.g. pregabalin or doxepin) or intervention (PPG radiofrequency).
The effect of live demonstration and flipped classroom with continuous formative assessment on dental students’ orthodontic wire-bending performance
Authors: Sivarajan Saritha , Soh Eunice Xinwei , Zakaria Nor Nadia , Kamarudin Yasmin , Lau May Nak , Bahar Aufa D. , Mohd Tahir Norhidayah , Wan Hassan Wan Nurazreena , Wey Mang Chek , Othman Siti Adibah , M Razi Roziana , Naimie Zahra
Published: June 2021

Background

Wire-bending skills is commonly taught through live demonstrations (LD) though flipped classroom (FC) method has gained popularity. Continuous formative assessment promotes personalised learning via closely monitored progress, with the identification of students’ strengths and weaknesses. This study aims to evaluate the effects of LD and FC teaching methods, supplemented with continuous formative assessment, on dental students’ learning of wire-bending skills for six types of removable orthodontic appliance components. A deeper understanding of the relative effectiveness between LD and FC teaching methods can help identify the most appropriate method to achieve student learning objectives, which is especially important given the current Covid-19 pandemic.

Methods

Forty third-year undergraduate dental students were randomly assigned into FC (n = 20) or LD (n = 20) cohort. Each student attended six teaching sessions, each to teach students’ competency in fabricating one type of wire component, for a total competency in fabricating six wire components over the course of six teaching sessions. Either LD or FC teaching methods were used. After each session, wire assignments had to be submitted. Wire assignments were then evaluated using a blinded wire-bending assessment protocol. As part of their formative assessment, the assessment results were distributed to students, lecturers, and technicians before the next session. After the first session (T0) and at the end of all six sessions (T1), students completed a self-reported questionnaire.

Results

The mean wire-bending scores for FC were significantly higher than LD for two of the six assignments, namely the Adams clasp (p < 0.01) and Z-spring (p = 0.03). Scores for both LD and FC increased significantly over time, which may be attributed to formative assessment. There was no statistically significant correlation between wire-bending scores and video usage. Students were satisfied with both teaching methods, according to T0 and T1 questionnaires.

Conclusions

Both LD and FC are equally effective in transferring practical orthodontic wire-bending skills and well-received by students. Continuous formative assessment may have enhanced students’ learning of orthodontic wire-bending skills. Further studies with control group are recommended to investigate the effect of formative assessment on teaching practical dental skills.
Reflecting on the challenges encountered by nurses at the great Kermanshah earthquake: a qualitative study
Authors: Abdi Alireza , Vaisi -Raygani Aliakbar , Najafi Bahareh , Saidi Hamid , Moradi Khalil
Published: June 2021

Background

Iran has experienced an increasing number of earthquake in the past three decades. Nurses are the largest group of healthcare providers that play an important role in responding to disasters. Based on previous studies, they experienced challenges providing care in the previous disasters. Therefore, this study aimed to explore the nursing challenges to provide care to the injured in the Kermanshah earthquake, Iran.

Methods

This is a qualitative study with conventional content analysis using Granheim and Landman approach. In this study, 16 nurses involved in providing care to the injured in the Kermanshah earthquake were selected by purposeful sampling method. Data were collected using in-depth semi-structured interviews. The criteria proposed by Guba and Lincoln were used to ensure the validity of the study.

Results

Data analysis led to the emergence of 453 primary codes, 14 subcategories, and 5 categories. The five categories were as follows: (a) organizational and managerial challenges; (b) human resources; (c) infrastructure; (d) educational preparations; (e) and ethical.

Conclusions

The results of this study showed that nurses faced several challenges in providing care to earthquake victims. Based on these findings, better educational management and planning, infrastructure reform, and establishment of a crisis nursing national team seem necessary.
Understanding providers’ attitudes and key concerns toward incorporating CVD risk prediction into clinical practice: a qualitative study
Authors: Takamine Linda , Forman Jane , Damschroder Laura J. , Youles Bradley , Sussman Jeremy
Published: June 2021

Background

Although risk prediction has become an integral part of clinical practice guidelines for cardiovascular disease (CVD) prevention, multiple studies have shown that patients’ risk still plays almost no role in clinical decision-making. Because little is known about why this is so, we sought to understand providers’ views on the opportunities, barriers, and facilitators of incorporating risk prediction to guide their use of cardiovascular preventive medicines.

Methods

We conducted semi-structured interviews with primary care providers (n = 33) at VA facilities in the Midwest. Facilities were chosen using a maximum variation approach according to their geography, size, proportion of MD to non-MD providers, and percentage of full-time providers. Providers included MD/DO physicians, physician assistants, nurse practitioners, and clinical pharmacists. Providers were asked about their reaction to a hypothetical situation in which the VA would introduce a risk prediction-based approach to CVD treatment. We conducted matrix and content analysis to identify providers’ reactions to risk prediction, reasons for their reaction, and exemplar quotes.

Results

Most providers were classified as Enthusiastic (n = 14) or Cautious Adopters (n = 15), with only a few Non-Adopters (n = 4). Providers described four key concerns toward adopting risk prediction. Their primary concern was that risk prediction is not always compatible with a “whole patient” approach to patient care. Other concerns included questions about the validity of the proposed risk prediction model, potential workflow burdens, and whether risk prediction adds value to existing clinical practice. Enthusiastic, Cautious, and Non-Adopters all expressed both doubts about and support for risk prediction categorizable in the above four key areas of concern.

Conclusions

Providers were generally supportive of adopting risk prediction into CVD prevention, but many had misgivings, which included concerns about impact on workflow, validity of predictive models, the value of making this change, and possible negative effects on providers’ ability to address the whole patient. These concerns have likely contributed to the slow introduction of risk prediction into clinical practice. These concerns will need to be addressed for risk prediction, and other approaches relying on “big data” including machine learning and artificial intelligence, to have a meaningful role in clinical practice.
Validity of algorithms for identifying five chronic conditions in MedicineInsight, an Australian national general practice database
Authors: Havard Alys , Manski-Nankervis Jo-Anne , Thistlethwaite Jill , Daniels Benjamin , Myton Rimma , Tu Karen , Chidwick Kendal
Published: June 2021

Background

MedicineInsight is a database containing de-identified electronic health records (EHRs) from over 700 Australian general practices. It is one of the largest and most widely used primary health care EHR databases in Australia. This study examined the validity of algorithms that use information from various fields in the MedicineInsight data to indicate whether patients have specific health conditions. This study examined the validity of MedicineInsight algorithms for five common chronic conditions: anxiety, asthma, depression, osteoporosis and type 2 diabetes.

Methods

Patients’ disease status according to MedicineInsight algorithms was benchmarked against the recording of diagnoses in the original EHRs. Fifty general practices contributing data to MedicineInsight met the eligibility criteria regarding patient load and location. Five were randomly selected and four agreed to participate. Within each practice, 250 patients aged ≥ 40 years were randomly selected from the MedicineInsight database. Trained staff reviewed the original EHR for as many of the selected patients as possible within the time available for data collection in each practice.

Results

A total of 475 patients were included in the analysis. All the evaluated MedicineInsight algorithms had excellent specificity, positive predictive value, and negative predictive value (above 0.9) when benchmarked against the recording of diagnoses in the original EHR. The asthma and osteoporosis algorithms also had excellent sensitivity, while the algorithms for anxiety, depression and type 2 diabetes yielded sensitivities of 0.85, 0.89 and 0.89 respectively.

Conclusions

The MedicineInsight algorithms for asthma and osteoporosis have excellent accuracy and the algorithms for anxiety, depression and type 2 diabetes have good accuracy. This study provides support for the use of these algorithms when using MedicineInsight data for primary health care quality improvement activities, research and health system policymaking and planning.
The detection of canine parvovirus type 2c of Asian origin in dogs in Romania evidenced its progressive worldwide diffusion
Authors: Balboni Andrea , Niculae Mihaela , Di Vito Serena , Urbani Lorenza , Terrusi Alessia , Muresan Cosmin , Battilani Mara
Published: June 2021

Background

Canine parvovirus (CPV) is one of the most important pathogens of dogs. Despite vaccination, CPV infections are still ubiquitous in dogs, and the three antigenic variants 2a, 2b and 2c are variously distributed in the canine population worldwide. To date, no information is available on CPV variants circulating in some European countries. The aim of this study was to genetically characterise the CPV detected in ten dogs with clinical signs of acute gastroenteritis in Romania. The presence of Carnivore protoparvovirus 1 DNA was investigated in faecal samples using an end-point PCR targeting the complete VP2 gene and positive amplicons were sequenced and analysed.

Results

All ten dogs with acute gastroenteritis tested positive to Carnivore protoparvovirus 1 DNA in faecal samples. The identified viruses belonged to CPV-2c type, showed identical sequences of the VP2 gene and were characterised by distinctive amino acid residues in the deduced VP2 protein: 5-glicine (5Gly), 267-tirosine (267Tyr), 324-isoleucine (324Ile) and 370-arginine (370Arg). These distinctive amino acid residues have already been reported in CPV-2c widespread in Asia and occasionally detected in Italy and Nigeria.

Conclusions

Since CPV-2c with VP2 amino acid residues 5Gly, 267Tyr, 324Ile and 370Arg were never reported before 2013, it can be assumed that this virus is progressively expanding its spread in the world dog population. This study adds new data about the presence of this new virus in Europe and underline worrying questions about its potential impact on the health of the canine population.
Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis
Authors: Wu Jing , Li Wei , Zhao Shi-guang , Qian Sen-he , Wang Zhou , Zhou Meng-jie , Hu Wen-song , Wang Jian , Hu Liu-xiu , Liu Yan , Xue Zheng-lian
Published: June 2021

Background

Menaquinone (MK-7) is a highly valuable vitamin K2produced byBacillus subtilis. Common static metabolic engineering approaches for promoting the production of MK-7 have been studied previously. However, these approaches caused an accumulation of toxic substances and reduced product yield. Hence, dynamic regulation by the quorum sensing (QS) system is a promising method for achieving a balance between product synthesis and cell growth.

Results

In this study, the QS transcriptional regulator SinR, which plays a significant role in biofilm formation and MK production simultaneously, was selected, and its site-directed mutants were constructed. Among these mutants,sinRknock out strain (KO-SinR) increased the biofilm biomass by 2.8-fold compared to the wild-type. SinRquadmaximized the yield of MK-7 (102.56 ± 2.84 mg/L). To decipher the mechanism of how this mutant regulates MK-7 synthesis and to find additional potential regulators that enhance MK-7 synthesis, RNA-seq was used to analyze expression changes in the QS system, biofilm formation, and MK-7 synthesis pathway. The results showed that the expressions oftapA,tasAandepsEwere up-regulated 9.79-, 0.95-, and 4.42-fold, respectively. Therefore, SinRquadformed more wrinkly and smoother biofilms than BS168. The upregulated expressions ofglpF,glpk, andglpDin this biofilm morphology facilitated the flow of glycerol through the biofilm. In addition, NADH dehydrogenases especiallysdhA,sdhB,sdhCandglpD, increased 1.01-, 3.93-, 1.87-, and 1.11-fold, respectively. The increased expression levels of NADH dehydrogenases indicated that more electrons were produced for the electron transport system. Electrical hyperpolarization stimulated the synthesis of the electron transport chain components, such as cytochrome c and MK, to ensure the efficiency of electron transfer. Wrinkly and smooth biofilms formed a network of interconnected channels with a low resistance to liquid flow, which was beneficial for the uptake of glycerol, and facilitated the metabolic flux of four modules of the MK-7 synthesis pathway.

Conclusions

In this study, we report for the first time that SinRquadhas significant effects on MK-7 synthesis by forming wrinkly and smooth biofilms, upregulating the expression level of most NADH dehydrogenases, and providing higher membrane potential to stimulate the accumulation of the components in the electron transport system.
Mapathons versus automated feature extraction: a comparative analysis for strengthening immunization microplanning
Authors: Mendes Amalia , Palmer Tess , Berens Andrew , Espey Julie , Price Rhiannan , Mallya Apoorva , Brown Sidney , Martinez Maureen , Farag Noha , Kaplan Brian
Published: June 2021

Background

Social instability and logistical factors like the displacement of vulnerable populations, the difficulty of accessing these populations, and the lack of geographic information for hard-to-reach areas continue to serve as barriers to global essential immunizations (EI). Microplanning, a population-based, healthcare intervention planning method has begun to leverage geographic information system (GIS) technology and geospatial methods to improve the remote identification and mapping of vulnerable populations to ensure inclusion in outreach and immunization services, when feasible. We compare two methods of accomplishing a remote inventory of building locations to assess their accuracy and similarity to currently employed microplan line-lists in the study area.

Methods

The outputs of a crowd-sourced digitization effort, or mapathon, were compared to those of a machine-learning algorithm for digitization, referred to as automatic feature extraction (AFE). The following accuracy assessments were employed to determine the performance of each feature generation method: (1) an agreement analysis of the two methods assessed the occurrence of matches across the two outputs, where agreements were labeled as “befriended” and disagreements as “lonely”; (2) true and false positive percentages of each method were calculated in comparison to satellite imagery; (3) counts of features generated from both the mapathon and AFE were statistically compared to the number of features listed in the microplan line-list for the study area; and (4) population estimates for both feature generation method were determined for every structure identified assuming a total of three households per compound, with each household averaging two adults and 5 children.

Results

The mapathon and AFE outputs detected 92,713 and 53,150 features, respectively. A higher proportion (30%) of AFE features were befriended compared with befriended mapathon points (28%). The AFE had a higher true positive rate (90.5%) of identifying structures than the mapathon (84.5%). The difference in the average number of features identified per area between the microplan and mapathon points was larger (t = 3.56) than the microplan and AFE (t = − 2.09) (alpha = 0.05).

Conclusions

Our findings indicate AFE outputs had higher agreement (i.e., befriended), slightly higher likelihood of correctly identifying a structure, and were more similar to the local microplan line-lists than the mapathon outputs. These findings suggest AFE may be more accurate for identifying structures in high-resolution satellite imagery than mapathons. However, they both had their advantages and the ideal method would utilize both methods in tandem.