bluuebunny/crossref_metadata_2025 huggingface dataset:
iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks
Authors: Nguyen Binh P. , Nguyen Quang H. , Doan-Ngoc Giang-Nam , Nguyen-Vo Thanh-Hoang , Rahardja Susanto
Published: December 2019

Background

Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of post-genomic where data on protein sequences have expanded very fast. In this study, we propose iProDNA-CapsNet – a new prediction model identifying protein-DNA binding residues using an ensemble of capsule neural networks (CapsNets) on position specific scoring matrix (PSMM) profiles. The use of CapsNets promises an innovative approach to determine the location of DNA-binding residues. In this study, the benchmark datasets introduced by Hu et al. (2017), i.e., PDNA-543 and PDNA-TEST, were used to train and evaluate the model, respectively. To fairly assess the model performance, comparative analysis between iProDNA-CapsNet and existing state-of-the-art methods was done.

Results

Under the decision threshold corresponding to false positive rate (FPR) ≈ 5%, the accuracy, sensitivity, precision, and Matthews’s correlation coefficient (MCC) of our model is increased by about 2.0%, 2.0%, 14.0%, and 5.0% with respect to TargetDNA (Hu et al., 2017) and 1.0%, 75.0%, 45.0%, and 77.0% with respect to BindN+ (Wang et al., 2010), respectively. With regards to other methods not reporting their threshold settings, iProDNA-CapsNet also shows a significant improvement in performance based on most of the evaluation metrics. Even with different patterns of change among the models, iProDNA-CapsNets remains to be the best model having top performance in most of the metrics, especially MCC which is boosted from about 8.0% to 220.0%.

Conclusions

According to all evaluation metrics under various decision thresholds, iProDNA-CapsNet shows better performance compared to the two current best models (BindN and TargetDNA). Our proposed approach also shows that CapsNet can potentially be used and adopted in other biological applications.
Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies
Authors: Wang Haohan , Yue Tianwei , Yang Jingkang , Wu Wei , Xing Eric P.
Published: December 2019

Background

Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as follow-ups to detect interactions between SNPs, epistasis are still yet to be modeled and discovered more thoroughly.

Results

In this paper, following the previous study of detecting marginal epistasis signals, and motivated by the universal approximation power of deep learning, we propose a neural network method that can potentially model arbitrary interactions between SNPs in genetic association studies as an extension to the mixed models in correcting confounding factors. Our method, namely Deep Mixed Model, consists of two components: 1) a confounding factor correction component, which is a large-kernel convolution neural network that focuses on calibrating the residual phenotypes by removing factors such as population stratification, and 2) a fixed-effect estimation component, which mainly consists of an Long-short Term Memory (LSTM) model that estimates the association effect size of SNPs with the residual phenotype.

Conclusions

After validating the performance of our method using simulation experiments, we further apply it to Alzheimer’s disease data sets. Our results help gain some explorative understandings of the genetic architecture of Alzheimer’s disease.
Modelling the evolution of cognitive styles
Authors: Liedtke Jannis , Fromhage Lutz
Published: December 2019

Background

Individuals consistently differ in behaviour, exhibiting so-called personalities. In many species, individuals differ also in their cognitive abilities. When personalities and cognitive abilities occur in distinct combinations, they can be described as ‘cognitive styles’. Both empirical and theoretical investigations produced contradicting or mixed results regarding the complex interplay between cognitive styles and environmental conditions.

Results

Here we use individual-based simulations to show that, under just slightly different environmental conditions, different cognitive styles exist and under a variety of conditions, can also co-exist. Co-existences are based on individual specialization on different resources, or, more generally speaking, on individuals adopting different niches or microhabitats.

Conclusions

The results presented here suggest that in many species, individuals of the same population may adopt different cognitive styles. Thereby the present study may help to explain the variety of styles described in previous studies and why different, sometimes contradicting, results have been found under similar conditions.
Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle
Authors: Lee Isaiah Paolo A. , Andam Cheryl P.
Published: December 2019

Background

Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources.

Results

The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production.

Conclusions

Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.
Evaluation of peripheral perfusion index and heart rate variability as early predictors for intradialytic hypotension in critically ill patients
Authors: Mostafa Hanan , Shaban Mohamed , Hasanin Ahmed , Mohamed Hassan , Fathy Shymaa , Abdelreheem Hossam M. , Lotfy Ahmed , Abougabal Ayman , Mukhtar Ahmed , El-adawy Akram
Published: December 2019

Background

Intradialytic hypotension is a serious complication during renal replacement therapy in critically ill patients. Early prediction of intradialytic hypotension could allow adequate prophylactic measures. In this study we evaluated the ability of peripheral perfusion index (PPI) and heart rate variability (HRV) to predict intradialytic hypotension.

Methods

A prospective observational study included 36 critically ill patients with acute kidney injury during their first session of intermittent hemodialysis. In addition to basic vital signs, PPI was measured using Radical-7 (Masimo) device. Electrical cardiometry (ICON) device was used for measuring cardiac output, systemic vascular resistance, and HRV. All hemodynamic values were recorded at the following time points: 30 min before the hemodialysis session, 15 min before the start of hemodialysis session, every 5 min during the session, and 15 min after the conclusion of the session. The ability of all variables to predict intradialytic hypotension was assessed through area under receiver operating characteristic (AUROC) curve calculation.

Results

Twenty-three patients (64%) had intradialytic hypotension. Patients with pulmonary oedema showed higher risk for development of intradialytic hypotension {Odds ratio (95% CI): 13.75(1.4–136)}. Each of baseline HRV, and baseline PPI showed good predictive properties for intradialytic hypotension {AUROC (95% CI): 0.761(0.59–0.88)}, and 0.721(0.547–0.857)} respectively.

Conclusions

Each of low PPI, low HRV, and the presence of pulmonary oedema are good predictors of intradialytic hypotension.
The prevalence and clinical correlates of adverse childhood experiences in a cross-sectional study of primary care patients with cardiometabolic disease or risk factors
Authors: Maunder Robert G. , Tannenbaum David W. , Permaul Joanne A. , Nutik Melissa , Haber Cleo , Mitri Mira , Costantini Daniela , Hunter Jonathan J.
Published: December 2019

Background

Adverse childhood experiences (ACEs) are associated with risk of poor adult health, including cardiometabolic diseases. Little is known about the correlates of ACEs for adults who have already developed cardiometabolic diseases, or who are at elevated risk.

Methods

Adult primary care patients with cardiometabolic disease (hypertension, diabetes, stroke, angina, myocardial infarction, coronary artery bypass graft, angioplasty) or with a risk factor (obesity, smoking, high cholesterol, family history) were surveyed regarding ACEs, psychological distress, attachment insecurity, quality of life, behavior change goals, stages of change, and attitudes toward potential prevention strategies.

Results

Of 387 eligible patients, 74% completed the ACEs survey. Exposure to ACEs was reported by 174 participants (61%). Controlling for age, gender, relationship status and income, number of ACEs was associated with psychological distress (F = 3.7, p = .01), quality of life (F = 8.9, p = .001), attachment anxiety (F = 3.4, p = .02), drinking alcohol most days (F = 4.0, p = .008) and smoking (F = 2.7, p = .04). Greater ACE exposure was associated with less likelihood of selecting diet or physical activity as a behavior change goal (linear-by-linear association p = .009). Stage of change was not associated with ACEs. ACEs exposure was not related to preferred resources for behavior change.

Conclusions

ACEs are common among patients at cardiometabolic risk and are related to quality of life, psychological factors that influence cardiometabolic outcomes and behavior change goals. ACEs should be taken into account when managing cardiometabolic risk in family medicine.
Improvement of Asia-Pacific colorectal screening score and evaluation of its use combined with fecal immunochemical test
Authors: He Xu-xia , Yuan Si-yi , Li Wen-bin , Yang Hong , Ji Wen , Wang Zhi-qiang , Hao Jian-yu , Chen Chuan , Chen Wei-qing , Gao Ying-xin , Li Ling-bo , Cheng Kai-liang , Qian Jia-ming , Wang Li , Li Jing-nan
Published: December 2019

Background

The Asia-Pacific Colorectal Screening (APCS) score is effective to screen high-risk groups of advanced colorectal neoplasia (ACN) patients but needs revising and can be combined with the fecal immunochemical test (FIT). This paper aimed to improve the APCS score and evaluate its use with the FIT in stratifying the risk of ACN.

Methods

This prospective and multicenter study enrolled 955 and 1201 asymptomatic Chinese participants to form the derivation and validation set, respectively. Participants received the risk factor questionnaire, colonoscopy and FIT. Multiple logistic regression was applied, and C-statistic, sensitivity and negative predictive values (NPVs) were used to compare the screening efficiency.

Results

A modified model was developed incorporating age, body mass index (BMI), family history, diabetes, smoking and drinking as risk factors, stratifying subjects into average risk (AR) or high risk (HR). In the validation set, the HR tier group had a 3.4-fold (95% CI 1.8–6.4) increased risk for ACN. The C-statistic for the modified score was 0.69 ± 0.04, and 0.67 ± 0.04 for the original score. The sensitivity of the modified APCS score combined with FIT for screening ACN high-risk cohorts was 76.7% compared with 36.7% of FIT alone and 70.0% of the modified APCS score alone. The NPVs of the modified score combined with FIT for ACN were 98.0% compared with 97.0% of FIT alone and 97.9% of the modified APCS score alone.

Conclusions

The modified score and its use with the FIT are efficient in selecting the HR group from a Chinese asymptomatic population.
Time to viral load suppression and its associated factors in cohort of patients taking antiretroviral treatment in East Shewa zone, Oromiya, Ethiopia, 2018
Authors: Ali Jemal Hassen , Yirtaw Tewodros Getinet
Published: December 2019

Background

A key goal of Antiretroviral Treatment (ART) is to achieve and maintain durable viral suppression. Thus, the most important use of viral load measurement is to monitor the effectiveness of therapy after initiation of ART. The main objective of the study was to determine the time for virological suppression and its associated factors among people living with HIV taking antiretroviral treatments in East Shewa Zone, Oromiya, Ethiopia.

Methods

Patients diagnosed with Human Immunodeficiency Virus presenting to the study health centers between October 3, 2011 and March 1, 2013 were included in the study given the following criteria: age 18 years or greater, eligible to start ART. All patients with baseline viral load measurements were included in the study. Interaction between explanatory variables with the response variable was analyzed by using cross tab features of (Statistical Package for the Social Sciences) SPSS, International Business Machines (IBM) Inc. Significance group comparison was done by Kaplan Meier log-rank test. Cox proportional hazard model was used to select significant factors to the variability between groups.

Result

Plasma viral load was suppressed below the detection level in 72% of individuals taking a different regimen of ART. The median Human Immunodeficiency virus (HIV)-1 plasma viral load in the cohort was estimated to be log 5.3111 copies/ml. The study observed Survival curve difference in the category of marital status (p-value 0.023) and baseline cluster of differentiation 4 (CD4) value (p-value 0.023). The estimated median time to Plasma Viral Load (PVL) suppression was 181 days (CI: 140.5–221.4) with the age group of 30–39 years having minimum time to achieve suppression with 92 days (CI: 60.1–123.8) and the maximum time required to reach the level was found among the age group between 50 and 59 years.

Conclusion

The study found that the estimated time to achieve PVL after taking ART to be 181 days. Factors affecting time to suppression level were marital status and baseline CD4.
Evaluation of long-term intravitreal anti-vascular endothelial growth factor injections on renal function in patients with and without diabetic kidney disease
Authors: O’Neill Rachael Ann , Gallagher Patrick , Douglas Tricia , Little Julie-Anne , Maxwell Alexander Peter , Silvestri Giuliana , McKay Gareth
Published: December 2019

Background

Administering anti-vascular endothelial growth factor (anti-VEGF) by intraocular injection has been shown to have a safe systemic profile. Nevertheless, incidents of acute kidney injury following anti-VEGF injection have been reported. We assessed the long-term effect of multiple intravitreal anti-VEGF injections on measures of renal function in patients with diabetes including rate of change of estimated glomerular filtration rate (eGFR) and urine albumin-to-creatinine ratio (ACR).

Methods

A retrospective review of patients receiving diabetic macular oedema (DMO) treatment was undertaken. Serum creatinine, ACR, number of intravitreal anti-VEGF injections and clinical characteristics were collected from electronic healthcare records (EHR). A co-efficient of eGFR and ACR change with time was calculated over a mean duration of 2.6 years. Regression modelling was used to assess variation in the number of anti-VEGF injections and change in eGFR and ACR.

Results

The EHR of 85 patients with DMO (59% male, 78% type 2 diabetes mellitus [T2DM]) were reviewed. On average, 26.8 intravitreal anti-VEGF injections were given per patient over a mean duration of 31 months. No association between increasing number of anti-VEGF injections and rate of eGFR decline (beta = 0.04, 95% confidence intervals [CI]: − 0.02, 0.09;p = 0.22) or ACR change over time (beta = 0.02, CI: − 0.19, 0.23;p = 0.86) was detected, following adjustment for hypertension, cerebrovascular disease, T2DM, and medications taken.

Conclusion

Our data suggests regular long-term intravitreal VEGF inhibition does not significantly alter the rate of change in eGFR and/or ACR with increasing number of treatment injections.
Physical activity and somatic symptoms among hemodialysis patients: a multi-center study in Zhejiang, China
Authors: Lou Xiaowei , Li Yiwen , Shen Huajuan , Juan Jin , He Qiang
Published: December 2019

Background

Somatic symptoms are commonly reported by patients on maintenance hemodialysis. Based on evidence that exercise can improve psychological state among the general population, we aimed to evaluate the effects of physical activity on somatic symptoms specifically in this clinical population.

Methods

This was a multicenter, cross-sectional study that included patients receiving hemodialysis treatment ≥3 times per week for > 3 months, aged 18 years or older, and who were willing to complete our study questionnaires and wear a pedometer; they were recruited from four hemodialysis centers in Zhejiang, China. Physical activity was quantified using pedometer data, with somatic symptoms quantified using the Symptom Checklist-90 (SCL-90). Hemodialysis information and blood laboratory tests were obtained from patients’ medical record. The score on the somatic dimension of the SCL-90 (S1-score) subdivided into tertiles for analysis: ≤1.17 (Q1), 1.17–1.58 (Q2) and ≥ 1.58 (Q3). A multivariate logistic regression analysis was performed to estimate the crude and adjusted odd ratios (ORs) and 95% confidence intervals (CIs) for the S1- somatic score according to the physical activity level during the last week. For this analysis, patients were stratified in a high and low exercise group using a cutoff of 3000 MET-min/week. Model 1 was adjusted for skinfold thickness of the triceps, upper arm circumference, grip strength, 5-m walking time, and 30-s sit-to-stand test. In model 2, we further adjusted for the leukocyte count, high-sensitivity C-reactive protein level, and albumin level.

Results

After screening, 320 patients were enrolled into the study group (37.50% male, average age of 58.60 ± 14.2 years and mean average number of steps per day of 3725.92 ± 2663.47). The S1-score (1.51 ± 0.39) was significantly higher for patients than for the normal reference population (P < 0.001). As the S1-score increased, the average number of steps per day decreased, both on dialysis and non-dialysis days. Total physical activity, measured by pedometry, showed the best correlation to S1 scores (r = − 0.813; P < 0.01). The OR of a high S1-score was 1.97 [95% CI, 0.63–4.08] for patients in the low physical activity group.

Conclusion

Higher S1 (somatic symptom) score was related to low physical activity among patients on maintenance hemodialysis.
Multimodal MRI of grey matter, white matter, and functional connectivity in cognitively healthy mutation carriers at risk for frontotemporal dementia and Alzheimer's disease
Authors: Feis Rogier A. , Bouts Mark J. R. J. , Dopper Elise G. P. , Filippini Nicola , Heise Verena , Trachtenberg Aaron J. , van Swieten John C. , van Buchem Mark A. , van der Grond Jeroen , Mackay Clare E. , Rombouts Serge A. R. B.
Published: December 2019

Background

Frontotemporal dementia (FTD) and Alzheimer’s disease (AD) are associated with divergent differences in grey matter volume, white matter diffusion, and functional connectivity. However, it is unknown at what disease stage these differences emerge. Here, we investigate whether divergent differences in grey matter volume, white matter diffusion, and functional connectivity are already apparent between cognitively healthy carriers of pathogenic FTD mutations, and cognitively healthy carriers at increased AD risk.

Methods

We acquired multimodal magnetic resonance imaging (MRI) brain scans in cognitively healthy subjects with (n=39) and without (n=36) microtubule-associated protein Tau (MAPT) or progranulin (GRN) mutations, and with (n=37) and without (n=38) apolipoprotein E ε4 (APOE4) allele. We evaluated grey matter volume using voxel-based morphometry, white matter diffusion using tract-based spatial statistics (TBSS), and region-to-network functional connectivity using dual regression in the default mode network and salience network. We tested for differences between the respective carriers and controls, as well as for divergence of those differences. For the divergence contrast, we additionally performed region-of-interest TBSS analyses in known areas of white matter diffusion differences between FTD and AD (i.e., uncinate fasciculus, forceps minor, and anterior thalamic radiation).

Results

MAPT/GRN carriers did not differ from controls in any modality. APOE4 carriers had lower fractional anisotropy than controls in the callosal splenium and right inferior fronto-occipital fasciculus, but did not show grey matter volume or functional connectivity differences. We found no divergent differences between both carrier-control contrasts in any modality, even in region-of-interest analyses.

Conclusions

Concluding, we could not find differences suggestive of divergent pathways of underlying FTD and AD pathology in asymptomatic risk mutation carriers. Future studies should focus on asymptomatic mutation carriers that are closer to symptom onset to capture the first specific signs that may differentiate between FTD and AD.
Retrospective cohort study of trifluridine/tipiracil (TAS-102) plus bevacizumab versus trifluridine/tipiracil monotherapy for metastatic colorectal cancer
Authors: Kotani Daisuke , Kuboki Yasutoshi , Horasawa Satoshi , Kaneko Asumi , Nakamura Yoshiaki , Kawazoe Akihito , Bando Hideaki , Taniguchi Hiroya , Shitara Kohei , Kojima Takashi , Tsuji Akihito , Yoshino Takayuki
Published: December 2019

Background

A previous phase I/II C-TASK FORCE study of trifluridine/tipiracil plus bevacizumab for patients with heavily pretreated metastatic colorectal cancer (mCRC) showed promising activity with an acceptable toxicity profile. This retrospective study aimed to investigate the safety and efficacy of trifluridine/tipiracil plus bevacizumab compared with trifluridine/tipiracil monotherapy in patients with heavily pretreated mCRC in clinical settings.

Methods

Records of patients with mCRC refractory to standard therapies who initiated trifluridine/tipiracil plus bevacizumab from January 2016 to March 2018 or trifluridine/tipiracil monotherapy from June 2014 to December 2015 were retrospectively reviewed at our institution.

Results

Totally, 60 patients received trifluridine/tipiracil plus bevacizumab and 66 received trifluridine/tipiracil monotherapy. All patients had previously received standard chemotherapy. Median progression-free survival (PFS) was 3.7 months [95% confidence interval (CI), 2.3–5.1] in the trifluridine/tipiracil plus bevacizumab group and 2.2 months (95% CI, 1.8–2.6) in the trifluridine/tipiracil monotherapy group [hazards ratio (HR) 0.69; 95% CI 0.48–0.99]. PFS rate at 16 weeks was 46.6% for the trifluridine/tipiracil plus bevacizumab group and 33.9% for the trifluridine/tipiracil monotherapy group. Although a relatively higher incidence of grade ≥ 3 neutropenia was observed in the trifluridine/tipiracil plus bevacizumab group than that in the other group (50.0% vs. 40.9%, p = 0.371), the incidence of febrile neutropenia was not high (3.3% vs. 7.8%, p = 0.444).

Conclusions

In real-world settings, trifluridine/tipiracil plus bevacizumab prolonged PFS and helped achieve higher 16-week PFS rate compared with trifluridine/tipiracil monotherapy in patients with heavily pretreated mCRC with manageable toxicities.

Trial registration

Retrospectively registered.
Psychological intimate partner violence against women in the European Union: a cross-national invariance study
Authors: Martín-Fernández Manuel , Gracia Enrique , Lila Marisol
Published: December 2019

Background

Intimate partner violence against women (IPVAW) is a worldwide public health problem. One of the most frequent forms of this type of violence in western societies is psychological IPVAW. According to the European Union (EU) Fundamental Rights Association (FRA) the prevalence of psychological IPVAW in the EU is 43%. However, the measurement invariance of the measure addressing psychological IPVAW in this survey has not yet been assessed.

Methods

The aim of this study is to ensure the cross-national comparability of this measure, by evaluating its measurement invariance across the 28 EU countries in a sample of 37,724 women, and to examine how the levels of this type of violence are distributed across the EU.

Results

Our results showed that the psychological IPVAW measure presented adequate psychometric properties (reliability and validity) in all countries. A latent structure of one factor was supported and scalar invariance was established in all countries. The average levels of psychological IPVAW were higher in countries like Finland, Latvia, Lithuania, and Sweden compared to the rest of the EU countries. In many of the other countries the levels of this type of violence overlapped.

Conclusion

Our findings underlined the importance of using appropriate statistical methods to make valid cross-national comparisons in large population surveys.
Gender-specific prevalence and associated factors of major depressive disorder and generalized anxiety disorder in a Chinese rural population: the Henan rural cohort study
Authors: Luo Zhicheng , Li Yuqian , Hou Yitan , Liu Xiaotian , Jiang Jingjing , Wang Yan , Liu Xue , Qiao Dou , Dong Xiaokang , Li Ruiying , Wang Fang , Wang Chongjian
Published: December 2019

Background

This study aims to investigate the prevalence and associated factors of major depressive disorder (MDD) and generalized anxiety disorder (GAD) by gender in Chinese rural adults.

Methods

A total of 29,993 participants aged from 18 to 79 years from the Henan Rural Cohort Study were included in this study. The Patient Health Questionnaire-2 (PHQ-2) and Generalized Anxiety Disorder-2 (GAD-2) were used to assess MDD and GAD through a face-to-face interview. Multivariate logistic regression model was conducted to analyze the associated factors for MDD and GAD.

Results

The age-standardized prevalence of MDD and GAD (and 95%CI) in the total sample were 5.41% (5.17–5.66%) and 4.94% (4.71–5.18%), respectively. Besides, the crude prevalence in women were significantly higher than men for both MDD (6.81% vs. 4.77%) and GAD (6.63% vs. 3.93%) (both P < 0.001). Tetrachoric correlation test showed high comorbidity between MDD and GAD (r = 0.88, P = 0.01). Further analysis revealed that age, sex, marital status, educational level, per capita monthly income, drinking, physical activity, and body mass index were associated with MDD and GAD in the overall sample. Gender difference was found among age groups for MDD (Pinteraction < 0.001).

Conclusions

These findings showed that Chinese rural adults were at low risk for prevalence of MDD and GAD. Women had higher prevalence and risks for MDD and GAD compared with men, indicating that women deserved more attention. Gender-specific interventions on the modifiable associated factors are urgently needed to improve the mental conditions for Chinese rural population.

Clinical trial registration

The Henan Rural Cohort Study has been registered in the Chinese Clinical Trial Register (Registration number: ChiCTR-OOC-15006699). Date of registration: 2015-07-06.
The cost-effectiveness of screening tools used in the diagnosis of fetal alcohol spectrum disorder: a modelled analysis
Authors: Berrigan Patrick , Andrew Gail , Reynolds James N. , Zwicker Jennifer D.
Published: December 2019

Background

Fetal Alcohol Spectrum Disorder (FASD) is characterized by physical and neurological abnormalities resulting from prenatal alcohol exposure. Though diagnosis may help improve patient outcomes, the diagnostic process can be costly. Subsequently, screening children suspected of FASD prior to diagnostic testing has been suggested, to avoid administering testing to children who are unlikely to receive a diagnosis. The present study set out to assess the cost-effectiveness of currently recommended FASD screening tools.

Methods

The screenings tools evaluated were chosen from Children’s Healthcare Canada’s National Screening Toolkit for Children and Youth Identified and Potentially Affected by FASD and include meconium testing of fatty acid ethyl esters (meconium testing) and the neurobehavioral screening tool (NST). An economic model was constructed to assess cost-effectiveness. One-way and probabilistic sensitivity analyses were conducted to assess the robustness of findings. Costs reflect 2017 Canadian dollars and the perspective is the public healthcare system.

Results

Both screening tools evaluated resulted in reduced costs and fewer diagnosed years of life than a no screening strategy in which all children suspected of FASD receive diagnostic testing. The model predicts that screening newborns with meconium testing results in a reduced cost of $89,186 per 100 individuals screened and 38 fewer diagnosed years of life by age 18, corresponding to an incremental cost-effectiveness ratio (ICER) of $2359. Screening children with the NST resulted in a reduced cost of $183,895 per 100 individuals screened and 77 fewer diagnosed years of life by age 18, corresponding to an ICER of $2390.

Conclusion

Findings suggest that screening is associated with less use of healthcare recourses but also fewer years of life with an FASD diagnosis over a no screening strategy. Since diagnosis can be key to children receiving timely and appropriate health and educational services, cost-savings must be weighed against the fewer years of life with a diagnosis associated with screening.
High-energy dose of therapeutic ultrasound in the treatment of patellar tendinopathy: protocol of a randomized placebo-controlled clinical trial
Authors: de Jesus Julio Fernandes , de Albuquerque Tadeu Aldrovando Brihy , Shimba Leandro Girardi , Bryk Flavio Fernandes , Cook Jill , Pinfildi Carlos Eduardo
Published: December 2019

Background

Patellar tendinopathy is an extremely debilitating condition and its treatment usually requires a combination of clinical approaches. Therapeutic ultrasound (TUS) is one of the most available electrophysical agent in rehabilitation settings; however, there is also a lack of high-quality studies that test different dosimetric aspects of TUS. Thus, the purpose of this study is to evaluate the short-, medium-, and long-term effects of the combination of high-energy TUS with a rehabilitation program for patellar tendinopathy.

Methods

This will be a randomized, placebo-controlled trial with blinding of patients, assessors, and therapist. The setting is an outpatient physical therapy clinic. We will recruit 66 participants (male and female) aged between 18 and 40 years and presenting with patellar tendinopathy. A treatment combining high-energy dose TUS and a rehabilitation program for patellar tendinopathy will be delivered twice a week for 8 weeks. The control group will receive the same treatment, but with a placebo TUS. The effectiveness of the intervention will be measured at the beginning (baseline), midpoint (4 weeks), and end of treatment (8 weeks), as well as at 3- and 6-months post-treatment. Primary outcomes will be pain intensity (visual analogue scale, VAS), and VISA-P questionnaire and primary time points will be baseline (T0) and the end of the program (T2). Also, IPAQ-short form questionnaire, muscle strength (manual dynamometry), 2D kinematics, pain pressure threshold (PPT) algometry, thermography, and magnetic resonance imaging (MRI) will be collected.

Discussion

TUS will be applied in an attempt to enhance the results obtained with the rehabilitation program proposed in this study, as well as stimulate some repair responses in individuals undergoing treatment for patellar tendinopathy, which in turn may optimize and improve treatment programs for patellar tendinopathy as well as to establish new guidelines for the application of TUS.

Trial registration

This study was prospectively registered at April-3rd-2018 and updated at September-1st-2019 in the Brazilian Registry of Clinical Trials (REBEC) under the registration number:RBR-658n6w.
The resonance® metallic ureteral stent in the treatment of malignant ureteral obstruction: a prospective observational study
Authors: Miyazaki Jun , Onozawa Mizuki , Takahashi Satoshi , Maekawa Yuka , Yasuda Mitsuru , Wada Koichiro , Maeda Yuji , Masaki Takuro , Yamaguchi Akito , Suzuki Masahiko , Sakai Yasuyuki , Kimura Tomokazu , Takai Manabu , Seike Kensaku , Hashimoto Takahiko , Yamamoto Shingo
Published: December 2019

Background

To study the outcomes and experiences of using metallic stents in treating patients with malignant ureteral obstruction (MUO), we examined the effects of metallic ureteral stenting using the Cook Resonance® stent in the treatment of MUO.

Methods

All patients who had a Resonance metallic stent inserted between April 2015 and March 2018 at one of multiple facilities were prospectively observed with a 1-year follow-up. The primary outcome was the patency rate of the metallic ureteral stent. The secondary outcomes included the complications (e.g., infection and fever).

Results

Although stent insertion was attempted in 50 patients, the stent could not be inserted as a ureteral stent in three patients due to severe ureteral stricture, and one ureteral cancer patient was excluded from the analysis. The remaining 46 patients’ median age was 67 years (range 28–85 years) (16 males, 30 females). Twenty-four patients died during the study; their median survival time was 226 days. The median follow-up period for the censored patients was 355 days (range 16–372 days), and just seven patients were still alive without Resonance failure > 1 year later. The women’s IPSS scores tended to be lower than those of the men. Regarding the OABSS score, although the women’s total score tended to be low, the difference between the men’s and women’s scores was nonsignificant. The bacteria detected from urine culture after stent insertion were more gram-positive than gram-negative.

Conclusion

Metallic ureteric stenting using the Resonance stent is safe and effective for treating MUO. Subjective symptoms were relatively less in the female patients.
Family history information extraction via deep joint learning
Authors: Shi Xue , Jiang Dehuan , Huang Yuanhang , Wang Xiaolong , Chen Qingcai , Yan Jun , Tang Buzhou
Published: December 2019

Background

Family history (FH) information, including family members, side of family of family members (i.e., maternal or paternal), living status of family members, observations (diseases) of family members, etc., is very important in the decision-making process of disorder diagnosis and treatment. However FH information cannot be used directly by computers as it is always embedded in unstructured text in electronic health records (EHRs). In order to extract FH information form clinical text, there is a need of natural language processing (NLP). In the BioCreative/OHNLP2018 challenge, there is a task regarding FH extraction (i.e., task1), including two subtasks: (1) entity identification, identifying family members and their observations (diseases) mentioned in clinical text; (2) family history extraction, extracting side of family of family members, living status of family members, and observations of family members. For this task, we propose a system based on deep joint learning methods to extract FH information. Our system achieves the highest F1- scores of 0.8901 on subtask1 and 0.6359 on subtask2, respectively.
Translating academic research into guidance to support healthcare improvement: how should guidance development be reported?
Authors: Turner Simon , Sharp Charlotte A. , Sheringham Jessica , Leamon Shaun , Fulop Naomi J.
Published: December 2019

Background

There is interest internationally in improving the uptake of research evidence to inform health care quality and safety. This article focusses on guidance development from research studies as one method for improving research uptake. While we recognise that implementation strategies on the ´demand´ side for encouraging the uptake of research are important, e.g. knowledge brokers and university-practice collaborations, this article focusses on the ´production´ aspect of how guidance development is reported and the consequent influence this may have on end-users´ receptivity to evidence, in addition to other demand-side processes.

Main text

The article considers the following question: how is guidance developed and what are the implications for reporting? We address this question by reviewing examples of guidance development reporting from applied health research studies, then describe how we produced guidance for a national study of evidence use in decision-making on adopting innovations. The starting point for reflecting on our experiences is a vignette of the guidance ´launch´ event at a national conference.

Conclusions

Implications for reporting guidance development and supporting improvement are discussed. These include the need to (a) produce reporting standards for the production of guidance to match reporting standards for other research methods, (b) acknowledge the ´informal´ or emergent aspects of producing guidance and its role within a wider knowledge mobilization strategy, (c) consider guidance development from projects as part of a wider knowledge mobilization strategy, and (d) encourage a receptive environment for guidance development and use, including researcher training, durable funding to support impact, and closer relations between research and practice.
Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018
Authors: Zhang Fanfan , Luo Suxian , Gu Jun , Li Zhiquan , Li Kai , Yuan Weifeng , Ye Yu , Li Hao , Ding Zhen , Song Deping , Tang Yuxin
Published: December 2019

Background

In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. To investigate the prevalence and genetic evolution of diarrhea-associated viruses responsible for the outbreaks, a total of 2987 field diarrheal samples collected from 168 pig farms in five provinces in Southern China during 2012–2018 were tested.

Results

Porcine epidemic diarrhea virus (PEDV) was most frequently detected virus with prevalence rates between 50.21 and 62.10% in samples, and 96.43% (162/168) in premises, respectively. Porcine deltacoronavirus (PDCoV) was the second prevalent virus with prevalence rates ranging from 19.62 to 29.19% in samples, and 70.24% (118/168) in premises, respectively. Both transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PoRV) were detected at low prevalence rates of < 3% in samples and 10.12% in premises. In this study, we identified a newly emerged swine acute diarrhea syndrome coronavirus (SADS-CoV) in diarrheal samples of piglets from Fujian province in Southern China, and the prevalence rate of SADS-CoV was 10.29% (7/68). Co-infections of these diarrhea-associated viruses were common. The most frequent co-infection was PEDV with PDCoV, with an average detection rate of 12.72% (380/2987, ranging from 8.26–17.33%). Phylogenetic analysis revealed that PEDVs circulating in Southern China during the last 7 years were clustered with the variant strains of PEDV in genotype IIa. The most frequent mutations were present in the collagenase equivalent (COE) and epitope regions of the spike gene of the PEDVs currently circulating in the field. Genetic relationships of PDCoVs were closely related with Chinese strains, other than those present in the USA, South Korea, Thailand and Lao’s public.

Conclusions

The findings of this study indicated that variant PEDV, PDCoV, and SADS-CoV were leading etiologic agents of porcine diarrhea, and either mono-infections or co-infections of pathogenic enteric CoVs were common in pigs in Southern China during 2012–2018. Thus, significant attention should be paid in order to effectively prevent and control porcine viral diarrhea.
Comparative metabolome analysis of serum changes in sheep under overgrazing or light grazing conditions
Authors: Zhang Jize , Gao Yang , Guo Huiqin , Ding Yong , Ren Weibo
Published: December 2019

Background

Overgrazing is a primary contributor to severe reduction in forage quality and production in Inner Mongolia, leading to extensive ecosystem degradation, sheep health impairment and growth performance reduction. Further studies to identify serum biomarkers that reflect changes in sheep health and nutritional status following overgrazing would be beneficial. We hereby hypothesize that reduced sheep growth performance under overgrazing conditions would be associated with metabolic and immune response alterations. This study used an untargeted metabolomics analysis by conducting ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) of sheep serum under overgrazing and light grazing conditions to identify metabolic disruptions in response to overgrazing.

Results

The sheep body weight gains as well as serum biochemical variables associated with immune responses and nutritional metabolism (immunoglobulin G, albumin, glucose, and nonesterified fatty acids) were significantly decreased with overgrazing compared with light grazing condition. In contrast, other serum parameters such as alanine and aspartate aminotransferase, alkaline phosphatase, total bilirubin, blood urea nitrogen, and interleukin-8 were markedly higher in the overgrazing group. Principal component analysis discriminated the metabolomes of the light grazing from the overgrazing group. Multivariate and univariate analyses revealed changes in the serum concentrations of 15 metabolites (9 metabolites exhibited a marked increase, whereas 6 metabolites showed a significant decrease) in the overgrazing group. Major changes of fatty acid oxidation, bile acid biosynthesis, and purine and protein metabolism were observed.

Conclusions

These findings offer metabolic evidence for putative biomarkers for overgrazing-induced changes in serum metabolism. Target-identification of these particular metabolites may potentially increase our knowledge of the molecular mechanisms of altered immune responses, nutritional metabolism, and reduced sheep growth performance under overgrazing conditions.
Synchronous and metachronous liver metastases in patients with colorectal cancer—towards a clinically relevant definition
Authors: Engstrand Jennie , Strömberg Cecilia , Nilsson Henrik , Freedman Jacob , Jonas Eduard
Published: December 2019

Background

Approximately 25% of patients with colorectal cancer (CRC) will have liver metastases classified as synchronous or metachronous. There is no consensus on the defining time point for synchronous/metachronous, and the prognostic implications thereof remain unclear. The aim of the study was to assess the prognostic value of differential detection at various defining time points in a population-based patient cohort and conduct a literature review of the topic.

Methods

All patients diagnosed with CRC in the counties of Stockholm and Gotland, Sweden, during 2008 were included in the study and followed for 5 years or until death to identify patients diagnosed with liver metastases. Patients with liver metastases were followed from time of diagnosis of liver metastases for at least 5 years or until death. Different time points defining synchronous/metachronous detection, as reported in the literature and identified in a literature search of databases (PubMed, Embase, Cochrane library), were applied to the cohort, and overall survival was calculated using Kaplan-Meier curves and compared with log-rank test. The influence of synchronously or metachronously detected liver metastases on disease-free and overall survival as reported in articles forthcoming from the literature search was also assessed.

Results

Liver metastases were diagnosed in 272/1026 patients with CRC (26.5%). No statistically significant difference in overall survival for synchronous vs. metachronous detection at any of the defining time points (CRC diagnosis/surgery and 3, 6 and 12 months post-diagnosis/surgery) was demonstrated for operated or non-operated patients. In the literature search, 41 publications met the inclusion criteria. No clear pattern emerged regarding the prognostic significance of synchronous vs. metachronous detection.

Conclusion

Synchronous vs. metachronous detection of CRC liver metastases lacks prognostic value. Using primary tumour diagnosis/operation as standardized cut-off point to define synchronous/metachronous detection is semantically correct. In synchronous detection, it defines a clinically relevant group of patients where individualized multimodality treatment protocols will apply.