bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of the COVID-19 epidemic in Ireland under mitigation
Authors: Cazelles Bernard , Yen Benjamin Nguyen Van , Champagne Clara , Comiskey Catherine 
Published: January 2021

Abstract
Background: In Ireland and across the European Union, cases of COVID-19 continue to rise with recent increases in reported cases following a period of stability. Public health interventions continue in their attempts to control the epidemic in spite of a lack of information on the scale of silent transmission. Methods: To tackle this challenge and the non-stationary aspect of the epidemic we used a modified SEIR stochastic model with time-varying parameters, following Brownian process. This model is coupled with Bayesian inference (PMCMC) for parameter estimation and used mainly confirmed reported hospitalized cases. Results: Mitigation measures provided an 80% reduction in transmission between March and May 2020. By end of October our estimated seroprevalence rate was 1.1% (95% CI: 0.5%–2.8%) far from herd immunity. We estimated that the proportion of asymptomatic transmission was approximately 40% but with large uncertainty (95% CI: 14%–73%). Finally we demonstrate that the available observed confirmed cases are not reliable for any analysis owing to the fact that their reporting rate has greatly evolved. Conclusion: We provide the first estimations of the dynamics of the COVID-19 epidemic in Ireland and its key parameters. We also quantify the effects of mitigation measures on the virus transmission before, during and after mitigation. Our results demonstrate that Ireland has significantly reduced transmission by employing mitigation measures, physical distancing and lockdown. This has to date avoided the saturation of healthcare infrastructures, flattened the epidemic curve and likely reduced mortality. However, as mitigation measures change silent transmission remain an ongoing challenge.
Adherence to TB Treatment Remains Low during Continuation Phase among Adult Patients in Northwest Ethiopia
Authors: Gashu kassahun Dessie , Gelaye Kassahun Alemu , Tilahun Binyam 
Published: January 2021

Abstract
Background: Adherence to Tuberculosis (TB) treatment remained a challenge for TB treatment programs. However, paucity of evidences specifically during continuation phase where the treatment is mainly patient-centered. This study aimed to determine the level and determinants of adherence to TB treatment among adult patients during continuation phase.Methods: We deployed a facility-based cross-sectional study design supplemented with lived experiences and perspectives of focal care providers. The study population included all adult (≥18 years) TB patients enrolled in the continuation treatment phase and TB focal care providers (for key-informant interviews). The study included 307 participants from 22 health facilities. Nine TB focal care providers were purposively selected for key-informant interviews. A shorter form, 11-item ARMS (adherence to refill and medication scale) was used for measuring adherence. Binary logistic regression was applied to identify factors associated with patient adherence. The audio data was transcribed, coded and categorized into themes using OpenCode software. The interpretation and analysis were conducted using thematic analysis.Results: Among 307 participants, 197 (64.2%) [95% CI (58.6% - 69.4%)] were adhere to TB treatment. A multi-variable analysis shown that secondary education (AOR = 4.138, 95% CI; 1.594-10.74); good provider-patient relationship (AOR=1.863, 95% CI; 1.014-3.423); good knowledge on TB treatment (AOR=1.845, 95% CI; 1.012-3.362) and middle family wealth (AOR= 2.646, 95% CI; 1.360-5.148) have shown significant association with adherence. Many patients mentioned that forgetfulness, traveling away from home without pills, and feeling sick were major reasons for non-adherence to TB treatment. Conclusions: The study indicated that patients’ adherence to TB treatment remains low during continuation phase. The patient’s education level, knowledge, family wealth, and provider-patient relationship were found positively associated with patient adherence. Forgetfulness, traveling away, and feeling sick were major reasons for non-adherence to TB treatment. Interventional studies are needed on those factors to improve patient adherence to TB treatment during continuation phase.
Analysis of Financial Performance and Environmental Sustainability of Coldwater Inland Fisheries in Sikkim Himalaya
Authors: Chettri Kul Bahadur , Kundu Ruma 
Published: January 2021

Abstract
This paper analyses the financial performances in terms of productivity and profitability indices and environmental sustainability with regards to Maximum Sustainable Yield (MSY) through the application of the Gordon-Schaefer Model for the coldwater Primary Fishermen Cooperative Society (PFCS). For this purpose, data has been collected from the secondary sources for the periods 2013-14 to 2018-19. The panel data analysis was carried out to derived the results using the method of ordinary least squares. The study found that PFCS such as Sribadam, Maneybong-Sopakha and Mangshilla have performed better in financial management but there is a probability of thread of sustainability in the future because in some of the periods their actual yield surpasses the MSY. On the other hand, PFCS like Rimbik, Chujachen and Dalep have not been able to bring their financial performances up to the mark because they were more concerned for sustainability. Excessive extraction of fishes from the water bodies for higher profit motive may lead to less availability for the coming generations. The study suggests that in aquaculture or fish farming, there should maintain an equilibrium between financial benefits and environmental sustainability and the resource should be utilised on a sustainable basis.
Extreme Ecological Niche Differences Lead to Extreme Postzygotic Ecological Isolation: A Case of Hybridization Between Carnivorous and Herbivorous Cyprinidae Fishes
Authors: Gu Haoran , Wang Yuanfu , Wang Haoyu , He You , Deng Sihong , He Xingheng , Wu Yi , Xing Kaiyan , Gao Xue , He Xuefu , Wang Zhijian 
Published: January 2021

Abstract
Background: Postzygote isolation is an important part of species isolation, especially for fish, and it can be divided into two aspects: genetic isolation and ecological isolation. With the increase in parental genetic distance, the intensity of genetic isolation between them also increases. Will the increase in parental ecological niche differences also lead to the increase in ecological isolation intensity between them? This question is difficult to answer based on the current literature due to the lack of hybridization cases of extreme ecological niche parents.Results: Cyprinidae fish parents (Schizothorax wangchiachii and Percocypris pingi) with extreme ecological niches (herbivorous and carnivorous) and their F1 hybrids were used as research objects. Fish and periphytic algae were selected as food corresponding to different parental resources. The foraging-related traits of these hybrids are generally the same between parents; however, the intermediate foraging traits of hybrids did not result in intermediate foraging performance for parental resources, and these hybrids could hardly forage for parental resources. The poor foraging performance of these hybrids for parental resources was caused not only by the decline in the foraging ability of these hybrids but, more importantly, by the decrease in foraging activity. Interestingly, these hybrids initially showed a high interest in foraging small fishes; however, after the first successful capture, these hybrids had difficulty ingesting fish and spit them out, which led to the subsequent decrease in foraging activity. We designed a series of experiments to explore the mechanism of the fish spitting of these hybrids, excluding the taste and the size of prey, and found that the decrease in their pharyngeal tooth puncture ability may be the reason. Conclusions: This study was the first to demonstrate that these parents with extreme niche differences will produce extreme postzygotic ecological isolation for parental resources. The poor foraging performance of these hybrids for parental resources is mainly due to the decrease in foraging activity. Interestingly, these hybrids have obvious fish-spitting behaviour, which is a typical example of the contradiction between intermediate traits and parental resources.
Charlson Comorbidity Index Is Predictive of Postoperative Clinical Outcome After Single Level Posterior Lumbar Interbody Fusion Surgery: a Single-center Study
Authors: Shinohara Kensuke , Ugawa Ryo , Arataki Shinya , Nakahara Shinnosuke , Takeuchi Kazuhiro 
Published: January 2021

Abstract
Background. In several previous studies Charlson comorbidity Index (CCI) score was associated with postoperative complications, mortality and re-admission. There are few reports about the influence of CCI score on postoperative clinical outcome. The purpose of this study was to investigate the influence of comorbidities as calculated with CCI on postoperative clinical outcomes after PLIF.Methods. 366 patients who underwent an elective primary single level PLIF were included. Postoperative clinical outcome was evaluated with the Japanese Orthopaedic Association lumbar score (JOA score). The correlation coefficient between the CCI score and postoperative improvement in JOA score was investigated. Patients were divided into three groups according to their CCI score (0, 1 and 2+). JOA improvement rate, length of stay (LOS) and direct cost were compared between each group. Postoperative complications were also investigated.Results. There was a weak negative relationship between CCI score and JOA improvement rate (r = -0.20). LOS and direct cost had almost no correlation with CCI score. The JOA improvement rate of Group 0 and Group 1 was significantly higher than Group 2+. LOS and direct cost were also significantly different etween Group 0 and Group 2+. There were 14 postoperative complications. Adverse postoperative complications were equivalently distributed in each group, and not associated with the number of comorbidities.Conclusions. A higher CCI score leads to a poor postoperative outcome. The recovery rate of patients with two or more comorbidities was significantly higher than in patients without comorbidities. However, the CCI score did not influence LOS and increased direct costs. The surgeon must take into consideration the patient’s comorbidities when planning a surgical intervention in order to achieve a good clinical outcome.
Evaluation of Sleep Disorder in Orthopaedic Trauma Patients: a Retrospective Analysis of 1129 Cases
Authors: Yang Hai , Liu Yi-jia , Ye Jia-lu , Zhao Li-hong , Li Ling-li , Hou Xiao-ling 
Published: January 2021

Abstract
Background In the ward of trauma center, It’s not unusual that the patients have sleep disorder, especially in the acute injury patients. Meanwhile, there is substantial evidence that sleep disorder is a predictor of depression and the important features of posttraumatic stess disorder.Methods From April 2018 to July 2019, all orthopaedic trauma patients were included in the retrospective study. Patients with mental impairment and craniocerebral injury were excluded from the study. Basic demographic data were collected. Pittsburgh sleep quality index(PSQI) was used to evaluate sleep quality, Visual Analog Scale (VAS) was used to evaluate physical pain, Pittsburgh sleep quality index(PSQI) was used to evaluate sleep quality, Barthel Index (BI) was used to evaluate activities of daily living(ADL) and Injury Severity Score (ISS) classification in medical records were collected. Univariate linear regression analysis and multivariate linear regression analysis were used to identify independently related factors.Results The average PSQI score was 6.3 (±4.0). Five hundred eighty-one (51.4%) patients had a PSQI score more than 5, indicating the presence of sleep disorder. The PSQI score was more than 10 in one hundred seventy-four (15.4%) patients. Univariate statistical analysis showed that age, gender, education, ADL (activities of daily living), and ISS classification were associated with increased PSQI scores. Marital status and pain were not associated with increased PSQI scores. When we used multivariate analysis to control for confounding variables, the gender, ADL, and ISS classification remained independently associated with PSQI (P =0.002, <0.000, and 0.002, respectively).Conclusions In our study, the sleep disorder is both common (51.4% PSQI >5) and serious (15.4% PSQI >10) in patients who suffered from traumatic orthopaedic injury. The following factors are closed associated with sleep disorder: gender, ADL and ISS classification. Besides, age and education level have independently impact on sleep quality. Unexpectedly, we find the VAS of pain was not independently associated with seriousness of sleep quality. This is inconsistent with the results reported in some literature.
DNA Repair-related Gene Signature In Predicting Prognosis Of Colorectal Cancer Patients
Authors: Lv Min-Yi , Wang Wei , Zhong Min-Er , Cai Du , Fan Dejun , Li Cheng-Hang , Kou Wei-Bin , Huang Ze-Ping , Duan Xin , Zhu Qi-Qi , Hu Chuling , He Xiaosheng , Gao Feng 
Published: January 2021

Abstract
Background: Increasing evidence has depicted that DNA repair-related genes (DRGs) are associated with the prognosis of colorectal cancer (CRC) patients. Thus, the aim of this study was to evaluate the impact of DNA repair-related gene signature (DRGS) in predicting the prognosis of CRC patients.Method: In this study, we retrospectively analyzed the gene expression profiles from six CRC cohorts. A total of 1,768 CRC patients with complete prognostic information were divided into training cohort (n=566) and 2 validation cohorts (n=624 and 578, respectively). LASSO-Cox model was applied to construct a prediction model.Results: Among 1,376 DRGs, a prognostic DRGS consisting of 11 distinct genes stratified patients into high and low -risk groups. In all cohorts, patients in the high -risk groups had significantly worse disease-free survival (DFS) compared with those in the low-risk groups (training cohort: hazard ratio (HR) = 2.40, 95% confidence interval (CI) = 1.67-3.44, P < 0.001; validation-1: HR = 2.20, 95% CI = 1.38-3.49, P < 0.001; validation-2 cohort: HR = 2.12, 95% CI = 1.40-3.21, P < 0.001). After adjusting for clinical features and molecular types, DRGS still remained as an independent prognostic marker in multivariable analysis (training cohort: HR = 1.80; 95% CI = 1.22-2.64, P = 0.0028; validation-1: HR = 1.85, 95% CI = 1.13-3.02, P = 0.015; validation-2 cohort: HR = 1.75, 95% CI = 1.15-2.65, P = 0.0085). Gene Set Enrichment Analysis (GSEA) showed significant dysregulated pathways in the high-risk involved in angiogenesis, KRAS signaling, epithelial mesenchymal transit (EMT) and myogenesis (P < 0.001).Conclusions: DNA repair-related gene signature is a favorable prognostic model for patients with CRC, and further studies are necessary to validate the exact biological mechanism.
Impact Of Pre-event Testing And Quarantine On Reducing The Risk Of COVID-19 Epidemic Rebound: A Modelling Study
Authors: WONG Ngai Sze , LEE Shui Shan , MITCHELL Kate M. , Yeoh Eng-kiong , Wang Cheng 
Published: January 2021

Abstract
BACKGROUND With the evolving growth of the COVID-19 epidemic, travel restriction policies would need to be adjusted accordingly. Prohibition of mass event may be relaxed for social and economic benefits when virus transmission stops but could bear the risk of epidemic rebound. Against the background of the varied SARS-CoV-2 prevalence internationally, we modelled the potential impacts of pre-event interventions on epidemic risk of holding a mass event when COVID-19 is under control. METHODS We developed a mathematical model of SARS-CoV-2 transmission in Guangdong Province, China, where local virus transmission ceased to occur. A large-scale international trade fair was assumed to be held, with influx of people from overseas and rest of China over a short period of time, who participated for 2-week. Scenarios of pre-event intervention (none, quarantine arrangement and polymerase chain reaction (PCR) testing for participants) were compared. The influence of contact pattern, SARS-CoV-2 prevalence outside the province and China, and testing coverage were examined in sensitivity analyses. RESULTS In basecase scenario (no event), the epidemic has been under control since March 2020. The event would lead to the detection of 1% more confirmed cases by 31 July when community contact rate increased to pre-epidemic level. In event scenario without additional interventions, there would be 599 (93%) more new infections comparing with basecase scenario. To avert new infections, quarantining all participants before the event would be the most effective strategy, followed by quarantining all overseas participants and testing all other participants, and testing all participants before the event and on day 7. However, testing strategy is likely to be affected by the SARS-CoV-2 prevalence outside the event province. CONCLUSIONS Pre-event interventions are effective for reducing the risk of epidemic rebound caused by an international large-scale event. Universal testing for participants is likely to be an effective and feasible intervention.
Machine Learning-based CT&nbsp;Radiomics Model Distinguishes COVID-19 From Non-COVID-19 Pneumonia&nbsp;
Authors: Chen Hui Juan , Mao Li , Chen Yang , Yuan Li , Wang Fei , Li Xiuli , Cai Qinlei , Qiu Jie , Tian Jie , Chen Feng 
Published: January 2021

Abstract
Background: To develop a machine learning-based CT radiomics model is critical for the accurate diagnosis of the rapid spread Coronavirus disease 2019 (COVID-19).Methods: In this retrospective study, a total of 326 chest CT exams from 134 patients (63 confirmed COVID-19 patients and 71 non-COVID-19 patients) were collected from January 20 to February 8, 2020. A semi-automatic segmentation procedure was used to delineate the region of interest (ROI), and the radiomic features were extracted. The Support Vector Machine(SVM) model was built on the combination of the 4 groups of features, including radiomic features, traditional radiological features, quantifying features and clinical features, by repeated cross-validation procedure and the performance on the time-independent testing cohort was evaluated by the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity and specificity. Results: For the SVM model that built on the combination of 4 groups of features(integrated model), the per-exam AUC of 0.925(95% CI: 0.856 to 0.994) was reached for differentiating COVID-19 on the testing cohort, and the sensitivity and specificity were 0.816(95% CI: 0.651 to 0.917) and 0.923(95% CI: 0.621 to 0.996), respectively. For the SVM models that built on radiomic features, radiological features, quantifying features and clinical features individually, the AUC on the testing cohort reached 0.765, 0.818, 0.607 and 0.739 respectively, significantly lower than the integrated model, except for the radiomic model.Conclusion: The machine learning-based CT radiomics models may accurately detect COVID-19, helping clinicians and radiologists to identify COVID-19 positive cases.
The Magnitude and Profile, Distribution Patterns and Associated Factors of AIDS-related Opportunistic Diseases in Adults on Antiretroviral Therapy in Malawi
Authors: Salema Hemson Hendrix 
Published: January 2021

Abstract
Background

Over one million people in Malawi are HIV infected and many suffer from AIDS-related opportunistic diseases (ODs). However, little is known about the clinical profiles of these ODs and their associated risk factors. We describe the burden and spectrum of ODs in HIV-infected adults on combined antiretroviral therapy (cART) since the countrywide scale-up of free HIV treatment.
Methods

A retrospective chart review was conducted across all three regions in Malawi. Clinical data on prevalent and incident AIDS-related ODs in patients commenced cART from 2004–2015 were abstracted from case notes between March and May 2016.
Results

A total of 9,953 patients were included in the analysis. 60.84% were females and relatively younger than males with mean age difference of 4.75 ± 2.9 years. Overall mean age was 40.72 ± 12.19 years. 86.85% were young and middle-aged adults of productive age-group (15–54 years). 65.08% were urban residents and 59.55% were from Southern region. 12,814 AIDS-related opportunistic events were extracted: 56.54% were prevalent AIDS-defining clinical conditions and the rest were incident AIDS-recurrent cases. 7.65% of patients had no OD manifestation. Commonly occurring aetiological agents were mycobacterial (36.31%), bacterial (20.77%), fungal (15.77%) and viral (15.11%) pathogens. Overall, the most prevalent ODs were mycobacterium tuberculosis (34.39%), bacterial pneumonia (11.21%), nontyphoid Salmonella bacteraemia (9.57%), HIV-wasting syndrome (8.93%), candidiasis (6.81%), isosporiasis (5.24%), pneumocystis pneumonia (4.02%) and cryptococcal meningitis (3.72%). In the multivariable logistic regression, healthcare facility types, gender, age-group, geographical location, CD4 cell count, viral load levels, treatment initiation eligibility criteria and low socio-economic status were statistically significantly associated with manifestation of AIDS-related opportunistic diseases.
Conclusion

ODs were highly pervasive among HIV-infected adults in Malawi including treatment-experienced patients which affect largely the productive population. Strategies for effective prevention, early detection and proactive management of AIDS-related opportunistic diseases need to be established and strengthened across all patient groups, in all regions and across all ART health facilities regardless of their levels.
Fatty Acid Composition and Eco-Agronomical Traits of Lallemantia Species Modulated Upon Exposed To Arbuscular Mycorrhizal Fungi and Nano Iron Chelate Fertilizers Under Water Deficit Conditions
Authors: Paravar Arezoo , Farahani Saeideh Maleki , Rezazadeh Ali Reza 
Published: January 2021

Abstract
Background: Application nano iron chelate and AMF fertilizer can increase plants' tolerance against water deficit stress. The main objectives of the current study were to investigate the effect of arbuscular mycorrhizal fungi (AMF) and nano iron chelate fertilizer under drought stress on grain yield, leaf chlorophyll contents, root colonization, oil percentage, and fatty acids profile of Lallemantia species. The experiment was carried out as a factorial based on a complete randomized block design consisting of three factors of irrigation levels of 90 (I90), 60 (I60), and 30% (I30) depletion of available soil water (ASW)), fertilizer levels of control (no fertilizer), AMF inoculation, and nano iron chelate, and plant species of Lallemantia (L. iberica and L. royleana) at the Research Farm of College of Agriculture, Shahed University, Tehran, Iran, in 2018/2019. Results: The results showed that increasing water deficit stress significantly decreased the above traits while applying nano iron and AMF fertilizers significantly increased them across water treatments. AMF fertilizer inoculation significantly improved both species yield. Higher root colonization by AMF inoculation enhanced seed oil and fatty acids (palmitic acid, stearic acid, oleic acid, linoleic acid, linolenic acid, arachidic acid, and Eicosenoic acid). In contrast, applying nano iron chelate by increasing chlorophyll content in any irrigation regime could enhance seed oil and some fatty acids such as palmitoleic acid. Conclusions: Water deficit stress and application of fertilizers had different effects on both species. L. iberica, compared to L. royleana, had the most tolerance to water deficit stress and the highest dependence on AMF inoculation. Overall, these results demonstrated that the application of AMF could improve major features of Lallemantia species under deficit irrigation conditions, especially at the I60 irrigation level.