Tag: pubmed

PLoS Pathog. 2021 Sep 7;17(9):e1009883. doi: 10.1371/journal.ppat.1009883. Online ahead of print.

ABSTRACT

SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.

PMID:34492088 | DOI:10.1371/journal.ppat.1009883

PLoS One. 2021 Sep 7;16(9):e0256978. doi: 10.1371/journal.pone.0256978. eCollection 2021.

ABSTRACT

Kenaf (Hibiscus cannabinus L.) is an industrial crop used as a raw material in various fields and is cultivated worldwide. Compared to high potential for its utilization, breeding sector is not vigorous partially due to laborous breeding procedure. Thus, efficient breeding methods are required for varieties that can adapt to various environments and obtain optimal production. For that, identifying kenaf’s characteristics is very important during the breeding process. Here, we investigated if RGB based vegetative index (VI) could be associated with traits for biomass. We used 20 varieties and germplasm of kenaf and RGB images taken with unmanned aerial vehicles (UAVs) for field selection in early and late growth stage. In addition, measuring the stem diameter and the number of nodes confirmed whether the vegetative index value obtained from the RGB image could infer the actual plant biomass. Based on the results, it was confirmed that the individual surface area and estimated plant height, which were identified from the RGB image, had positive correlations with the stem diameter and node number, which are actual growth indicators of the rate of growth further, biomass could also be estimated based on this. Moreover, it is suggested that VIs have a high correlation with actual growth indicators; thus, the biomass of kenaf could be predicted. Interstingly, those traits showing high correlation in the late stage had very low correlations in the early stage. To sum up, the results in the current study suggest a more efficient breeding method by reducing labor and resources required for breeding selection by the use of RGB image analysis obtained by UAV. This means that considerable high-quality research could be performed even with a tight budget. Furthermore, this method could be applied to crop management, which is done with other vegetative indices using a multispectral camera.

PMID:34492059 | DOI:10.1371/journal.pone.0256978

PLoS One. 2021 Sep 7;16(9):e0256799. doi: 10.1371/journal.pone.0256799. eCollection 2021.

ABSTRACT

BACKGROUND: Health facilities in developing countries are increasingly adopting Electronic Health Records systems (EHRs) to support healthcare processes. However, only limited studies are available that assess the actual use of the EHRs once adopted in these settings. We assessed the state of the 376 KenyaEMR system (national EHRs) implementations in healthcare facilities offering HIV services in Kenya.

METHODS: The study focused on seven EHRs use indicators. Six of the seven indicators were programmed and packaged into a query script for execution within each KenyaEMR system (KeEMRs) implementation to collect monthly server-log data for each indicator for the period 2012-2019. The indicators included: Staff system use, observations (clinical data volume), data exchange, standardized terminologies, patient identification, and automatic reports. The seventh indicator (EHR variable Completeness) was derived from routine data quality report within the EHRs. Data were analysed using descriptive statistics, and multiple linear regression analysis was used to examine how individual facility characteristics affected the use of the system.

RESULTS: 213 facilities spanning 19 counties participated in the study. The mean number of authorized users who actively used the KeEMRs was 18.1% (SD = 13.1%, p<0.001) across the facilities. On average, the volume of clinical data (observations) captured in the EHRs was 3363 (SD = 4259). Only a few facilities(14.1%) had health data exchange capability. 97.6% of EHRs concept dictionary terms mapped to standardized terminologies such as CIEL. Within the facility EHRs, only 50.5% (SD = 35.4%, p< 0.001) of patients had the nationally-endorsed patient identifier number recorded. Multiple regression analysis indicated the need for improvement on the mode of EHRs use of implementation.

CONCLUSION: The standard EHRs use indicators can effectively measure EHRs use and consequently determine success of the EHRs implementations. The results suggest that most of the EHRs use areas assessed need improvement, especially in relation to active usage of the system and data exchange readiness.

PMID:34492070 | DOI:10.1371/journal.pone.0256799

PLoS One. 2021 Sep 7;16(9):e0256630. doi: 10.1371/journal.pone.0256630. eCollection 2021.

ABSTRACT

Pneumonia is a respiratory infection caused by bacteria or viruses; it affects many individuals, especially in developing and underdeveloped nations, where high levels of pollution, unhygienic living conditions, and overcrowding are relatively common, together with inadequate medical infrastructure. Pneumonia causes pleural effusion, a condition in which fluids fill the lung, causing respiratory difficulty. Early diagnosis of pneumonia is crucial to ensure curative treatment and increase survival rates. Chest X-ray imaging is the most frequently used method for diagnosing pneumonia. However, the examination of chest X-rays is a challenging task and is prone to subjective variability. In this study, we developed a computer-aided diagnosis system for automatic pneumonia detection using chest X-ray images. We employed deep transfer learning to handle the scarcity of available data and designed an ensemble of three convolutional neural network models: GoogLeNet, ResNet-18, and DenseNet-121. A weighted average ensemble technique was adopted, wherein the weights assigned to the base learners were determined using a novel approach. The scores of four standard evaluation metrics, precision, recall, f1-score, and the area under the curve, are fused to form the weight vector, which in studies in the literature was frequently set experimentally, a method that is prone to error. The proposed approach was evaluated on two publicly available pneumonia X-ray datasets, provided by Kermany et al. and the Radiological Society of North America (RSNA), respectively, using a five-fold cross-validation scheme. The proposed method achieved accuracy rates of 98.81% and 86.85% and sensitivity rates of 98.80% and 87.02% on the Kermany and RSNA datasets, respectively. The results were superior to those of state-of-the-art methods and our method performed better than the widely used ensemble techniques. Statistical analyses on the datasets using McNemar’s and ANOVA tests showed the robustness of the approach. The codes for the proposed work are available at https://github.com/Rohit-Kundu/Ensemble-Pneumonia-Detection.

PMID:34492046 | DOI:10.1371/journal.pone.0256630

PLoS One. 2021 Sep 7;16(9):e0256612. doi: 10.1371/journal.pone.0256612. eCollection 2021.

ABSTRACT

This study aims to explore whether higher education and science popularization can achieve coordinated growth with temporal and spatial characteristics. Selecting the provincial regions of the Yangtze River Economic Belt in China as cases with data from the national statistics administrations (such as China Statistical Yearbook), this study uses entropy weight analysis, TOPSIS, GM(1,1) gray prediction methods and coupling coordination degree model to evaluate the coordinated growth status. The key findings are: (1) the annual budget per student, and the number of science and technology museums affect both systems more obviously; (2) the overall performances of science popularization fluctuate more obviously than those of higher education; (3) the coordinated growth performances of the two systems in most regions remain mild fluctuations and keep relatively stable coordinated status, however, temporal and spatial variation tendencies do exist among regions. Therefore, corresponding countermeasures should be implemented: generally, national authority needs to involve in coordination activities among regions; the regions with satisfactory coordinated growth performances need more creative approaches to maintain the coordinated growth interactions; the regions at the transitioning status need to prevent the grade decline and upgrade the performances; the regions with lagging performances need to stop the decline and reduce the gaps with others. The novelties include analyzing the coordinated growth interaction mechanism between the two, selecting indices to assess the abstract interaction mechanism precisely, proposing suggestions based on temporal and spatial comparisons of the coordinated growth performances, etc.

PMID:34492057 | DOI:10.1371/journal.pone.0256612

PLoS Negl Trop Dis. 2021 Sep 7;15(9):e0009762. doi: 10.1371/journal.pntd.0009762. Online ahead of print.

ABSTRACT

BACKGROUND: Entamoeba infections have major impact on millions of the people worldwide. Entamoeba histolytica has long been accepted as the only pathogenic species. However, recent reports of other Entamoeba spp. in symptomatic cases have raised questions on their pathogenicity.

METHODOLOGY/PRINCIPAL FINDINGS: Total 474 stool samples and 125 liver aspirates from patients with intestinal and extra intestinal manifestations and from community were included. Sewage samples from the hospital and the city were also included. Microscopic examination and molecular detection were performed to detect presence of E. histolytica/ dispar/ moshkovskii/ bangladeshi. The associated demographic and socioeconomic factors were statistically analyzed with the presence of Entamoeba. Microscopy detected Entamoeba spp. in 5.4% stool and 6.4% liver aspirate samples. Through nested multiplex PCR, prevalence of Entamoeba spp. in intestinal and extra-intestinal cases was 6.6% (20/301) and 86.4% (108/125) respectively and in asymptomatic population was 10.5% (13/123). Sewage samples did not show presence of any Entamoeba spp. Uneducated subjects, low economic conditions, untreated drinking water, consumption of raw vegetables and habit of not washing hands before meals were significantly associated with presence of Entamoeba spp.

CONCLUSIONS: E. histolytica still remains the only Entamoeba spp. in invasive extra intestinal infections. E. dispar was detected in both asymptomatic and symptomatic intestinal infections. Routine identification of Entamoeba spp. should incorporate PCR based detection methods.

PMID:34492023 | DOI:10.1371/journal.pntd.0009762

PLoS One. 2021 Sep 7;16(9):e0254287. doi: 10.1371/journal.pone.0254287. eCollection 2021.

ABSTRACT

Dog importation data from 2018-2020 were evaluated to ascertain whether the dog importation patterns in the United States changed during the COVID-19 pandemic, specifically with regard to denial of entry. Dog denial of entry reports from January 1, 2018, to December 31, 2020, stored within the Centers for Disease Control and Prevention (CDC) Quarantine Activity Reporting System (QARS), were reviewed. Basic descriptive statistics were used to analyze the data. Reason for denial, country of origin, and month of importation were all examined to determine which countries of origin resulted in the largest number of denials, and whether there was a seasonal change in importations during the COVID-19 pandemic (2020), compared to previous years (2018 and 2019). During 2020, CDC denied entry to 458 dogs. This represents a 52% increase in dogs denied entry compared to the averages in 2018 and 2019. Dogs were primarily denied entry for falsified rabies vaccination certificates (56%). Three countries exported 74% of all dogs denied entry into the United States, suggesting that targeted interventions may be needed for certain countries. Increased attempts to import inadequately vaccinated dogs from countries with canine rabies in 2020 may have been due to the increased demand for domestic pets during the COVID-19 pandemic. Educational messaging should highlight the risk of rabies and the importance of making informed pet purchases from foreign entities to protect pet owners, their families, and the public.

PMID:34492037 | DOI:10.1371/journal.pone.0254287

PLoS One. 2021 Sep 7;16(9):e0254577. doi: 10.1371/journal.pone.0254577. eCollection 2021.

ABSTRACT

BACKGROUND: Circulating levels of the endogenous inhibitor of nitric oxide synthase, asymmetric dimethylarginine (ADMA), are positively associated with the prevalence of metabolic syndrome (MetS) in cross-sectional investigations. It is unclear if circulating ADMA and other methylarginines are associated with incident MetS prospectively.

METHODS: We related circulating ADMA, symmetric dimethylarginine (SDMA), L-arginine (ARG) concentrations (measured with a validated tandem mass spectrometry assay) and the ARG/ADMA ratio to MetS and its components in 2914 (cross-sectional analysis, logistic regression; mean age 58 years, 55% women) and 1656 (prospective analysis, Cox regression; mean age 56 years, 59% women) individuals from the Framingham Offspring Study who attended a routine examination.

RESULTS: Adjusting for age, sex, smoking, and eGFR, we observed significant associations of ADMA (direct) and ARG/ADMA (inverse) with odds of MetS (N = 1461 prevalent cases; Odds Ratio [OR] per SD increment 1.13, 95%CI 1.04-1.22; and 0.89, 95%CI 0.82-0.97 for ADMA and ARG/ADMA, respectively). Upon further adjustment for waist circumference, systolic and diastolic blood pressure, glucose, high-density lipoprotein cholesterol, and triglycerides, we observed a positive relation between SDMA and MetS (OR per SD increment 1.15, 95% CI 1.01-1.30) but the other associations were rendered statistically non-significant. We did not observe statistically significant associations between any of the methylarginines and the risk of new-onset MetS (752 incident events) over a median follow-up of 11 years.

CONCLUSION: It is unclear whether dimethylarginines play an important role in the incidence of cardiometabolic risk in the community, notwithstanding cross-sectional associations. Further studies of larger samples are needed to replicate our findings.

PMID:34492019 | DOI:10.1371/journal.pone.0254577

PLoS One. 2021 Sep 7;16(9):e0255375. doi: 10.1371/journal.pone.0255375. eCollection 2021.

ABSTRACT

OBJECTIVE: Lung cancer patients with interstitial lung disease (ILD) are prone for higher morbidity and mortality and their treatment is challenging. The purpose of this study is to investigate whether the survival of lung cancer patients is affected by the presence of ILD documented on CT.

MATERIALS AND METHODS: 146 patients with ILD at initial chest CT were retrospectively included in the study. 146 lung cancer controls without ILD were selected. Chest CTs were evaluated for the presence of pulmonary fibrosis which was classified in 4 categories. Presence and type of emphysema, extent of ILD and emphysema, location and histologic type of cancer, clinical staging and treatment were evaluated. Kaplan-Meier estimates and Cox regression models were used to assess survival probability and hazard of death of different groups. P value < 0.05 was considered significant.

RESULTS: 5-year survival for the study group was 41% versus 48% for the control group (log-rank test p = 0.0092). No significant difference in survival rate was found between the four different categories of ILD (log-rank test, p = 0.195) and the different histologic types (log-rank test, p = 0.4005). A cox proportional hazard model was used including presence of ILD, clinical stage and age. The hazard of death among patients with ILD was 1.522 times that among patients without ILD (95%CI, p = 0.029).

CONCLUSION: Patients with lung cancer and CT evidence of ILD have a significantly shorter survival compared to patients with lung cancer only. Documenting the type and grading the severity of ILD in lung cancer patients will significantly contribute to their challenging management.

PMID:34492020 | DOI:10.1371/journal.pone.0255375

PLoS Comput Biol. 2021 Sep 7;17(9):e1009347. doi: 10.1371/journal.pcbi.1009347. Online ahead of print.

ABSTRACT

We construct a recursive Bayesian smoother, termed EpiFilter, for estimating the effective reproduction number, R, from the incidence of an infectious disease in real time and retrospectively. Our approach borrows from Kalman filtering theory, is quick and easy to compute, generalisable, deterministic and unlike many current methods, requires no change-point or window size assumptions. We model R as a flexible, hidden Markov state process and exactly solve forward-backward algorithms, to derive R estimates that incorporate all available incidence information. This unifies and extends two popular methods, EpiEstim, which considers past incidence, and the Wallinga-Teunis method, which looks forward in time. We find that this combination of maximising information and minimising assumptions significantly reduces the bias and variance of R estimates. Moreover, these properties make EpiFilter more statistically robust in periods of low incidence, where several existing methods can become destabilised. As a result, EpiFilter offers improved inference of time-varying transmission patterns that are advantageous for assessing the risk of upcoming waves of infection or the influence of interventions, in real time and at various spatial scales.

PMID:34492011 | DOI:10.1371/journal.pcbi.1009347