bluuebunny/crossref_metadata_2025 huggingface dataset:
Cutandia rigescens (Poaceae) a new species to the flora of Iran: distribution, taxonomy and ecology

Authors: TIRGAN SAMEREH , NAQINEZHAD ALIREZA , HOSEINZADEH ZEINAB
Published: October 2019

During a revision of the genera Cutandia and Catapodium in Iran (Poaceae: subtribe Parapholiinae), the occurrence of Cutandia rigescens was confirmed for the first time on sand dunes along the southern shore of the Caspian Sea in the northern part of the country. Twenty-five important morphological and anatomical characters were examined in an attempt to separate this species from Cutandia dichotoma, C. memphitica and Catapodium rigidum, similar taxa already recorded from Iran. In addition to the morphology of the glume, lemma and palea, the most diagnostic characters proved to be: size and shape of long cells in the intercostal zone of leaf epidermis, size of short cells and long cells in the costal zone of the leaf epidermis, size of angular prickles in the leaf epidermis, number and size of vascular bundles in a cross-section of the culm, the presence or absence of parenchymatous cells in the center of the culm and number of florets. Distribution map for Iran, together with vegetation data were presented for all four species.
Flood and Inundation Forecasting in the Sparsely Gauged Transboundary Chenab River Basin Using Satellite Rain and Coupling Meteorological and Hydrological Models
Authors: Asghar Malik Rizwan , Ushiyama Tomoki , Riaz Muhammad , Miyamoto Mamoru
Published: October 2019

Flood forecasting in a transboundary river basin is challenging due to insufficient data sharing between countries in the upper and lower reaches of a basin. A solution is the use of satellite-observed rainfall and numerical weather prediction (NWP) for hydrological forecasting. We applied this method to the transboundary sparsely gauged Chenab River basin in Pakistan and India to reproduce the exceptionally high flood in 2014. We employed global NWPs by three weather centers to consider forecast uncertainty and downscaled them using the Weather Research and Forecasting (WRF) Model to prepare precipitation inputs. For hydrological simulations, we used a kinematic wave model, the Integrated Flood Analysis System (IFAS), for the upper-reach basin with high mountains and steep slopes, and we used a diffusive-wave rainfall–runoff–inundation (RRI) model for low altitudes and mild slopes. In our forecasting experiment, the precipitation by the global NWP was not able to predict flood peaks consistently. However, the downscaled rainfall by regional NWP showed good performance in predicting flood waves quantitatively, and a multimodel approach provided added value in issuing reliable warning as early as 6 days in advance. A confident streamflow forecasting near the border of the countries also led to reliable inundation forecasting by the RRI model in the lower-reach basin.
Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs
Authors: Gyawali Abiskar , Shrestha Vivek , Guill Katherine E. , Flint-Garcia Sherry , Beissinger Timothy M.
Published: October 2019

Background

Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs.

Results

In this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960’s, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306 k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P ≤ 0.00001) for PH. The results from our single-plant GWAS were further validated by bulk segregant analysis (BSA) for PH. BSA sequencing was performed on the same population by selecting tall and short plants as separate bulks. This approach identified 37 genomic regions for plant height. Of the 25 significant SNPs from GWAS, the three most significant SNPs co-localize with regions identified by BSA.

Conclusion

Overall, this study demonstrates that sp-GWAS coupled with BSA can be a useful tool for detecting significant SNPs and identifying candidate genes. This result is particularly useful for species/populations where association panels are not readily available.
New different origins and evolutionary processes of AP2/EREBP transcription factors in Taxus chinensis
Authors: Zhang Meng , Chen Ying , Jin Xiaofei , Cai Yuxin , Yuan Yuanyuan , Fu Chunhua , Yu Longjiang
Published: October 2019

Background

Taxusspp. produces the anticancer drug, taxol, and hence is planted as an industrial crop in China. APETALA2/ethylene response element binding proteins (AP2/EREBPs) are the key regulators of plant development, growth, and stress responses. Several homologues control taxol biosynthesis. Identifying the AP2/EREBP proteins fromTaxusis important to increase breeding and production and clarify their evolutionary processes.

Results

Among the 90 genes from multiTaxus chinensistranscriptome datasets, 81 encoded full-length AP2-containing proteins. A domain structure highly similar to that of angiosperm AP2/EREBPs was found in 2 AP2, 2 ANT, 1 RAV, 28 dehydration-responsive element-binding proteins, and 47 ethylene-responsive factors contained, indicating that they have extremely conservative evolution processes. A new subgroup protein, TcA3Bz1, contains three conserved AP2 domains and, a new domain structure of AP2/EREBPs that is different from that of known proteins. The new subtype AP2 proteins were also present in several gymnosperms (Gingko biloba) and bryophytes (Marchantia polymorpha). However, no homologue was found inSelaginella moellendorffii, indicating unknown evolutionary processes accompanying this plant’s evolution. Moreover, the structures of the new subgroup AP2/EREBPs have different conserved domains, such as B3, zf-C3Hc3H, and agent domains, indicating their divergent evolution in bryophytes and gymnosperms. Interestingly, three repeats of AP2 domains have separately evolved from mosses to gymnosperms for most of the new proteins, but the AP2 domain of Gb_11937 has been replicated.

Conclusion

The new subtype AP2/EREBPs have different origins and would enrich our knowledge of the molecular structure, origin, and evolutionary processes of AP2/EREBP transcription factors in plants.
Cognitive impairments in patients with persistent symptoms attributed to Lyme disease
Authors: Berende Anneleen , Agelink van Rentergem Joost , Evers Andrea W. M. , ter Hofstede Hadewych J. M. , Vos Fidel J. , Kullberg Bart Jan , Kessels Roy P. C.
Published: October 2019

Background

Persistent symptoms attributed to Lyme borreliosis often include self-reported cognitive impairment. However, it remains unclear whether these symptoms can be substantiated by objective cognitive testing.

Methods

For this observational study, cognitive performance was assessed in 280 adults with persistent symptoms attributed to Lyme borreliosis (as part of baseline data collected for the Dutch PLEASE study). Cognitive testing covered the five major domains: episodic memory, working memory / attention, verbal fluency, information-processing speed and executive function. Patients’ profiles of test scores were compared to a large age-, education- and sex-adjusted normative sample using multivariate normative comparison. Performance validity was assessed to detect suboptimal effort, and questionnaires were administered to measure self-reported cognitive complaints, fatigue, anxiety, depressive symptoms and several other psychological factors.

Results

Of 280 patients, one was excluded as the test battery could not be completed. Of the remaining 279 patients, 239 (85.4%) displayed sufficient performance validity. Patients with insufficient performance validity felt significantly more helpless and physically fatigued, and less orientated. Furthermore, they had a lower education level and less often paid work. Of the total study cohort 5.7% (n = 16) performed in the impaired range. Among the 239 patients who displayed sufficient performance validity, 2.9% (n = 7) were classified as cognitively impaired. No association between subjective cognitive symptoms and objective impairment was found.

Conclusions

Only a small percentage of patients with borreliosis-attributed persistent symptoms have objective cognitive impairment. Performance validity should be taken into account in neuropsychological examinations of these patients. Self-report questionnaires are insufficiently valid to diagnose cognitive impairment.

Trial registration

ClinicalTrials.gov NCT01207739. Registered 23 September 2010.
Forecasting incidence of hand, foot and mouth disease using BP neural networks in Jiangsu province, China
Authors: Liu Wendong , Bao Changjun , Zhou Yuping , Ji Hong , Wu Ying , Shi Yingying , Shen Wenqi , Bao Jing , Li Juan , Hu Jianli , Huo Xiang
Published: October 2019

Background

Hand, foot and mouth disease (HFMD) is a rising public health problem and has attracted considerable attention worldwide. The purpose of this study was to develop an optimal model with meteorological factors to predict the epidemic of HFMD.

Methods

Two types of methods, back propagation neural networks (BP) and auto-regressive integrated moving average (ARIMA), were employed to develop forecasting models, based on the monthly HFMD incidences and meteorological factors during 2009–2016 in Jiangsu province, China. Root mean square error (RMSE) and mean absolute percentage error (MAPE) were employed to select model and evaluate the performance of the models.

Results

Four models were constructed. The multivariate BP model was constructed using the HFMD incidences lagged from 1 to 4 months, mean temperature, rainfall and their one order lagged terms as inputs. The other BP model was fitted just using the lagged HFMD incidences as inputs. The univariate ARIMA model was specified as ARIMA (1,0,1)(1,1,0)12(AIC = 1132.12, BIC = 1440.43). And the multivariate ARIMAX with one order lagged temperature as external predictor was fitted based on this ARIMA model (AIC = 1132.37, BIC = 1142.76). The multivariate BP model performed the best in both model fitting stage and prospective forecasting stage, with a MAPE no more than 20%. The performance of the multivariate ARIMAX model was similar to that of the univariate ARIMA model. Both performed much worse than the two BP models, with a high MAPE near to 40%.

Conclusion

The multivariate BP model effectively integrated the autocorrelation of the HFMD incidence series. Meanwhile, it also comprehensively combined the climatic variables and their hysteresis effects. The introduction of the climate terms significantly improved the prediction accuracy of the BP model. This model could be an ideal method to predict the epidemic level of HFMD, which is of great importance for the public health authorities.
Risk factors and survival of patients infected with carbapenem-resistant Klebsiella pneumoniae in a KPC endemic setting: a case-control and cohort study
Authors: Cienfuegos-Gallet Astrid V. , Ocampo de Los Ríos Ana M. , Sierra Viana Patricia , Ramirez Brinez Faiver , Restrepo Castro Carlos , Roncancio Villamil Gustavo , del Corral Londoño Helena , Jiménez J. Natalia
Published: October 2019

Background

Many gaps in the burden of resistant pathogens exist in endemic areas of low- and middle-income economies, especially those endemic for carbapenem resistance. The aim of this study is to evaluate risk factors for carbapenem-resistance, to estimate the association between carbapenem-resistance and all-cause 30-day mortality and to examine whether mortality is mediated by inappropriate therapy.

Methods

A case-control and a cohort study were conducted in one tertiary-care hospital in Medellín, Colombia from 2014 to 2015. Phenotypic and genotypic characterization of isolates was performed. In the case-control study, cases were defined as patients infected with carbapenem-resistantK. pneumoniae(CRKP) and controls as patients infected with carbapenem-susceptibleK. pneumoniae(CSKP). A risk factor analysis was conducted using logistic regression models. In the cohort study, the exposed group was defined as patients infected with CRKP and the non-exposed group as patients infected with CSKP. A survival analysis using an accelerated failure time model with a lognormal distribution was performed to estimate the association between carbapenem resistance and all-cause 30-day-mortality and to examine whether mortality is mediated by inappropriate therapy.

Results

A total of 338 patients were enrolled; 49 were infected with CRKP and 289 with CSKP. Among CRKP isolates CG258 (n = 29), ST25 (n = 5) and ST307 (n = 4) were detected. Of importance, every day of meropenem (OR 1.18, 95%CI 1.10–1.28) and cefepime (OR 1.22, 95%CI 1.03–1.49) use increase the risk of carbapenem resistance. Additional risk factors were previous use of ciprofloxacin (OR 2.37, 95%CI 1.00–5.35) and urinary catheter (OR 2.60, 95%CI 1.25–5.37). Furthermore, a significant lower survival time was estimated for patients infected with CRKP compared to CSKP (Relative Times 0.44, 95%CI 0.24–0.82). The strength of association was reduced when appropriate therapy was included in the model (RT = 0.81 95%CI 0.48–1.37).

Conclusion

Short antibiotic courses had the potential to reduce the selection and transmission of CRKP. A high burden in mortality occurred in patients infected with CRKP in a KPC endemic setting and CRKP leads to increased mortality via inappropriate antibiotic treatment. Furthermore, dissemination of recognized hypervirulent clones could add to the list of challenges for antibiotic resistance control.
Prognostic value of estrogen receptor-α and progesterone receptor in curatively resected colorectal cancer: a retrospective analysis with independent validations
Authors: Ye Shu-Biao , Cheng Yi-Kan , Zhang Lin , Wang Xue-Ping , Wang Lei , Lan Ping
Published: October 2019

Background

Prognostic assessment is crucial for optimal treatment. The aim of our study was to investigate the potential impact of estrogen receptor-α (ER-α) and progesterone receptor (PR) on the prognosis of colorectal cancer (CRC) patients who received curative resection.

Methods

Retrospective evaluation of two independent cohorts of CRC patients maintained prospectively in 2009–2010 (training set) (n = 148) and 2007–2009 (internal validation set) (n = 485). Furthermore, we used an external independent CRC cohort from The Cancer Genome Atlas (TCGA) (n = 511) for further validation. ER-α and PR expression as well as other potential prognostic factors were retrospectively evaluated in training set with respect to overall survival (OS), local relapse free survival (LRFS) and distant metastasis free survival (DMFS). The prognostic factors found in training set will be validated in two validation cohorts.

Results

On univariate analysis for the training set, OS, LRFS and DMFS were not associated with PR expression. While patients with ER-αexpression were found to have poor prognosis. In addition, multivariate analysis showed that ER-αexpression maintained significance with respect to OS (HR, 5.06; p = 0.002), LRFS (HR, 8.81; p = 0.002) and DMFS (HR, 8.07; p = 0.004). Similarly, ER-α expression showed prognostic significance with respect to OS with hazard ratios (HRs) of 1.572 (95% CI: 1.001–2.467, p = 0.049) and 1.624 (95% CI: 1.047–2.520, p = 0.031) for the internal and external validation cohort, respectively.

Conclusion

ER-α expression was a biomarker of poor prognosis and it might inform treatment decision for high risk CRC patients. However, PR expression was not associated with survival outcomes.
Peripapillary retinal artery in first diagnosed and untreated normal tension glaucoma
Authors: Rong Xin , Cai Yu , Li Mei , Fang Yuan , Tian Tian , Pan Yingzi
Published: October 2019

Background

Glaucoma, an important cause of visual impairment in many countries, remains a common eye condition due to difficulties in its early diagnosis. We analyzed the characteristics of retinal arteries to add a valuable technology for helping the normal tension glaucoma (NTG) diagnosis.

Methods

This study included 51 patients with newly diagnosed NTG with hemifield defects and 60 age-matched controls. Peripapillary retinal arteriolar calibers (PRACs) photoed by non-mydriatic retinal camera were measured using ImageJ by two masked readers. We also performed spectral-domain optical coherence tomography to evaluate retinal nerve fiber layer thickness (RNFLT) and optic disc parameters. Their relations to retinal arteriolar calibers were investigated by univariate and multivariate linear regression. The area under the receiver operating characteristic curve (AUROC) was used to confirm the powers to detect NTG by PRACs.

Results

PRACs in four quadrants were significantly reduced in individuals with first diagnosed NTG (82 ± 15.1 μm, 80 ± 13.6 μm, 71 ± 11.6 μm, and 64 ± 10.0 μm) compared with those in age-matched controls (101 ± 9.8 μm, 105 ± 8.7 μm, 90 ± 7.5 μm, and 82 ± 9.8 μm). Superotemporal and inferotemporal PRACs in the visual field-affected hemifield were narrower than those in the unaffected hemifield in NTG group (P ≤ 0.004). Temporal PRACs in the RNFL unaffected hemifield were significantly narrower than in healthy eyes (P < 0.001). Superotemporal PRAC showed a significant correlation with superior RNFLT (β = 0.659,P < 0.001), and a similar relationship was found between inferotemporal PRAC and inferior RNFLT (β = 0.227,P = 0.015). The diagnostic capability of temporal PRACs was satisfactory (superotemporal PRAC; AUROC 0.983, cut-off value 84.7 μm, inferotemporal PRAC; AUROC 0.946, cut-off value 94.2 μm).

Conclusions

PRAC and inferotemporal PRAC are valid parameters for discriminating patients with NTG.
Acteoside inhibits inflammatory response via JAK/STAT signaling pathway in osteoarthritic rats
Authors: Qiao Zhiguang , Tang Jiaxin , Wu Wen , Tang Jian , Liu Ming
Published: October 2019

Background

Osteoarthritis (OA) is a common degenerative disease of synovial joints caused by inflammation. Acteoside (ACT), a major component and lipase inhibitor from the Chinese tea Ligustrum purpurascens kudingcha, has been reported to regulate the inflammation and immune response. The study aims to investigate the effects of ACT on inflammatory responses and joint protection in OA rats.

Methods

Cell proliferation was examined by MTT and colony formation assay. Apoptosis was analyzed using flow cytometry with Annexin V/PI staining. ELISA was employed to examine the concentration of inflammatory cytokines. OA rat model was established by surgery stimulation.

Results

ACT treatment significantly inhibited the upregulation of inflammatory cytokines induced by IL-1β in primary chondrocytes, including IL-6, IL-12, TNF-α and IFN-γ. ACT stimulation also enhanced the cell proliferation, while inhibited cell apoptosis in IL-1β-treated chondrocytes. Consistently, ACT treatment led to downregulation of cleaved-caspase-3 and apoptosis regulator Bax, and upregulation of Bcl-2. Furthermore, ACT treatment inhibited IL-1β-induced activation of JAK/STAT pathway. The results were confirmed in surgery-induced OA rat model. Moreover, ACT treatment significantly inhibited synovial inflammation and articular chondrocyte apoptosis in OA rats.

Conclusion

Our findings indicate that ACT has the potential therapeutic effect on OA through inhibiting the inflammatory responses via inactivating JAK/STAT signaling pathway.
Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches
Authors: Mutenherwa Farirai , Wassenaar Douglas R. , de Oliveira Tulio
Published: October 2019

Background

HIV molecular epidemiology is increasingly recognized as a vital source of information for understanding HIV transmission dynamics. Despite extensive use of these data-intensive techniques in both research and public health settings, the ethical issues associated with this science have received minimal attention. As the discipline evolves, there is reasonable concern that existing ethical and legal frameworks and standards might lag behind the rapid methodological developments in this field. This is a follow-up on our earlier work that applied a predetermined analytical framework to examine the perspectives of a sample of scientists from the fields of epidemiology, public health, virology and bioethics on key ethical issues associated with HIV molecular epidemiology in HIV network research.

Methods

Fourteen in-depth interviews were conducted with scientists from the fields of molecular epidemiology, public health, virology and bioethics. Inductive analytical approaches were applied to identify key themes that emerged from the data.

Results

Our interviewees acknowledged the potential positive impact of molecular epidemiology in the fight against HIV. However, they were concerned that HIV phylogenetics research messages may be incorrectly interpreted if not presented at the appropriate level. There was consensus that HIV phylogenetics research presents a potential risk to privacy, but the probability and magnitude of this risk was less obvious. Although participants acknowledged the social value that could be realized from the analysis of HIV genetic sequences, there was a perceived fear that the boundaries for use of HIV sequence data were not clearly defined.

Conclusions

Our findings highlight distinct ethical issues arising from HIV molecular epidemiology. As the discipline evolves and HIV sequence data become increasingly available, it is critical to ensure that ethical standards keep pace with biomedical advancements. We argue that the ethical issues raised in this study, whether real or perceived, require further conceptual and empirical examination.
Analysis of Plasmodium falciparum Pfcrt and Pfmdr1 genes in parasite isolates from asymptomatic individuals in Southeast Nigeria 11 years after withdrawal of chloroquine
Authors: Ikegbunam Moses N. , Nkonganyi Charles N. , Thomas Bolaji N. , Esimone Charles O. , Velavan Thirumalaisamy P. , Ojurongbe Olusola
Published: October 2019

Background

A reversal of chloroquine (CQ) resistance following a period of withdrawal has raised the possibility of its re-introduction. This study evaluated the current prevalence ofPfcrtandPfmdr1alleles inPlasmodium falciparumisolates, 11 years after CQ withdrawal in Southeast Nigeria.

Methods

Filter-paper blood samples were collected from 725 non-febrile individuals, comprising 250 children (≤ 12 years), 250 pregnant women and 225 other adults, between October 2014 and February 2015 in Nnewi town, Southeast Nigeria. Nested PCR followed by direct sequencing was employed for the genotyping ofPfcrtandPfmdr1genes.

Results

A total of 103 parasites-positive samples were recovered, comprising of 48 (19.20%) among children, 20 (20.00%) among pregnant women and 35 (15.50%) among other adults cohort. The frequency of the mutant genotype ofPfcrt76T, 75E and 74I was 94.50% each. Parasite isolates from children had a frequency of 100% for mutant alleles in allPfcrtcodons while isolates from pregnant women and other adults had a frequency of 91% each in all codons. Haplotype distribution ofpfcrtgene were 5.45, 0.00 and 76.37% for CVMNK, SVMNT and CVIET, respectively. ForPfmdr1gene, the frequency of 86Y, 184F and 1246Y mutant alleles were 8.54, 29.27 and 3.66%, respectively. Amongst thePfmdr1haplotypes analysed, NFD had the highest frequency of 24.4%, followed by YFD at 6.10%. NYF and NYY occurred the least (1.20%).

Conclusion

The high level ofPfcrtmutations is suggestive of a sustained CQ pressure onP. falciparumisolates in the study area, despite the change of first line treatment from CQ to artemisinin combination therapy for 11 years. A new strategy to ensure the complete withdrawal of CQ from the country is recommended.
Detection of malaria parasites in dried human blood spots using mid-infrared spectroscopy and logistic regression analysis
Authors: Mwanga Emmanuel P. , Minja Elihaika G. , Mrimi Emmanuel , Jiménez Mario González , Swai Johnson K. , Abbasi Said , Ngowo Halfan S. , Siria Doreen J. , Mapua Salum , Stica Caleb , Maia Marta F. , Olotu Ally , Sikulu-Lord Maggy T. , Baldini Francesco , Ferguson Heather M. , Wynne Klaas , Selvaraj Prashanth , Babayan Simon A. , Okumu Fredros O.
Published: October 2019

Background

Epidemiological surveys of malaria currently rely on microscopy, polymerase chain reaction assays (PCR) or rapid diagnostic test kits for Plasmodium infections (RDTs). This study investigated whether mid-infrared (MIR) spectroscopy coupled with supervised machine learning could constitute an alternative method for rapid malaria screening, directly from dried human blood spots.

Methods

Filter papers containing dried blood spots (DBS) were obtained from a cross-sectional malaria survey in 12 wards in southeastern Tanzania in 2018/19. The DBS were scanned using attenuated total reflection-Fourier Transform Infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra in the range 4000 cm−1 to 500 cm−1. The spectra were cleaned to compensate for atmospheric water vapour and CO2 interference bands and used to train different classification algorithms to distinguish between malaria-positive and malaria-negative DBS papers based on PCR test results as reference. The analysis considered 296 individuals, including 123 PCR-confirmed malaria positives and 173 negatives. Model training was done using 80% of the dataset, after which the best-fitting model was optimized by bootstrapping of 80/20 train/test-stratified splits. The trained models were evaluated by predicting Plasmodium falciparum positivity in the 20% validation set of DBS.

Results

Logistic regression was the best-performing model. Considering PCR as reference, the models attained overall accuracies of 92% for predicting P. falciparum infections (specificity = 91.7%; sensitivity = 92.8%) and 85% for predicting mixed infections of P. falciparum and Plasmodium ovale (specificity = 85%, sensitivity = 85%) in the field-collected specimen.

Conclusion

These results demonstrate that mid-infrared spectroscopy coupled with supervised machine learning (MIR-ML) could be used to screen for malaria parasites in human DBS. The approach could have potential for rapid and high-throughput screening of Plasmodium in both non-clinical settings (e.g., field surveys) and clinical settings (diagnosis to aid case management). However, before the approach can be used, we need additional field validation in other study sites with different parasite populations, and in-depth evaluation of the biological basis of the MIR signals. Improving the classification algorithms, and model training on larger datasets could also improve specificity and sensitivity. The MIR-ML spectroscopy system is physically robust, low-cost, and requires minimum maintenance.
Dietary seaweed intake and depressive symptoms in Japanese adults: a prospective cohort study
Authors: Guo Feng , Huang Cong , Cui Yufei , Momma Haruki , Niu Kaijun , Nagatomi Ryoichi
Published: October 2019

Background

This prospective cohort study aimed to investigate the association between daily seaweed intake and depressive symptoms.

Methods

In a prospective study conducted between 2008 and 2011, 500 Japanese adult employees aged 20–74 years participated and were included in the final analysis. Consumption of seaweed was assessed using a brief self-administered diet history questionnaire, and changes in seaweed consumption were divided into three categories (decreased, unchanged, and increased). Depressive symptoms were assessed using a Japanese version of the Self-Rating Depression Scale (SDS). Depressive symptoms were defined as an SDS score of ≥50 in the present study.

Results

At the 3-year follow-up, 46 participants (9.2%) showed depressive symptoms. Multivariate analysis showed that baseline seaweed intakes were not significantly associated with the incidence of depressive symptoms (p for trend = 0.501). Conversely, odds ratios (95% CI) for depressive symptoms were lower in the participants who had higher seaweed intake than in those who had lower seaweed intake (decreased, 1.00; unchanged, 0.32 [0.13–0.81]; increased, 0.34 [0.13–0.88]; p for trend = 0.032) after adjusting for confounding factors.

Conclusions

This study revealed a relationship between higher seaweed intake and a lower incidence of depressive symptoms in Japanese adults.
Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases
Authors: Zanfardino Mario , Franzese Monica , Pane Katia , Cavaliere Carlo , Monti Serena , Esposito Giuseppina , Salvatore Marco , Aiello Marco
Published: October 2019

Genomic and radiomic data integration, namely radiogenomics, can provide meaningful knowledge in cancer diagnosis, prognosis and treatment. Despite several data structures based on multi-layer architecture proposed to combine multi-omic biological information, none of these has been designed and assessed to include radiomic data as well. To meet this need, we propose to use the MultiAssayExperiment (MAE), an R package that provides data structures and methods for manipulating and integrating multi-assay experiments, as a suitable tool to manage radiogenomic experiment data. To this aim, we first examine the role of radiogenomics in cancer phenotype definition, then the current state of radiogenomics data integration in public repository and, finally, challenges and limitations of including radiomics in MAE, designing an extended framework and showing its application on a case study from the TCGA-TCIA archives. Radiomic and genomic data from 91 patients have been successfully integrated in a single MAE object, demonstrating the suitability of the MAE data structure as container of radiogenomic data.
Development, acceptability, appropriateness and appeal of a cancer clinical trials implementation intervention for rural- and minority-serving urology practices
Authors: Ellis Shellie , Geana Mugur , Griebling Tomas , McWilliams Charles , Gills Jessie , Stratton Kelly , Mackay Christine , Shifter Ariel , Zganjar Andrew , Thrasher Brantley
Published: October 2019

Background

Few community urologists offer cancer patients the opportunity to participate in cancer clinical trials, despite national guidelines that recommend it, depriving an estimated 260,000 urological cancer patients of guideline-concordant care each year. Existing strategies to increase urologists’ offer of clinical trials are designed for resource-rich environments and are not feasible for many community urologists. We sought to design an implementation intervention for dissemination in under-resourced community urology practices and to compare its acceptability, appropriateness and adoption appeal among trial-naïve and trial-experienced urologists.

Methods

We used a design-for-dissemination approach, informed by the Theoretical Domains Framework and Behavior Change Wheel, to match determinants of the clinical trial offer to theoretically informed implementation strategies. We described the implementation intervention in evaluation workshops offered at urology professional society meetings. We surveyed participants to assess the implementation intervention’s acceptability and appropriateness using validated instruments. We also measured adoption appeal, intention to adopt and previous trial offer.

Results

Our design process resulted in a multi-modal implementation intervention, comprised of multiple implementation strategies designed to address six domains from the Theoretical Domains Framework. Evaluation workshops delivered at four meetings, convened five separate professional societies. Sixty-one percent of those offered an opportunity to participate in the implementation intervention indicated intention to adopt. Average implementation intervention acceptability and appropriateness ratings were 4.4 and 4.4 (out of 5), respectively. Acceptability scores were statistically significantly higher among those offering trials compared to those not (p = 0.03). Appropriateness scores did not differ between those offering trials and those not (p = 0.24). After urologists ranked their top three innovation attributes, 43% of urologists included practice reputation in their top three reasons for offering clinical trials; 30% listed practice differentiation among their top three reasons. No statistically significant differences were found between those who offered trials and those who did not among any of the innovation attributes.

Conclusions

LEARN|INFORM|RECRUIT is a promising implementation intervention to address low accrual to clinical trials, poised for implementation and effectiveness testing. The implementation intervention is appealing to its target audience and may have equal uptake among trial-naïve and trial-experienced practices.
The effect of training and awareness of subtle control on the frequency of hand hygiene among intensive care unit nurses
Authors: Farmani Zeinab , Kargar Marzieh , Khademian Zahra , Paydar Shahram , Zare Najaf
Published: October 2019

Objective

This study aimed to determine the effect of awareness of subtle control after training on the hand hygiene compliance among nurses in intensive care units (ICUs). The study was conducted in two ICUs of a trauma center in Shiraz, Iran on 48 nurses. The nurses of one ICU were randomly allocated to the intervention and the nurses of the other ICU were allocated to the control group. All nurses were trained on hand hygiene. Then a fake closed camera television (CCTV) was visibly installed in the intervention group’s ICU, while the nurses were aware of it. The degree of compliance with hand hygiene was observed in both groups before and after the intervention. Data were gathered using a checklist based on the World Health Organization hand hygiene protocol and analyzed using SPSS 16 and the Chi square, Wilcoxon, Mann–Whitney U, and Independent T-tests, were performed.

Results

The mean percentage of hand hygiene compliance in the intervention group after the intervention was significantly higher than before the intervention (p < 0.001). Additionally, the changes in the mean percentage of the intervention group was significantly higher than that for the control group (p = 0.001). The findings showed that a fake CCTV after training, installed in ICUs, can improve hand hygiene compliance.
Maternal and fetal outcomes of cesarean delivery and factors associated with its unfavorable management outcomes; in Ayder Specialized Comprehensive Hospital, Mekelle, Tigray, Ethiopia, 2017
Authors: Mengesha Meresa Berwo , Adhanu Hadgay Hagos , Weldegeorges Desta Abraha , Assefa Natnael Etsay , Werid Weldu Mammo , Weldemariam Mulu Gebretsadik , Welay Fissaha Tekulu , Hidru Hagos Degefa , Gebru Tesfay Tsegay
Published: October 2019

Objectives

This study aimed to determine the unfavorable outcomes and to assess factors contribute to the unfavorable management outcomes after cesarean deliveries in Ayder Specialized Comprehensive Hospital, Mekelle, Tigray, Ethiopia, 2017.

Results

The unfavorable maternal management outcomes were Adhesion 28 (8.3%), excessive blood loss and blood transfusion 19 (5.6%), cesarean hysterectomy 10 (3%), relaparotomy 5 (1.5%), wound infection and wound dehiscence 23 (6.8%). Unfavorable fetal outcomes were were stillbirth 9 (2.6%), early neonatal death 8 (2.4%), low birth weight 58 (17.2%). women who did not book for Antenatal Care and having a history of previous cesarean delivery were found to be associated with unfavorable maternal outcomes and indications of cesarean delivery as obstructed labor was associated with unfavorable fetal outcomes.
Respiratory variations of inferior vena cava fail to predict fluid responsiveness in mechanically ventilated patients with isolated left ventricular dysfunction
Authors:   Chinese Critical Ultrasound Study Group (CCUSG), Zhang Hongmin , Zhang Qing , Chen Xiukai , Wang Xiaoting , Liu Dawei
Published: October 2019

Background

Respiratory variation of inferior vena cava is problematic in predicting fluid responsiveness in patients with right ventricular dysfunction. However, its effectiveness in patients with isolated left ventricular systolic dysfunction (ILVD) has not been reported. We aimed to explore whether inferior vena cava diameter distensibility index (dIVC) can predict fluid responsiveness in mechanically ventilated ILVD patients.

Methods

Patients admitted to the intensive care unit who were on controlled mechanical ventilation and in need of a fluid responsiveness assessment were screened for enrolment. Several echocardiographic parameters, including dIVC, tricuspid annular plane systolic excursion (TAPSE), left ventricular ejection fraction (LVEF), and LV outflow tract velocity–time integral (VTI) before and after passive leg raising (PLR) were collected. Patients with LV systolic dysfunction only (TAPSE ≥ 16 mm, LVEF < 50%) were considered to have isolated left ventricular systolic dysfunction (ILVD).

Results

One hundred and twenty-nine subjects were enrolled in this study, among them, 28 were labelled ILVD patients, and the remaining 101 were patients with normal LV function (NLVF). The value of dIVC in ILVD patients was as high as that in NLVF patients, (20% vs. 16%, p = 0.211). The ILVD group contained a much lower proportion of PLR responders than NLVF patients did (17.9% vs. 53.2%, p < 0.001). No correlation was detected between dIVC and ΔVTI in ILVD patients (r = 0.196, p = 0.309). dIVC was correlated with ΔVTI in NLVF patients (r = 0.722, p < 0.001), and the correlation was strengthened compared with that derived from all patients (p = 0.020). A receiver-operating characteristic (ROC) analysis showed that the area-under-the-curve (AUC) of dIVC for determining fluid responsiveness from ILVD patients was not statistically significant (p = 0.251). In NLVF patients, ROC analysis revealed an AUC of 0.918 (95% CI 0.858–0.978; p < 0.001), which was higher than the AUC derived from all patients (p = 0.033). Patients with LVEF below 40% had a lower ΔVTI and fewer PLR responders than those with LVEF 40–50% and LVEF above 50% (p < 0.001).

Conclusion

dIVC should be used with caution when critically ill patients on controlled mechanical ventilation display normal right ventricular function in combination with abnormal left ventricular systolic function.
Students’ perceptions of a food safety and quality e-learning course: a CASE study for a MSC in food consumption
Authors: Vaz-Fernandes Paula , Caeiro Sandra
Published: October 2019

Life long training and education in food safety is a crucial issue in particular for professionals working in the field. At the same time there is a need to evaluate the effectiveness of that training in particular when is given in e-learning. The purpose of this explorative work is to evaluate the Food Safety and Quality e-learning course within a Master program offered in the National Distance Learning University in Portugal. Following a case study methodology a mixed methods approached was used, based on an online questionnaire survey to students that enrolled the course, followed by a Focus Group Discussion to better discuss the weak points addressed by the students in the questionnaire. The questionnaire aimed to assess students perceptions about the course organization, recourses, assignments, acquired competences, change attitudes and behaviour and link with the professional activity Students who enrolled the course during 2016/17 and 2017/18 were surveyed in the fourth semester of the curricular year, in the period of development of the master thesis dissertation. In addition a quantitative analysis was conducted in the temporal distributions of messages published on the Moodle platform (learning analytics) to evaluate students’ interactions and engagement during the course.

This study has shown that overall, students are very satisfied with the course, however they suggested improvements that are needed considering the pedagogical model used and their availability to learn as students with full time jobs, most related with the food science. This explorative research aimed to contribute to the improvement of food safety and quality training based also on recent tools and recommendations within e-learning in science education.
Development and implementation of an emission optimization model for passenger flight bookings
Authors: Schennings Andreas , Larsson Joel , Robèrt Markus
Published: October 2019

In this analysis we discover the potential of a more transparent emission declaration system, in order to a) facilitate for environmentally concerned consumers to choose low-emission flights, and b) provide data for a future emission trading system where the aviation industry is accounted for its emission costs. Some air travel consumers book flights through low-cost flight ticket price comparison websites, that offer comparisons on price, convenience, travel time, and other factors relevant to the consumer. As a basis for this study, an algorithm designed for “flight CO2 emissions comparisons”, was developed and implemented on Sweden’s largest flight ticket price comparison website that compares flights by CO2 emissions in kg per passenger and trip. A visitor to the site can now also select a flight based on the ranking of carbon emission levels from each flight. In addition to the implementation of the algorithm in a commercial aviation booking system, a survey was conducted to analyze consumer preference data to glean insights and make conclusions about flight ticket price sensitivity, convenience, environmental awareness and potential for behavioral change among air travel consumers.

The findings from this study indicate that the algorithm will not act as a catalyst for emission reductions in the aviation sector, unless it is complemented by emission reduction policies and/or introduction of a fair emission taxation system. Furthermore, the aviation sector should be obliged to report accurate emission data on all tickets in order to bring full transparency to consumers searching low emission transport modes.
Green production of silver nanoparticles, evaluation of their nematicidal activity against Meloidogyne javanica and their impact on growth of faba bean
Authors: Hamed Seham M. , Hagag Eman S. , El-Raouf Neveen Abd
Published: October 2019

Background

Cyanobacterium-based silver nanoparticles are considered not only as an efficient nano-nematicide but also as a bio-stimulant material for plant growth. They could be employed as a part of an integrated program for controlling some plant diseases.

Results

In this study, silver nanoparticles (Ag-NPs) were biosynthesized from aqueous extract of the cyanobacterium,Nostocsp. PCC7524. Full characterization of the biosynthesized Ag-NPs was monitored by UV-vis spectroscopy, transmission electron microscopy, X-ray diffraction pattern, Zeta sizer, and Fourier transform infrared spectroscopy. In vitro assay against the root-knot nematodeMeloidogyne javanicashowed that Ag-NPs significantly decreased egg hatching ofM. javanicaat different applied concentrations (3, 6, 12, 25, and 50%, v/v). Fifty percent of Ag-NPs induced the highest reduction percent (94.66%). Moreover, Ag-NPs and AgNO3significantly increased the percentages of larval mortality of the second-stage juveniles (J2) with concentration and time-dependent responses. Ag-NPs or AgNO3at 2.4 ml/l, 24 h, completely inhibited the growth of J2compared to 23% inhibition using aqueous cyanobacterial extract (ACE). In vivo effect of Ag-NPs on faba bean-infected plant under greenhouse conditions was achieved by treating soil with three different concentrations of 1, 2, and 3 ml/kg soil over two consecutive seasons. Ag-NPs significantly reduced root galling from 39.6 to 78.7% and J2population in the soils from 32.2% to 86.7% in the 2018 season and from 21.9 to 78.1% and 40.0 to 81.0% in the 2019 season, respectively. Moreover, 3 ml/kg soil of Ag-NP treatment showed statistically comparable effects to that of vydate nematicide but with remarkable enhancement of faba bean growth parameters as compared to those of vydate or AgNO3treatments in the two seasons.

Conclusions

The considerable in vitro and in vivo nematicidal potential of the cyanobacterium-based Ag-NPs, besides their bio-stimulant effect on plant growth, makes them feasible for the biological control ofM. javanica.
Iterative magnetic forward modeling for high susceptibility based on integral equation and Gauss-fast Fourier transform
Authors: Ouyang Fang , Chen Longwei
Published: October 2019

Self-demagnetization due to strongly magnetic bodies can seriously affect the interpretation of magnetic anomalies. Conventional numerical methods often neglect the self-demagnetization effects and limit their use to low susceptibilities ([Formula: see text]). We have developed a novel iterative method based on the integral equation and the Gauss-fast Fourier transform (FFT) technique for calculating the magnetic field from finite bodies of high magnetic susceptibility and arbitrary shapes. The method uses a segmented model consisting of prismatic voxels to approximate a complex target region. In each voxel, the magnetization is assumed to be constant, so that the integral equation in the spatial domain can reduce to a simple form with lots of merit in numerical calculation after the 2D Fourier transform. Moreover, a contraction operator is derived to ensure the convergence of the iterative calculation, and the Gauss-FFT technique is applied to reduce numerical errors due to edge effects. Our modeling results indicate that this new iterative scheme performs well in a wide range of magnetic susceptibilities (1–1000 SI). For lower susceptibilities ([Formula: see text]), the iterative algorithm converges rapidly and indicates very good correlation with the analytical solutions. At higher susceptibilities ([Formula: see text]), our method still performs well, but the numerical accuracy improves with a relatively slow speed. In the extreme case ([Formula: see text]), an acceptable result is also obtained after sufficient iterative computation. A further improvement in the numerical precision can be achieved by increasing the number of prismatic voxels, but at the same time, the computational time increases linearly with the size of the voxels.