bluuebunny/crossref_metadata_2025 huggingface dataset:
mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes
Authors: Song Bing , Woerner August E. , Planz John
Published: January 2021

Background

Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data.

Results

This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested.

Conclusion

The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology.

Availability

The R packagemixIndependR,is available on the Comprehensive R Archive Network (CRAN) at:https://cran.r-project.org/web/packages/mixIndependR/index.html.
Dynamic conversion of cell sorting patterns in aggregates of embryonic stem cells with differential adhesive affinity
Authors: Tse Jeffrey D. , Moore Robert , Meng Yue , Tao Wensi , Smith Elizabeth R. , Xu Xiang-Xi
Published: January 2021

Background

Mammalian early development comprises the proliferation, differentiation, and self-assembly of the embryonic cells. The classic experiment undertaken by Townes and Holtfreter demonstrated the ability of dissociated embryonic cells to sort and self-organize spontaneously into the original tissue patterns. Here, we further explored the principles and mechanisms underlying the phenomenon of spontaneous tissue organization by studying aggregation and sorting of mouse embryonic stem (ES) cells with differential adhesive affinity in culture.

Results

As observed previously, in aggregates of wild-type and E-cadherin-deficient ES cells, the cell assemblies exhibited an initial sorting pattern showing wild-type cells engulfed by less adhesive E-cadherin-deficient ES cells, which fits the pattern predicted by the differential adhesive hypothesis proposed by Malcom Steinberg. However, in further study of more mature cell aggregates, the initial sorting pattern reversed, with the highly adhesive wild-type ES cells forming an outer shell enveloping the less adhesive E-cadherin-deficient cells, contradicting Steinberg’s sorting principle. The outer wild-type cells of the more mature aggregates did not differentiate into endoderm, which is known to be able to sort to the exterior from previous studies. In contrast to the naive aggregates, the mature aggregates presented polarized, highly adhesive cells at the outer layer. The surface polarity was observed as an actin cap contiguously spanning across the apical surface of multiple adjacent cells, though independent of the formation of tight junctions.

Conclusions

Our experimental findings suggest that the force of differential adhesive affinity can be overcome by even subtle polarity generated from strong bilateral ligation of highly adhesive cells in determining cell sorting patterns.
Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome
Authors: Tan Xiaodong , Liu Ranran , Zhang Yonghong , Wang Xicai , Wang Jie , Wang Hailong , Zhao Guiping , Zheng Maiqing , Wen Jie
Published: January 2021

Background

DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Herein, we compared the methylome and transcriptome of chickens with and without FLHS.

Results

We found genome-wide dysregulated DNA methylation pattern in which regions up- and down-stream of gene body were hypo-methylated in chickens with FLHS. A total of 4155 differentially methylated genes and 1389 differentially expressed genes were identified. Genes were focused when a negative relationship between mRNA expression and DNA methylation in promoter and gene body were detected. Based on pathway enrichment analysis, we found expression of genes related to lipogenesis and oxygenolysis (e.g., PPAR signaling pathway, fatty acid biosynthesis, and fatty acid elongation) to be up-regulated with associated down-regulated DNA methylation. In contrast, genes related to cellular junction and communication pathways (e.g., vascular smooth muscle contraction, phosphatidylinositol signaling system, and gap junction) were inhibited and with associated up-regulation of DNA methylation.

Conclusions

In the current study, we provide a genome-wide scale landscape of DNA methylation and gene expression. The hepatic hypo-methylation feature has been identified with FLHS chickens. By integrated analysis, the results strongly suggest that increased lipid accumulation and hepatocyte rupture are central pathways that are regulated by DNA methylation in chickens with FLHS.
Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat
Authors: Alemu Admas , Feyissa Tileye , Maccaferri Marco , Sciara Giuseppe , Tuberosa Roberto , Ammar Karim , Badebo Ayele , Acevedo Maricelis , Letta Tesfaye , Abeyo Bekele
Published: January 2021

Background

Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety-two Ethiopian durum wheat accessions comprising 167 historical landraces and 25 modern cultivars were assembled for GWAS analysis to identify QTLs for root system architecture (RSA) traits and genotyped with a high-density 90 K wheat SNP array by Illumina.

Results

Using a non-roll, paper-based root phenotyping platform, a total of 2880 seedlings and 14,947 seminal roots were measured at the three-leaf stage to collect data for total root length (TRL), total root number (TRN), root growth angle (RGA), average root length (ARL), bulk root dry weight (RDW), individual root dry weight (IRW), bulk shoot dry weight (SDW), presence of six seminal roots per seedling (RT6) and root shoot ratio (RSR). Analysis of variance revealed highly significant differences between accessions for all RSA traits. Four major (− log10P≥ 4) and 34 nominal (− log10P≥ 3) QTLs were identified and grouped in 16 RSA QTL clusters across chromosomes. A higher number of significant RSA QTL were identified on chromosome 4B particularly for root vigor traits (root length, number and/or weight).

Conclusions

After projecting the identified QTLs on to a high-density tetraploid consensus map along with previously reported RSA QTL in both durum and bread wheat, fourteen nominal QTLs were found to be novel and could potentially be used to tailor RSA in elite lines. The major RGA QTLs on chromosome 6AL detected in the current study and reported in previous studies is a good candidate for cloning the causative underlining sequence and identifying the beneficial haplotypes able to positively affect yield under water- or nutrient-limited conditions.
Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum
Authors: Xu Peng , Guo Qi , Meng Shan , Zhang Xianggui , Xu Zhenzhen , Guo Wangzhen , Shen Xinlian
Published: January 2021

Background

Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance.

Results

In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response.

Conclusions

These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.
Comparative transcriptome analysis uncovers roles of hydrogen sulfide for alleviating cadmium toxicity in Tetrahymena thermophila
Authors: Lv Hongrui , Xu Jing , Bo Tao , Wang Wei
Published: January 2021

Background

Cadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfide (H2S) effectively alleviates heavy metal toxicity in plants and reduces oxidative stress in mammals. However, the function of H2S for alleviating heavy metal toxicity in aquatic organisms remains less clear. Tetrahymena thermophila is an important model organism to evaluate toxic contaminants in an aquatic environment. In this study, the molecular roles of exogenously H2S application were explored by RNA sequencing under Cd stress in T. thermophila.

Results

The exposure of 30 μM Cd resulted in T. thermophila growth inhibition, cell nigrescence, and malondialdehyde (MDA) content considerably increase. However, exogenous NaHS (donor of H2S, 70 μM) significantly alleviated the Cd-induced toxicity by inhibiting Cd absorbtion, promoting CdS nanoparticles formation and improving antioxidant system. Comparative transcriptome analysis showed that the expression levels of 9152 genes changed under Cd stress (4658 upregulated and 4494 downregulated). However, only 1359 genes were differentially expressed with NaHS treatment under Cd stress (1087 upregulated and 272 downregulated). The functional categories of the differentially expressed genes (DEGs) by gene ontology (GO) revealed that the transcripts involved in the oxidation–reduction process, oxidoreductase activity, glutathione peroxidase activity, and cell redox homeostasis were the considerable enrichments between Cd stress and NaHS treatment under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the carbon metabolism, glutathione metabolism, metabolism of xenobiotics by cytochrome P450, and ABC transporters were significantly differentially expressed components between Cd stress and NaHS treatment under Cd stress in T. thermophila. The relative expression levels of six DEGs were further confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).

Conclusion

NaHS alleviated Cd stress mainly through inhibiting Cd absorbtion, promoting CdS nanoparticles formation, increasing oxidation resistance, and regulation of transport in free-living unicellular T. thermophila. These findings will expand our understanding for H2S functions in the freshwater protozoa.
A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration
Authors: Kampers Linde F. C. , Koehorst Jasper J. , van Heck Ruben J. A. , Suarez-Diez Maria , Stams Alfons J. M. , Schaap Peter J.
Published: January 2021

Background

Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions.

Results

Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa.

Conclusions

The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments
Authors: Schmautz Zala , Espinal Carlos A. , Bohny Andrea M. , Rezzonico Fabio , Junge Ranka , Frossard Emmanuel , Smits Theo H. M.
Published: January 2021

Background

An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured.

Results

We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed.

Conclusion

Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.
Cloning and characterization of KoOsmotin from mangrove plant Kandelia obovata under cold stress
Authors: Fei Jiao , Wang You-shao , Cheng Hao , Su Yu-bin , Zhong Yongjia , Zheng Lei
Published: January 2021

Background

Low temperature is a major abiotic stress that seriously limits mangrove productivity and distribution. Kandelia obovata is the most cold-resistance specie in mangrove plants, but little is known about the molecular mechanism underlying its resistance to cold. Osmotin is a key protein associated with abiotic and biotic stress response in plants but no information about this gene in K. obovata was reported.

Results

In this study, a cDNA sequence encoding osmotin, KoOsmotin (GenBank accession no. KP267758), was cloned from mangrove plant K. obovata. The KoOsmotin protein was composed of 221 amino acids and showed a calculated molecular mass of 24.11 kDa with pI 4.92. The KoOsmotin contained sixteen cysteine residues and an N-terminal signal peptide, which were common signatures to most osmotins and pathogenesis-related 5 proteins. The three-dimensional (3D) model of KoOsmotin, contained one α-helix and eleven β-strands, was formed by three characteristic domains. Database comparisons of the KoOsmotin showed the closest identity (55.75%) with the osmotin 34 from Theobroma cacao. The phylogenetic tree also revealed that the KoOsmotin was clustered in the branch of osmotin/OLP (osmotin-like protien). The KoOsmotin protein was proved to be localized to both the plasma membrane and cytoplasm by the subcellular localization analysis. Gene expression showed that the KoOsmotin was induced primarily and highly in the leaves of K. obovata, but less abundantly in stems and roots. The overexpressing of KoOsmotin conferred cold tolerance in Escherichia coli cells.

Conclusion

As we known, this is the first study to explore the osmotin of K. obovata. Our study provided valuable clues for further exploring the function of KoOsmotin response to stress.
The role of JrPPOs in the browning of walnut explants
Authors: Zhao Shugang , Wang Hongxia , Liu Kai , Li Linqing , Yang Jinbing , An Xiuhong , Li Pingping , Yun Linying , Zhang Zhihua
Published: January 2021

Background

Tissue culture is an effective method for the rapid breeding of seedlings and improving production efficiency, but explant browning is a key limiting factor of walnut tissue culture. Specifically, the polymerization of PPO-derived quinones that cause explant browning of walnut is not well understood. This study investigated explants of ‘Zanmei’ walnut shoot apices cultured in agar (A) or vermiculite (V) media, and the survival percentage, changes in phenolic content, POD and PPO activity, and JrPPO expression in explants were studied to determine the role of PPO in the browning of walnut explants.

Results

The results showed that the V media greatly reduced the death rate of explants, and 89.9 and 38.7% of the explants cultured in V media and A media survived, respectively. Compared with that of explants at 0 h, the PPO of explants cultured in A was highly active throughout the culture, but activity in those cultured in V remained low. The phenolic level of explants cultured in A increased significantly at 72 h but subsequently declined, and the content in the explants cultured in V increased to a high level only at 144 h. The POD in explants cultured in V showed high activity that did not cause browning. Gene expression assays showed that the expression of JrPPO1 was downregulated in explants cultured in both A and V. However, the expression of JrPPO2 was upregulated in explants cultured in A throughout the culture and upregulated in V at 144 h. JrPPO expression analyses in different tissues showed that JrPPO1 was highly expressed in stems, young leaves, mature leaves, catkins, pistils, and hulls, and JrPPO2 was highly expressed in mature leaves and pistils. Moreover, browning assays showed that both explants in A and leaf tissue exhibited high JrPPO2 activity.

Conclusion

The rapid increase in phenolic content caused the browning and death of explants. V media delayed the rapid accumulation of phenolic compounds in walnut explants in the short term, which significantly decreased explants mortality. The results suggest that JrPPO2 plays a key role in the oxidation of phenols in explants after branch injury.
Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L
Authors: Xiong Yi , Lei Xiong , Bai Shiqie , Xiong Yanli , Liu Wenhui , Wu Wendan , Yu Qingqing , Dong Zhixiao , Yang Jian , Ma Xiao
Published: January 2021

Background

Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process.

Results

In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness.

Conclusions

This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.
Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus
Authors: Wang Haoyi , Wang Qian , Pak Haksong , Yan Tao , Chen Mingxun , Chen Xiaoyang , Wu Dezhi , Jiang Lixi
Published: January 2021

Background

Rapeseed (Brassica napusL.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC.

Results

We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identifiedBnaC07g30920D, apatatin-like lipase(PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region ofBnaC07g30920Dwere associated with the significant reduction of SOC, leading to a 4.7–6.2% reduction of SOCs. We performed in silico analysis to show a total of 40PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes ofBrassica napus. RNA-seq analysis unveiled thatBnPTLswere preferentially expressed in reproductive tissues especially maturing seeds.

Conclusions

We identifiedBnaC07g30920D, aBnPTLgene, that was associated with SOC using GWAS and performed in silico analysis of 40PTLsinBrassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization ofBnPTLgenes.
Improved selection of participants in genetic longevity studies: family scores revisited
Authors: Rodríguez-Girondo Mar , van den Berg Niels , Hof Michel H. , Beekman Marian , Slagboom Eline
Published: January 2021

Background

Although human longevity tends to cluster within families, genetic studies on longevity have had limited success in identifying longevity loci. One of the main causes of this limited success is the selection of participants. Studies generally include sporadically long-lived individuals, i.e. individuals with the longevity phenotype but without a genetic predisposition for longevity. The inclusion of these individuals causes phenotype heterogeneity which results in power reduction and bias. A way to avoid sporadically long-lived individuals and reduce sample heterogeneity is to include family history of longevity as selection criterion using a longevity family score. A main challenge when developing family scores are the large differences in family size, because of real differences in sibship sizes or because of missing data.

Methods

We discussed the statistical properties of two existing longevity family scores: the Family Longevity Selection Score (FLoSS) and the Longevity Relatives Count (LRC) score and we evaluated their performance dealing with differential family size. We proposed a new longevity family score, the mLRC score, an extension of the LRC based on random effects modeling, which is robust for family size and missing values. The performance of the new mLRC as selection tool was evaluated in an intensive simulation study and illustrated in a large real dataset, the Historical Sample of the Netherlands (HSN).

Results

Empirical scores such as the FLOSS and LRC cannot properly deal with differential family size and missing data. Our simulation study showed that mLRC is not affected by family size and provides more accurate selections of long-lived families. The analysis of 1105 sibships of the Historical Sample of the Netherlands showed that the selection of long-lived individuals based on the mLRC score predicts excess survival in the validation set better than the selection based on the LRC score .

Conclusions

Model-based score systems such as the mLRC score help to reduce heterogeneity in the selection of long-lived families. The power of future studies into the genetics of longevity can likely be improved and their bias reduced, by selecting long-lived cases using the mLRC.
Development and validation of prediction model to estimate 10-year risk of all-cause mortality using modern statistical learning methods: a large population-based cohort study and external validation
Authors: Ajnakina Olesya , Agbedjro Deborah , McCammon Ryan , Faul Jessica , Murray Robin M. , Stahl Daniel , Steptoe Andrew
Published: January 2021

Background

In increasingly ageing populations, there is an emergent need to develop a robust prediction model for estimating an individual absolute risk for all-cause mortality, so that relevant assessments and interventions can be targeted appropriately. The objective of the study was to derive, evaluate and validate (internally and externally) a risk prediction model allowing rapid estimations of an absolute risk of all-cause mortality in the following 10 years.

Methods

For the model development, data came from English Longitudinal Study of Ageing study, which comprised 9154 population-representative individuals aged 50–75 years, 1240 (13.5%) of whom died during the 10-year follow-up. Internal validation was carried out using Harrell’s optimism-correction procedure; external validation was carried out using Health and Retirement Study (HRS), which is a nationally representative longitudinal survey of adults aged ≥50 years residing in the United States. Cox proportional hazards model with regularisation by the least absolute shrinkage and selection operator, where optimisation parameters were chosen based on repeated cross-validation, was employed for variable selection and model fitting. Measures of calibration, discrimination, sensitivity and specificity were determined in the development and validation cohorts.

Results

The model selected 13 prognostic factors of all-cause mortality encompassing information on demographic characteristics, health comorbidity, lifestyle and cognitive functioning. The internally validated model had good discriminatory ability (c-index=0.74), specificity (72.5%) and sensitivity (73.0%). Following external validation, the model’s prediction accuracy remained within a clinically acceptable range (c-index=0.69, calibration slope β=0.80, specificity=71.5% and sensitivity=70.6%). The main limitation of our model is twofold: 1) it may not be applicable to nursing home and other institutional populations, and 2) it was developed and validated in the cohorts with predominately white ethnicity.

Conclusions

A new prediction model that quantifies absolute risk of all-cause mortality in the following 10-years in the general population has been developed and externally validated. It has good prediction accuracy and is based on variables that are available in a variety of care and research settings. This model can facilitate identification of high risk for all-cause mortality older adults for further assessment or interventions.
Factors associated with caregiving self-efficacy among primary informal caregivers of persons with dementia in Singapore
Authors: Tan Gregory Tee Hng , Yuan Qi , Devi Fiona , Wang Peizhi , Ng Li Ling , Goveas Richard , Chong Siow Ann , Subramaniam Mythily
Published: January 2021

Background

Informal caregivers of persons with dementia (PWD) are often associated with negative health outcomes. Self-efficacy in dementia caregiving has been reported to have protective effects on caregiver’s health. This study aims to examine the factors associated with the domains of caregiving self-efficacy among informal caregivers in Singapore, a country with a rapidly aging population and a 10% prevalence of dementia among older adults.

Methods

Two hundred eighty-two informal caregivers were recruited and data including participant’s caregiving self-efficacy, sociodemographic information, perceived social support, positive aspects of caregiving, knowledge of dementia, as well as behavioral and memory problems of care recipients were collected. A confirmatory factor analysis (CFA) was performed for the 3-factor model of the Revised Scale for Caregiving Self-Efficacy (RSCSE), and multiple linear regressions were conducted using the RSCSE subscales as dependent variables.

Results

Our CFA found that the RSCSE 3-factor model proposed by the original scale developer was an acceptable fit among informal caregivers in Singapore. Having established that the 3-factor model of the RSCSE was compatible among our sample, a series of multiple regressions were conducted using each of the factors as a dependent variable. Regressions revealed several factors that were significantly associated with caregiving self-efficacy. Importantly, outlook on life was positively associated to all 3 domains of the RSCSE, while social support was positively associated with self-efficacy in obtaining respite and controlling upsetting thoughts.

Conclusion

The 3-factor model of the RSCSE was found to be an appropriate fit for our sample. Findings from this study elucidated important novel insights into the factors that influences caregiving self-efficacy amongst informal caregivers in Singapore. Crucially, caregivers’ outlook on life and social support should be improved in order to enhance their caregiving self-efficacy.
Campylobacter-associated hospitalisations in an Australian provincial setting
Authors: Moffatt Cameron R. M. , Kennedy Karina J. , Selvey Linda , Kirk Martyn D.
Published: January 2021

Background

Campylobacter spp. infections are a globally important cause of enterocolitis, causing substantial morbidity. Capturing accurate information on hospitalisations is challenging and limited population-level data exist to describe the clinico-epidemiological characteristics of hospitalised cases.

Methods

Hospital administrative and laboratory datasets were linked to identify Campylobacter-associated hospitalisations between 2004 and 2013. Accuracy of morbidity coding was assessed using laboratory diagnosis as a gold standard, with health department surveillance data used to calculate population-based rates. Additional patient-level data were collected via review of medical records. Descriptive statistics were used to assess changes in rates and proportions and to assess relationships between key variables including age, length of stay, comorbidity and complications.

Results

In total 685 Campylobacter-associated hospital admissions were identified, with the sensitivity of morbidity coding 52.8% (95% CI 48.9–56.7%). The mean annual rate of hospitalisation was 13.6%. Hospitalisation rates were higher for females across most age-groups, while for both genders marked increases were observed for those aged ≥60 years. Median admission age was 39.5 years, with an average length of stay of 3.5 days. Comorbidities were present in 34.5% (237/685) of admissions, with these patients more likely to develop electrolyte disturbances, hypotension, renal impairment or acute confusion (all p < 0.001). Bacteraemia and acute kidney injury were observed in 4.1% (28/685) and 3.6% (23/685) of admissions, respectively. Inpatient mortality was low (0.15%).

Conclusion

Under reporting of Campylobacter-associated hospitalisations is substantial but can be improved through data linkage. We observed demographic differences among those hospitalised but further work is needed to determine risk factors and predictors for hospitalisation.
High prevalence of multidrug resistant ESBL- and plasmid mediated AmpC-producing clinical isolates of Escherichia coli at Maputo Central Hospital, Mozambique
Authors: Estaleva Calvina E. L. , Zimba Tomas F. , Sekyere John Osei , Govinden Usha , Chenia Hafizah Y. , Simonsen Gunnar S. , Haldorsen Bjørg , Essack Sabiha Y. , Sundsfjord Arnfinn
Published: January 2021

Background

Epidemiological data of cephalosporin-resistant Enterobacterales in Sub-Saharan Africa is still restricted, and in particular in Mozambique. The aim of this study was to detect and characterize extended-spectrum β-lactamase (ESBL) - and plasmid-mediated AmpC (pAmpC)-producing clinical strains of Escherichia coli at Maputo Central Hospital (MCH), a 1000-bed reference hospital in Maputo, Mozambique.

Methods

A total of 230 clinical isolates of E. coli from urine (n = 199) and blood cultures (n = 31) were collected at MCH during August–November 2015. Antimicrobial susceptibility testing was performed by the disc diffusion method and interpreted according to EUCAST guidelines. Isolates with reduced susceptibility to 3rd generation cephalosporins were examined further; phenotypically for an ESBL−/AmpC-phenotype by combined disc methods and genetically for ESBL- and pAmpC-encoding genes by PCR and partial amplicon sequencing as well as genetic relatedness by ERIC-PCR.

Results

A total of 75 isolates with reduced susceptibility to cefotaxime and/or ceftazidime (n = 75) from urine (n = 58/199; 29%) and blood (n = 17/31; 55%) were detected. All 75 isolates were phenotypically ESBL-positive and 25/75 (33%) of those also expressed an AmpC-phenotype. ESBL-PCR and amplicon sequencing revealed a majority of blaCTX-M (n = 58/75; 77%) dominated by blaCTX-M-15. All AmpC-phenotype positive isolates (n = 25/75; 33%) scored positive for one or more pAmpC-genes dominated by blaMOX/FOX. Multidrug resistance (resistance ≥ three antibiotic classes) was observed in all the 75 ESBL-positive isolates dominated by resistance to trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin. ERIC-PCR revealed genetic diversity among strains with minor clusters indicating intra-hospital spread.

Conclusion

We have observed a high prevalence of MDR pAmpC- and/or ESBL-producing clinical E. coli isolates with FOX/MOX and CTX-Ms as the major β-lactamase types, respectively. ERIC-PCR analyses revealed genetic diversity and some clusters indicating within-hospital spread. The overall findings strongly support the urgent need for accurate and rapid diagnostic services to guide antibiotic treatment and improved infection control measures.
Melanoma diagnosis using deep learning techniques on dermatoscopic images
Authors: Jojoa Acosta Mario Fernando , Caballero Tovar Liesle Yail , Garcia-Zapirain Maria Begonya , Percybrooks Winston Spencer
Published: January 2021

Background

Melanoma has become more widespread over the past 30 years and early detection is a major factor in reducing mortality rates associated with this type of skin cancer. Therefore, having access to an automatic, reliable system that is able to detect the presence of melanoma via a dermatoscopic image of lesions and/or skin pigmentation can be a very useful tool in the area of medical diagnosis.

Methods

Among state-of-the-art methods used for automated or computer assisted medical diagnosis, attention should be drawn to Deep Learning based on Convolutional Neural Networks, wherewith segmentation, classification and detection systems for several diseases have been implemented. The method proposed in this paper involves an initial stage that automatically crops the region of interest within a dermatoscopic image using the Mask and Region-based Convolutional Neural Network technique, and a second stage based on a ResNet152 structure, which classifies lesions as either “benign” or “malignant”.

Results

Training, validation and testing of the proposed model was carried out using the database associated to the challenge set out at the 2017 International Symposium on Biomedical Imaging. On the test data set, the proposed model achieves an increase in accuracy and balanced accuracy of 3.66% and 9.96%, respectively, with respect to the best accuracy and the best sensitivity/specificity ratio reported to date for melanoma detection in this challenge. Additionally, unlike previous models, the specificity and sensitivity achieve a high score (greater than 0.8) simultaneously, which indicates that the model is good for accurate discrimination between benign and malignant lesion, not biased towards any of those classes.

Conclusions

The results achieved with the proposed model suggest a significant improvement over the results obtained in the state of the art as far as performance of skin lesion classifiers (malignant/benign) is concerned.
Quick evaluation of lower leg ischemia in patients with peripheral arterial disease by time maximum intensity projection CT angiography: a pilot study
Authors: Zhang Daming , Zhou Xueyan , Zhang Haiping , Fan Xiaobing , Lin Zehong , Xue Huadan , Wang Yining , Jin Zhengyu , Chen Yuexin
Published: January 2021

Background

The purpose of this study is to evaluate a new method involving time maximum intensity projection (t-MIP) postprocessed from dynamic computed tomographic angiography (dyn-CTA) in diagnosing peripheral arterial disease (PAD).

Methods

A population of 34 patients with known PAD was examined with a combined CTA protocol consisting of a standard CTA (s-CTA) scan of the lower extremities and a dyn-CTA scan of the calves. For each lower leg, t-MIP images consisting of the MIP0 (sagittal MIP), MIP+θ (45° lateral MIP), and MIP−θ (− 45° lateral MIP) were automatically generated from dyn-CTA. An objective evaluation of the vascular CT attenuation of the best enhancement phase of dyn-CTA and t-MIP was measured; a subjective evaluation of vessel stenosis and occlusion was performed, assigning a score for t-MIP and s-CTA. The CT attenuation of t-MIP and dyn-CTA was compared, as were the runoff scores of t-MIP and s-CTA.

Results

The CT attenuation of t-MIP CTA of three vascular segments from 68 lower extremities was higher than that of the best enhancement phase of dyn-CTA and s-CTA, with statistically significant differences at the posterior tibial artery and fibular artery (all p < 0.05). There were strong correlations (r ≥ 0.75, p < 0.05) of the runoff scores between t-MIP and s-CTA.

Conclusions

There is potential clinical applicability of t-MIP in assisting with the diagnosis of lower leg vascular stenosis in dyn-CTA with reliable diagnostic accuracy and convenient immediacy.
Metal artifacts in intraoperative O-arm CBCT scans
Authors: Peltonen Juha I. , Kaasalainen Touko , Kortesniemi Mika
Published: January 2021

Background

Cone-beam computed tomography (CBCT) has become an increasingly important medical imaging modality in orthopedic operating rooms. Metal implants and related image artifacts create challenges for image quality optimization in CBCT. The purpose of this study was to develop a robust and quantitative method for the comprehensive determination of metal artifacts in novel CBCT applications.

Methods

The image quality of an O-arm CBCT device was assessed with an anthropomorphic pelvis phantom in the presence of metal implants. Three different kilovoltage and two different exposure settings were used to scan the phantom both with and without the presence of metal rods.

Results

The amount of metal artifact was related to the applied CBCT imaging protocol parameters. The size of the artifact was moderate with all imaging settings. The highest applied kilovoltage and exposure level distinctly increased artifact severity.

Conclusions

The developed method offers a practical and robust way to quantify metal artifacts in CBCT. Changes in imaging parameters may have nonlinear effects on image quality which are not anticipated based on physics.
What stakeholders think: perceptions of perinatal depression and screening in China’s primary care system
Authors: Premji Shahirose Sadrudin , Dobson Keith S. , Prashad Anupa , Yamamoto Shelby , Tao Fangbiao , Zhu Beibei , Wu Xiaoyan , Lu Mengjuan , Shao Shanshan
Published: January 2021

Background

Mental health in China is a significant issue, and perinatal depression has been recognized as a concern, as it may affect pregnancy outcomes. There are growing calls to address China’s mental health system capacity issues, especially among vulnerable groups such as pregnant women due to gaps in healthcare services and inadequate access to resources and support. In response to these demands, a perinatal depression screening and management (PDSM) program was proposed. This exploratory case study identified strategies for successful implementation of the proposed PDSM intervention, informed by the Consolidated Framework for Implementation Research (CFIR) framework, in Ma’anshan city, Anhui province.

Methods

This qualitative study included four focus group discussions and two in-depth individual interviews with participants using a semi-structured interview guide. Topics examined included acceptance, utility, and readiness for a PDSM program. Participants included perinatal women and their families, policymakers, and healthcare providers. Interviews were transcribed verbatim, coded, and analyzed for emergent themes.

Results

The analysis revealed several promising factors for the implementation of the PDSM program including: utilization of an internet-based platform, generation of perceived value among health leadership and decision-makers, and the simplification of the screening and intervention components. Acceptance of the pre-implementation plan was dependent on issues such as the timing and frequency of screening, ensuring high standards of quality of care, and consideration of cultural values in the intervention design. Potential challenges included perceived barriers to the implementation plan among stakeholders, a lack of trained human health resources, and poor integration between maternal and mental health services. In addition, participants expressed concern that perinatal women might not value the PDSM program due to stigma and limited understanding of maternal mental health issues.

Conclusion

Our analysis suggests several factors to support the successful implementation of a perinatal depression screening program, guidelines for successful uptake, and the potential use of internet-based cognitive behavioral therapy. PDSM is a complex process; however, it can be successfully navigated with evidence-informed approaches to the issues presented to ensure that the PDSM is feasible, effective, successful, and sustainable, and that it also improves maternal health and wellbeing, and that of their families.
Low birth weight trends in Organisation for Economic Co-operation and Development countries, 2000–2015: economic, health system and demographic conditionings
Authors: Erasun Diego , Alonso-Molero Jéssica , Gómez-Acebo Inés , Dierssen-Sotos Trinidad , Llorca Javier , Schneider José
Published: January 2021

Background

Low birth weight rates are increasing in both developed and developing countries. Although several maternal factors have been identified as associated with low birth weight, little is known of economic or organization factors influencing this increase. This study aims to ascertain the twenty-first century relationships between the contextual country factors and low birth weight rates.

Methods

We analyse trends of low birth weight rates in Organisation for Economic Co-operation and Development (OECD) countries. Data from 2000 to 2015 were obtained from the OECD data base. Their relationships with demographic and economic variables, health habits, woman-related preventive measures, health care system organization and funding, health care work force and obstetric care were analysed using random-effects linear regression.

Results

Low birth weight rates are higher in Southern Europe (7.61%) and lower in Northern Europe (4.68%). Low birth weight rates escalated about 20% in Southern Europe and to less extent in Easter Europe (7%) and Asian/Oceanian countries, while remained stable in America, Central Europe and Northern Europe. Investment in health care, private health system coverage, ratios of paediatricians and obstetricians, average length of admission due to pregnancy or birth and Caesarean section rate were associated with higher low birth weight rates. Factors associated with lower low birth weight rates were health care coverage, public health system coverage, hospitals per million inhabitants, and ratios of health care workers, physicians, midwives and nurses.

Conclusions

In OECD countries, LBW rates are related to contextual country characteristics such as GDP per capita, which is inversely related to LBW rate. Health care system factors, including health care coverage or investment in public health system, are directly associated with lower LBW rates.