bluuebunny/crossref_metadata_2025 huggingface dataset:
Challenges in measuring integrated care models: International knowledge and the case of Québec
Authors: Wankah Paul , Guillette Maxime , Lemaitre Thomas , Belzile Louise , Couturier Yves
Published: July 2020

Introduction

The implementation of integrated care models requires significant efforts, especially due to institutional and organisational inertial forces that characterize health and social care systems of developed countries. It is therefore crucial to deploy strategies that promote continuous adjustment to these barriers so as to improve the benefits of integrating care. Measuring the implementation and effects of integrated care models are key component of these strategies. However, measuring integrated care also faces major challenges. This study aims to identify and characterise integrated care measurement challenges.

Methods

A review of reviews on the measurement of integrated care identified 12 papers. A thematic analysis was conducted to identify and categorize measurement challenges. Document analysis was done on the measurement of an integrated care model for older adults in Québec.

Results

Eight categories of measurement challenges were identified. These challenges include difficulties in measuring structures, processes, and effects of models; conceptual ambiguity and heterogeneity of organisational forms; involving multiple actors in the measurement strategy; and including multiple data sources, amongst others. These challenges revealed and explained potential gaps in the measurement of integrated care for older adults in Québec. For instance, the Québec measurement strategy did not include effects indicators.

Conclusion

Although the measurement of integrated care is a complex endeavour, there is a need for adequate measurement strategies that allow to appreciate important elements of integrate care. The findings of this study could be used as a reflexive tool in advancing research and practice of measuring integrated care.
Adolescent Girl–Mother Communication on Sexual and Reproductive Health Issues Among Students in Fiche Town, Oromia, Central Ethiopia
Authors: Feyissa Mulugeta , Nigussie Tadesse , Mamo Yitagesu , Aferu Temesgen
Published: July 2020

Background: Adolescents who have communication about sexual and reproductive health (SRH) with their parents are less likely to participate in risky sexual behaviors and to utilize modern contraceptives. However, communication on SRH issues between adolescents and their parents continues to be below the desired goals in low- and middle-income countries. Objective: To assess SRH communication between adolescent girls and their mothers among students in secondary and preparatory schools in Fiche town, Oromia, Central Ethiopia. Method: An institution-based cross-sectional study was conducted from March 27 to March 30, 2017, using a structured self-administered questionnaire. A total of 181 adolescent female students selected from 2 schools in the town participated in the study. Data were collected on sociodemographic characteristics, student-mother communication, and knowledge about and attitudes toward SRH issues. Multivariable logistic regression analysis was performed, and variables with a P value less than .05 were considered statistically significant. Results: A total of 103 (56.9%) of the students had discussed SRH issues with their mothers. The mothers’ educational status (ie, primary school and above, adjusted odds ratio [AOR] = 10.01, 95% CI = 3.55-28.19; the student living with friends, AOR = 5.29, 95% CI = 1.09-25.47; the students’ knowledge about SRH issues, AOR = 8.57, 95% CI = 3.61-20.35; and students’ attitude toward SRH issues, AOR = 2.79, 95% CI = 1.26-6.15) were identified as independent positive predictors of student-mother communication on selected SRH issues. Conclusion: More than half of the study participants had communication on SRH issues with their mothers. SRH communication was positively associated with maternal educational status, the students’ living with friends, and the student’s knowledge of and attitude toward SRH issues.
The Rio 2016 Paralympic Games: The Visibility of People With Disabilities in Brazil as a Possible Legacy
Authors: de Souza Doralice Lange , Brittain Ian
Published: July 2020

There are claims that the Paralympic Games (PG) might contribute to a better world for people with disabilities (PWD). However, there are also claims that the PG might in fact be counterproductive to the PWD’s rights movement because they might promote the medical model of disability and/or ableism. In this context, we developed a qualitative exploratory study to investigate the legacies of the Rio 2016 PG from the perspective of disability rights activists and people involved in Paralympic sport managerial positions. In this article, we discuss one of the main perceived legacies that the PG fostered PWD’s visibility and a change in society’s perception of PWD. We conducted 24 open in-depth interviews and found that, for our participants, the PG worked as a showcase for PWD who were rarely seen in the media and in public spaces before the Games. This visibility helped to challenge negative stereotypes and stigmas associated with PWD, as well as possibly opening new doors for them. Our interviewees believe that we shouldn’t expect that the PG alone can change people’s perceptions and PWD’s status overnight. They are part of a larger and complex set of actions that are slowly contributing to this process.
Return to Play in Athletes After Thumb Ulnar Collateral Ligament Repair With Suture Tape Augmentation
Authors: Gibbs Daniel B. , Shin Steven S.
Published: July 2020

Background:

Thumb ulnar collateral ligament (UCL) tears are common in competitive athletes. These tears often occur as a result of a radially directed force on an extended thumb. To date, no literature exists on the use of suture tape augmentation for repair of the thumb UCL in a competitive athlete cohort.

Hypothesis:

Using suture tape augmentation for the thumb UCL will allow for a safe and expedient return to play in competitive athletes.

Study Design:

Case series; Level of evidence, 4.

Methods:

A retrospective chart review was completed to identify all patients who underwent operative primary thumb UCL repair between 2014 and 2018. All procedures were performed at a single institution by the senior author. Inclusion criteria were acute complete tears of the thumb metacarpophalangeal joint UCL, treated with primary repair via suture tape augmentation in competitive high school, collegiate, or professional athletes. Exclusion criteria included recreational athletes, patients who underwent reconstruction (rather than repair), and patients with insufficient follow-up to establish return to play. Charts of patients identified through the retrospective review were further evaluated to determine patient- and injury-related variables. Return to play was defined as return to game competition and stratified as to whether this was at the same level of competition or any level of competition.

Results:

A total of 18 thumbs in 17 competitive high school, collegiate, and professional athletes were included in this study. One of the professional basketball players sustained injury to both thumbs approximately 10 months apart. The study group comprised 4 collegiate baseball players, 6 professional baseball players, 3 professional basketball players, 1 professional hockey player, 1 amateur-level hockey player, 1 high school basketball player, and 1 high school volleyball player. Mean follow-up was 27.9 months, and no complications were noted. Athletes who sustained an in-season injury (n = 13; 72.2%) returned to play at any level at a mean ± SD of 30.9 ± 10.1 days and at the same level at 36.3 ± 11.2 days. Athletes who sustained an out-of-season injury (n = 5; 27.8%) returned to play at any level at 101.4 ± 86.6 days and at the same level at 114.6 ± 87.0 days.

Conclusion:

The findings presented here offer evidence for return to play in competitive high school, collegiate, and professional athletes with a thumb UCL tear treated with repair and suture tape augmentation. All athletes returned to the same level of play. Those attempting to return in-season returned to the same level of play at a mean of just under 5 weeks. Augmenting the repair with anchored suture may prevent prolonged immobilization, expedite thumb motion, and improve postoperative recovery.
A comparative analysis of profit inefficiency and productivity convergence between Taiwanese and Chinese banks
Authors: Chen Xiang , Fu Tsu-Tan , Juo Jia-Ching , Yu Ming-Miin
Published: July 2020

To insure a proper and meaningful productivity assessment of DMUs with different production technologies, this article develops a difference-based profit metafrontier Luenberger productivity indicator. Adopting the proposed model, we empirically measure the profit inefficiency and examine the profit productivity convergence for samples banks consisting of 31 Taiwanese banks and 50 Chinese city banks over 2010–2014. Empirical results show that Chinese banks perform better in profit efficiency than Taiwanese banks. While Chinese banks have better technology in profit creation than Taiwanese banks, the latter may reap much higher profit gain than the former if they can adopt the profit metafrontier. The results of the profit metafrontier Luenberger productivity indicator analysis show that both Chinese and Taiwanese banks have experienced declines in profit productivity. However, the results also indicate a divergence in productivity growth for Chinese city banks and a convergent productivity growth for Taiwanese banks.

JEL CLASSIFICATION: D20, G21, P34
A nonparametric analysis of competitiveness efficiency: The relevance of firm size and the configuration of competitive pillars
Authors: Lafuente Esteban , Leiva Juan Carlos , Moreno-Gómez Jorge , Szerb László
Published: July 2020

This study employs a data envelopment analysis (DEA) model with a single constant input to analyze the competitiveness performance of a unique sample of 103 knowledge-intensive business service (KIBS) firms from Hungary, Spain, Colombia, and Costa Rica for the year 2017. Also, we assess how the configuration of competitive pillars—strengths and weaknesses—affects efficiency and how firm size moderates this relationship. The mean efficiency scores by which the competitiveness output can be optimized is 47.43%. The results suggest that the configuration of competitive pillars has important implications for efficiency analyses. For small businesses, competitive-enhancing actions should focus on mitigating competitive weaknesses that are detrimental to efficiency. Also, a configuration of competitive pillars in which one or various competitive strengths prevail is more beneficial for small businesses. Managerial tools such as the proposed competitiveness measure may offer useful information on what strategic actions can contribute to optimize business competitiveness.

JEL CLASSIFICATION C14; L19; L25
Institutional shareholding as a corporate governance mechanism that drives Chief Executive Officer pay
Authors: Pucheta-Martínez María Consuelo , Chiva-Ortells Carlos
Published: July 2020

We explore the effect of institutional directors on Chief Executive Officer (CEO) pay (total, fixed, and variable compensation). We delve particularly into the impact of pressure-sensitive and pressure-resistant institutional directors, who, respectively, represent institutional investors who maintain and investors who do not maintain a business relationship with the firm whose board they serve on. Focusing on CEO total pay, the findings show that institutional and pressure-resistant directors on boards behave similarly, affecting CEO total pay in a nonlinear way: as the presence of institutional and pressure-resistant directors on boards increases, the monitoring hypothesis prevails, and subsequently, better corporate governance decreases CEO total pay. However, when their presence on boards exceeds a critical point, the entrenchment hypothesis holds, thereby leading to an increase in CEO total pay. Contrary to our predictions, pressure-sensitive directors do not affect CEO total pay. Regarding the CEO’s compensation structure (fixed and variable), the results suggest that institutional and pressure-resistant directors increase fixed compensation and reduce variable pay, while pressure-sensitive directors affect neither fixed nor variable compensation. This evidence supports the view that institutional directors should be considered as a heterogeneous collective.

JEL CLASSIFICATION: G3, G34, M12
Net operating working capital and firm value: A cross-country analysis
Authors: Baños-Caballero Sonia , García-Teruel Pedro J , Martínez-Solano Pedro
Published: July 2020

Here, we use a sample of firms from 30 countries during the period 1995–2013 to examine the relationship between net operating working capital (NWC) and firm value. Specifically, we show that the value of NWC varies across countries and that it depends on both investor protection and a country’s financial and economic development. Our findings imply that shareholders value NWC more in countries with strong enforcement of investor rights, and greater financial and economic development.

Jel Classification: G15; G18; G31; G32
Planning participants’ preferential differences under immersive virtual reality and conventional representations: An experiment of street renewal
Authors: Zhu Wei , Guo Shaoyu , Zhao Jinhua
Published: July 2020

Immersive virtual reality is a promising technology for planning participation. The paper contributes to the literature by comparing the latest virtual reality technology using head-mounted display with conventional graphic representation (pictures of rendered three-dimensional environments in this case) in terms of the effects on the participants’ preferences for the plans and their underlying decision mechanisms. Using a stated choice experiment based on a real-world project of street renewal, we collected choice data from 48 university students from non-design majors. We found significant quantitative but limited qualitative differences between the aggregate preferences under virtual reality and conventional graphic representation, and some generally unappealing features under conventional graphic representation were more favored under virtual reality. Results of the discrete choice modeling showed the individual decision mechanisms became more homogeneous under virtual reality. Virtual reality had stronger impacts on the female participants than the male participants. The females had more aggregate preference reversals, larger preference differences, and stronger changes in the decision mechanism. But the mechanisms of the two genders converged under virtual reality. The findings can be used to design better participatory processes with virtual reality and conventional graphic representation properly applied according to their capabilities.
Soil drugs of the future: The sustainability of BioAg and the repair of arable land
Authors: Oviatt Peter
Published: July 2020

BioAg, short for biological agriculture, is an umbrella term used by agricultural conglomerates to market biologically active products used for pest control and fertilization. Within this framing, I investigate the commodification of a type of fungus that forms a beneficial relationship with plant roots. Mycorrhizal fungi connect with root tips to exchange photosynthesized sugars for an array of what biologists call “ecosystem services,” which include the translocation of soil minerals, water, and pathogen antagonism. I discuss three conditions that now give rise to the commodification of mycorrhizal fungi in industrial agriculture: the creation of an inoculant form produced under sterile (in vitro) conditions; the declaration of industrial arable soils as lacking functioning communities of mycorrhizal fungi, a deficit most easily remedied through the application of industrially produced inoculants; the build-up of a broader mycorrhizal subjectivity, which has made the loss of mycorrhizal fungi in agricultural lands a concern for those beyond agricultural and scientific communities. To analyze these three stages of the commodification of mycorrhizal fungi, I engage the framework of accumulation by restoration as part of the economy of repair. Following the work of Christopher Henke, I discuss how mycorrhizal inoculants are poised to bring about two forms of repair to soil ecologies and industrial agriculture: maintenance and transformation. I examine the challenges and controversies surrounding the efficacy of mycorrhizal inoculants, testing claims about ecological restoration and how an emergent and heavily promoted agricultural commodity might impact regional agricultural infrastructures, rural ecologies, and agrarian livelihoods. I use the case of mycorrhizal inoculants within BioAg to sort out promissory claims of sustainability, and look at how agricultural conglomerates are now building their envisioned future of industrial agriculture.
Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN
Authors: Gleitz Hélène F. E. , Dugourd Aurélien J. F. , Leimkühler Nils B. , Snoeren Inge A. M. , Fuchs Stijn N. R. , Menzel Sylvia , Ziegler Susanne , Kröger Nicolaus , Triviai Ioanna , Büsche Guntram , Kreipe Hans , Banjanin Bella , Pritchard Jessica E. , Hoogenboezem Remco , Bindels Eric M. , Schumacher Neele , Rose-John Stefan , Elf Shannon , Saez-Rodriguez Julio , Kramann Rafael , Schneider Rebekka K.
Published: July 2020

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm (MPN) that leads to progressive bone marrow (BM) fibrosis. Although the cellular mutations involved in the pathogenesis of PMF have been extensively investigated, the sequential events that drive stromal activation and fibrosis by hematopoietic–stromal cross-talk remain elusive. Using an unbiased approach and validation in patients with MPN, we determined that the differential spatial expression of the chemokine CXCL4/platelet factor-4 marks the progression of fibrosis. We show that the absence of hematopoietic CXCL4 ameliorates the MPN phenotype, reduces stromal cell activation and BM fibrosis, and decreases the activation of profibrotic pathways in megakaryocytes, inflammation in fibrosis-driving cells, and JAK/STAT activation in both megakaryocytes and stromal cells in 3 murine PMF models. Our data indicate that higher CXCL4 expression in MPN has profibrotic effects and is a mediator of the characteristic inflammation. Therefore, targeting CXCL4 might be a promising strategy to reduce inflammation in PMF.
SnxPy Monolayers: a New Type of Two-Dimensional Materials with High Stability, Carrier Mobility, and Magnetic Properties
Authors: Dou Yan-Mei , Zhang Chang-Wen , Li Ping , Wang Pei-Ji
Published: July 2020

Searching for two-dimensional (2D) group V materials with ferromagnetism, elastic anisotropy, and carrier mobility and tunable band structure is one key to developing constantly developing nanodevices. The 2D monolayers SnxPy with x/y (1/1, 1/2, 1/3, and so on) coordination number are studied based on the particle-swarm optimization technique combined with the density functional theory optimization. Its thermal stability can be confirmed by molecular dynamics at 70K and 300K, indicating that the novel 2D materials have a stable existence. The electronic band structures of four stable structures suggest that all the monolayers of SnxPy are fully adjustable and flexible tunable band gaps semiconductors under the biaxial strain. The monolayer of P$$ \overline{4}{2}_1 $$

4
¯

2
1

m-SnP2 with unique valence band structure can go from nonmagnetic to ferromagnetic by the hole doping because of the “Stoner criterion,” and Pmc21-SnP2 is a direct-like gap semiconductor with in-plane elastic anisotropy to possess a high electron mobility as high as 800 cm2V−1 s−1 along the kb direction, which is much higher than that of MoS2 (∼ 200 cm2V−1 s−1). The optical absorption peak of the material is in the ultraviolet region. These discoveries expand the potential applications of the emerging field of 2D SnxPy structures in nanoelectronics.
Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations
Authors: Papachristou Dimitris , Koutsouli Panagiota , Laliotis George P. , Kunz Elisabeth , Upadhyay Maulik , Seichter Doris , Russ Ingolf , Gjoko Bunevski , Kostaras Nikolaos , Bizelis Iosif , Medugorac Ivica
Published: July 2020

Background

The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs).

Results

We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support forBos indicusintrogression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps.

Conclusions

All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
Statistical shape analysis of tap roots: a methodological case study on laser scanned sugar beets
Authors: Heeren Behrend , Paulus Stefan , Goldbach Heiner , Kuhlmann Heiner , Mahlein Anne-Katrin , Rumpf Martin , Wirth Benedikt
Published: July 2020

Background

The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D shape of plant surfaces. The computation of a shape based principal component analysis (PCA) built on concepts from continuum mechanics has proven to be an effective tool for a qualitative and quantitative shape examination.

Results

The shape based PCA was used for a statistical analysis of 140 sugar beet roots of different cultivars. The calculation of the mean sugar beet root shape and the description of the main variations was possible. Furthermore, unknown and individual tap roots could be attributed to their cultivar by means of a robust classification tool based on the PCA results.

Conclusion

The method demonstrates that it is possible to identify principal modes of root shape variations automatically and to quantify associated variances out of laserscanned 3D sugar beet tap root models. The introduced approach is not limited to the 3D shape description by laser scanning. A transfer to 3D MRI or radar data is also conceivable.
The insights into the systematic relationship of Gastrostyla-affinitive genera, with report on a new saline soil ciliate genus and new species (Protozoa, Ciliophora)
Authors: Lu Xiaoteng , Wang Yuanyuan , Al-Farraj Saleh A. , El-Serehy Hamed , Huang Jie , Shao Chen
Published: July 2020

Background

Hypotrichia are a group with the most complex morphology and morphogenesis within the ciliated protists. The classification ofGastrostyla-like species, a taxonomically difficult group of hypotrichs with a common ventral cirral pattern but various dorsal and ontogenetic patterns, is poorly understood. Hence, systematic relationships within this group and with other taxa in the subclass Hypotrichia remain unresolved.

Results

18S rRNA gene sequence of a newGastrostyla-like taxon was obtained. Phylogenetic analyses based on the 18S rRNA gene sequences indicate that this ciliate represents a new genus that is closely related toHeterourosomoidaandKleinstylawithin the oxytrichid clade of the Hypotrichia. However, the position of this cluster remains unresolved. All three genera deviate from the typical oxytrichids by their incomplete (or lack of) dorsal kinety fragmentation during morphogenesis. Morphology and morphogenesis of this newly discovered form,Heterogastrostyla salinanov. gen., nov. spec., are described.Heterogastrostylanov. gen., is characterised as follows: more than 18 fronto-ventral-transverse cirri, cirral anlagen V and VI develop pretransverse cirri, and dorsal ciliature inUrosomoida-like pattern.

Conclusions

Similar to the CEUU-hypothesis about convergent evolution of urostylids and uroleptids, we speculate that the shared ventral cirral patterns ofGastrostyla-like taxa might have resulted from convergent evolution.
CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
Authors: Patel Manthan , Patel Divyesh , Datta Subhamoy , Singh Umashankar
Published: July 2020

Background

The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown.

Results

By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1.

Conclusion

Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution
Authors: Höglund Andrey , Strempfl Katharina , Fogelholm Jesper , Wright Dominic , Henriksen Rie
Published: July 2020

Background

Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver).

Results

We identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus).

Conclusion

The candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.
Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools
Authors: Derakhshani Hooman , Bernier Steve P. , Marko Victoria A. , Surette Michael G.
Published: July 2020

Background

Illumina technology currently dominates bacterial genomics due to its high read accuracy and low sequencing cost. However, the incompleteness of draft genomes generated by Illumina reads limits their application in comprehensive genomics analyses. Alternatively, hybrid assembly using both Illumina short reads and long reads generated by single molecule sequencing technologies can enable assembly of complete bacterial genomes, yet the high per-genome cost of long-read sequencing limits the widespread use of this approach in bacterial genomics. Here we developed a protocol for hybrid assembly of complete bacterial genomes using miniaturized multiplexed Illumina sequencing and non-barcoded PacBio sequencing of a synthetic genomic pool (SGP), thus significantly decreasing the overall per-genome cost of sequencing.

Results

We evaluated the performance of SGP hybrid assembly on the genomes of 20 bacterial isolates with different genome sizes, a wide range of GC contents, and varying levels of phylogenetic relatedness. By improving the contiguity of Illumina assemblies, SGP hybrid assembly generated 17 complete and 3 nearly complete bacterial genomes. Increased contiguity of SGP hybrid assemblies resulted in considerable improvement in gene prediction and annotation. In addition, SGP hybrid assembly was able to resolve repeat elements and identify intragenomic heterogeneities, e.g. different copies of 16S rRNA genes, that would otherwise go undetected by short-read-only assembly. Comprehensive comparison of SGP hybrid assemblies with those generated using multiplexed PacBio long reads (long-read-only assembly) also revealed the relative advantage of SGP hybrid assembly in terms of assembly quality. In particular, we observed that SGP hybrid assemblies were completely devoid of both small (i.e. single base substitutions) and large assembly errors. Finally, we show the ability of SGP hybrid assembly to differentiate genomes of closely related bacterial isolates, suggesting its potential application in comparative genomics and pangenome analysis.

Conclusion

Our results indicate the superiority of SGP hybrid assembly over both short-read and long-read assemblies with respect to completeness, contiguity, accuracy, and recovery of small replicons. By lowering the per-genome cost of sequencing, our parallel sequencing and hybrid assembly pipeline could serve as a cost effective and high throughput approach for completing high-quality bacterial genomes.
Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach
Authors: Rawandoozi Zena J. , Hartmann Timothy P. , Carpenedo Silvia , Gasic Ksenija , da Silva Linge Cassia , Cai Lichun , Van de Weg Eric , Byrne David H.
Published: July 2020

Background

Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica(L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time.

Results

Phenotypic data of seven F1low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40–46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles.

Conclusions

A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.
Proteomic responses to progressive dehydration stress in leaves of chickpea seedlings
Authors: Vessal Saeedreza , Arefian Mohammad , Siddique Kadambot H. M.
Published: July 2020

Background

Chickpea is an important food legume crop with high protein levels that is widely grown in rainfed areas prone to drought stress. Using an integrated approach, we describe the relative changes in some physiological parameters and the proteome of a drought-tolerant (MCC537, T) and drought-sensitive (MCC806, S) chickpea genotype.

Results

Under progressive dehydration stress, the T genotype relied on a higher relative leaf water content after 3 and 5 d (69.7 and 49.3%) than the S genotype (59.7 and 40.3%) to maintain photosynthetic activities and improve endurance under stress. This may have been facilitated by greater proline accumulation in the T genotype than the S genotype (14.3 and 11.1 μmol g− 1 FW at 5 d, respectively). Moreover, the T genotype had less electrolyte leakage and lower malondialdehyde contents than the S genotype under dehydration stress, indicating greater membrane stability and thus greater dehydration tolerance. The proteomic analysis further confirmed that, in response to dehydration, the T genotype activated more proteins related to photosynthesis, stress response, protein synthesis and degradation, and gene transcription and signaling than the S genotype. Of the time-point dependent proteins, the largest difference in protein abundance occurred at 5 d, with 29 spots increasing in the T genotype and 30 spots decreasing in the S genotype. Some of the identified proteins—including RuBisCo, ATP synthase, carbonic anhydrase, psbP domain-containing protein, L-ascorbate peroxidase, 6-phosphogluconate dehydrogenase, elongation factor Tu, zinc metalloprotease FTSH 2, ribonucleoproteins and auxin-binding protein—may play a functional role in drought tolerance in chickpea.

Conclusions

This study highlights the significance of genotype- and time-specific proteins associated with dehydration stress and identifies potential resources for molecular drought tolerance improvement in chickpea.
Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed
Authors: Fang Lin , Xu Xin , Li Ji , Zheng Feng , Li Mingzhi , Yan Jingwei , Li Yuan , Zhang Xinhua , Li Lin , Ma Guohua , Zhang Aying , Lv Fubing , Wu Kunlin , Zeng Songjun
Published: July 2020

Backgrounds

Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.

Results

In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues.

Conclusions

This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.
Polyploidization and pseudogenization in allotetraploid frog Xenopus laevis promote the evolution of aquaporin family in higher vertebrates
Authors: Jia Yanglei , Liu Xiao
Published: July 2020

Background

Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and function due to genome wide duplication. While some AQP orthologs have been lost in higher vertebrates through evolution.

Result

Genome-wide comparative analyses of the AQP family between allotetraploid frog Xenopus laevis (Xla) and diploid frog Xenopus tropicalis (Xtr), based on the genome assemblies, revealed that the number of AQPs in Xla genome nearly doubled that in Xtr (32 vs. 19). Synteny analysis indicated that the distribution of the retained AQPs in Xla subgenomes (17 in Xla. L, the longer homeolog of Xla genome and 15 in Xla. S, the shorter homeolog of Xla genome) were highly symmetrical when compared with that in Xtr genome. Remarkably, two members in Xla. L and four members in Xla. S were lost through evolution. Blast analysis revealed that the lost AQPs in Xla are pseudogenized via either the deletion of some exons or some single nucleotide insertions or deletions that lead the reading frame shift. Additionally, comparative genomic analyses suggested that the orthologs of AQPs that with one copy absence in Xla are also prone to be lost in higher vertebrates.

Conclusion

This study revealed that polyploidization and subsequent pseudogenization and deletion in Xla genome promote the evolution of AQP family in higher vertebrates. Besides, our results would also contribute to understanding the evolution of AQP family.
Changes in the vaginal microbiota associated with primary ovarian failure
Authors: Wang Juan , Xu Jieying , Han Qixin , Chu Weiwei , Lu Gang , Chan Wai-Yee , Qin Yingying , Du Yanzhi
Published: July 2020

Background

Primary ovarian failure (POF) is defined as follicular failure in women of reproductive age. Although many factors are speculated to contribute to the occurrence of POF, the exact aetiology remains unclear. Moreover, alterations in the microbiome of patients with POF are poorly studied.

Results

This study investigated the vaginal microbiota of 22 patients with POF and 29 healthy individuals. High-throughput Illumina MiSeq sequencing targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to evaluate the relationships between the vaginal flora and clinical characteristics of POF. Different from results of previous studies, we found that the diversity and richness of the vaginal flora of patients with POF was significantly different from those of healthy controls. Comparison of the vaginal flora of patients with POF with that of menopausal women revealed that the relative abundance of Lactobacillus was significantly reduced in the latter. A reduced abundance of Lactobacillus was furthermore associated with a lower pregnancy success rate. Of particular interest is that L. gallinarum especially appeared to be beneficially associated with reproductive-related indicators (FSH, E2, AMH, PRL) whilst L. iners appeared to have a detrimental effect. The result of the present study may enable the identification of microbiota associated with POF, however, further investigations of differences in the microbiota in the context of POF will enable a deeper understanding of the disease pathogenesis that involves modification of the vaginal microbiota.

Conclusions

The present study identified the microbiota associated with POF. Further investigations on the differences in the microbiota in the context of POF will improve our understanding of the pathogenesis of the disease which involves modification of the vaginal microbiota.
Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in safflower (Carthamus tinctorius L.) under MeJA treatment
Authors: Chen Jiang , Wang Jie , Wang Rui , Xian Bin , Ren Chaoxiang , Liu Qianqian , Wu Qinghua , Pei Jin
Published: July 2020

Background

Safflower (Carthamus tinctorius L.) is an important cash crop, of which the dried tube flower is not only an important raw material for dyes and cosmetics but also an important herb widely used in traditional Chinese medicine. The pigment and bioactive compounds are composed of flavonoids (mainly quinone chalcones), and studies have reported that MeJA can promote the biosynthesis of quinone chalcones, but the mechanism underlying the effect of MeJA in safflower remains unclear. Here, we attempt to use metabolomics and transcriptome technologies to analyse the molecular mechanism of flavonoid biosynthesis under MeJA treatment in safflower.

Results

Based on a UHPLC-ESI-MS/MS detection platform and a self-built database (including hydroxysafflor yellow A, HSYA), a total of 209 flavonoid metabolites were detected, and 35 metabolites were significantly different after treatment with MeJA. Among them, 24 metabolites were upregulated upon MeJA treatment, especially HSYA. Eleven metabolites were downregulated after MeJA treatment. Integrated metabolomics and transcriptome analysis showed that MeJA might upregulate the expression of upstream genes in the flavonoid biosynthesis pathway (such as CHSs, CHIs and HCTs) and downregulate the expression of downstream genes (such as F3Ms, ANRs and ANSs), thus promoting the biosynthesis of quinone chalcones, such as HSYA. The transcription expressions of these genes were validated by real-time PCR. In addition, the promoters of two genes (CtCHI and CtHCT) that were significantly upregulated under MeJA treatment were cloned and analysed. 7 and 3 MeJA response elements were found in the promoters, respectively.

Conclusions

MeJA might upregulate the expression of the upstream genes in the flavonoid biosynthesis pathway and downregulate the expression of the downstream genes, thus promoting the biosynthesis of quinone chalcones. Our results provide insights and basic data for the molecular mechanism analysis of flavonoid synthesis in safflower under MeJA treatment.
De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics
Authors: Vu Dinh Duy , Shah Syed Noor Muhammad , Pham Mai Phuong , Bui Van Thang , Nguyen Minh Tam , Nguyen Thi Phuong Trang
Published: July 2020

Background

Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management.Panax vietnamensisHa et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers.

Results

In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes ofP. vietnamensis(roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances.

Conclusion

Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.