bluuebunny/crossref_metadata_2025 huggingface dataset:
Genus level molecular phylogeny of Aegisthidae Gisbrecht, 1893 (Copepoda: Harpacticoida) reveals morphological adaptations to deep-sea and plagic habitats
Authors: Khodami Sahar , Mercado-Salas Nancy F. , Martìnez Arbizu Pedro
Published: March 2020

Background

The family Aegisthidae is known as typical component of deep-sea hyperbenthic waters that gradually colonized other marine environments. The phylogenetic relationships within this family have been examined here including hyperbenthic, planktonic, benthic forms and two associated Aegisthidae species.

Results

Ninety four specimens belong to 14 genera were studied using 18S and 28S rRNA and COI mtDNA. Bayesian analysis supports the monophyly of 10 genera whereas Andromastax, Jamstecia, Nudivorax and Aegisthus revealed to be paraphyletic. The first offshoot of the phylogenetic tree is a clade consists of the undescribed genus Aegisthidae gen.1 sister to the two monophyletic genera Cerviniella and Hase, whereas the other Cerviniinae members (represented by Cervinia and Expansicervinia) assemble a monophylum, sister to the hyperbenthic and planktonic aegisthid genera, resulting in the paraphyly of the subfamily Cerviniinae. Hence, we defined the new subfamily Cerviniellinae subfam. nov. encompassing the three benthic genera Cerviniella, Hase and Eucanuella. The subfamily Cerviniinae has been re-defined to include Cervinia, Expansicervinia and Paracerviniella. Members of the subfamily Pontostratiotinae were clustered into two clades, one consists of the genus Stratiopontotes sister to an undescribed genus + Cerviniopsis and Siphonis. The second contains Pontostratiotes sister to the members of the planktonic subfamily Aegisthinae, resulting in the paraphyly of the Pontostratiotinae. Therefore, the Pontostratiotinae has been re-defined to include only members of the genus Pontostratiotes; whereas the subfamily Cerviniopseinae has been re-erected and re-defined containing Stratiopontotes, Cerviniopsis, Siphonis, Aegisthidae gen. 2, Herdmaniopsis, Hemicervinia and Tonpostratiotes. Within this subfamily, the associated Siphonis clusters as sister to the Cerviniopsis represents an example of convergent evolution in which the possession of a stylet-like mandible and an oral cone reminiscent of the Siphonostomatoida. The planktonic Aegisthus, Andromastax, Jamstecia, Nudivorax and Scabrantenna confirm the monophylom Aegisthinae, sister to the Pontostratiotinae.

Conclusions

Our DNA based phylogeny reveals the deep-sea origin of Aegisthidae by placing benthic Aegisthidae gen.1 and Cerviniellinae subfam. nov. as the most basal lineages. Secondary adaptations to hyperbenthic and planktonic realms, as well as associated lifestyle were discovered here by the derived positions of Pontostratiotinae, Aegisthinae and Siphonis respectively.
Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene
Authors: Obert Tomáš , Vďačný Peter
Published: March 2020

Background

Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms.

Results

Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms.

Conclusions

The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.
The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa
Authors: Al-Jumaili Ahmed S. , Boudali Selma Farah , Kebede Adebabay , Al-Bayatti Sahar A. , Essa Abdulamir A. , Ahbara Abulgasim , Aljumaah Riyadh S. , Alatiyat Raed M. , Mwacharo Joram M. , Bjørnstad Gro , Naqvi Arifa N. , Gaouar Semir Bechir Suheil , Hanotte Olivier
Published: March 2020

Background

Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. In this paper, using theD-loop of mitochondrial DNA as a maternally inherited genetic marker, we address the question of the origin and dispersal routes of domestic chicken of the Middle East (Iraq and Saudi Arabia), the northern part of the African continent (Algeria and Libya) and the Horn of Africa (Ethiopia).

Results

The analysis of the mtDNAD-loop of 706 chicken samples from Iraq (n = 107), Saudi Arabia (n = 185), Algeria (n = 88), Libya (n = 23), Ethiopia (n = 211) and Pakistan (n = 92) show the presence of five haplogroups (A, B, C, D and E), suggesting more than one maternal origin for the studied populations. Haplogroup E, which occurred in 625 samples, was the most frequent in all countries. This haplogroup most likely originates from the Indian subcontinent and probably migrated following a terrestrial route to these different countries. Haplotypes belonging to haplogroup D were present in all countries except Algeria and Libya, it is likely a legacy of the Indian Ocean maritime trading network. Haplogroup A was present in all countries and may be of commercial origin. Haplogroup B was found only in Ethiopia. Haplogroup C was only detected in the South-Western region of Saudi Arabia and in Ethiopia.

Conclusion

The results support a major influence of the Indian subcontinent on the maternal diversity of the today’s chicken populations examined here. Most of the diversity occurs within rather than between populations. This lack of phylogeographic signal agrees with both ancient and more recent trading networks having shaped the modern-day diversity of indigenous chicken across populations and countries.
Selected neuropeptide genes show genetic differentiation between Africans and non-Africans
Authors: Tai Kah Yee , Wong KokSheik , Aghakhanian Farhang , Parhar Ishwar S , Dhaliwal Jasbir , Ayub Qasim
Published: March 2020

Background

Publicly available genome data provides valuable information on the genetic variation patterns across different modern human populations. Neuropeptide genes are crucial to the nervous, immune, endocrine system, and physiological homeostasis as they play an essential role in communicating information in neuronal functions. It remains unclear how evolutionary forces, such as natural selection and random genetic drift, have affected neuropeptide genes among human populations. To date, there are over 100 known human neuropeptides from the over 1000 predicted peptides encoded in the genome. The purpose of this study is to analyze and explore the genetic variation in continental human populations across all known neuropeptide genes by examining highly differentiated SNPs between African and non-African populations.

Results

We identified a total of 644,225 SNPs in 131 neuropeptide genes in 6 worldwide population groups from a public database. Of these, 5163 SNPs that had ΔDAF |(African - non-African)| ≥ 0.20 were identified and fully annotated. A total of 20 outlier SNPs that included 19 missense SNPs with a moderate impact and one stop lost SNP with high impact, were identified in 16 neuropeptide genes. Our results indicate that an overall strong population differentiation was observed in the non-African populations that had a higher derived allele frequency for 15/20 of those SNPs. Highly differentiated SNPs in four genes were particularly striking: NPPA (rs5065) with high impact stop lost variant; CHGB (rs6085324, rs236150, rs236152, rs742710 and rs742711) with multiple moderate impact missense variants; IGF2 (rs10770125) and INS (rs3842753) with moderate impact missense variants that are in linkage disequilibrium. Phenotype and disease associations of these differentiated SNPs indicated their association with hypertension and diabetes and highlighted the pleiotropic effects of these neuropeptides and their role in maintaining physiological homeostasis in humans.

Conclusions

We compiled a list of 131 human neuropeptide genes from multiple databases and literature survey. We detect significant population differentiation in the derived allele frequencies of variants in several neuropeptide genes in African and non-African populations. The results highlights SNPs in these genes that may also contribute to population disparities in prevalence of diseases such as hypertension and diabetes.
Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest
Authors: Sparks Michael E. , Bansal Raman , Benoit Joshua B. , Blackburn Michael B. , Chao Hsu , Chen Mengyao , Cheng Sammy , Childers Christopher , Dinh Huyen , Doddapaneni Harsha Vardhan , Dugan Shannon , Elpidina Elena N. , Farrow David W. , Friedrich Markus , Gibbs Richard A. , Hall Brantley , Han Yi , Hardy Richard W. , Holmes Christopher J. , Hughes Daniel S. T. , Ioannidis Panagiotis , Cheatle Jarvela Alys M. , Johnston J. Spencer , Jones Jeffery W. , Kronmiller Brent A. , Kung Faith , Lee Sandra L. , Martynov Alexander G. , Masterson Patrick , Maumus Florian , Munoz-Torres Monica , Murali Shwetha C. , Murphy Terence D. , Muzny Donna M. , Nelson David R. , Oppert Brenda , Panfilio Kristen A. , Paula Débora Pires , Pick Leslie , Poelchau Monica F. , Qu Jiaxin , Reding Katie , Rhoades Joshua H. , Rhodes Adelaide , Richards Stephen , Richter Rose , Robertson Hugh M. , Rosendale Andrew J. , Tu Zhijian Jake , Velamuri Arun S. , Waterhouse Robert M. , Weirauch Matthew T. , Wells Jackson T. , Werren John H. , Worley Kim C. , Zdobnov Evgeny M. , Gundersen-Rindal Dawn E.
Published: March 2020

Background

Halyomorpha halys(Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies.

Results

Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely supportH. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

Conclusions

Availability of theH. halysgenome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics
Authors: Hodonsky Chani J. , Baldassari Antoine R. , Bien Stephanie A. , Raffield Laura M. , Highland Heather M. , Sitlani Colleen M. , Wojcik Genevieve L. , Tao Ran , Graff Marielisa , Tang Weihong , Thyagarajan Bharat , Buyske Steve , Fornage Myriam , Hindorff Lucia A. , Li Yun , Lin Danyu , Reiner Alex P. , North Kari E. , Loos Ruth J. F. , Kooperberg Charles , Avery Christy L.
Published: March 2020

Background

Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asian-ancestry populations, despite evidence that rare or ancestry-specific variation contributes substantially to RBC trait heritability. Recently developed combined-phenotype methods which leverage genetic trait correlation to improve statistical power have not yet been applied to these traits. Here we leveraged correlation of seven quantitative RBC traits in performing a combined-phenotype analysis in a multi-ethnic study population.

Results

We used the adaptive sum of powered scores (aSPU) test to assess combined-phenotype associations between ~ 21 million SNPs and seven RBC traits in a multi-ethnic population (maximum n = 67,885 participants; 24% African American, 30% Hispanic/Latino, and 43% European American; 76% female). Thirty-nine loci in our multi-ethnic population contained at least one significant association signal (p < 5E-9), with lead SNPs at nine loci significantly associated with three or more RBC traits. A majority of the lead SNPs were common (MAF > 5%) across all ancestral populations. Nineteen additional independent association signals were identified at seven known loci (HFE, KIT, HBS1L/MYB, CITED2/FILNC1, ABO, HBA1/2, and PLIN4/5). For example, the HBA1/2 locus contained 14 conditionally independent association signals, 11 of which were previously unreported and are specific to African and Amerindian ancestries. One variant in this region was common in all ancestries, but exhibited a narrower LD block in African Americans than European Americans or Hispanics/Latinos. GTEx eQTL analysis of all independent lead SNPs yielded 31 significant associations in relevant tissues, over half of which were not at the gene immediately proximal to the lead SNP.

Conclusion

This work identified seven loci containing multiple independent association signals for RBC traits using a combined-phenotype approach, which may improve discovery in genetically correlated traits. Highly complex genetic architecture at the HBA1/2 locus was only revealed by the inclusion of African Americans and Hispanics/Latinos, underscoring the continued importance of expanding large GWAS to include ancestrally diverse populations.
A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing
Authors: Huang Tinghua , Yang Min , Dong Kaihui , Xu Mingjiang , Liu Jinhui , Chen Zhi , Zhu Shijia , Chen Wang , Yin Jun , Jin Kai , Deng Yu , Guan Zhou , Huang Xiali , Yang Jun , Han Rongxun , Yao Min
Published: March 2020

Background

Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals.

Results

In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth was achieved for each multiplexed library, and replicated samples from the same tissues clustered together, demonstrating the high quality of Super deepSAGE data. Comparison with previous research indicated that our results not only have good reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis revealed ten groups of genes showing distinct expression patterns among these samples. Our analysis of over-represented binding motifs identified 41 regulators, and we demonstrated a potential application of this dataset in infectious diseases and immune biology research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways.

Conclusions

The Super deepSAGE technology and tissue-differential expression profiles are valuable resources for investigating the porcine gene expression regulation. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making them novel potential targets for the diagnosis and therapy of bacterial infections and other immune disorders.
Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency
Authors: Zhang Xiao-Yong , Qiu Jie-Ya , Hui Qiu-Ling , Xu Yuan-Yuan , He Yi-Zhong , Peng Liang-Zhi , Fu Xing-Zheng
Published: March 2020

Background

Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown.

Results

In this study, we identified a total of 128 CgbHLHs from pummelo (Citrus grandis) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency.

Conclusions

In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.
Specific humoral response in cancer patients treated with a VEGF-specific active immunotherapy procedure within a compassionate use program
Authors:   Team of Investigators of Compassionate use Program, Sánchez Ramírez Javier , Morera Díaz Yanelys , Bequet-Romero Mónica , Hernández-Bernal Francisco , Martín Bauta Yenima , Selman-Housein Bernal Katty-Hind , de la Torre Santos Ana Victoria , Pérez de la Iglesia Mariela , Trimiño Lorenzo Lian , Ayala Avila Marta
Published: March 2020

Background

CIGB-247 is a cancer therapeutic vaccine that uses as antigen a variant of human vascular endothelial growth factor (VEGF) mixed with the bacterially-derived adjuvant VSSP. CIGB-247 has been already evaluated in two phase I clinical trials (CENTAURO and CENTAURO-2), showing to be safe and immunogenic in advanced cancer patients selected under well-defined and controlled clinical conditions. Surviving patients were submitted to monthly re-immunizations and some of them showed objective clinical benefits. Based on these results, a compassionate use program (CUP) with CIGB-247 was initiated for patients that did not meet the strict entry criteria applied for the CENTAURO and CENTAURO-2 clinical trials, but could potentially benefit from the application of this cancer therapeutic vaccine.

Results

Polyclonal IgM, IgA and IgG antibodies specific for VEGF were detected by ELISA in serum samples from patients vaccinated with 400 μg of antigen combined with 200 μg of VSSP. Polyclonal antibody response showed no cross reactivity for other VEGF family member molecules like VEGF-C and VEGF-D. Serum from immunized individuals was able to block the binding of VEGF to its receptors VEGFR2 and VEGFR1. IgG fraction purified from immune sera shared the aforementioned characteristics and also inhibited the interaction between VEGF and the therapeutic recombinant antibody bevacizumab, an anti-angiogenic drug approved for the treatment of different tumors. No serious adverse events attributable to CIGB-247 have been documented yet in participants of the CIGB-247 CUP.

The present paper is a first report of our findings concerning the humoral response and safety characteristics in treated CIGB-247 CUP cancer patients. The study has provided the unique opportunity of not only testing CIGB-247 in a broader clinical spectrum sample of Cuban cancer patients, but also within the context of the day-to-day clinical practice and treatment settings for these diseases in Cuban medical institutions.

Conclusions

The CIGB-247 CUP has demonstrated that immunization and follow-up of a variety of cancer patients, under day-to-day clinical practice conditions in several Cuban medical institutions, replicate our previous findings in clinical trials: CIGB-247 is safe and immunogenic.
Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud
Authors: Wang Jingjing , An Cong , Guo Hailin , Yang Xiangyang , Chen Jingbo , Zong Junqin , Li Jianjian , Liu Jianxiu
Published: March 2020

Background

Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown.

Results

The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family.

Conclusions

Zoysia salt treatment transcriptome shows the 24-h and roots may make significant contributions to the salt tolerance. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation.
QTL mapping and transcriptome analysis identify candidate genes regulating pericarp thickness in sweet corn
Authors: Wu Xiaming , Wang Bo , Xie Fugui , Zhang Liping , Gong Jie , Zhu Wei , Li Xiaoqin , Feng Faqiang , Huang Jun
Published: March 2020

Background

In recent years, the planting area of sweet corn in China has expanded rapidly. Some new varieties with high yields and good adaptabilities have emerged. However, the improvement of edible quality traits, especially through the development of varieties with thin pericarp thickness, has not been achieved to date. Pericarp thickness is a complex trait that is the key factor determining the edible quality of sweet corn. Genetic mapping combined with transcriptome analysis was used to identify candidate genes controlling pericarp thickness.

Results

To identify novel quantitative trait loci (QTLs) for pericarp thickness, a sweet corn BC4F3population of 148 lines was developed using the two sweet corn lines M03 (recurrent parent) and M08 (donor parent). Additionally, a high-density genetic linkage map containing 3876 specific length amplified fragment (SLAF) tags was constructed and used for mapping QTLs for pericarp thickness. Interestingly, 14 QTLs for pericarp thickness were detected, and one stable QTL (qPT10–5)was detected across multiple years, which explained 7.78–35.38% of the phenotypic variation located on chromosome 10 (144,631,242-145,532,401). Forty-two candidate genes were found within the target region ofqPT10–5. Moreover, of these 42 genes, five genes (GRMZM2G143402,GRMZM2G143389,GRMZM2G143352,GRMZM6G287947, andAC234202.1_FG004) were differentially expressed between the two parents, as revealed by transcriptome analysis. According to the gene annotation information, three genes might be considered candidates for pericarp thickness.GRMZM2G143352andGRMZM2G143402have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, whileGRMZM2G143389has been annotated as FATTY ACID EXPORT 2, chloroplastic.

Conclusions

This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.
Genome-wide survey of the bHLH super gene family in Brassica napus
Authors: Ke Yun-Zhuo , Wu Yun-Wen , Zhou Hong-Jun , Chen Ping , Wang Mang-Mang , Liu Ming-Ming , Li Peng-Feng , Yang Jin , Li Jia-Na , Du Hai
Published: March 2020

Background

The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop,Brassica napus.

Results

We identified 602 potential bHLHs in theB. napusgenome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions ofBnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization betweenBrassica rapaandBrassica oleraceawas the main expansion mechanism forBnabHLHs. Expression analyses showed thatBnabHLHswere widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects ofB. napusdevelopment. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles ofBnabHLHschanged significantly, with many showing increased expression. The induction of five candidateBnabHLHswas confirmed following the five hormone treatments via qRT-PCR. Up to 246BnabHLHsfrom nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function.

Conclusion

The 602 BnabHLHs identified fromB. napuswere classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development inB. napus. Moreover, this study provides important insights into the potential functions of theBnabHLHssuper gene family and thus will be useful in future gene function research.
Metabolic profiling and scavenging activities of developing circumscissile fruit of psyllium (Plantago ovata Forssk.) reveal variation in primary and secondary metabolites
Authors: Patel Manish Kumar , Mishra Avinash , Jaiswar Santlal , Jha Bhavanath
Published: March 2020

Background

Developing fruit is considered as an excellent model to study the complex network of metabolites which are altered rapidly during development.

Results

Metabolomics revealed that developing psyllium fruit is a rich source of primary metabolites (ω-3 and ω-6 fatty acids and amino-acids), secondary metabolites and natural antioxidants. Eidonomy and anatomy confirmed that psyllium fruit followed five stages of development. Total lipids and fatty acids were synthesized differentially; saturated fatty acids (FAs) increased, whereas total polyunsaturated FAs decreased with increasing developmental stage. The unsaturation index and degree of unsaturation showed a catenary curve. Principal component analysis confirmed a significant shift in the FA profile from bud initiation to the maturation stage. Similarly, a similar level of total amino acids was present at different developmental stage following a temporal biosynthesis pathway. Total phenolic and flavonoid contents decreased in tandem with fruit development. Twenty-two different metabolites were identified, and metabolic changes were also observed during fruit development. Six metabolites were detected exclusively in the flowering stage, whereas two were detected in each of early and maturity stages of development. The metabolites apigenin and kaempferol were detected ubiquitously in all developmental stages. Time-dependent metabolomics revealed a shift in metabolite biosynthesis.

Conclusion

During fruit development, metabolites, FAs, amino acids, total phenolics, total flavonoids, antioxidants and scavenging activities changed progressively and were co-ordinately linked to each other. As a future perspective, further studies will focus on the validation of identified metabolites, which integrated with transcriptomics data and will reveal the metabolic regulatory network of development psyllium fruit.
Uncontrolled and apparent treatment resistant hypertension: a cross-sectional study of Russian and Norwegian 40–69 year olds
Authors: Petersen Jakob , Malyutina Sofia , Ryabikov Andrey , Kontsevaya Anna , Kudryavtsev Alexander V. , Eggen Anne Elise , McKee Martin , Cook Sarah , Hopstock Laila A. , Schirmer Henrik , Leon David A.
Published: March 2020

Background

Uncontrolled hypertension is a major cardiovascular risk factor. We examined uncontrolled hypertension and differences in treatment regimens between a high-risk country, Russia, and low-risk Norway to gain better understanding of the underlying factors.

Methods

Population-based survey data on 40–69 year olds with hypertension defined as taking antihypertensives and/or having high blood pressure (140+/90+ mmHg) were obtained from Know Your Heart Study (KYH, N = 2284), Russian Federation (2015–2018) and seventh wave of The Tromsø Study (Tromsø 7, N = 5939), Norway (2015–2016). Uncontrolled hypertension was studied in the subset taking antihypertensives (KYH: N = 1584; Tromsø 7: 2792)and defined as having high blood pressure (140+/90+ mmHg). Apparent treatment resistant hypertension (aTRH) was defined as individuals with uncontrolled hypertension on 3+ OR controlled on 4+ antihypertensive classes in the same subset.

Results

Among all those with hypertension regardless of treatment status, control of blood pressure was achieved in 22% of men (KYH and Tromsø 7), while among women it was 33% in Tromsø 7 and 43% in KYH. When the analysis was limited to those on treatment for hypertension, the percentage uncontrolled was higher in KYH (47.8%, CI 95 44.6–50.9%) than Tromsø 7 (38.2, 36.1–40.5%). The corresponding figures for aTRH were 9.8% (8.2–11.7%) and 5.7% (4.8–6.8%).

Antihypertensive monotherapies were more common than combinations and used by 58% in Tromsø 7 and 44% in KYH. In both KYH and Tromsø 7, untreated hypertension was higher in men, those with no GP visit in the past year and problem drinkers. In both studies, aTRH was associated with older age, CVD history, obesity, and diabetes. In Tromsø 7, also male gender and any drinking. In KYH, also chronic kidney disease.

Conclusion

There is considerable scope for promoting combination therapies in line with European treatment guidelines in both study populations. The factors associated with untreated hypertension overlap with known correlates of treatment non-adherence and health check non-attendance. In contrast, aTRH was characterised by obesity and underlying comorbidities potentially complicating treatment.
Hidden analyses: a review of reporting practice and recommendations for more transparent reporting of initial data analyses
Authors:   on behalf of the Topic Group “Initial Data Analysis” of the STRATOS Initiative (STRengthening Analytical Thinking for Observational Studies, http://www.stratos-initiative.org), Huebner Marianne , Vach Werner , le Cessie Saskia , Schmidt Carsten Oliver , Lusa Lara
Published: March 2020

Background

In the data pipeline from the data collection process to the planned statistical analyses, initial data analysis (IDA) typically takes place between the end of the data collection and do not touch the research questions. A systematic process for IDA and clear reporting of the findings would help to understand the potential shortcomings of a dataset, such as missing values, or subgroups with small sample sizes, or shortcomings in the collection process, and to evaluate the impact of these shortcomings on the research results. A clear reporting of findings is also relevant when making datasets available to other researchers. Initial data analyses can provide valuable insights into the suitability of a data set for a future research study. Our aim was to describe the practice of reporting of initial data analyses in observational studies in five highly ranked medical journals with focus on data cleaning, screening, and reporting of findings which led to a potential change in the analysis plan.

Methods

This review was carried out using systematic search strategies with eligibility criteria for articles to be reviewed. A total of 25 papers about observational studies were selected from five medical journals published in 2018. Each paper was reviewed by two reviewers and IDA statements were further discussed by all authors. The consensus was reported.

Results

IDA statements were reported in the methods, results, discussion, and supplement of papers. Ten out of 25 papers (40%) included a statement about data cleaning. Data screening statements were included in all articles, and 18 (72%) indicated the methods used to describe them. Item missingness was reported in 11 papers (44%), unit missingness in 15 papers (60%). Eleven papers (44%) mentioned some changes in the analysis plan. Reported changes referred to missing data treatment, unexpected values, population heterogeneity and aspects related to variable distributions or data properties.

Conclusion

Reporting of initial data analyses were sparse, and statements on IDA were located throughout the research articles. There is a lack of systematic reporting of IDA. We conclude the article with recommendations on how to overcome shortcomings in the practice of IDA reporting in observational studies.
Non-participation and attrition in a longitudinal study of civilians exposed to the January 2015 terrorist attacks in Paris, France
Authors: Vuillermoz Cécile , Stene Lise Eilin , Aubert Lydéric , Motreff Yvon , Pirard Philippe , Baubet Thierry , Lesieur Sophie , Chauvin Pierre , Vandentorren Stéphanie
Published: March 2020

Background

Non-participation and attrition are rarely studied despite being important methodological issues when performing post-disaster studies. A longitudinal survey of civilians exposed to the January 2015 terrorist attacks in Paris, France, was conducted 6 (Wave 1) and 18 months (Wave 2) after the attacks. We described non-participation in Wave 1 and determined the factors associated with attrition in Wave 2.

Methods

Multivariate logistic regression models were used to compare participants in both waves with those who participated in the first wave only. Analyses were performed taking the following factors into account: socio-demographic characteristics, exposure to terror, peri-traumatic reactions, psychological support, perceived social support, impact on work, social and family life, and mental health disorders. Characteristics of new participants in Wave 2 were compared with participants in both waves using a chi-square test.

Results

Of the 390 persons who were eligible to participate in the survey, 190 participated in Wave 1 (participation rate: 49%). The most frequently reported reason for non-participation was to avoid being reminded of the painful event (32%, n = 34/105). In Wave 2, 67 were lost to follow-up, 141 people participated, of whom 123 participated in Wave 1 (re-participation rate: 65%) and 18 were new. Attrition in Wave 2 was associated with socio-demographic characteristics (age, French origin) and location during the attacks, but not with terror exposure or mental health disorders. Compared with those who participated in both waves, new participants declared less social and psychological support since the attacks.

Conclusions

Attrition at 6 months was not associated with exposure to terror or mental health disorders, which indicates that any bias in future analyses on IMPACTS on mental health outcomes will be limited. Our findings suggest the importance of adapting similar surveys for people of foreign origin and of improving strategies to avoid attrition of younger people, for example by using social media, peers, and the educational environment. The present study also revealed that a high level of exposure to terror and a lack of social and psychological support after a terrorist event could impede individuals’ participation in similar surveys in the short term.
Evaluation of confounding in epidemiologic studies assessing alcohol consumption on the risk of ischemic heart disease
Authors: Wallach Joshua D. , Serghiou Stylianos , Chu Lingzhi , Egilman Alexander C. , Vasiliou Vasilis , Ross Joseph S. , Ioannidis John P. A.
Published: March 2020

Background

Among different investigators studying the same exposures and outcomes, there may be a lack of consensus about potential confounders that should be considered as matching, adjustment, or stratification variables in observational studies. Concerns have been raised that confounding factors may affect the results obtained for the alcohol-ischemic heart disease relationship, as well as their consistency and reproducibility across different studies. Therefore, we assessed how confounders are defined, operationalized, and discussed across individual studies evaluating the impact of alcohol on ischemic heart disease risk.

Methods

For observational studies included in a recent alcohol-ischemic heart disease meta-analysis, we identified all variables adjusted, matched, or stratified for in the largest reported multivariate model (i.e. potential confounders). We recorded how the variables were measured and grouped them into higher-level confounder domains. Abstracts and Discussion sections were then assessed to determine whether authors considered confounding when interpreting their study findings.

Results

85 of 87 (97.7%) studies reported multivariate analyses for an alcohol-ischemic heart disease relationship. The most common higher-level confounder domains included were smoking (79, 92.9%), age (74, 87.1%), and BMI, height, and/or weight (57, 67.1%). However, no two models adjusted, matched, or stratified for the same higher-level confounder domains. Most (74/87, 85.1%) articles mentioned or alluded to “confounding” in their Abstract or Discussion sections, but only one stated that their main findings were likely to be affected by residual confounding. There were five (5/87, 5.7%) authors that explicitly asked for caution when interpreting results.

Conclusion

There is large variation in the confounders considered across observational studies evaluating the impact of alcohol on ischemic heart disease risk and almost all studies spuriously ignore or eventually dismiss confounding in their conclusions. Given that study results and interpretations may be affected by the mix of potential confounders included within multivariate models, efforts are necessary to standardize approaches for selecting and accounting for confounders in observational studies.
Promoting rational antibiotic prescribing for non-complicated infections: understanding social influence in primary care networks in Germany
Authors: Poss-Doering Regina , Kamradt Martina , Glassen Katharina , Andres Edith , Kaufmann-Kolle Petra , Wensing Michel
Published: March 2020

Background

Primary care networks in Germany are formalized regional collaborations of physicians and other healthcare providers. Common goals are optimized healthcare processes and services for patients, enhanced communication, agency for professional concerns and strengthened economic power. In the ARena study (Sustainable reduction of antibiotic-induced antimicrobial resistance), 14 primary care networks in two federal German states aimed to promote appropriate antibiotics use for acute non-complicated infections by fostering awareness and understanding. Factors related to the role of primary care networks were to be identified.

Methods

For this study, audio-recorded telephone interviews were conducted with physicians, non-physician health professionals and stakeholder representatives. Pseudonymized verbatim transcripts were coded using thematic analysis. In-depth analysis was based on the inductive categories ‘social support’, ‘social learning’, ‘social normative pressures’ and ‘social contagion’ to reflect social influence processes. Data generated through a survey with physicians and non-physician health professionals were analyzed descriptively to foster understanding of the networks’ potential impact on antibiotic prescribing.

Results

Social influence processes proved to be relevant regarding knowledge transfer, manifestation of best-practice care and self-reflection. Peer communication was seen as a great asset, the main reason for membership and affirmative for own perspectives. All interviewed physicians (n = 27) considered their network to be a strong support factor for daily routines, introduction of new routines, and continuity of care. They utilized network-offered training programs focusing on best practice guideline-oriented use of antibiotics and considered their networks supportive in dealing with patient expectations. A shared attitude combined with ARena intervention components facilitated reflective management of antibiotic prescribing. Non-physician health professionals (n = 11) also valued network peer exchange. They assumed their employers joined networks to offer improved and continuous care. Stakeholders (n = 7) expected networks and their members to be drivers for care optimization.

Conclusion

Primary care networks play a crucial role in providing a platform for professional peer exchange, social support and reassurance. With regards to their impact on antibiotic prescribing for acute non-complicated infections, networks seem to facilitate and amplify quality improvement programs by providing a platform for refreshing awareness, knowledge and self-reflection among care providers. They are well suited to promote a rational use of antibiotics.

Trial registration

ISRCTN, ISRCTN58150046. Registered 24 August 2017.
The effects of health literacy in influenza vaccination competencies among community-dwelling older adults in Hong Kong
Authors: Zhang Fan , Or Peggy Pui-Lai , Chung Joanne Wai-Yee
Published: March 2020

Background

Poor health literacy was found to be one of the key barriers in older adults’ disease prevention practice. However, it has still been unclear how different processes in health literacy play a role in older adult’s vaccination-related competencies. By adopting the European Health Literacy Survey (HLS-EU), the current study aimed to examine older adults’ competences in accessing, understanding, evaluating and applying health information, as well as how they are related to perceived difficulties in vaccination-related practices. .

Methods

With a cross-sectional design, a quantitative exploratory study was conducted using structured questionnaires. Four-hundred and 86 community-dwelling older adults aged 65 and above were recruited from non-government organizations in Hong Kong. Health literacy was measured by the Chinese version of 47-item HLS-EU (HLS-Asia-Q), which assesses the competences in accessing, understanding, evaluating and applying health information across the domains of health care, disease prevention, and health promotion. Linear regression was performed to test the association between different aspects of health literacy and vaccination-related information processing.

Results

The findings showed that the health literacy of Hong Kong older adults has been limited, particularly in information appraisal. Poorer competences in accessing and appraising health information were associated with greater difficulties in making vaccination decision.

Conclusions

By identifying the health literacy processes associated with vaccination, our findings suggested that health-promotion programs strengthening the appraisal and comparison of vaccination information should be provided for the general public. Meanwhile, health professionals and mass media should reduce the complexity when delivering the health messages, and make it easier for older adults to access and comprehend, thus increasing the inclination to take vaccine and preventing the spread of communicable diseases.
The influence of the age of dementia onset on college students’ stigmatic attributions towards a person with dementia
Authors: Werner Perla , Raviv-Turgeman Lilach , Corrigan Patrick W.
Published: March 2020

Background

Research in the area of public stigma and Alzheimer’s disease (AD) is limited to examining stigmatic beliefs towards persons aged 65 and over (i.e., persons with late-onset dementia). The aim of the present study was to compare college students’ stigmatic attributions towards an older and a younger person with AD, using an attributional model of stigma.

Method

A cross-sectional study was conducted with 375 college students (mean age = 25.5, 58.9% female, 64.3% Jewish) who answered a computerized, self-administered, structured questionnaire after being presented with one of two randomly distributed vignettes varying in the age of the person with AD – 80 or 50 years of age. Cognitive, emotional and behavioral attributions of stigma were assessed using an adapted version of the Attribution Questionnaire. Other variables examined included background information, experiences and concerns about developing AD. T-tests and Ordinary Least Square (OLS) hierarchical regressions were used to analyze results.

Results

Similar to previous studies, students’ levels of dementia stigma were low to moderate. Negative attributions were consistently and significantly higher (β = .17 to .33,p < .01), and positive attributions were significantly lower (β = −.26, p < .01) when the target person was younger rather than older.

Conclusion

The differences in stigmatic beliefs towards a younger and older person with AD point to the theoretical and practical importance of clearly stating the age of the target person in stigma studies as well as in programs aimed at reducing public stigma towards persons with AD.