bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS unveils features between early- and late-flowering pearl millets
Authors: Diack Oumar , Kanfany Ghislain , Gueye Mame Codou , Sy Ousmane , Fofana Amadou , Tall Hamidou , Serba Desalegn D. , Zekraoui Leila , Berthouly-Salazar Cécile , Vigouroux Yves , Diouf Diaga , KANE NDJIDO ARDO 
Published: August 2020

Abstract
Background: Pearl millet, a dietary food for around 100 million people in Africa and in India, has a large diversity due to an extensive genetic diversity combined with a high degree of admixture with wild relatives. In Senegal, two major morphotypes are distinguished: early-flowering and late-flowering millets. The phenotypic variabilities according to the flowering time plays an important role in pearl millet adaptation to climate variability. A better understanding of the genetic makeup of these variabilities would allow breeding of pearl millet fitting different climatic areas. In this study, we aimed to characterize the genetic basis of these phenotypic differences. Results: We defined a core collection capturing most of the diversity of cultivated pearl millet of Senegal, which includes 60 early-flowering Souna and 31 late-flowering Sanio. This panel was evaluated during the 2016 and 2017 rainy seasons at Nioro for 16 agro-morphological traits. Phenological and phenotypic traits linked with yield, flowering time, and biomass helped differentiated early- and late-flowering millets. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) with minor allele frequencies of more than 5% were identified. Sparse Non-Negative Matrix Factorization (sNMF) analysis confirms the genetic structure in two gene pools associated with flowering time differences. Moreover, two chromosomal regions on linkage groups (LG 3) (~89.7Mb) and (LG 6) (~68.1Mb) differentiated the early-flowering into two clusters. Genome-wide association study (GWAS) was used to associate phenotypic variation to the SNPs and 18 genes were linked to flowering time, plant height, nodal tiller number, and biomass (P-value ˂ 2.3E-06). Conclusions: The diversity of early- and late-flowering pearl millet landraces of Senegal was captured using a heuristic approach. Key phenology and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were implicated as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes would have paramount importance in breeding strategies under climate change scenarios.
Using Routine Health Information Data for Research in Low- and Middle-Income Countries: A Systematic Review
Authors: Hung Yuen Wai , Hoxha Klesta , Irwin Bridget R. , Law Michael R. , Grépin Karen Ann 
Published: August 2020

Abstract
Background : Routine health information systems (RHISs) support resource allocation and management decisions at all levels of the health system, as well as strategy development and policy-making in many low- and middle-income countries (LMICs). Although RHIS data represent a rich source of information, such data are currently underused for research purposes, largely due to concerns over data quality. Given that substantial investments have been made in strengthening RHISs in LMICs in recent years and that there is a growing demand for more real-time data from researchers, this systematic review builds upon the existing literature to summarize the extent to which RHIS data have been used in peer-reviewed research publications. Methods : Using terms ‘routine health information system’, ‘health information system’, or ‘health management information system’ and a list of LMICs, four electronic peer-review literature databases were searched from inception to February 20 2019: PubMed, Scopus, EMBASE, and EconLit. Articles were assessed for inclusion based on pre-determined eligibility criteria and study characteristics were extracted from included articles using a piloted data extraction form. Results : We identified 132 studies that met our inclusion criteria, originating in 37 different countries. Overall, the majority of the studies identified were from Sub-Saharan Africa and were published within the last five years. Malaria and maternal health were the most commonly studied health conditions, although a number of other health conditions and health services were also explored. Conclusions : Our study identified an increasing use of RHIS data for research purposes, with many studies applying rigorous study designs and analytic methods to advance program evaluation, monitoring and assessing services, and epidemiological studies in LMICs. RHIS data represent an underused source of data and should be made more available and further embraced by the research community in LMIC health systems.
Perceptions of patients with end-stage kidney disease (ESKD) and their informal caregivers on palliative care as a treatment option: a qualitative study
Authors: Sarfo-Walters Catherine , Boateng Edward Appiah 
Published: August 2020

Abstract
Background: Palliative care is increasingly becoming an accepted treatment choice for many individuals diagnosed with end-stage kidney disease (ESKD). Yet, its utilisation is non-existent in many lower- and middle-income countries (LMICs). This study explored the perceptions of individuals with ESKD and their informal caregivers on palliative care as a treatment option for the disease in Ghana.Methods: This was a phenomenological study, with an in-depth analysis of data collected from nine individuals with ESKD and six informal caregivers through individual, face-to-face semi-structured interviews. The study was conducted in two renal centres within the Kumasi metropolis, Ghana among individuals with ESKD seeking care from both renal centres and their informal caregivers.Results: Three main themes were derived from this study – motivation for initiating haemodialysis, facing realities of haemodialysis, and considering palliative care. Participants felt that haemodialysis (HD) was not meeting their health expectations and demonstrated a general willingness to utilise palliative care if it would reduce suffering. Conclusions: This study has shown that individuals with ESKD or their informal caregivers would consider palliative care services, if available. It paves the way for discussions about palliative care for ESKD to begin across renal centres within Ghana and other similar settings. Exploring perspectives of clinicians in such settings could inform strategies on how to implement palliative care for ESKD management in such settings.
The Professional Contribution of Chiropractors to Danish elite football clubs: A qualitative exploration of role and perceived value in an interprofessional service provision context.
Authors: Hostrup Joachim , Koza Anders , Myburgh Corrie 
Published: August 2020

Abstract
Background: Interprofessional team-based care has been widely adopted in elite level athletic health and performance practice. Although chiropractors can claim some penetration as health care service providers in high level sport, their position as valued members of interprofessional health care teams, especially those built around traditional medical organisational structures, is unclear. As a first step to map the professional practice landscape of Danish sports chiropractors, this investigation sought to explore the perceived role and value of chiropractors as service providers in elite Danish football clubs. Methods: A comparative qualitative case study using semi-structured individual interviews was conducted. Six Danish Superliga clubs were purposively sampled to compare and contrast instances where chiropractors were absent from the health care team, contracted as in-house health care team members or engaged as external service providers. Triangulated responses were solicited from healthcare co-ordinators, chiropractors and athletes within each club’s organisation through short semi-structured individual interviews. The audio-recorded responses were transcribed verbatim and thematically analysed using a framework approach. Results: Inductive and deductive coding revealed 14 unique codes, which were further organised into 4 code families relating to the role of chiropractors, benefits of utilizing chiropractic care and facilitators and barriers to interprofessional practice. From this framework 3 themes were abstracted, these being: “Broadening horizons”, “In-house preferred to take-away” and “Already covered, or even necessary?”. Conclusion: In this practice context, chiropractors fill the role of musculoskeletal health care service providers. Their perceived value stems from additional expert disciplinary knowledge, improved diagnostic triage and increased treatment flexibility. However, where not utilized, the role of the spinal health expert is questioned and when acknowledged, limited to that of a technician/therapist. It is unclear whether chiropractors can claim core team member status. Further exploration of this interesting context of interprofessional practice is warranted.
High conservation combined with high plasticity: genomics and evolution of Borrelia bavariensis
Authors: Becker Noémie S , Rollins Robert Ethan , Nosenko Kateryna , Paulus Alexander , Martin Samantha , Krebs Stefan , Takano Ai , Sato Kozue , Kovalev Sergey Y , Kawabata Hiroki , Fingerle Volker , Margos Gabriele 
Published: August 2020

Abstract
Background

Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis , is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge.

Results

We present a genome reconstruction for 33 B. bavariensis isolates from Eurasia based on long-read (Pacific Bioscience, for three isolates) and short-read (Illumina) data. We show that the combination of both sequencing techniques allows proper genome reconstruction of all plasmids in most cases but use of a very close reference is necessary when only short-read sequencing data is available. B. bavariensis genomes combine a high degree of genetic conservation with high plasticity: all isolates share the main chromosome and five plasmids, but the repertoire of other plasmids is highly variable. In addition to plasmid losses and gains through horizontal transfer, we also observe several fusions between plasmids. Although European isolates of B. bavariensis have little diversity in genome content, there is some geographic structure to this variation. In contrast, each Asian isolate has a unique plasmid repertoire and we observe no geographically based differences between Japanese and Russian isolates. Comparing the genomes of Asian and European populations of B. bavariensis suggests that some genes which are markedly different between the two populations may be good candidates for adaptation to the tick vector, ( Ixodes ricinus in Europe and I. persulcatus in Asia).

Conclusions

We present the characterization of genomes of a large sample of B. bavariensis isolates and show that their plasmid content is highly variable. This study opens the way for genomic studies seeking to understand host and vector adaptation as well as human pathogenicity in Eurasian Lyme Borreliosis agents.
Operative invasiveness does not affect the prognosis of patients with non-small cell lung cancer
Authors: Motono Nozomu , Iwai Shun , Iijima Yoshihito , Usuda katsuo , Uramoto Hidetaka 
Published: August 2020

Abstract
Background: The relationship between operative invasiveness and the prognosis in non-small cell lung cancer (NSCLC) patients who have undergone surgery has been controversial.Methods: Clinical data were analyzed for 463 NSCLC patients. Operative invasiveness was defined by wound length, operation time, and the postoperative C-reactive protein (postCRP) level. The operative approach was divided into video-assisted thoracic surgery (VATS) and thoracotomy.Results: The wound length and operation time were significantly correlated with the postCRP level (correlation coefficient (CC) = 0.39, p<0.01; CC = 0.54, p<0.01, respectively). The postCRP level in the VATS group was significantly lower than that in the thoracotomy group (12.2 mg/dl vs 20.58 mg/dl, p<0.01). The relapse-free survival differed significantly based on wound length (p<0.01), operation time (p=0.01), CRP level (p<0.01), and operative approach (p<0.01). The carcinoembryonic antigen level (hazard ratio [HR], 1.58; p = 0.02), pathological stage (pStage) (HR, 2.57; p < 0.01), vascular invasion (HR, 1.95; p = 0.01), and preoperative CRP level (preCRP) (HR, 1.91; p < 0.01) were identified as significant prognostic factors for relapse-free survival in a multivariate analysis. Furthermore, the multivariate analysis showed that smoking history (HR, 2.36; p = 0.03), pStage (HR, 3.26; p < 0.01), and preCRP level were significant prognostic factors for overall survival.Conclusion: Preoperative CRP level was associated with poor prognosis. Although the VATS approach might be less invasive procedure for NSCLC patients, operative invasiveness does not affect the prognosis.
Presence of Fermentable Oligo-, Di-, Monosaccharides, and Polyols (FODMAPs) in commonly eaten foods: Extension of a database to indicate dietary FODMAP content and calculation of intake in the general population from food diary data
Authors: Liljebo Therese , Störsrud Stine , Andreasson Anna 
Published: August 2020

Abstract
Background: FODMAPs (Fermentable Oligo-, Di-, Monosaccharides And Polyols) are known for their health benefits but their fermentation may trigger gastrointestinal symptoms and a low-FODMAP diet is a commonly used intervention for functional gastrointestinal disorders. The use of direct measures of FODMAP is labor intensive and expensive and to facilitate the assessment of FODMAP intake in research and clinical work, a nutritional content database with good quality estimates on FODMAP values is needed. Further, the average intake of FODMAP in a general population would be a useful reference and knowledge the most commonly eaten foods containing FODMAPs would facilitate clinical work utilizing FODMAP diet interventions. Methods: A nutritional content database was extended with published FODMAP content data. The database was used to calculate FODMAP intake from four-day food diaries from 117 individuals from the general population in Sweden and the most common food items containing FODMAPs were identified. Results: FODMAP content for 1060 food items were added to the database resulting in 1805 listed FODMAP values. Mean intake of total FODMAP in the diaries was 19g (fructose: 15.2g; fructan: 3.5g; lactose: 14.1g; galacto-oligosaccharides (GOS) 0.43g and polyols 1.3g per day. Overall the most common eaten food items containing FODMAPs were rye and wheat based foods. Conclusion: Intake of FODMAPs as calculated using the extended database were in line with previous studies supporting its use of the database both research and in clinical interventions. The lists of the most commonly eaten FODMAP food items are provided and may be used to facilitate FODMAP diet interventions.
Quantifying the advantages of conducting a prospective meta-analysis (PMA): a case study of early childhood obesity prevention
Authors: Seidler Anna Lene , Hunter Kylie E , Espinoza David , Mihrshahi Seema , Askie Lisa M 
Published: August 2020

Abstract
Background: For prospective meta-analyses (PMA), eligible studies are identified and the PMA hypotheses, selection criteria and analysis methods are pre-specified before results of any of the studies are known. This reduces publication bias and selective outcome reporting and provides a unique opportunity for outcome standardisation/harmonisation. We conducted a world-first PMA of four trials investigating interventions to prevent early childhood obesity. The aims of this study were to quantitatively analyse the effects of prospective planning on variations across trials, outcome harmonisation, and the power to detect intervention effects, and to derive recommendations for future PMA.Methods: We examined intervention design, participant characteristics and outcomes collected across the four trials included in the EPOCH PMA using their registration records, protocol publications and variable lists. The outcomes trials that planned to collect prior to inclusion in the PMA were compared to the outcomes trials collected after PMA inclusion. We analysed the proportion of matching outcome definitions across trials, the number of outcomes per trial, and how collaboration increased the statistical power to detect intervention effects.Results: The included trials varied in intervention design and participants, which improved external validity and the ability to perform subgroup analyses for the meta-analysis. While individual trials had limited power to detect the main intervention effect (BMI z-score), synthesising data substantially increased statistical power. Prospective planning led to an increase in number of collected outcome categories (e.g. weight, child’s diet, sleep), and greater outcome harmonisation. Prior to PMA inclusion, only 18% of outcome categories were included in all trials. After PMA inclusion this increased to 91% of outcome categories. However, whilst trials mostly collected the same outcome categories after PMA inclusion, some inconsistencies in how the outcomes were measured remained (such as measuring physical activity by hours of outside play versus using an activity monitor).Conclusion: Prospective planning led to greater outcome harmonisation and greater power to detect intervention effects, while maintaining acceptable variation in trial designs and populations, which improved external validity. Recommendations for future PMA include more detailed harmonisation of outcome measures, and careful pre-specification of analyses to avoid research waste by unnecessary over-collection of data.
Deciphering the transcriptional changes in Escherichia coli strains C41(DE3) and C43(DE3) that makes them a superior choice for membrane protein production.
Authors: Webb Chaille Teresa , Lithgow Trevor 
Published: August 2020

Abstract
Background: The production of membrane proteins for functional and structural protein analysis remains a bottleneck in the continuing quest for understanding biological systems. For recombinant membrane proteins, the Walker strains C41(DE3) and C43(DE3) are a valuable tool because they are capable of producing levels of functional protein that would otherwise be toxic to the cell. At the genome level, amongst only a handful of genetic changes, mutations in the lacUV5 promoter region upstream from the bacteriophage T7 RNA polymerase gene distinguish these strains from BL21(DE3) but do not inform on how the strains have adapted for superior production of recombinant membrane proteins. Results: Comparative transcriptomic analyses revealed a moderate change in gene expression in C41(DE3) and C43(DE3) compared to their parent strain BL21(DE3) under standard growth conditions. However, under the conditions used for membrane protein production (with plasmid carriage and addition of IPTG), the differential response of C41(DE3) and C43(DE3) compared to their parent strain BL21(DE3) was striking. Over 2000 genes were differentially expressed in C41(DE3) with a two-fold change and false discover rate < 0.01 and 1700 genes differentially expressed in C43(DE3) compared to their parent strain BL21(DE3). Conclusion: These results illuminate the cellular adaptations occurring in the Walker strains to alleviate the toxic effects that can occur during membrane protein production, whilst providing changes in metabolism pathways required for membrane protein biogenesis. The BL21(DE3) derivatives strains C41(DE3) and C43(DE3), are adept to the process of membrane biogenesis in E. coli, making them superior to their parent strain for the production of membrane proteins and potentially other toxic proteins.
Effects of various nitrogen regimes on the ability of rapeseed (Brassica napus L.) to suppress littleseed canarygrass (Phalaris minor Retz.)
Authors: Xu Gaofeng , Shen Shicai , Zhang Yun , Clements David Roy , Yang Shaosong , Dong Liyao , Zhang Fudou 
Published: August 2020

Abstract
Background: Littleseed canarygrass (Phalaris minor Retz.) is one of the most troublesome invasive weeds infesting winter crops in Yunnan Province, China. Our previous study found that rapeseed (Bassica napus L.) was a logical candidate crop to control littleseed canarygrass in agroecosystems. Nitrogen (N) could impact plant community composition by altering competitive interactions, however, the effects of different N regimes on weed control efficacy of rapeseed were unknown. Here, we report the effects of different N regimes on the control efficacy of littleseed canarygrass by rapeseed and their competitive effects and photosynthetic characteristics. Results: The results showed that the rapeseed yield and its control efficacy on littleseed canarygrass were significantly affected (P<0.05) under different N regimes, and the control efficacy of littleseed canarygrass by rapeseed increased first and then decreased with the increase of basal nitrogen rates, while increasing topdressing N rates increased control efficacy of littleseed canarygrass by rapeseed only. In fact, yield and weed control efficacy of rapeseed was most ideal when both basal and top-dressing N was 90 kg·ha-1. We also found that N significantly impacted the competitive ability of rapeseed to littleseed canarygrass and rapeseed had a highest competitive ability when both basal and top-dressing N was 90 kg·ha-1. With the increase of basal nitrogen rates, competitive balance index (CB) of rapeseed increased first and then decreased, but which gradually increased with increasing of topdressing N rates. Our research also showed level and period of N application had a significant effect (P<0.01) on the photosynthetic rate (Pn) and chlorophyll content (Chl) of both rapeseed and littleseed canarygrass. Under the same N application regime, the Pn and Chl of littleseed canarygrass were higher than that of rapeseed in December, while the Pn and Chl of rapeseed was higher than that of littleseed canarygrass in February. Our study indicated that photosynthetic characteristics of rapeseed and littleseed canarygrass in different growth stages differ in their sensitivity to N regimes, creating a dynamic competitive relationship. Conclusions: Together, our results demonstrated that rational application of fertilizer N could help rapeseed produce higher yields and greater weed control efficacy, suggesting that future modeling or experimental studies on utilizing crops to control invasive weeds should carefully consider both timing and placement of N.