bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal dietary resistant starch does not improve piglet’s gut and liver metabolism when challenged with a high fat diet
Authors: Schroyen Martine , Leblois Julie , Uerlings Julie , Li Bing , Sureda Ester Arévalo , Massart Sébastien , Wavreille José , Bindelle Jérôme , Everaert Nadia 
Published: June 2020

Abstract
Background
In the past several years, the use of resistant starch (RS) as prebiotic has extensively been studied in pigs, and this mostly in the critical period around weaning. RS is believed to exert beneficial effects on the gastrointestinal tract mainly due to higher levels of short chain fatty acids (SCFAs) and an improved microbiota profile. In this study, sows were fed digestible starch (DS) or RS during late gestation and lactation and the possible maternal effect of RS on the overall health of the progeny was assessed. Since RS is also described to have a positive effect on metabolism, and to investigate a metabolic programming of the progeny, half of the piglets per maternal diet were assigned to a high fat diet from weaning on to 10 weeks after.

Results
No bodyweight differences were found between the four experimental piglet groups. The high fat diet did however impact back fat thickness and meat percentage whereas maternal diet did not influence these parameters. The impact of the high fat diet was also reflected in higher levels of serum cholesterol. No major differences in microbiota could be distinguished, although higher levels of SCFA were seen in the colon of piglets born from RS fed sows, and some differences in SCFA production were observed in the caecum, mainly due to piglet diet. RNA-sequencing on liver and colon scrapings revealed minor differences between the maternal diet groups. Merely a handful of genes was differentially expressed between piglets from DS and RS sows, and network analysis showed only one significant cluster of genes in the liver due to the maternal diet that did not point to meaningful biological pathways. However, the high fat diet resulted in liver gene clusters that were significantly correlated with piglet diet, of which one is annotated for lipid metabolic processes. These clusters were not correlated with maternal diet.

Conclusions
There is only a minor impact of maternal dietary RS on the progeny, reflected in SCFA changes. A high fat diet given to the progeny directly evokes metabolic changes in the liver, without any maternal programming by a RS diet.
Prevalence and phylogeny of Chlamydiae and hemotropic mycoplasma species in captive and free-living bats
Authors: Fritschi Janine , Marti Hanna , Seth-Smith Helena M. B. , Aeby Sébastien , Greub Gilbert , Meli Marina L. , Hofmann-Lehmann Regina , Mühldorfer Kristin , Stokar-Regenscheit Nadine , Wiederkehr Danja , Pilo Paola , Van Den Broek Peggy Rüegg- , Borel Nicole 
Published: June 2020

Abstract
Background
Bats are hosts for a variety of microorganisms, however, little is known about the presence of Chlamydiales and hemotropic mycoplasmas. This study investigated 475 captive and free-living bats from Switzerland, Germany, and Costa Rica for Chlamydiales and hemotropic mycoplasmas by PCR to determine the prevalence and phylogeny of these organisms.

Results
Screening for Chlamydiales resulted in a total prevalence of 31.4%. Positive samples originated from captive and free-living bats from all three countries. Sequencing of 15 samples allowed the detection of two phylogenetically distinct groups. These groups share sequence identities to Chlamydiaceae, and to Chlamydia-like organisms including Rhabdochlamydiaceae and unclassified Chlamydiales from environmental samples, respectively.
PCR analysis for the presence of hemotropic mycoplasmas resulted in a total prevalence of 0.7%, comprising free-living bats from Germany and Costa Rica. Phylogenetic analysis revealed three sequences related to other unidentified mycoplasmas found in vampire bats and Chilean bats.

Conclusions
Bats can harbor Chlamydiales and hemotropic mycoplasmas and the newly described sequences in this study indicate that the diversity of these bacteria in bats is much larger than previously thought. Both, Chlamydiales and hemotropic mycoplasmas are not restricted to certain bat species or countries and captive and free-living bats can be colonized. In conclusion, bats represent another potential host or vector for novel, previously unidentified, Chlamydiales and hemotropic mycoplasmas.
Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level
Authors: Kang Wenjuan , Jiang Zhehao , Chen Yonggang , Wu Fang , Liu Chang , Wang Haifang , Shi Shangli , Zhang Xue-Xian 
Published: June 2020

Abstract
Background
Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness.

Results
Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P < 0.01). A total of 8111 genes was differentially expressed, representing ~ 17.1% of the M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants.

Conclusions
Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.
Comparison of methods for handling covariate missingness in propensity score estimation with a binary exposure
Authors: Coffman Donna L. , Zhou Jiangxiu , Cai Xizhen 
Published: June 2020

Abstract
Background
Causal effect estimation with observational data is subject to bias due to confounding, which is often controlled for using propensity scores. One unresolved issue in propensity score estimation is how to handle missing values in covariates.

Method
Several approaches have been proposed for handling covariate missingness, including multiple imputation (MI), multiple imputation with missingness pattern (MIMP), and treatment mean imputation. However, there are other potentially useful approaches that have not been evaluated, including single imputation (SI) + prediction error (PE), SI + PE + parameter uncertainty (PU), and Generalized Boosted Modeling (GBM), which is a nonparametric approach for estimating propensity scores in which missing values are automatically handled in the estimation using a surrogate split method. To evaluate the performance of these approaches, a simulation study was conducted.

Results
Results suggested that SI + PE, SI + PE + PU, MI, and MIMP perform almost equally well and better than treatment mean imputation and GBM in terms of bias; however, MI and MIMP account for the additional uncertainty of imputing the missingness.

Conclusions
Applying GBM to the incomplete data and relying on the surrogate split approach resulted in substantial bias. Imputation prior to implementing GBM is recommended.
Applying an intersectionality lens to the theoretical domains framework: a tool for thinking about how intersecting social identities and structures of power influence behaviour
Authors: Etherington Cole , Rodrigues Isabel Braganca , Giangregorio Lora , Graham Ian D. , Hoens Alison M. , Kasperavicius Danielle , Kelly Christine , Moore Julia E. , Ponzano Matteo , Presseau Justin , Sibley Kathryn M. , Straus Sharon 
Published: June 2020

Abstract
Background
A key component of the implementation process is identifying potential barriers and facilitators that need to be addressed. The Theoretical Domains Framework (TDF) is one of the most commonly used frameworks for this purpose. When applying the TDF, it is critical to understand the context in which behaviours occur. Intersectionality, which accounts for the interface between social identity factors (e.g. age, gender) and structures of power (e.g. ageism, sexism), offers a novel approach to understanding how context shapes individual decision-making and behaviour. We aimed to develop a tool to be used alongside applications of the TDF to incorporate an intersectionality lens when identifying implementation barriers and enablers.

Methods
An interdisciplinary Framework Committee (n = 17) prioritized the TDF as one of three models, theories, and frameworks (MTFs) to enhance with an intersectional lens through a modified Delphi approach. In collaboration with the wider Framework Committee, a subgroup considered all 14 TDF domains and iteratively developed recommendations for incorporating intersectionality considerations within the TDF and its domains. An iterative approach aimed at building consensus was used to finalize recommendations.

Results
Consensus on how to apply an intersectionality lens to the TDF was achieved after 12 rounds of revision. Two overarching considerations for using the intersectionality alongside the TDF were developed by the group as well as two to four prompts for each TDF domain to guide interview topic guides. Considerations and prompts were designed to assist users to reflect on how individual identities and structures of power may play a role in barriers and facilitators to behaviour change and subsequent intervention implementation.

Conclusions
Through an expert-consensus approach, we developed a tool for applying an intersectionality lens alongside the TDF. Considering the role of intersecting social factors when identifying barriers and facilitators to implementing research evidence may result in more targeted and effective interventions that better reflect the realities of those involved.
The outcomes of modified endoscopic mucosal resection and endoscopic submucosal dissection for the treatment of rectal neuroendocrine tumors and the value of endoscopic morphology classification in endoscopic resection
Authors: Wang Xiang-Yao , Chai Ning-Li , Linghu En-Qiang , Qiu Shao-Tian , Li Long-Song , Zou Jia-Le , Xiang Jing-Yuan , Li Xing-Xing 
Published: June 2020

Abstract
Background
To compare the outcomes of modified endoscopic mucosal resection (m-EMR) and endoscopic submucosal dissection (ESD) for rectal neuroendocrine tumors (NETs) and evaluate the value of endoscopic morphology classification in endoscopic resection (ER).

Methods
Patients with rectal NET diameters less than 2 cm who were treated between April 2007 and January 2019 were enrolled. The endoscopic morphology of rectal NETs was classified based on the endoscopic views. Patients who underwent ESD and m-EMR were compared. Baseline characteristics as well as en bloc resection, complete resection, the procedure time, adverse events and the risk factors associated with incomplete resection were analyzed.

Results
A total of 429 patients with 449 rectal NETs were enrolled for the classification of endoscopic morphology and were classified into four types (Ia, IIb, II, and III). There were 79 patients in the m-EMR group and 259 patients in the ESD group before matching. Propensity score matching created 77 pairs between the two groups that were well balanced. The mean procedure time was significantly shorter for m-EMR than for ESD (9.1 ± 4.4 min vs 16.0 ± 7.9 min, P = 0.000). The rates of en bloc resection (98.7% vs 100%; P = 1.000), complete resection (90.9% vs 93.5%, P = 0.548) and adverse events (2.6% vs 2.6%, P = 1.000) were similar between the two groups. Univariate and multivariate analyses showed that histopathological grade and endoscopic morphology were associated with incomplete resection.

Conclusion
Both ESD and m-EMR are effective and safe for the treatment of rectal NETs. Endoscopic morphology should be considered along with histopathological grade for ER.
Association between chronic diseases and falls among a sample of older people in Finland
Authors: Immonen Milla , Haapea Marianne , Similä Heidi , Enwald Heidi , Keränen Niina , Kangas Maarit , Jämsä Timo , Korpelainen Raija 
Published: June 2020

Abstract
Background
Falls are a major problem for older people and recurrent fallers are especially prone to severe consequences due to falls. This study investigated the association between chronic conditions and falls.

Methods
Responses from 872 older persons (age 65–98) to a health questionnaire were used in the analyses. Characteristics and disease prevalence between recurrent fallers, one-time fallers and non-fallers were compared. A hierarchical clustering method was applied to find combinations of chronic conditions that were associated with recent recurrent falling.

Results
The results showed that recurrent fallers had a higher number of diseases (median 4, interquartile range, IQR = 2.0–5.0) compared to non-fallers (median 2, IQR = 1.0–3.0). Eight clusters were formed based on the data. The participants in the low chronic disease cluster were younger, more physically active, not frail, and had fewer geriatric conditions. Multiple chronic disease cluster participants were older, less physically active, overweight (body mass index, BMI > 30), at risk of malnutrition, and had more geriatric conditions. Significantly increased risk of recurrent falls relative to the low chronic cluster was found for respondents in the osteoporosis cluster and multiple chronic disease cluster (OR = 5.65, 95% confidence interval CI: 1.23–25.85, p = 0.026, and OR = 13.42, 95% CI: 2.47–72.96, p = 0.002, respectively). None of the clusters were associated with increased risk of one-time falling.

Conclusions
The results implicate that the number of chronic diseases is related with risk of recurrent falling. Furthermore, the results implicate the potential of identifying certain combinations of chronic diseases that increase fall risk by analyzing health record data, although further studies are needed with a larger population sample.
Tick-borne encephalitis (TBE) cases are not random: explaining trend, low- and high-frequency oscillations based on the Austrian TBE time series
Authors: Rubel Franz , Walter Melanie , Vogelgesang Janna R. , Brugger Katharina 
Published: June 2020

Abstract
Background
Why human tick-borne encephalitis (TBE) cases differ from year to year, in some years more 100%, has not been clarified, yet. The cause of the increasing or decreasing trends is also controversial. Austria is the only country in Europe where a 40-year TBE time series and an official vaccine coverage time series are available to investigate these open questions.

Methods
A series of generalized linear models (GLMs) has been developed to identify demographic and environmental factors associated with the trend and the oscillations of the TBE time series. Both the observed and the predicted TBE time series were subjected to spectral analysis. The resulting power spectra indicate which predictors are responsible for the trend, the high-frequency and the low-frequency oscillations, and with which explained variance they contribute to the TBE oscillations.

Results
The increasing trend can be associated with the demography of the increasing human population. The responsible GLM explains 12% of the variance of the TBE time series. The low-frequency oscillations (10 years) are associated with the decadal changes of the large-scale climate in Central Europe. These are well described by the so-called Scandinavian index. This 10-year oscillation cycle is reinforced by the socio-economic predictor net migration. Considering the net migration and the Scandinavian index increases the explained variance of the GLM to 44%. The high-frequency oscillations (2–3 years) are associated with fluctuations of the natural TBE transmission cycle between small mammals and ticks, which are driven by beech fructification. Considering also fructification 2 years prior explains 64% of the variance of the TBE time series. Additionally, annual sunshine duration as predictor for the human outdoor activity increases the explained variance to 70%.

Conclusions
The GLMs presented here provide the basis for annual TBE forecasts, which were mainly determined by beech fructification. A total of 3 of the 5 years with full fructification, resulting in high TBE case numbers 2 years later, occurred after 2010. The effects of climate change are therefore not visible through a direct correlation of the TBE cases with rising temperatures, but indirectly via the increased frequency of mast seeding.
Pharmacokinetic study of two different rifabutin doses co-administered with lopinavir/ritonavir in African HIV and tuberculosis co-infected adult patients
Authors: Kouanda Seni , Ouedraogo Henri Gautier , Cisse Kadari , Compaoré Tegwinde Rebeca , Sulis Giorgia , Diagbouga Serge , Roggi Alberto , Tarnagda Grissoum , Villani Paola , Sangare Lassana , Simporé Jacques , Regazzi Mario , Matteelli Alberto 
Published: June 2020

AbstractBackgroundThis study aimed to assess the pharmacokinetic profile of 150 mg rifabutin (RBT) taken every other day (every 48 h) versus 300 mg RBT taken every other day (E.O.D), both in combination with lopinavir/ritonavir (LPV/r), in adult patients with human immunodeficiency virus (HIV) and tuberculosis (TB) co-infection.MethodsThis is a two-arm, open-label, pharmacokinetic, randomised study conducted in Burkina Faso between May 2013 and December 2015. Enrolled patients were randomised to receive either 150 mg RBT EOD (arm A, 9 subjects) or 300 mg RBT EOD (arm B, 7 subjects), both associated with LPV/r taken twice daily. RBT plasma concentrations were evaluated after 2 weeks of combined HIV and TB treatment. Samples were collected just before drug ingestion and at 1, 2, 3, 4, 6, 8, and 12 h after drug ingestion to measure plasma drug concentration using an HPLC-MS/MS assay.ResultsThe Cmax and AUC0–12hmedians in arm A (Cmax = 296 ng/mL, IQR: 205–45; AUC0–12h = 2528 ng.h/mL, IQR: 1684–2735) were lower than those in arm B (Cmax = 600 ng/mL, IQR: 403–717; AUC0–12h = 4042.5 ng.h/mL, IQR: 3469–5761), with a statistically significant difference in AUC0–12h(p = 0.044) but not in Cmax (p = 0.313). No significant differences were observed in Tmax (3 h versus 4 h). Five patients had a Cmax below the plasma therapeutic limit (< 300 ng/mL) in the 150 mg RBT arm, while the Cmax was above this threshold for all patients in the 300 mg RBT arm. Additionally, at 48 h after drug ingestion, all patients had a mycobacterial minimum inhibitory concentration (MIC) above the limit (> 64 ng/mL) in the 300 mg RBT arm, while 4/9 patients had such values in the 150 mg RBT arm.ConclusionThis study confirmed that the 150 mg dose of rifabutin ingested EOD in combination with LPV/r is inadequate and could lead to selection of rifamycin-resistant mycobacteria.Trial registrationPACTR201310000629390, 28th October 2013.
Monitoring progress towards the first UNAIDS 90-90-90 target in key populations living with HIV in Norway
Authors: Whittaker Robert , Case Kelsey K. , Nilsen Øivind , Blystad Hans , Cowan Susan , Kløvstad Hilde , van Sighem Ard 
Published: June 2020

Abstract
Background
In line with the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 target, Norway aims for at least 90% of people living with HIV (PLHIV) to know their HIV-status. We produced current estimates of the number of PLHIV and undiagnosed population in Norway, overall and for six key subpopulations: Norwegian-born men who have sex with men (MSM), migrant MSM, Norwegian-born heterosexuals, migrant Sub-Saharan Africa (SSA)-born heterosexuals, migrant non-SSA-born heterosexuals and people who inject drugs.

Methods
We used the European Centre for Disease Prevention and Control (ECDC) HIV Modelling Tool on Norwegian HIV surveillance data through 2018 to estimate incidence, time from infection to diagnosis, PLHIV, and the number and proportion undiagnosed. As surveillance data on CD4 count at diagnosis were not collected in Norway, we ran two models; using default model CD4 assumptions, or a proxy for CD4 distribution based on Danish national surveillance data. We also generated alternative overall PLHIV estimates using the Spectrum AIDS Impact Model, to compare with those obtained from the ECDC tool.

Results
Estimates of the overall number of PLHIV in 2018 using different modelling approaches aligned at approximately 5000. In both ECDC models, the overall number undiagnosed decreased continuously from 2008. The proportion undiagnosed in 2018 was lower using default model CD4 assumptions (7.1% [95%CI: 5.3–8.9%]), than the Danish CD4 proxy (10.2% [8.3–12.1%]). This difference was driven by results for heterosexual migrants. Estimates for Norwegian-born MSM, migrant MSM and Norwegian-born heterosexuals were similar in both models. In these three subpopulations, incidence in 2018 was < 30 new infections, and the number undiagnosed had decreased in recent years. Norwegian-born MSM had the lowest estimated number of undiagnosed infections (45 [30–75], using default CD4 assumptions) and undiagnosed fraction (3.6% [2.4–5.7%], using default CD4 assumptions) in 2018.

Conclusions
Results allow cautious confidence in concluding that Norway has achieved the first UNAIDS 90–90-90 target, and clearly highlight the success of prevention strategies among MSM. Estimates for subpopulations strongly influenced by migration remain less clear, and future modelling should appropriately account for all-cause mortality and out-migration, and adjust for time of in-migration.