bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homeobox B9 integrates bone morphogenic protein 4 with inflammation at atheroprone sites
Authors: Souilhol Celine , Gauci Ismael , Feng Shuang , Tardajos Ayllon Blanca , Mahmoud Marwa , Canham Lindsay , Fragiadaki Maria , Serbanovic-Canic Jovana , Ridger Victoria , Evans Paul Charles 
Published: August 2019

Abstract

Aims
Atherosclerosis develops near branches and bends of arteries that are exposed to disturbed blood flow which exerts low wall shear stress (WSS). These mechanical conditions alter endothelial cells (EC) by priming them for inflammation and by inducing turnover. Homeobox (Hox) genes are developmental genes involved in the patterning of embryos along their anterior–posterior and proximal–distal axes. Here we identified Hox genes that are regulated by WSS and investigated their functions in adult arteries.

Methods and results
EC were isolated from inner (low WSS) and outer (high WSS) regions of the porcine aorta and the expression of Hox genes was analysed by quantitative real-time PCR. Several Hox genes (HoxA10, HoxB4, HoxB7, HoxB9, HoxD8, HoxD9) were significantly enriched at the low WSS compared to the high WSS region. Similarly, studies of cultured human umbilical vein EC (HUVEC) or porcine aortic EC revealed that the expression of multiple Hox genes (HoxA10, HoxB9, HoxD8, HoxD9) was enhanced under low (4 dyn/cm2) compared to high (13 dyn/cm2) WSS conditions. Gene silencing studies identified Hox genes (HoxB9, HoxD8, HoxD9) that are positive regulators of inflammatory molecule expression in EC exposed to low WSS, and others (HoxB9, HoxB7, HoxB4) that regulated EC turnover. We subsequently focused on HoxB9 because it was strongly up-regulated by low WSS and, uniquely, was a driver of both inflammation and proliferation. At a mechanistic level, we demonstrate using cultured EC and murine models that bone morphogenic protein 4 (BMP4) is an upstream regulator of HoxB9 which elicits inflammation via induction of numerous inflammatory mediators including TNF and downstream NF-κB activation. Moreover, the BMP4-HoxB9-TNF pathway was potentiated by hypercholesterolaemic conditions.

Conclusions
Low WSS induces multiple Hox genes that control the activation state and turnover of EC. Notably, low WSS activates a BMP4-HoxB9-TNF signalling pathway to initiate focal arterial inflammation, thereby demonstrating integration of the BMP and Hox systems in vascular pathophysiology.
Understory Vegetation Richness and Diversity of Eucalyptus benthamii and Pinus elliottii Plantations in the Midsouth US
Authors: De Stefano Andrea , Blazier Michael A , Comer Christopher E , Dean Thomas J , Wigley T Bently 
Published: August 2019

AbstractIn the Western Gulf region of the United States cold-tolerant eucalyptus have been explored as pulpwood feedstock. However, non-native plantations may alter understory species diversity, modifying environmental conditions and soil characteristics. Few studies have compared eucalyptus plantations with native ecosystems to understand the impact on understory vegetation in the United States. In this study, we compared understory plant species richness and diversity during 2014–2016 in (1) slash pine (Pinus elliottii) established in 2008, (2) slash pine established in 2013, and (3) and Camden white gum (Eucalyptus benthamii) established in 2013. Overstory characteristics, soil pH, and soil nutrient concentrations were measured to understand factors that affected understory species richness and diversity. Results indicated a decline in understory species richness over time, with Camden white gum in an intermediate condition between same-age slash pine (highest richness) and older slash pine (lowest richness). Leaf area index, soil pH and K, and tree height were the most important factors influencing understory species richness and diversity. The adoption of fast-growing eucalyptus on these sites will probably accelerate the deterioration of natural habitats and reduce open-condition species in favor of shade-tolerant species, overturning the conservation efforts already put in place by governmental agencies and conservation groups.
The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species
Authors: Faber-Hammond Joshua J , Bezault Etienne , Lunt David H , Joyce Domino A , Renn Suzy C P 
Published: August 2019

AbstractThe initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50–100 CNVEs per individual. For those species represented by multiple samples, we identify 150–200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in “hotspots” and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.
Allele-Specific Transcript Abundance: A Pilot Study in Healthy Centenarians
Authors: Tindale Lauren C , Thiessen Nina , Leach Stephen , Brooks-Wilson Angela R 
Published: August 2019

Abstract
The genetic basis of healthy aging and longevity remains largely unexplained. One hypothesis as to why long-lived individuals do not appear to have a lower number of common-complex disease variants, is that despite carrying risk variants, they express disease-linked alleles at a lower level than the wild-type alleles. Allele-specific abundance (ASA) is the different transcript abundance of the two haplotypes of a diploid individual. We sequenced the transcriptomes of four healthy centenarians and four mid-life controls. CIBERSORT was used to estimate blood cell fractions: neutrophils were the most abundant source of RNA, followed by CD8+ T cells, resting NK cells, and monocytes. ASA variants were more common in noncoding than coding regions. Centenarians and controls had a comparable distribution of ASA variants by predicted effect, and we did not observe an overall bias in expression toward major or minor alleles. Immune pathways were most highly represented among the gene set that showed ASA. Although we found evidence of ASA in disease-associated genes and transcription factors, we did not observe any differences in the pattern of expression between centenarians and controls in this small pilot study.
The Predictive Performance of Objective Measures of Physical Activity Derived From Accelerometry Data for 5-Year All-Cause Mortality in Older Adults: National Health and Nutritional Examination Survey 2003–2006
Authors: Smirnova Ekaterina , Leroux Andrew , Cao Quy , Tabacu Lucia , Zipunnikov Vadim , Crainiceanu Ciprian , Urbanek Jacek K 
Published: August 2019

AbstractBackgroundDeclining physical activity (PA) is a hallmark of aging. Wearable technology provides reliable measures of the frequency, duration, intensity, and timing of PA. Accelerometry-derived measures of PA are compared with established predictors of 5-year all-cause mortality in older adults in terms of individual, relative, and combined predictive performance.MethodsParticipants aged between 50 and 85 years from the 2003–2006 National Health and Nutritional Examination Survey (NHANES, n = 2,978) wore a hip-worn accelerometer in the free-living environment for up to 7 days. A total of 33 predictors of 5-year all-cause mortality (number of events = 297), including 20 measures of objective PA, were compared using univariate and multivariate logistic regression.ResultsIn univariate logistic regression, the total activity count was the best predictor of 5-year mortality (Area under the Curve (AUC) = 0.771) followed by age (AUC = 0.758). Overall, 9 of the top 10 predictors were objective PA measures (AUC from 0.771 to 0.692). In multivariate regression, the 10-fold cross-validated AUC was 0.798 for the model without objective PA variables (9 predictors) and 0.838 for the forward selection model with objective PA variables (13 predictors). The Net Reclassification Index was substantially improved by adding objective PA variables (p &lt; .001).ConclusionsObjective accelerometry-derived PA measures outperform traditional predictors of 5-year mortality, including age. This highlights the importance of wearable technology for providing reproducible, unbiased, and prognostic biomarkers of health.
Mineral exploration with 3-D controlled-source electromagnetic method: a synthetic study of Sukhoi Log gold deposit
Authors: Malovichko M , Tarasov A V , Yavich N , Zhdanov M S 
Published: August 2019

SUMMARY
This paper presents a feasibility study of using the controlled-source frequency-domain electromagnetic (CSEM) method in mineral exploration. The method has been widely applied for offshore hydrocarbon exploration; however, nowadays this method is rarely used on land. In order to conduct this study, we have developed a fully parallelized forward modelling finite-difference (FD) code based on the iterative solver with contraction-operator preconditioner. The regularized inversion algorithm uses the Gauss–Newton method to minimize the Tikhonov parametric functional with the Laplacian-type stabilizer. A 3-D parallel inversion code, based on the iterative finite-difference solver with the contraction-operator preconditioner, has been evaluated for the solution of the large-scale inverse problems. Using the computer simulation for a synthetic model of Sukhoi Log gold deposit, we have compared the CSEM method with the conventional direct current sounding and the CSEM survey with a single remote transmitter. Our results suggest that, a properly designed electromagnetic survey together with modern 3-D inversion could provide detailed information about the geoelectrical structure of the mineral deposit.
A point dislocation in a layered, transversely isotropic and self-gravitating Earth — Part II: accurate Green's functions
Authors: Zhou J , Pan E , Bevis M 
Published: August 2019

SUMMARYWe present an accurate approach for calculating the point-dislocation Green's functions (GFs) for a layered, spherical, transversely-isotropic and self-gravitating Earth. The formalism is based on the approach recently used to find analytical solutions for the dislocation Love numbers (DLNs). However, in order to make use of the DLNs, we first analyse their asymptotic behaviour, and then the behaviour of the GFs computed from the DLNs. We note that the summations used for different GF components evolve at different rates towards asymptotic convergence, requiring us to use two new and different truncation values for the harmonic degree (i.e. the index of summation). We exploit this knowledge to design a Kummer transformation that allows us to reduce the computation required to evaluate the GFs at the desired level of accuracy. Numerical examples are presented to clarify these issues and demonstrate the advantages of our approach. Even with the Kummer transformation, DLNs of high degree are still needed when the earth model contains very fine layers, so computational efficiency is important. The effect of anisotropy is assessed by comparing GFs for isotropic and transversely isotropic media. It is shown that this effect, though normally modest, can be significant in certain contexts, even in the far field.
Education inequalities in adult all-cause mortality: first national data for Australia using linked census and mortality data
Authors: Korda Rosemary J , Biddle Nicholas , Lynch John , Eynstone-Hinkins James , Soga Kay , Banks Emily , Priest Naomi , Moon Lynelle , Blakely Tony 
Published: August 2019

Abstract

Background
National linked mortality and census data have not previously been available for Australia. We estimated education-based mortality inequalities from linked census and mortality data that are suitable for international comparisons.

Methods
We used the Australian Bureau of Statistics Death Registrations to Census file, with data on deaths (2011–2012) linked probabilistically to census data (linkage rate 81%). To assess validity, we compared mortality rates by age group (25–44, 45–64, 65–84 years), sex and area-inequality measures to those based on complete death registration data. We used negative binomial regression to quantify inequalities in all-cause mortality in relation to five levels of education [‘Bachelor degree or higher’ (highest) to ‘no Year 12 and no post-secondary qualification’ (lowest)], separately by sex and age group, adjusting for single year of age and correcting for linkage bias and missing education data.

Results
Mortality rates and area-based inequality estimates were comparable to published national estimates. Men aged 25–84 years with the lowest education had age-adjusted mortality rates 2.20 [95% confidence interval (CI): 2.08‒2.33] times those of men with the highest education. Among women, the rate ratio was 1.64 (1.55‒1.74). Rate ratios were 3.87 (3.38‒4.44) in men and 2.57 (2.15‒3.07) in women aged 25–44 years, decreasing to 1.68 (1.60‒1.76) in men and 1.44 (1.36‒1.53) in women aged 65–84 years. Absolute education inequalities increased with age. One in three to four deaths (31%) was associated with less than Bachelor level education.

Conclusions
These linked national data enabled valid estimates of education inequality in mortality suitable for international comparisons. The magnitude of relative inequality is substantial and similar to that reported for other high-income countries.
Effectiveness of BCG Vaccination Against Mycobacterium tuberculosis Infection in Adults: A Cross-sectional Analysis of a UK-Based Cohort
Authors: Katelaris Anthea L , Jackson Charlotte , Southern Jo , Gupta Rishi K , Drobniewski Francis , Lalvani Ajit , Lipman Marc , Mangtani Punam , Abubakar Ibrahim 
Published: August 2019

Abstract

Background
BCG appears to reduce acquisition of Mycobacterium tuberculosis infection in children, measured using interferon-gamma release assays (IGRAs). We explored whether BCG vaccination continues to be associated with decreased prevalence of M. tuberculosis infection in adults.

Methods
We conducted a cross-sectional analysis of data from adult contacts of tuberculosis cases participating in a UK cohort study. Vaccine effectiveness (VE) of BCG, ascertained based on presence of a scar or vaccination history, against latent tuberculosis infection (LTBI), measured via IGRA, was assessed using multivariable logistic regression. The effects of age at BCG and time since vaccination were also explored.

Results
Of 3453 recent tuberculosis contacts, 27.5% had LTBI. There was strong evidence of an association between BCG and LTBI (adjusted odds ratio = 0.70; 95% confidence interval, .56–.87; P = .0017) yielding a VE of 30%. VE declined with time since vaccination but there was evidence that LTBI prevalence was lower amongst vaccinated individuals even &gt;20 years after vaccination, compared with nonvaccinated participants.

Conclusions
BCG is associated with lower prevalence of LTBI in adult contacts of tuberculosis. These results contribute to growing evidence that suggests BCG may protect against M. tuberculosis infection as well as disease. This has implications for immunization programs, vaccine development, and tuberculosis control efforts worldwide.

Clinical trials registration
NCT01162265.
Drug-Drug Interactions of Glecaprevir and Pibrentasvir Coadministered With Human Immunodeficiency Virus Antiretrovirals
Authors: Kosloski Matthew P , Oberoi Rajneet , Wang Stanley , Viani Rolando M , Asatryan Armen , Hu Beibei , Ding Bifeng , Qi Xin , Kim Elaine J , Mensa Federico , Kort Jens , Liu Wei 
Published: August 2019

AbstractBackgroundTreatment of patients coinfected with hepatitis C and human immunodeficiency viruses (HCV; HIV) requires careful consideration of potential drug-drug interactions between HCV direct-acting antiviral agents (DAA) and HIV antiretrovirals. Glecaprevir/pibrentasvir is a fixed-dose combination of an NS3/4A protease inhibitor and an NS5A inhibitor approved for the treatment of chronic HCV genotype 1–6 infection, including patients with HIV coinfection.MethodsA series of phase 1 studies was conducted to evaluate potential interactions of glecaprevir and pibrentasvir with elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide, abacavir/dolutegravir/lamivudine, raltegravir, rilpivirine, atazanavir/ritonavir, darunavir/ritonavir, lopinavir/ritonavir, or efavirenz/emtricitabine/tenofovir disoproxil fumarate. Pharmacokinetics of the antiretrovirals and DAAs were characterized when administered alone and in combination to quantify changes in systemic drug exposure.ResultsGlecaprevir area under the curve increased &gt;4-fold in the presence of ritonavir-boosted HIV protease inhibitors, while pibrentasvir concentrations were not significantly affected; elevations in alanine transaminase occurred in combination with atazanavir/ritonavir only. Exposures of glecaprevir and pibrentasvir may be significantly decreased by efavirenz. Coadministration with glecaprevir and pibrentasvir did not result in clinically significant changes in the exposure of any antiretroviral agents.ConclusionsAtazanavir is contraindicated with glecaprevir/pibrentasvir and use of boosted protease inhibitors or efavirenz is not recommended. No clinically significant interactions were observed with other studied antiretrovirals.
Investigating the prevalence of and factors associated with depressive symptoms among urban and semi-urban school adolescents in Bangladesh: a pilot study
Authors: Anjum Afifa , Hossain Sahadat , Sikder Tajuddin , Uddin Md Elias , Rahim Dewan Abdur 
Published: August 2019

Abstract

Background
Adolescent depression is an alarming issue for Bangladesh since a large number of Bangladeshi adolescents suffer from depression but cannot get proper treatment. This study aimed to investigate the prevalence of depression and factors associated with this psychological health hazard among urban and semi-urban adolescents of the Dhaka region in Bangladesh.

Methods
A cross-sectional pilot study was performed among 311 adolescents, grades 8–10, in Dhaka city and Savar Upazila, adjacent to the city, in 2018. Data were collected using a questionnaire consisting of items on sociodemographics, lifestyle information, screen-based sedentary behaviour (SBSB) and mental health.

Results
A total of 36.6% of the adolescents reported depressive symptoms, with a greater prevalence among females (42.9%) than males (25.7%). Sociodemographic factors including being female, residence and grade in school were significantly associated with depression. Logistic regression analysis showed that SBSBs, such as the use of social media (odds ratio [OR] 2.06 [95% confidence interval {CI} 1.27–3.35]), high screen time (&gt;120 min/day; OR 2.35 [95% CI 1.30–4.25]) and sleep disturbance (OR 3.93 [95% CI 2.37–6.50]) were significantly linked with depressive symptoms.

Conclusions
Depressive symptoms are prevalent among urban and semi-urban adolescents of Dhaka, Bangladesh. Therefore, urgent initiatives should be taken to curb the spread of depression among Bangladeshi adolescents.
Short-course antibiotic treatment of bone and joint infections in children: a retrospective study at Montpellier University Hospital from 2009 to 2013
Authors: Filleron A , Laurens M E , Marin G , Marchandin H , Prodhomme O , Alkar F , Godreuil S , Nagot N , Cottalorda J , L’Kaissi M , Rodiere M , Vigue M G , Didelot M N , Michon A L , Delpont M , Louahem D , Jeziorski E 
Published: August 2019

Abstract

Background
Acute haematogenous bone and joint infections (AHBJI) represent a diagnostic and therapeutic emergency in children, with significant potential sequelae in the case of delayed treatment. Although historically the recommendations for treatment have been based on surgery and prolonged antibiotic therapy, recent studies have demonstrated that short-course antibiotic therapy is also effective.

Objectives
We evaluated a short-term antibiotic protocol for both osteomyelitis and septic arthritis in a 6 year retrospective study at the University Hospital of Montpellier.

Methods
This protocol was based on an initial intravenous treatment with a re-evaluation after 48 h and an early switch to oral therapy in the case of a favourable clinical course for a minimum total duration of 15 days. Antibiotics were selected based on local microbiological epidemiology and systematically adapted to bacteriological results.

Results
One hundred and seventy-six cases of AHBJI were included, comprising 56 patients with osteomyelitis, 95 with septic arthritis and 25 who had both of these. The aetiological agent was identified in 42% of the cases, with the main pathogens being Staphylococcus aureus (39%) and Kingella kingae (27%). The mean intravenous treatment duration was 4 days, while the total treatment duration was 15 days. There were no treatment failures, mild sequelae occurred in 1% of the cases and the secondary surgical revision rate was 7%.

Conclusions
The results of this study are comparable to those reported for evaluations of prolonged antibiotic therapy protocols, thus indicating that a common short-term antimicrobial therapy for the management of both osteomyelitis and septic arthritis (minimum of 15 days) is a viable option for treating AHBJI in children. Further prospective studies to confirm these findings are hence warranted.
The fifth vital sign? Nurse worry predicts inpatient deterioration within 24 hours
Authors: Romero-Brufau Santiago , Gaines Kim , Nicolas Clara T , Johnson Matthew G , Hickman Joel , Huddleston Jeanne M 
Published: August 2019

Abstract

Introduction
Identification of hospitalized patients with suddenly unfavorable clinical course remains challenging. Models using objective data elements from the electronic health record may miss important sources of information available to nurses.

Methods
We recorded nurses’ perception of patient potential for deterioration in 2 medical and 2 surgical adult hospital units using a 5-point score at the start of the shift (the Worry Factor [WF]), and any time a change or an increase was noted by the nurse. Cases were evaluated by three reviewers. Intensive care unit (ICU) transfers were also tracked.

Results
31 159 patient-shifts were recorded for 3185 unique patients during 3551 hospitalizations, with 169 total outcome events. Out of 492 potential deterioration events identified, 380 (77%) were confirmed by reviewers as true deterioration events. Likelihood ratios for ICU transfer were 17.8 (15.2–20.9) in the 24 hours following a WF &gt; 2, and 40.4 (27.1–60.1) following a WF &gt; 3. Accuracy rates were significantly higher in nurses with over a year of experience (68% vs 79%, P = 0.04). The area under the receiver operator characteristic curve (AUROC) was 0.92 for the prediction of ICU transfer within 24 hours.

Discussion
This is a higher accuracy than most published early warning scores.

Conclusion
Nurses’ pattern recognition and sense of worry can provide important information for the detection of acute physiological deterioration and should be included in the electronic medical record.