bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping evidence on the distribution of paediatric cancers in sub-Saharan Africa: a scoping review protocol
Authors: Ndlovu Sehlisiwe R. , Kuupiel Desmond , Ginindza Themba G. 
Published: November 2019

AbstractBackgroundPaediatric cancers account for a minor fraction of deaths and hence receive little attention from policymakers. In low-income countries, the absence of comprehensive national paediatric strategies results in a lack of access for a majority of children with cancer. In sub-Saharan Africa (SSA), the burden of childhood cancers is underestimated due to a lack of paediatric cancer registries, poor health care systems and competing healthcare needs. The objective of this study is to map evidence on the distribution of paediatric cancers in the SSA region.MethodA scoping review will be conducted to map literature on the distribution of paediatric cancers in SSA.An electronic literature search will be conducted from the following databases: PubMed, Google Scholar, EBSCOhost (CINAHL and Health Source) and World Health Organization (WHO)/International Agency for Research in Cancer (IARC) (GLOBOCAN databases). We will also search the reference lists of included studies to source relevant literature. A pilot search was conducted to determine the feasibility of the study. Study selection will be guided by the inclusion and exclusion criteria. After charting the data, a descriptive overview of the studies will be presented in a narrative format. An account of the study characteristics will be described in this narrative. The analysis will be mainly based on mapping the country-specific outcomes emerging from the studies, and a numerical summary of these outcomes will be conducted. Tables, maps and charts will be produced and presented in the result section.DiscussionThis review study will identify existing research gaps for future research to influence policy implementation and to improve the availability of diagnosis and treatment of paediatric cancers in SSA.
Intervention components, mediators, and mechanisms of change of Internet- and mobile-based interventions for post-traumatic stress disorder: protocol for a systematic review and meta-analysis
Authors: Steubl Lena , Sachser Cedric , Baumeister Harald , Domhardt Matthias 
Published: November 2019

Abstract

Background
While Internet- and mobile-based interventions (IMIs) might possess the potential to increase access to evidence-based therapies for post-traumatic stress disorder (PTSD), comprehensive knowledge on active intervention components and change mechanisms underlying their efficacy is largely pending so far. The proposed systematic review and meta-analysis will systematically review the current status of research on the efficacy of IMIs for adult PTSD compared to active control conditions and identify active intervention components and mediators responsible for therapeutic change.

Methods
A systematic literature search (PsycINFO, Medline/PubMed, Embase, CENTRAL, ICTRP, and Web of Science) will be conducted using keywords targeting “PTSD” and “Internet- and mobile-based interventions”. Two independent researchers will retrieve studies eligible for inclusion and extract and evaluate data (design, population, outcomes, sample size, duration of intervention and follow-up, drop-out rate). Risk of bias will be assessed, and results will be synthesized qualitatively and evaluated meta-analytically when possible.

Discussion
The results of this systematic review and meta-analysis might further contribute to the development of IMIs for PTSD by highlighting intervention components and mediators associated with their efficacy. Knowledge about the active ingredients might ultimately lead to more effective interventions and treatment packages, with implications for clinical practice and dissemination of these rather novel interventions.

Systematic review registration
PROSPERO (CRD42019130314).
Study of genetic diversity, biofilm formation, and detection of Carbapenemase, MBL, ESBL, and tetracycline resistance genes in multidrug-resistant Acinetobacter baumannii isolated from burn wound infections in Iran
Authors: Ranjbar Reza , Farahani Abbas 
Published: November 2019

Abstract

Background
Antimicrobial resistance in multidrug-resistant Acinetobacter baumannii (MDR-AB) isolated from burn wound infections is a major concern in intensive care or burns units worldwide, and molecular studies are considered critical strategies for control of MDR-AB outbreaks in this regard. Thus, in this study, antibiotic resistance, biofilm-forming ability, molecular epidemiology of MDR A. baumannii strains recovered from patients with burns were investigated in three major hospital centers of Iran.

Methods
In this cross-sectional research, 163 non-repetitive A. baumannii strains were tested for susceptibility to antimicrobial agents. Polymerase chain reaction (PCR) was performed to characterize ambler classes A, B, and D β-lactamases, ISAba1 and integrons, biofilm formation was also investigated. Clonal relatedness was analyzed using Pulsed-Field Gel Electrophoresis (PFGE).

Results
Among 163 A. baumannii strains collected, 94.5% of them were Carbapenem-Non-Susceptible A. baumannii (CNSAB) and also 90.1 and 52.2% of them were Metallo-β-Lactamases (MBL) and Extended-Spectrum β-Lactamases (ESBL) producing isolates, respectively. Colistin and polymyxin B exhibited excellent activity against CNSAB strains. High prevalence of blaOXA − 23-like (85.1%), blaVIM (60.5%), blaPER − 1 (42.3%), tetB (67.8%), and Class 1 integrons (65.6%) were identified in CNSAB strains. ISAba1 element was associated with 42 (25.8%) and 129 (98.5%) of blaOXA-51-like and blaOXA-23-like genes, respectively. 6 clusters with the ability to form strong biofilms were found to be dominant and endemic in our entire areas.

Conclusions
Results of the present study show that antimicrobial resistance in CNSAB isolates from burn wound infections in monitored hospitals in Iran is multifactorial, and also findings of the study suggested that local antibiotic prescription policies should be regularly reviewed, and efficient infection control measures should be observed. Therefore, further strengthening of surveillance of antimicrobial resistance is urgently needed in these regions.
Time–frequency dependency of financial risk and economic risk: evidence from Greece
Authors: Kirikkaleli Dervis 
Published: November 2019

Abstract
This study aims to shed some light on the one of the most popular phenomena in the economics and finance literature—nexus between economic growth and financial development—for the case of Greece over 1990Q1 to 2018Q4 within the framework of risk. In other words, this study investigates the causal link between financial risk and economic risk in Greece using wavelet coherence tests while answering the following questions: (i) does financial risk lead to economic risk in Greece and/or does economic risk lead to financial risk in Greece, and (ii) if so, why? The wavelet coherence approach allows the study to capture the long-run and short-run causal linkages among the time series variables since the approach combines time and frequency domain causalities. The findings from wavelet coherence supports the Schumpeter hypothesis since the findings proves that there is unidirectional causality from financial risk to economic risk in Greece (i) between 1995 and 1998; (ii) between 2003 and 2013; (iii) between 2013 and 2017 at different frequency levels. The findings clearly reveal how financial risk is important predictor for economic risk in Greece over the period of 1990–2018.
Copy number of 8q24.3 drives HSF1 expression and patient outcome in cancer: an individual patient data meta-analysis
Authors: Brusselaers Nele , Ekwall Karl , Durand-Dubief Mickael 
Published: November 2019

Abstract

Background
The heat-shock transcription factor 1 (HSF1) has been linked to cell proliferation and survival in cancer and has been proposed as a biomarker for poor prognosis. Here, we assessed the role of HSF1 expression in relation to copy number alteration (CNA) and cancer prognosis.

Methods
Using 10,287 cancer genomes from The Cancer Genome Atlas and Cbioportal databases, we assessed the association of HSF1 expression with CNA and cancer prognosis. CNA of 8q24.3 was categorized as diploid (reference), deletion (fewer copies), gain (+ 1 copy) and amplification (≥ + 2 copies). Multivariate logistic regression modeling was used to assess 5-year survival among those with a first cancer diagnosis and complete follow-up data (N = 9568), categorized per anatomical location and histology, assessing interaction with tumor stage, and expressed as odds ratios and 95% confidence intervals.

Results
We found that only 54.1% of all tumors have a normal predicted 8q24.3 copy number and that 8q24.3 located genes including HSF1 are mainly overexpressed due to increased copies number of 8q24.3 in different cancers. The tumor of patients having respectively gain (+ 1 copy) and amplification (≥ + 2 copies) of 8q24.3 display a global increase of 5-year mortality (odds ratio = 1.98, 95% CI 1.22–3.21) and (OR = 2.19, 1.13–4.26) after full adjustment. For separate cancer types, tumor patients with 8q24.3 deletion showed a marked increase of 5-year mortality in uterine (OR = 4.84, [2.75–8.51]), colorectal (OR = 4.12, [1.15–14.82]), and ovarian (OR = 1.83, [1.39–2.41]) cancers; and decreased mortality in kidney cancer (OR = 0.41, [0.21–0.82]). Gain of 8q24.3 resulted in significant mortality changes in 5-year mortality for cancer of the uterus (OR = 3.67, [2.03–6.66]), lung (OR = 1.76, [1.24–2.51]), colorectal (OR = 1.75, [1.32–2.31]) cancers; and amplification for uterine (OR = 4.58, [1.43–14.65]), prostate (OR = 4.41 [3.41–5.71]), head and neck (OR = 2.68, [2.17–3.30]), and stomach (OR = 0.56, [0.36–0.87]) cancers.

Conclusions
Here, we show that CNAs of 8q24.3 genes, including HSF1, are tightly linked to 8q24.3 copy number in tumor patients and can affect patient outcome. Our results indicate that the integration of 8q24.3 CNA detection may be a useful predictor for cancer prognosis.
Simultaneous estimation of in situ porosity and thermal structure from core sample measurements and resistivity log data at Nankai accretionary prism
Authors: Yabe Suguru , Fukuchi Rina , Hamada Yohei , Kimura Gaku 
Published: November 2019

Abstract
The shallow accretionary prism of the Nankai Trough is a location where both large interplate earthquakes and slow earthquakes occur. Since the physical properties of sedimentary materials are important topics for understanding the structure of the prism, numerous ocean drilling expeditions have been conducted in that region to obtain logging data and core samples. Although the physical properties of the obtained samples are normally measured onboard immediately after coring, estimations of in situ physical properties are difficult because of differences in laboratory and in situ physical conditions. Herein, we propose a new method for estimating in situ porosity from downhole electrical resistivity log data that evaluates in situ porosity and thermal structure simultaneously using correlations between the porosity and resistivity, and between the porosity and thermal conductivity that were established based on laboratory measurements. When constructing physical property correlations, X-ray computed tomography data play an important role in estimating the porosity of samples from which resistivity or thermal conductivity were measured. To validate our method, we compared the estimation with density log data collected at Site C0002 and found that the estimated in situ porosity shows good agreement with the in situ porosity converted from density log data. A comparison with porosity measured onboard for core and cutting samples showed that they are consistent with each other. With this new method, continuous distributions of in situ porosity and thermal structure can be estimated simultaneously based on resistivity log data and heat flow, which are basic quantities acquired during ocean drilling science expeditions.
Mechanical strength of a new plate compared to six previously tested opening wedge high tibial osteotomy implants
Authors: Diffo Kaze Arnaud , Maas Stefan , Belsey James , Hoffmann Alexander , Seil Romain , van Heerwaarden Ronald , Pape Dietrich 
Published: November 2019

Abstract

Background
This study aimed to assess the mechanical static and fatigue strength provided by the FlexitSystem plate in medial opening wedge high tibial osteotomies (MOWHTO), and to compare it to six previously tested implants: the TomoFix small stature, the TomoFix standard, the ContourLock, the iBalance, the second generation PEEKPower and the size 2 Activmotion. Thus, this will provide surgeons with data that will help in the choice of the most appropriate implant for MOWHTO.

Methods
Six fourth-generation tibial bone composites underwent a MOWHTO and each was fixed using six FlexitSystem plates, according to standard techniques. The same testing procedure that has already been previously defined, used and published, was used to investigate the static and dynamic strength of the prepared bone-implant constructs. The test consisted of static loading and cyclical loading for fatigue testing.

Results
During static testing, the group constituted by the FlexitSystem showed a fracture load higher than the physiological loading of slow walking (3.7 kN > 2.4 kN). Although this fracture load was relatively small compared to the average values for the other Implants from our previous studies, except for the TomoFix small stature and the Contour Lock. During fatigue testing, FlexitSystem group showed the smallest stiffness and higher lifespan than the TomoFix and the PEEKPower groups.

Conclusions
The FlexitSystem plate showed sufficient strength for static loading, and average fatigue strength compared to the previously tested implants. Full body dynamic loading of the tibia after MOWHTO with the investigated implants should be avoided for at least 3 weeks. Implants with a wider T-shaped proximal end, positioned onto the antero-medial side of the tibia head, or inserted in the osteotomy opening in a closed-wedge construction, provided higher mechanical strength than implants with small a T-shaped proximal end, centred onto the medial side of the tibia head.
PDIL1-2 can indirectly and negatively regulate expression of the AGPL1 gene in bread wheat
Authors: Dong Jie , Zheng Yongxing , Fu Yihan , Wang Jinxi , Yuan Shasha , Wang Yonghua , Zhu Qidi , Ou Xingqi , Li Gezi , Kang Guozhang 
Published: November 2019

Abstract

Background
ADP-glucose pyrophosphorylase (AGPase), the key enzyme in plant starch biosynthesis, is a heterotetramer composed of two identical large subunits and two identical small subunits. AGPase has plastidial and cytosolic isoforms in higher plants, whereas it is mainly detected in the cytosol of grain endosperms in cereal crops. Our previous results have shown that the expression of the TaAGPL1 gene, encoding the cytosolic large subunit of wheat AGPase, temporally coincides with the rate of starch accumulation and that its overexpression dramatically increases wheat AGPase activity and the rate of starch accumulation, suggesting an important role.

Methods
In this study, we performed yeast one-hybrid screening using the promoter of the TaAGPL1 gene as bait and a wheat grain cDNA library as prey to screen out the upstream regulators of TaAGPL1 gene. And the barley stripe mosaic virus-induced gene-silencing (BSMV-VIGS) method was used to verify the functional characterization of the identified regulators in starch biosynthesis.

Results
Disulfide isomerase 1-2 protein (TaPDIL1-2) was screened out, and its binding to the TaAGPL1-1D promoter was further verified using another yeast one-hybrid screen. Transiently silenced wheat plants of the TaPDIL1-2 gene were obtained by using BSMV-VIGS method under field conditions. In grains of BSMV-VIGS-TaPDIL1-2-silenced wheat plants, the TaAGPL1 gene transcription levels, grain starch contents, and 1000-kernel weight also significantly increased.

Conclusions
As important chaperones involved in oxidative protein folding, PDIL proteins have been reported to form hetero-dimers with some transcription factors, and thus, our results suggested that TaPDIL1-2 protein could indirectly and negatively regulate the expression of the TaAGPL1 gene and function in starch biosynthesis.
Evaluation of the association of C5 with neovascular age-related macular degeneration and polypoidal choroidal vasculopathy
Authors: Liu Ke , Ma Li , Lai Timothy Y. Y. , Brelen Marten E. , Tam Pancy O. S. , Tham Clement C. , Pang Chi Pui , Chen Li Jia 
Published: November 2019

AbstractBackgroundNeovascular age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV) are sight-threatening maculopathies with both environmental and genetic risk factors. We have previously shown relative risks posed by genes of the complement pathways to neovascular AMD and PCV.MethodsIn this study, we investigated the haplotype-tagging single nucleotide polymorphisms (SNPs) in thecomplement component 5(C5) gene in 708 unrelated Chinese individuals: 200 neovascular AMD patients, 233 PCV patients and 275 controls. Six tagging SNPs inC5were genotyped. Univariate single SNP association analysis, haplotype-based association analysis and gene-gene interaction analysis betweenC5and other AMD-associated genes were performed.ResultsThe results revealed none of the six tagging SNPs of theC5gene had a significant association with neovascular AMD or PCV (P > 0.05). We also found insignificant haplotype-based association, and no significant SNP-SNP interaction betweenC5and other genes (includingC2-CFB-RDBP-SKIV2L,SERPING1,CETP,ABCG1,PGF,ANGPT2,CFHandHTRA1) for neovascular AMD and PCV.ConclusionsThis study showed no statistical significance in the genetic association ofC5with neovascular AMD or PCV in a Hong Kong Chinese population. Further studies in large samples from different populations are warranted to elucidate the role ofC5in the genetic susceptibility of AMD and PCV.
Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease
Authors: Radl Viviane , Winkler Jana Barbro , Kublik Susanne , Yang Luhua , Winkelmann Traud , Vestergaard Gisle , Schröder Peter , Schloter Michael 
Published: November 2019

Abstract

Background
Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear.

Results
As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression.

Conclusions
Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.
A step towards equitable clinical trial recruitment: a protocol for the development and preliminary testing of an online prostate cancer health information and clinical trial matching tool
Authors: Borno Hala T. , Bakke Brian M. , Kaplan Celia , Hebig-Prophet Anke , Chao Jessica , Kim Yoon-Ji , Yeager Jan , Cinar Pelin , Small Eric , Boscardin Christy , Gonzales Ralph 
Published: November 2019

Abstract

Background
Recruitment of a diverse participant pool to cancer clinical trials is an essential component of clinical research as it improves the generalizability of findings. Investigating and piloting novel recruitment strategies that take advantage of ubiquitous digital technologies has become an important component of facilitating broad recruitment and addressing inequities in clinical trial participation. Equitable and inclusive recruitment improves generalizability of clinical trial outcomes, benefiting patients, clinicians, and the research community. The increasing prevalence of online connectivity in the USA and use of the Internet as a resource for medical information provides an opportunity for digital recruitment strategies in cancer clinical trials. This study aims to measure the acceptability, preliminary estimates of efficacy, and feasibility of the Trial Library intervention, an Internet-based cancer clinical trial matching tool. This study will also examine the extent to which the Trial Library website, designed to address the linguistic and literacy needs of broader patient populations, influences patient-initiated conversations with physicians about clinical trial participation.

Methods
This is a study protocol for a non-randomized, single-arm pilot study. This is a mixed methods study design that utilizes the statistical analysis of quantitative survey data and the qualitative analysis of interview data to assess the participant experience with the Trial Library intervention. This study will examine (1) acceptability as a measure of participant satisfaction with this intervention, (2) preliminary measure of efficacy as a measure of proportion of participants with documented clinical trial discussion in the electronic medical record, and (3) feasibility of the intervention as a measure of duration of clinical visit.

Discussion
The principles that informed the design of the Trial Library intervention aim to be generalizable to clinical trials across many disease contexts. From the ground up, this intervention is built to be inclusive of the linguistic, literacy, and technological needs of underrepresented patient populations. This study will collect essential preliminary data prior to a multi-site randomized clinical trial of the Trial Library intervention.

Trial registration
This study has received institutional approval from the Committee of Human Subjects Research at the University of California, San Francisco.