bluuebunny/crossref_metadata_2025_split huggingface dataset:
Achieving the four dimensions of food security for resettled refugees in Australia: A systematic review
Authors: Lawlis Tanya , Islam Wasima , Upton Penney 
Published: December 2017

AimFood security is defined by four dimensions: food availability, access, utilisation and stability. Resettled refugees face unique struggles securing these dimensions and, thus, food security when moving to a new country. This systematic review aimed to identify the challenges Australian refugees experience in achieving the four dimensions of food security.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines were followed; the SPIDER tool was used to determine eligibility criteria. Three databases were searched using terms relating to food in/security and refugees from 2000 to 20 May 2017.ResultsSeven articles were retained for analysis. Studies were categorised against the four dimensions, with four studies identifying challenges against all dimensions. Challenges contributing to high levels of food insecurity in each dimension included: availability and cost of traditional foods, difficulty in accessing preferred food outlets, limited food knowledge and preparation skills and food stability due to low income and social support.ConclusionsFood insecurity adversely impacts refugee health and integration. Methodical research framed by the four dimensions of food security is imperative to address challenges to securing food security in refugee groups and assisting in the development of sustainable interventions.
dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing
Authors: Gruber Bernd , Unmack Peter J. , Berry Oliver F. , Georges Arthur 
Published: December 2017

AbstractAlthough vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user‐friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy–Weinberg equilibrium, gametic‐phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F‐statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user‐friendly approach to lower the hurdle to analyse such data—therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well‐established format—genlight from the adegenet package—as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub.
Identification of differential protein‐coding gene expressions in early phase lung adenocarcinoma
Authors: Zhou Li‐Na , Li Shi‐Cheng , Li Xue‐Ying , Ge Hong , Li Hong‐Mei 
Published: December 2017

BackgroundThe diagnosis of early phase lung adenocarcinoma (LADC) is associated with therapeutic strategy, effect, and survival time. However, the sensitive biomarkers of early phase LADC are still unclear. This study aimed to identify protein‐coding genes that can be used as biomarkers of early stage LADC.MethodsGene microarray analysis was performed to identify key hub genes that show different expression in lung adenocarcinoma compared to normal tissues. The microarray data of lung adenocarcinoma in stages IA, IB, IIA, IIB, and normal tissues (GSE10072) were downloaded from a free online database, Gene Expression Omnibus (GEO).ResultsA total of 572 differentially expressed genes (DEGs) were identified between early phase lung adenocarcinoma and normal tissues using R software. Database for Annotation, Visualization and Integrated Discovery online tools were used to obtain Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to analyze DEGs. Cytoscape software was used to express the protein‐protein interaction network. We found that some cancer‐related Gene Ontology terms and pathways (e.g. cell adhesion, cell surface receptor signaling pathway, PI3K‐Akt signaling pathway) were significantly enriched in DEGs.ConclusionProtein‐coding genes JUN, FYN, CAV1, and SFN may play vital roles in the progress of early‐stage lung adenocarcinoma. Consequently, through bioinformatics analysis, the key genes could be established to provide more potential references for the therapeutic targets of lung adenocarcinoma.
Survival analysis of patients with advanced non‐small cell lung cancer receiving tyrosine kinase inhibitor (TKI) treatment: A multi‐center retrospective study
Authors: Shi Qingming , Guan Maojing , Wang Yong , Xu Congjing , Tang Lei , Fu Wenhua , Bi Minghong , Sun Xiang , Gu Kangsheng , Pang Dongsheng 
Published: December 2017

BackgroundThe study was conducted to assess differences in overall survival (OS) in patients with non‐small cell lung cancer (NSCLC) receiving different treatment modalities of tyrosine kinase inhibitors (TKIs).MethodsA total of 463 NSCLC patients receiving TKI treatment were included. OS was compared according to treatment timing in all patients, the elderly, and patients positive for EGFR mutations.ResultsOne hundred and seventy two patients received TKIs as first‐line treatment, 220 as second‐line, and 67 as third‐line. The results between the three groups were not statistically significant: the one, two, and three‐year OS rates were: 55.3%, 22.3%, and 11.3% (first‐line); 59.6%, 27.8%, and 14.9% (second‐line); and 53.8%, 41.3%, and 29.5% (third‐line), respectively (P = 0.095). Results between the three groups of elderly patients were also not statistically significant (P = 0.469). The one and two‐year OS rates in EGFR mutation‐positive patients receiving first‐line treatment were 48% and 17.5%, respectively. The one, two, and three‐year OS rates of patients receiving second‐line treatment were: 54.2%, 30.3%, and 20.2%, respectively. There were no statistically significant differences between the groups with EGFR mutations receiving first‐line or second‐line treatment. Thirteen EGFR mutation‐positive patients received third‐line TKI treatment for a median duration of 7 months. Their one and two‐year OS rates were 69.8% and 58.2%, respectively, which were higher than in the other two groups (P = 0.015).ConclusionThree lines of TKI therapy can prolong survival in NSCLC patients. Elderly patients can benefit from TKI therapy. EGFR mutation‐positive patients can benefit from second‐line or third‐line TKI therapy.
Canine Conundrum: domestic dogs as an invasive species and their impacts on wildlife in India
Authors: Home C. , Bhatnagar Y. V. , Vanak A. T. 
Published: December 2017

AbstractDomestic dogs are increasingly being recognized as a conservation threat for native species. In many places, their impacts may be as severe as other invasive predators such as cats and rats. We conducted the first ever sub‐continent scale assessment of the impacts of dogs on native species in India using an online key informant survey and reports from national print media. Dogs reportedly attacked 80 species, of which 31 were IUCN Red list threatened species, including four Critically Endangered species. Larger bodied mammals such as ungulates and carnivores, were most commonly reported to be attacked, although this may be an observation bias. Approximately 68% of the attacks were carried out by dogs unaccompanied by humans. Most of the attacks were carried out by packs of dogs with 45% of these attacks leading to the death of the prey. Nearly 48% of the incidents were reported in and around wildlife protected areas, suggesting that dogs are an important large‐scale edge effect around protected areas in India. For Critically Endangered species that are already suffering from serious population declines due to other causes, the impact of dogs may seriously impede population recovery efforts. Mitigating the impacts of dogs on wildlife requires a multi‐pronged approach of responsible dog ownership, restriction in free‐ranging behaviour, and strong population control measures, especially around sensitive conservation areas.
Application of three‐dimensional print in minor hepatectomy following liver partition between anterior and posterior sectors
Authors: Igami Tsuyoshi , Nakamura Yoshihiko , Oda Masahiro , Tanaka Hiroshi , Nojiri Motoi , Ebata Tomoki , Yokoyama Yukihiro , Sugawara Gen , Mizuno Takashi , Yamaguchi Junpei , Mori Kensaku , Nagino Masato 
Published: December 2017

BackgroundMinor hepatectomy following liver partition between the right anterior and posterior sectors requires technical ingenuities. In such hepatectomy, we used three‐dimensional (3D) print; therefore, our procedure was introduced.MethodsDigital segmentation of anatomical structures from multidetector‐row computed tomography images utilized the original software ‘PLUTO’, which was developed by Graduate School of Information Science, Nagoya University. After changing the final segmentation data to the stereolithography files, 3D‐printed liver at 70% scale was produced. The support material was washed and mould charge was removed from 3D‐printed hepatic veins. The surface of 3D‐printed model was abraded and coated with urethane resin paint. After natural drying, 3D‐printed hepatic veins were coloured by injection of a dye. The 3D‐printed portal veins were whitish because mould charge remained. All procedures after 3D printing were performed by hand work. A 3D‐printed model of the right posterior sector and a 3D‐printed model of other parenchyma were produced, respectively. Measuring the length between the main structures on the liver surface and the planned partition line on the 3D‐printed model, land mark between the right anterior and posterior sectors on the real liver surface was produced with scale adjustment.ResultsMinor hepatectomy following liver partition between the right anterior and posterior sectors was performed referring to 3D‐printed model. The planned liver partition and resection were successful.ConclusionsApplication of 3D‐printed liver to minor hepatectomy following liver partition between the right anterior and posterior sectors is easy and a suitable procedure.
Neutrophil Gelatinase‐Associated Lipocalin as a Biomarker of Allograft Function After Renal Transplantation: Evaluation of the Current Status and Future Insights
Authors: Cappuccilli Maria , Capelli Irene , Comai Giorgia , Cianciolo Giuseppe , La Manna Gaetano 
Published: December 2017

AbstractNeutrophil gelatinase‐associated lipocalin (NGAL), a protein belonging to the lipocalin superfamily initially found in activated neutrophils, is expressed by several cell types, including kidney tubule. The increase in NGAL production and release from tubular cells in response to various insults has been proven to predict acute kidney injury (AKI). For this reason, it has emerged as a valuable noninvasive biomarker of AKI in clinical nephrology. Also in the renal transplant setting, different studies have indicated NGAL as a valuable tool, especially in the early postoperative period, since the currently available clinical and laboratory parameters remain poorly sensitive to monitor immediate posttransplant graft function. This is an analysis of the recent literature to assess the utility of plasma and urinary NGAL, exosomal mRNA for NGAL, and NGAL levels in the perfusate of machine‐perfused kidneys for the prediction of graft function recovery in the early postsurgery phase after renal transplantation. We found that NGAL appears as a promising troponin‐like biomarker to detect short‐term impairment of graft function after renal transplant, but there are still some limitations in its clinical application, essentially related to its low specificity. Moreover, comparing NGAL assayed in serum, urine, machine‐perfusate, or as exosomal mRNA, each one has shown limitations and benefits in terms of predictive performance for DGF, according to various existing studies, feasibly due to different cut‐off levels, designs and patient sample sizes.
Pediatric femoral hernia in the laparoscopic era
Authors: Aneiros Castro Belén , Cano Novillo Indalecio , García Vázquez Araceli , López Díaz María , Benavent Gordo María Isabel , Gómez Fraile Andrés 
Published: December 2017

AbstractIntroductionFemoral hernia is a rare and often misdiagnosed condition in childhood. The aim of our study was to demonstrate that the laparoscopic approach improves diagnostic accuracy and offers a safe and effective treatment.MethodsA retrospective study of 687 pediatric patients who underwent laparoscopic inguinal hernia repair from January 2000 to December 2015 was performed.ResultsFemoral hernias were identified in 16 patients (2.3%). The right side was affected in 10 cases (62.5%), the left side in 5 (31.2%), and 1 case was bilateral (6.2%). The mean age of patients was 8.00 ± 3.81 years, and there was a male predominance. Preoperative diagnosis was femoral hernia in eight cases (50%) and indirect inguinal hernia in the remaining eight (50%). Seven children (43.8%) presented with hernia recurrence after having undergone an open ipsilateral indirect hernia repair. A modified laparoscopic McVay technique was performed in 12 cases (70.6%). An epigastric artery injury by trocar occurred in one patient. All operations were completed laparoscopically. The mean surgical time was 45.6 ± 22.9 min for unilateral cases and 110 ± 10.0 min for bilateral cases. No immediate postoperative complications were noted. The mean postoperative hospital stay was 0.6 ± 0.4 days. No recurrence was observed after a median follow‐up of 11 years (range, 4–16 years).ConclusionFemoral hernia is a rare pathology in pediatric patients that is often difficult to diagnose. The laparoscopic approach is effective in the diagnosing and treating these hernias, and it allows for the simultaneous repair of multiple groin defects.
Logging, exotic plant invasions, and native plant reassembly in a lowland tropical rain forest
Authors: Döbert Timm F. , Webber Bruce L. , Sugau John B. , Dickinson Katharine J. M. , Didham Raphael K. 
Published: December 2017

AbstractHabitat modification and biological invasions are key drivers of global environmental change. However, the extent and impact of exotic plant invasions in modified tropical landscapes remain poorly understood. We examined whether logging drives exotic plant invasions and whether their combined influences alter understory plant community composition in lowland rain forests in Borneo. We tested the relationship between understory communities and local‐ and landscape‐scale logging intensity, using leaf area index (LAI) and aboveground biomass (AGB) data from 192 plots across a logging‐intensity gradient from primary to repeatedly logged forests. Overall, we found relatively low levels of exotic plant invasions, despite an intensive logging history. Exotic species were more speciose, had greater cover, and more biomass in sites with more local‐scale canopy loss. Surprisingly, though, exotic species invasion was not related to either landscape‐scale canopy loss or road configuration. Moreover, logging and invasion did not seem to be acting synergistically on native plant composition, except that seedlings of the canopy‐dominant Dipterocarpaceae family were less abundant in areas with higher exotic plant biomass. Current low levels of invasion, and limited association with native understory community change, suggest there is a window of opportunity to manage invasive impacts. We caution about potential lag effects and the possibly severe negative impacts of exotic plant invasions on the long‐term quality of tropical forest, particularly where agricultural plantations function as permanent seed sources for recurrent dispersal along logging roads. We therefore urge prioritization of strategic management plans to counter the growing threat of exotic plant invasions in modified tropical landscapes.
Antibacterial activities and molecular mechanism of amino‐terminal fragments from pig nematode antimicrobial peptide CP‐1
Authors: Dong Na , Wang Zhihua , Chou Shuli , Zhang Licong , Shan Anshan , Jiang Junguang 
Published: December 2017

High manufacturing costs and weak cell selectivity have limited the clinical application of naturally occurring peptides when faced with an outbreak of drug resistance. To overcome these limitations, a set of antimicrobial peptides was synthesized with the general sequence of (WL)n, where n = 1, 2, 3, and WL was truncated from the N‐terminus of Cecropin P1 without initial serine residues. The antimicrobial peptide WL3 exhibited stronger antimicrobial activity against both Gram‐negative and Gram‐positive microbes than the parental peptide CP‐1. WL3 showed no hemolysis even at the highest test concentrations compared to the parental peptide CP‐1. The condition sensitivity assays (salts, serum, and trypsin) demonstrated that WL3 had high stability in vitro. Fluorescence spectroscopy and electron microscopy indicated that WL3 killed microbes by means of penetrating the membrane and causing cell lysis. In a mouse model, WL3 was able to significantly reduce the bacteria load in major organs and cytokines (TNF‐α, IL‐6, and IL‐1β) levels in serum. In summary, these findings suggest that WL3, which was modified from a natural antimicrobial peptide, has enormous potential for application as a novel antibacterial agent.
Filaggrin mutations increase allergic airway disease in childhood and adolescence through interactions with eczema and aeroallergen sensitization
Authors: Chan Adrian , Terry William , Zhang Hongmei , Karmaus Wilfried , Ewart Susan , Holloway John W. , Roberts Graham , Kurukulaaratchy Ramesh , Arshad Syed Hasan 
Published: December 2017

SummaryBackgroundFilaggrin loss‐of‐function (FLG‐LOF) mutations are an established genetic cause of eczema. These mutations have subsequently been reported to increase the risk of aeroallergen sensitization and allergic airway disease. However, it is unclear whether FLG variants require both eczema and aeroallergen sensitization to influence airway disease development long‐term outcomes.ObjectiveTo examine the effects of FLG‐LOF mutations on allergic airway disease outcomes, with eczema and aeroallergen sensitization as intermediate variables, using the Isle of Wight birth cohort.MethodsStudy participants were evaluated at ages 1, 2, 4, 10 and 18 years to ascertain the development of allergic diseases (eczema, asthma and allergic rhinitis) and aeroallergen sensitization (determined by skin prick tests). FLG‐LOF mutations were genotyped in 1150 subjects. To understand the complex associations between FLG mutations, intermediate variables (eczema and aeroallergen sensitization) and airway disease, path analysis was performed.ResultsThere were significant total effects of FLG‐LOF mutations on both asthma and allergic rhinitis at all ages as well as on aeroallergen sensitization up till 10 years old. In the filaggrin‐asthma analysis, a direct effect of FLG‐LOF mutations was observed on early childhood eczema (age 1 and 2 years) (relative risk (RR) 2.01, 95% CI: 1.74‐2.31, P < .001), and all significant indirect pathways on asthma outcomes passed through eczema at these ages. In contrast, for the filaggrin‐rhinitis model, FLG‐LOF mutations exerted significant direct effects on early eczema as well as rhinitis at 10 years (RR 1.99; 95% CI: 1.72‐2.29, P = .002).ConclusionFLG‐LOF mutations are a significant risk factor for later childhood asthma and rhinitis. However, the pathway to asthma is only through early childhood eczema while a direct effect was observed for childhood rhinitis.
Therapeutic potential of phages in autoimmune liver diseases
Authors: Górski A , Jończyk-Matysiak E , Łusiak-Szelachowska M , Weber-Dąbrowska B , Międzybrodzki R , Borysowski J 
Published: December 2017

Summary
Autoimmune liver disease (ALD) poses a difficult medical challenge, as there is a significant number of patients in whom current therapy offers questionable or no benefit, yet its side effects may be serious, including the development of malignancy. Bacterial viruses (phages) have been recognized increasingly as immunomodulators contributing to immune homeostasis and curbing inflammation. Accumulating data suggest that phages may be useful in immunotherapy of ALD. Phages have been shown to down-regulate the expression and/or production and activity of factors associated with hepatic injury [reactive oxygen species, Toll-like receptor (TLR)-4 activation, nuclear factor kappa B (NF-κB) activation, proinflammatory and procoagulant activities of platelets] and up-regulate the expression and/or production of factors demonstrated as playing a protective role [interleukin (IL)-10, IL-1 receptor antagonist].
Randomized open‐label crossover assessment of Prograf vs Advagraf on immunosuppressant pharmacokinetics and pharmacodynamics in simultaneous pancreas‐kidney patients
Authors: Cattral Mark , Luke Sean , Knauer Michael J. , Norgate Andrea , Schiff Jeffrey , Muirhead Norman , Luke Patrick P. 
Published: December 2017

AbstractIntroductionWe assessed the pharmacokinetic and pharmacodynamic impact of converting stable simultaneous pancreas‐kidney (SPK) recipients from standard tacrolimus (Prograf) to long‐acting tacrolimus (Advagraf).MethodsIn a randomized prospective crossover study, stable SPK recipients on Prograf were assigned to Prograf with 1:1 conversion to Advagraf or vice versa. Demographics, tacrolimus, mycophenolic acid levels, and Cylex CD4 + ATP levels were taken at specified intervals in addition to standard blood work.ResultsTwenty‐one patients, who were a minimum of 1 year post‐transplant, were entered into the study. No difference in tacrolimus or mycophenolic acid levels was noted between patients who were first assigned to Prograf or Advagraf. Additionally, Cylex levels as well as serum creatinine, lipase, and blood sugar levels were unchanged. There were no episodes of rejection during the 6‐month study.ConclusionsIt is safe to convert between Prograf and Advagraf 1:1, without major impact on pharmacokinetics or pharmacodynamics in SPK recipients.