bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network‐ and distance‐based methods in bioregionalization processes at regional scale: An application to the terrestrial mammals of Iran
Authors: Yusefi Gholam Hosein , Safi Kamran , Brito José Carlos 
Published: August 2019

AbstractAimIn recent years, novel approaches have been proposed to improve current bioregionalization methods, but these have not been thoroughly compared. We assessed the applicability of the recently developed network‐based clustering method (Infomap algorithm) in bioregionalization analysis at regional spatial scales and compared the results with commonly used distance‐based methods (hierarchical clustering algorithm). We also identified climate regions by using a model‐based cluster analysis (Gaussian algorithm). Finally, we quantified the representation of climate regions and bioregions in current protected areas (PAs).LocationIran.TaxaTerrestrial mammals.MethodsTo define bioregions we used the Infomap algorithm and distance‐based clustering methods based on species distribution data (over 14,000 occurrence records for 188 species). The Infomap algorithm was applied using the interactive web application “INFOMAP BIOREGIONS” and the distance‐based clustering was based on unweighted pair‐group method using arithmetic averages (UPGMA). To identify climate regions we used principal components analysis and a model‐based cluster analysis both based on 15 climatic variables as well as a terrain ruggedness index.ResultsThe Infomap algorithm detected nine biogeographical units: seven bioregions and two transition zones. The distance‐based method suggested five bioregions. The identified bioregions differed between methods with some consistent spatial patterns across methods. Temperature and precipitation explained 85.8% of the environmental variation. Eight climate regions were identified. In general, climate variation and bioregional patterns are currently poorly represented in PAs (<25% coverage).Main conclusionsThe network‐based method allowed identifying bioregions at regional scale and was apparently more sensitive than the conventional distance‐based method. The detection of transition zones by the Infomap algorithm was an advantage, and stressed the fact that the distribution of Iranian mammalian fauna is complex, especially in the south‐eastern part where contact areas between several bioregions are found. The identified bioregions (especially the distance‐based bioregions) and climate regions tended to match well with previous bioregionalization studies and the global terrestrial ecoregions. When thoroughly compared and understood, bioregions and climate regions provide a framework for regional biodiversity conservation planning.
NCBP1 promotes the development of lung adenocarcinoma through up‐regulation of CUL4B
Authors: Zhang Huijun , Wang An , Tan Yulong , Wang Shaohua , Ma Qinyun , Chen Xiaofeng , He Zelai 
Published: August 2019

AbstractLung cancer is the most frequent cancer type and is the leading cause of tumour‐associated deaths worldwide. Nuclear cap‐binding protein 1 (NCBP1) is necessary for capped RNA processing and intracellular localization. It has been reported that silencing of NCBP1 resulted in cell growth reduction in HeLa cells. Nevertheless, its clinical significance and underlying molecular mechanisms in non–small‐cell lung cancer remain unclear. In this study, we found that NCBP1 was significantly overexpressed in lung cancer tissues and several lung cancer cell lines. Through knockdown and overexpression experiments, we showed that NCBP1 promoted lung cancer cell growth, wound healing ability, migration and epithelial‐mesenchymal transition. Mechanistically, we found that cullin 4B (CUL4B) was a downstream target gene of NCBP1 in NSCLC. NCBP1 up‐regulated CUL4B expression via interaction with nuclear cap‐binding protein 3 (NCBP3). CUL4B silencing significantly reversed NCBP1‐induced tumorigenesis in vitro. Based on these findings, we propose a model involving the NCBP1‐NCBP3‐CUL4B oncoprotein axis, providing novel insight into how CUL4B is activated and contributes to LUAD progression.
The Clinical Course after Long‐Term Acute Care Hospital Admission among Older Medicare Beneficiaries
Authors: Makam Anil N. , Tran Thu , Miller Michael E. , Xuan Lei , Nguyen Oanh Kieu , Halm Ethan A. 
Published: August 2019

ObjectivesLong‐term acute care (LTAC) hospitals provide extended complex post–acute care to more than 120 000 Medicare beneficiaries annually, with the goal of helping patients to regain independence and recover. Because little is known about patients’ long‐term outcomes, we sought to examine the clinical course after LTAC admission.DesignNationally representative 5‐year cohort study using 5% Medicare data from 2009 to 2013.SettingLTAC hospitals.ParticipantsHospitalized Medicare fee‐for‐service beneficiaries 65 years of age or older who were transferred to an LTAC hospital.MeasurementsMortality, recovery (defined as achieving 60 consecutive days alive without inpatient care), time spent in an inpatient facility following LTAC hospital admission, receipt of an artificial life‐prolonging procedure (feeding tube, tracheostomy, hemodialysis), and palliative care physician consultation.ResultsOf 14 072 hospitalized older adults transferred to an LTAC hospital, median survival was 8.3 months, and 1‐ and 5‐year survival rates were 45% and 18%, respectively. Following LTAC admission, 53% never achieved a 60‐day recovery. The median time of their remaining life a patient spent as an inpatient after LTAC admission was 65.6% (interquartile range = 21.4%‐100%). More than one‐third (36.9%) died in an inpatient setting, never returning home after the LTAC admission. During the preceding hospitalization and index LTAC admission, 30.9% received an artificial life‐prolonging procedure, and 1% had a palliative care physician consultation.ConclusionHospitalized older adults transferred to LTAC hospitals have poor survival, spend most of their remaining life as an inpatient, and frequently undergo life‐prolonging procedures. This prognostic understanding is essential to inform goals of care discussions and prioritize healthcare needs for hospitalized older adults admitted to LTAC hospitals. Given the exceedingly low rates of palliative care consultations, future research is needed to examine unmet palliative care needs in this population. J Am Geriatr Soc 67:2282–2288, 2019
GBSS‐BINDING PROTEIN, encoding a CBM48 domain‐containing protein, affects rice quality and yield
Authors: Wang Wei , Wei Xiangjin , Jiao Guiai , Chen Wenqiang , Wu Yawen , Sheng Zhonghua , Hu Shikai , Xie Lihong , Wang Jiayu , Tang Shaoqing , Hu Peisong 
Published: August 2019

AbstractThe percentage of amylose in the endosperm of rice (Oryza sativa) largely determines grain cooking and eating qualities. Granule‐bound starch synthase I (GBSSI) and GBSSII are responsible for amylose biosynthesis in the endosperm and leaf, respectively. Here, we identified OsGBP, a rice GBSS‐binding protein that interacted with GBSSI and GBSSII in vitro and in vivo. The total starch and amylose contents in osgbp mutants were significantly lower than those of wild type in leaves and grains, resulting in reduced grain weight and quality. The carbohydrate‐binding module 48 (CBM48) domain present in the C‐terminus of OsGBP is crucial for OsGBP binding to starch. In the osgbp mutant, the extent of GBSSI and GBSSII binding to starch in the leaf and endosperm was significantly lower than wild type. Our data suggest that OsGBP plays an important role in leaf and endosperm starch biosynthesis by mediating the binding of GBSS proteins to developing starch granules. This elucidation of the function of OsGBP enhances our understanding of the molecular basis of starch biosynthesis in rice and contributes information that can be potentially used for the genetic improvement of yield and grain quality.
Placental mesenchymal dysplasia with a good outcome: A case report
Authors: Oide Shiho , Kuwata Tomoyuki , Wang Liangcheng , Imai Ken , Chikazawa Kenro , Takagi Kenjiro 
Published: August 2019

AbstractPlacental mesenchymal dysplasia (PMD), characterized by an enlarged and thickened placenta with multiple hypoechoic cystic spaces, frequently leads to a poor infantile/fetal outcome. Here, we describe a case of PMD involving an infant delivered at term with a good outcome. The fetus was male, and the proportion of the PMD lesion to the entire placenta remained constant: the PMD lesion did not enlarge. Given what is known about the pathogenesis of PMD with its association with vascular endothelial growth factor‐D (VEGF‐D) encoded by an X‐linked gene and androgenetic/biparental mosaicism, which is consistent with female dominancy and a poor outcome, we suggest that a male sex of the fetus and non‐progressing PMD may have been associated with this good outcome.
Bronchiolitis at a specialist paediatric centre: The electronic medical record helps to evaluate low‐value care
Authors: Lawrence Joanna G , Andrew Lauren , Bracken Jenny , Voskoboynik Alice , Oakley Ed , South Mike , Middleton Katherine , Scanlan Barry , Marshall Tim , Hiscock Harriet 
Published: August 2019

AimLow‐value care (LVC) is common. We aimed, using infants presenting to a major tertiary paediatric hospital with bronchiolitis between April 2016 and July 2018, to: (i) assess rates of chest X‐ray (CXR) and medication use; (ii) identify associated factors; and (iii) measure the harm of not performing these practices.MethodsWe extracted data from the electronic medical record for all children aged 1–12 months given a diagnosis of bronchiolitis in the emergency department. Factors potentially associated with LVC practices were extracted, including patient demographics, ordering physician characteristics, order indication, medications prescribed and admission ward. To assess for harm, a radiologist, blinded to CXR indication, reviewed all CXRs ordered over the winter of 2017 for infants with bronchiolitis.ResultsA CXR was ordered for 439 (11.2%) infants, most commonly to rule out consolidation and collapse (65%). CXRs were more likely to be ordered for admitted infants (40.9% admitted to the general medical ward), and 62% were ordered by emergency department staff. Salbutamol was prescribed for 9.3% (n = 199). Amongst those who had a CXR, 28% were prescribed an antibiotic compared to 2.1% for those who did not. In an audit of 98 CXRs ordered over the winter of 2017, there were no CXR findings that meaningfully affected patient outcomes.ConclusionUsing electronic medical record data, we found that CXR and medication use in bronchiolitis were higher than expected given our hospital guideline advice. Future research needs to understand why and develop interventions to reduce LVC.
USF2 enhances the osteogenic differentiation of PDLCs by promoting ATF4 transcriptional activities
Authors: Liu Fan , Wang Xiaohong , Zheng Bowen , Li Danni , Chen Cen , Lee In‐seop , Zhong Jialin , Li Duo , Liu Yi 
Published: August 2019

AbstractObjectiveOur study aimed to elucidate the regulatory molecules related to the osteogenic differentiation of periodontal ligament cells (PDLCs).BackgroundPeriodontal ligament cells are a favorable source for cell‐based therapy in periodontal bone engineering and regeneration due to their potential multilineage differentiation ability. However, the molecular mechanism and signaling pathways related to the osteogenic differentiation of PDLCs are still unclear.MethodsOsteoblast‐specific protein expression levels were examined by ELISA in osteogenic‐induced PDLCs (induced‐PDLC group). A microarray assay and a bioinformatics analysis were carried out to reveal significantly expressed genes and the related pathways in induced‐PDLCs, and these findings were then confirmed by qRT‐PCR and a luciferase reporter assay. Finally, overexpressing and silencing gene systems were established to identify the specific transcriptional relationship and function of the target genes on the osteogenic differentiation of PDLCs.ResultsOsteogenically differentiated PDLCs with high levels of osteoblast‐specific proteins were established. The upstream stimulatory factor 2 (USF2) and activating transcription factor 4 (ATF4) mRNA levels were upregulated the most through the MAPK signaling pathway in the induced‐PDLC group. USF2 could bind to the transcriptional initiation region of ATF4 and regulate its transcriptional activities. Additionally, the overexpression of USF2 promoted osteoblast‐specific gene expression and the Alizarin red staining of PDLCs, while simultaneously overexpressing USF2 and silencing ATF4 reversed the favorable osteogenic effect of the induced‐PDLCs by reducing osteoblast‐specific gene expression and the Alizarin red staining level.ConclusionOur study demonstrated that USF2 could enhance the osteogenic differentiation of PDLCs by regulating ATF4 transcriptional activities, which provides a new strategy to utilize USF2 and ATF4 as potential target molecules for periodontal bone regeneration.
Evaluation of a hepatitis C virus core antigen assay from venepuncture and dried blood spot collected samples: A cohort study
Authors: Catlett Beth , Lamoury Francois M. J. , Bajis Sahar , Hajarizadeh Behzad , Martinez Danica , Mowat Yasmin , Cunningham Philip H. , Jacka Brendan P. , Cloherty Gavin A , Marks Philippa , Dore Gregory J. , Grebely Jason , Applegate Tanya L. 
Published: August 2019

AbstractThe global scale‐up of hepatitis C virus (HCV) diagnosis requires simplified and affordable HCV diagnostic pathways. This study evaluated the sensitivity and specificity of the HCV Architect core antigen (HCVcAg) assay for detection of active HCV infection in plasma and capillary whole blood dried blood spots (DBS) compared with HCV RNA testing in plasma (Abbott RealTime HCV Viral Load). Samples were collected from participants in an observational cohort enrolled at three sites in Australia (two‐drug treatment and alcohol clinics and one homelessness service). Of 205 participants, 200 had results across all samples and assay types and 186 were included in this analysis (14 participants receiving HCV therapy were excluded). HCV RNA was detected in 29% of participants ([95% CI: 22.6‐36.1], 54 of 186). The sensitivity of HCVcAg for detection of active HCV infection in plasma was 98.1% (95% CI: 90‐100) and 100% (95% CI: 93‐100) when compared to HCV RNA thresholds of ≥12 and ≥1000 IU/mL, respectively. The sensitivity of the HCVcAg assay for detection of active HCV infection in DBS was 90.7% (95% CI: 80‐97) and 92.5% (95% CI: 82‐98) when compared to HCV RNA thresholds of ≥12 and ≥1000 IU/mL, respectively. The specificity of HCV core antigen for detection of active infection was 100% (95% CI: 97‐100) for all samples and RNA thresholds. These data indicate that the detection of HCVcAg is a useful tool for determining active HCV infection; to facilitate enhanced testing, linkage to care and treatment particularly when testing plasma samples are collected by venepuncture.
Consistent high prevalence of undiagnosed blood‐borne virus infection in patients attending large urban emergency departments in England
Authors: Hopkins Mark J. , Todd Stacy , Beadsworth Mike , Anderson Charlotte , Mohamed Zameer , Muir David , Vivancos Roberto , Brown Ashley S. , Ruf Murad , Chawla Anu 
Published: August 2019

AbstractUnderstanding local viral hepatitis and HIV epidemiology is essential if WHO elimination targets are to be achieved. We demonstrate a consistently high prevalence of undiagnosed active infection in urban emergency department attendees in England, with variations in local risk groups crucial to informing targeted testing initiatives.
Comparative study of nutritional mode and mycorrhizal fungi in green and albino variants of Goodyera velutina, an orchid mainly utilizing saprotrophic rhizoctonia
Authors: Suetsugu Kenji , Yamato Masahide , Matsubayashi Jun , Tayasu Ichiro 
Published: August 2019

AbstractThe majority of chlorophyllous orchids form mycorrhizal associations with so‐called rhizoctonia fungi, a phylogenetically heterogeneous assemblage of predominantly saprotrophic fungi in Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae. It is still a matter of debate whether adult orchids mainly associated with rhizoctonia species are partially mycoheterotrophic. Here, we investigated the nutritional modes of green and albino variants of Goodyera velutina, an orchid species considered to be mainly associated with Ceratobasidium spp., by measuring their 13C and 15N abundances, and by molecular barcoding of their mycorrhizal fungi. Molecular analysis revealed that both green and albino variants of G. velutina harbored a similar range of mycobionts, mainly saprotrophic Ceratobasidium spp., Tulasnella spp., and ectomycorrhizal Russula spp. In addition, stable isotope analysis revealed that albino variants were significantly enriched in 13C but not so greatly in 15N, suggesting that saprotrophic Ceratobasidium spp. and Tulasnella spp. are their main carbon source. However, in green variants, 13C levels were depleted and those of 15N were indistinguishable from the co‐occurring autotrophic plants. Therefore, we concluded that the albino G. velutina variants are fully mycoheterotrophic plants whose C derives mainly from saprotrophic rhizoctonia, while the green G. velutina variants are mainly autotrophic plants, at least at our study site, in spite of their additional associations with ectomycorrhizal fungi. This is the first report demonstrating that adult nonphotosynthetic albino variants can obtain their nutrition mainly from nonectomycorrhizal rhizoctonia.
Broad learning for nonparametric spatial modeling with application to seismic attenuation
Authors: Kuok Sin‐Chi , Yuen Ka‐Veng 
Published: August 2019

AbstractSpatial modeling is a core element in geographical information science. It incorporates geographic information to construct the relationship for interpreting the behavior of spatial phenomena. In this paper, a broad learning framework for nonparametric spatial modeling is presented. Broad learning overcomes the obstacle of expensive computational consumption in deep learning and provides a powerful computationally efficient alternative. In contrast to the deep learning architecture that is configured with stacks of hierarchical layers, broad learning networks are established in a flat manner that can be flexibly reconfigured with the inherited information from the trained network. To develop the broad learning network, a simple prototype network is established as the initial trial and it is modified incrementally to enhance its data fitting capacity. Consequently, complex relationship of unstructured spatial data can be modeled efficiently. To demonstrate the efficacy and applicability of the broad learning framework, we will present a simulated example and a real application using the strong ground motion records on the 2008 great Wenchuan earthquake.
Periocular infantile hemangiomas: Characteristics, ocular sequelae, and outcomes
Authors: Zhao Jiawei , Huang Amy H. , Rainer Barbara M. , Kryatova Maria S. , Eghrari Allen O. , Wang Jiangxia , Puttgen Katherine B. , Cohen Bernard A. 
Published: August 2019

AbstractObjectivesTo identify clinical factors associated with complications of periocular infantile hemangioma (IH) and monitor improvement in complication rates post‐treatment.MethodsRetrospective cohort study. Eighty‐nine patients diagnosed with periocular IH at a pediatric dermatology clinic of a tertiary care center between 2001 and 2013 were included with parental approval. Parents were interviewed by telephone between July and September of 2015, then again in January 2018 to inquire about ophthalmologic follow‐up. Electronic medical records were reviewed from January 2001 through January 2018.ResultsSixty percent of patients demonstrated ocular sequelae, including astigmatism (33%), visual axis obstruction (29%), nasolacrimal duct obstruction (7%), ptosis (4%), amblyopia (3%), and strabismus (1%). Compared with superficial IH, deep and mixed IH had higher odds, 3.4 (P = 0.025) and 3.8 (P = 0.034), respectively, of developing ocular sequelae. All patients with astigmatism prior to involution of IH received systemic therapy, with a significant post‐treatment decrease in the proportion of patients with astigmatism (40% to 18%, P = 0.027). Three‐quarters of patients experienced complete IH involution by time of enrollment in kindergarten. Fifty‐one (57.3%) patients received formal ophthalmologic evaluation confirmed through chart review or phone interview, with average follow‐up duration of 51.2 months (range: 1.9, 99.3).ConclusionDeep and mixed IH were more likely to demonstrate ocular complications than superficial IH. Rate of astigmatism decreased with systemic therapy. Our study suggests that patients with periocular IH have a lower rate of amblyopia now compared with the prepropranolol era and emphasizes the importance of early treatment of periocular IH to prevent permanent visual sequelae.
Inclusion of Time-Varying Covariates in Cure Survival Models with an Application in Fertility Studies
Authors: Lambert Philippe , Bremhorst Vincent 
Published: August 2019

SummaryCure survival models are used when we desire to acknowledge explicitly that an unknown proportion of the population studied will never experience the event of interest. An extension of the promotion time cure model enabling the inclusion of time-varying covariates as regressors when modelling (simultaneously) the probability and the timing of the monitored event is presented. Our proposal enables us to handle non-monotone population hazard functions without a specific parametric assumption on the baseline hazard. This extension is motivated by and illustrated on data from the German Socio-Economic Panel by studying the transition to second and third births in West Germany.
A Hidden Semi-Markov Model for Characterizing Regime Shifts in Ocean Density Variability
Authors: Economou Theodoros , Menary Matthew B. 
Published: August 2019

SummarySocietally important decadal predictions of temperature and precipitation over Europe are largely affected by variability in the North Atlantic Ocean. Within this region, the Labrador Sea is of particular importance because of its link between surface-driven density variability and the Atlantic meridional overturning circulation. Using physical justifications, we propose a statistical model to describe the temporal variability of ocean density in terms of salinity-driven and temperature-driven density. This is a hidden semi-Markov model that allows for either a salinity-driven or a temperature-driven ocean density regime, such that the persistence in each regime is governed probabilistically by a semi-Markov chain. The model is fitted in the Bayesian framework, and a reversible jump Markov chain Monte Carlo algorithm is proposed to deal with a single-regime scenario. The model is first applied to a reanalysis data set, where model checking measures are also proposed. Then it is applied to data from 43 climate models to investigate whether and how ocean density variability differs between them and also the reanalysis data. Parameter estimates relating to the mean holding time for each regime are used to establish a link between regime behaviour and the Atlantic meridional overturning circulation.