bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines
Authors: Dutil Julie , Chen Zhihua , Monteiro Alvaro N. , Teer Jamie K. , Eschrich Steven A. 
Published: March 2019

Abstract
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.
The Critical Role of RNA m6A Methylation in Cancer
Authors: Lan Qing , Liu Pei Y. , Haase Jacob , Bell Jessica L. , Hüttelmaier Stefan , Liu Tao 
Published: March 2019

Abstract
Since the identification of the first RNA demethylase and the establishment of methylated RNA immunoprecipitation-sequencing methodology 6 to 7 years ago, RNA methylation has emerged as a widespread phenomenon and a critical regulator of transcript expression. This new layer of regulation is termed “epitranscriptomics.” The most prevalent RNA methylation, N6-methyladenosine (m6A), occurs in approximately 25% of transcripts at the genome-wide level and is enriched around stop codons, in 5′- and 3′-untranslated regions, and within long internal exons. RNA m6A modification regulates RNA splicing, translocation, stability, and translation into protein. m6A is catalyzed by the RNA methyltransferases METTL3, METTL14, and METTL16 (writers), is removed by the demethylases FTO and ALKBH5 (erasers), and interacts with m6A-binding proteins, such as YTHDF1 and IGF2BP1 (readers). RNA methyltransferases, demethylases, and m6A-binding proteins are frequently upregulated in human cancer tissues from a variety of organ origins, increasing onco-transcript and oncoprotein expression, cancer cell proliferation, survival, tumor initiation, progression, and metastasis. Although RNA methyltransferase inhibitors are not available yet, FTO inhibitors have shown promising anticancer effects in vitro and in animal models of cancer. Further screening for selective and potent RNA methyltransferase, demethylase, or m6A-binding protein inhibitors may lead to compounds suitable for future clinical trials in cancer patients.
An overlooked hotspot for birds in the Atlantic Forest
Authors: Cavarzere Vagner , Albano Ciro , Tonetti Vinicius Rodrigues , Pacheco José Fernando , Whitney Bret M. , Silveira Luís Fábio 
Published: March 2019

Montane and submontane forest patches in the state of Bahia, Brazil, are among the few large and preserved Atlantic Forests remnants. They are strongholds of an almost complete elevational gradient, which harbor both lowland and highland bird taxa. Despite being considered a biodiversity hotspot, few ornithologists have surveyed these forests, especially along elevational gradients. Here we compile bird records acquired from systematic surveys and random observations carried out since the 1980s in a 7,500 ha private protected area: Serra Bonita private reserve. We recorded 368 species, of which 143 are Atlantic Forest endemic taxa. Some 16 and 13 species are threatened at the global and national levels, respectively. If one accounts for subspecies, the number of Brazilian threatened taxa raises to 21. Species composition differs between lower and higher elevations, in which case lowlands harbor Amazonia-related taxa, whereas highlands are the home of Atlantic Forest-related taxa.
Belostomatidae (Heteroptera: Nepomorpha) held in the Invertebrate Collection of the Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil: inventory and new distributional records
Authors: Almeida Thaís Melo de , Stefanello Fabiano , Hamada Neusa 
Published: March 2019

Belostomatidae is a family of giant water bugs with 52 valid species in Brazil. Here, we list 33 valid species housed in the Invertebrates Collection of the Instituto Nacional de Pesquisas da Amazônia – INPA, Manaus, Brazil. Of the total species examined, 26 had their distributional ranges increased (new records provided in parentheses): Belostoma amazonum Estévez & Polhemus (Mato Grosso and Roraima); B. aurivillianum (Montandon) (Rondônia); B. bosqi De Carlo (Maranhão); B. candidulum Montandon (Mato Grosso do Sul); B. carajaensis Ribeiro & Estévez (Amazonas); B. dallasi De Carlo (Bahia and Pará); B. dentatum (Mayr) (Roraima); B. denticolle Montandon (Roraima); B. dilatatum (Dufour) (Maranhão); B. discretum Montandon (Rio Grande do Sul); B. elongatum Montandon (Paraná); B. estevezae Ribeiro & Alecrim (Amazonas); B. fittkaui De Carlo (Roraima); B. gestroi Montandon (Pará); B. guianae Lauck (Brazil, in Roraima); B. micantulum (Stål) (Maranhão, Rio Grande do Norte, Rondônia and Roraima); B. minusculum (Uhler) (Brazil, in Amazonas, Pará and Rio Grande do Norte); B. parvum Estévez & Polhemus (Amazonas and Roraima); B. plebejum (Stål) (Roraima); B. pygmeum (Dufour) (Pará); B. ribeiroi De Carlo (Mato Grosso do Sul); B. stollii (Amyot & Serville) (Roraima); Horvathinia pelocoroides Montandon (Rondônia); Lethocerus annulipes (Herrich-Schaeffer) (Maranhão, Paraíba and Paraná); L. delpontei De Carlo (Amazonas and Pará) and L. maximus De Carlo (Acre, Amapá, Amazonas and Roraima). In addition, we provide a list of type and non-type specimens of Belostomatidae from INPA’s collection identified to the species level, photographs of these species and relevant taxonomic notes, when available.
A new peculiar isometopine genus (Hemiptera: Heteroptera: Miridae) from the Eocene Baltic amber
Authors: HERCZEK ALEKSANDER , POPOV YURI A. 
Published: March 2019

This joint article should be considered as a continuation of a series of publications on fossil mirids from the Baltic amber (Prussian Formation). Miridae, or plant bugs, are the largest family of contemporary true bugs (Heteroptera) widespread all over the world, with about 1,500 genera and over 10,000 species (Schuh 1995, Kerzhner & Josifov 1999). Recent Isometopinae is a relatively small subfamily including about 190 species, strongly cryptic in habits and rare in world collections. Some are predaceous and may hunt soft-bodied, mostly aphids and scale insects. Most inclusions of fossil plant bugs are usually found in the Eocene Baltic amber, where mirids are mainly represented by the subfamilies Cylapinae, Isometopinae, and Mirinae (Popov & Herczek 2008). These fossil insects were rather scarce only in the first years of their discovery (Popov & Herczek 1992, 1993; Herczek 1993). Judging from the described and undescribed of Baltic amber mirids known to us just now, the isometopinae are not so rare among other fossil mirids and provide evidence for a considerable diversity at least since Eocene time.
On the Relative Sensitivity of a Tropical Deep Convective Storm to Changes in Environment and Cloud Microphysical Parameters
Authors: Posselt Derek J. , He Fei , Bukowski Jennifer , Reid Jeffrey S. 
Published: March 2019

Abstract
Monte Carlo and Morris screening techniques are used to examine the relative sensitivity of deep convective simulations to changes in initial conditions (IC) versus changes to microphysical parameters (MP). IC are perturbed using a set of empirical orthogonal function–principal component pairs obtained from a database of tropical soundings, while MP are perturbed consistent with their range of realistic values. Monte Carlo experiments provide a broad overview of parameter–output response, while Morris screening techniques identify the most significant influences on specific model output variables. Changes to MP produce a similar order-of-magnitude response in convective hydrologic cycle, dynamics, and latent heating as changes to IC. Changes in IC appear to have a larger effect on radiative fluxes than perturbations to MP. The distribution of low-level latent heating reveals that changes in MP have a larger influence on cold pool properties than changes to the environment. The dominant effects are produced by a subset of cloud MP and thermodynamic structure functions, indicating perturbation of a subset of the control factors may be used to produce most of the variability in a short-term convective-scale ensemble forecast. The most influential MP are the autoconversion threshold, the rain particle size distribution intercept, and the ice particle fall speed parameters. The most influential EOFs are those that correspond to variability in lower- to midtropospheric temperature and water vapor, as well as zonal low-level shear. The results have implications for both the understanding of what influences convective development and the design of ensemble-based prediction and data assimilation systems.
Stratospheric Trailing Gravity Waves from New Zealand
Authors: Jiang Qingfang , Doyle James D. , Eckermann Stephen D. , Williams Bifford P. 
Published: March 2019

AbstractGravity waves are frequently observed in the stratosphere, trailing long distances from mid- to high-latitude topography. Two such trailing-wave events documented over New Zealand are examined using observations, numerical simulations, and ray-tracing analysis to explore and document stratospheric trailing-wave characteristics and formation mechanisms. We find that the trailing waves over New Zealand are orographically generated and regulated by several processes, including interaction between terrain and mountaintop winds, critical-level absorption, and lateral wave refraction. Among these, the interaction between topography and low-level winds determines the perturbation energy distribution over horizontal scales and directions near the wave source, and accordingly, trailing waves are sensitive to terrain features and low-level winds. Terrain-forced wave modes are filtered by absorption associated with directional wind shear and Jones critical levels. The former plays a role in defining wave-beam orientation, and the latter sets an upper limit for the permissible horizontal wavelength of trailing waves. On propagating into the stratosphere, these orographic gravity waves are subject to horizontal refraction associated with the meridional shear in the stratospheric westerlies, which tends to elongate the wave beams pointing toward stronger westerlies and shorten the wave beams on the opposite side.
Hydrological Responses of Headwater Basins to Monthly Perturbed Climate in the North American Cordillera
Authors: Rasouli Kabir , Pomeroy John W. , Whitfield Paul H. 
Published: March 2019

Abstract
How mountain hydrology at different elevations will respond to climate change is a challenging question of great importance to assessing changing water resources. Here, three North American Cordilleran snow-dominated basins—Wolf Creek, Yukon; Marmot Creek, Alberta; and Reynolds Mountain East, Idaho—each with good meteorological and hydrological records, were modeled using the physically based, spatially distributed Cold Regions Hydrological Model. Model performance was verified using field observations and found adequate for diagnostic analysis. To diagnose the effects of future climate, the monthly temperature and precipitation changes projected for the future by 11 regional climate models for the mid-twenty-first century were added to the observed meteorological time series. The modeled future was warmer and wetter, increasing the rainfall fraction of precipitation and shifting all three basins toward rainfall–runoff hydrology. This shift was largest at lower elevations and in the relatively warmer Reynolds Mountain East. In the warmer future, there was decreased blowing snow transport, snow interception and sublimation, peak snow accumulation, and melt rates, and increased evapotranspiration and the duration of the snow-free season. Annual runoff in these basins did not change despite precipitation increases, warming, and an increased prominence of rainfall over snowfall. Reduced snow sublimation offset reduced snowfall amounts, and increased evapotranspiration offset increased rainfall amounts. The hydrological uncertainty due to variation among climate models was greater than the predicted hydrological changes. While the results of this study can be used to assess the vulnerability and resiliency of water resources that are dependent on mountain snow, stakeholders and water managers must make decisions under considerable uncertainty, which this paper illustrates.
Evaluation of Catch Efficiency Transfer Functions for Unshielded and Single-Alter-Shielded Solid Precipitation Measurements
Authors: Pierre Amandine , Jutras Sylvain , Smith Craig , Kochendorfer John , Fortin Vincent , Anctil François 
Published: March 2019

AbstractSolid precipitation undercatch can reach 20%–70% depending on meteorological conditions, the precipitation gauge, and the wind shield used. Five catch efficiency transfer functions were selected from the literature to adjust undercatch from unshielded and single-Alter-shielded precipitation gauges for different accumulation periods. The parameters from these equations were calibrated using data from 11 sites with a WMO-approved reference measurement. This paper presents an evaluation of these transfer functions using data from the Neige site, which is located in the eastern Canadian boreal climate zone and was not used to derive any of the transfer functions available for evaluation. Solid precipitation measured at the Neige site was underestimated by 34% and 21% when compared with a manual reference precipitation measurement for unshielded and single-Alter-shielded gauges, respectively. Catch efficiency transfer functions were used to adjust these solid precipitation measurements, but all equations overestimated amounts of solid precipitation by 2%–26%. Five different statistics evaluated the accuracy of the adjustments and the variance of the results. Regardless of the adjustment applied, the catch efficiency for the unshielded gauge increased after the adjustment. However, this was not the case for the single-Alter-shielded gauges, for which the improvement of the results after applying the adjustments was not seen in all of the statistics tests. The results also showed that using calibrated parameters on datasets with similar site-specific characteristics, such as the mean wind speed during precipitation and the regional climate, could guide the choice of adjustment methods. These results highlight the complexity of solid precipitation adjustments.
External validation of CLI Frailty Index and assessment of predictive value of modified CLI Frailty Index for patients with critical limb ischemia undergoing infrainguinal revascularization
Authors: Morisaki Koichi , Furuyama Tadashi , Matsubara Yutaka , Inoue Kentaro , Kurose Shun , Yoshino Shinichiro , Nakayama Ken , Yamashita Sho , Yoshiya Keiji , Yoshiga Ryosuke , Maehara Yoshihiko 
Published: March 2019

Objectives CLI Frailty is a useful diagnostic criterion of frailty in patients with critical limb ischemia (CLI). It is important to evaluate not only comorbidities but also frailty in decision making to select the type of treatment for CLI patients. The purposes of our study were to externally validate the CLI Frailty Index and to evaluate the modified CLI Frailty Index by measurement of skeletal muscle mass using computed tomography. Methods Patients who underwent preoperative computed tomography examination and infrainguinal revascularization between 2002 and 2015 were retrospectively analyzed. A patient was defined as CLI Frailty (+), if two or more of the following criteria were present: low Geriatric Nutritional Risk Index (GNRI), low skeletal muscle mass index (SMI) evaluated by prediction equations, and non-ambulatory status. For the modified CLI Frailty Index, skeletal muscle area was measured by computed tomography instead of prediction equations. Results During the study period, 226 patients with CLI underwent revascularization; we included 127 patients and excluded 99 patients who were treated only with iliac revascularization or did not undergo CT scans. The overall survival at two years after revascularization was 83.6% for the CLI Frailty (−) group versus 63.2% for the CLI Frailty (+) group ( P = .02). The overall survival at two years after revascularization was 89.7% for the modified CLI Frailty (−) group versus 60.5% for the modified CLI Frailty (+) group ( P < .01). Multivariate analysis 1 including CLI Frailty revealed that hemodialysis (HR, 3.71; 95% CI, 1.58–8.83; P < .01), CLI Frailty (HR, 3.22; 95% CI, 1.35–7.47; P < .01) and cerebrovascular disease (HR, 2.58; 95% CI, 1.09–5.91; P = .03) were risk factors for overall survival two years after revascularization. In multivariate analysis 2 including modified CLI Frailty, modified CLI Frailty (HR, 5.92; 95% CI, 2.49–15.7; P < .01), hemodialysis (HR, 4.03; 95% CI, 1.65–10.0; P < .01) and diabetes mellitus (HR, 0.41; 95% CI, 0.16–0.99; P = .05) were risk factors for overall survival two years after revascularization. Conclusions Both the CLI Frailty and the modified CLI Frailty Indexes were useful in predicting the two-year overall survival of patients with CLI after infrainguinal revascularization. Although the measurement of skeletal muscle mass using computed tomography may accurately predict two-year overall survival, SMI prediction is effective for patients with CLI who did not undergo preoperative CT.
A Comprehensive Systematic Review of the Association Between Airway Mucins and Chronic Rhinosinusitis
Authors: Kato Kosuke , Song Brian H. , Howe Carol L. , Chang Eugene H. 
Published: March 2019

ObjectiveAirway mucins are the major constituents of mucus and one of the first lines of host defense against inhaled pathogens. However, aberrant expression of mucins is associated with mucus hypersecretion resulting in chronic nasal drainage, a common complaint from patients with chronic rhinosinusitis (CRS). Our goal in this systematic review was to determine (1) expression profiles, (2) regulatory mechanisms, and (3) the pathologic roles of mucins associated with CRS.MethodsMEDLINE, Cochrane Library, Embase, Scopus, Web of Science, and ClinicalTrials.gov were searched for studies focused on the role of mucins in CRS. Quality was assessed using the Cochrane Risk of Bias tool. The full text articles selected were then categorized into 3 study groups: (1) clinical, (2) animal, and (3) in vitro cultures. Data regarding study design, population/setting, methods, and bias were extracted and synthesized.ResultsOur initial search generated 392 titles/abstracts. After the primary review, 111 articles underwent secondary review. The final review included 53 articles, including 34 articles (64%) in the clinical study group, 3 articles (6%) in the animal study group, and 16 articles (30%) in the in vitro study group. In total, aberrant expression of 8 mucins—6 secreted-mucins (MUC2, -5AC, -5B, -6, -7, and -8) and 2 membrane-bound mucins (MUC1 and -4)—were identified in CRS tissues compared to healthy controls. Mucin expression was associated with bacterial sinusitis, inflammatory markers, and the response to steroid therapy in patients with CRS with nasal polyposis.ConclusionThere is a strong correlation between alterations in mucin expression profiles and CRS. This systematic review highlights the most recent literature on the role of mucins in CRS. The analysis of these studies is limited by the heterogeneity in study designs, relatively few numbers of clinical samples, and lack of mechanistic studies in animal models and in vitro cultures.
Management of musculoskeletal foot and ankle conditions prior to public‐sector orthopaedic referral in South Australia
Authors: Walsh Tom P. , Ferris Linda R. , Cullen Nancy C. , Bourke Jared L. , Cooney Melissa J. , Gooi Chi K. , Brown Christopher H. , Arnold John B. 
Published: March 2019

AbstractBackgroundFoot and ankle pain is common in the Australian adult population. People with musculoskeletal foot and ankle conditions are often referred for surgical opinion, yet how patients are managed prior to referral is largely unknown. The aim of this study was to determine the characteristics and management of patients with musculoskeletal foot and ankle complaints prior to public‐sector orthopaedic referral in South Australia.MethodsPeople with non‐urgent foot or ankle complaints were recruited over a 12‐month period from the waiting‐lists of three tertiary hospitals in Adelaide, Australia. Participants completed a questionnaire on their medical history, duration and location of their foot or ankle complaint, diagnosis of their condition, previous treatment and medical imaging. The Manchester‐Oxford Foot and Ankle Questionnaire, and the EuroQol‐5D‐5 L measured foot/ankle pain severity and health‐related‐quality‐of‐life (HRQoL). Descriptive statistics were generated for sample demographics, medical history and foot/ankle symptoms. Multivariable regressions were used to explore factors associated with foot/ankle pain severity and whether participants considered an operation necessary.ResultsTwo hundred and thirty‐three adults returned questionnaires, with a survey response rate of 38.4% (66.1% female, median age 57.7 years IQR 18.5, BMI 29.3 kg/m2 IQR 8.7). Half of the participants had seen a podiatrist (52.8%), and 36.5% did not see any other health professional prior to orthopaedic referral. Sixty‐five (27.9%) had not yet been given a diagnosis. BMI was positively associated with foot/ankle pain severity (β 0.48, 95% CI 0.05, 0.92), while HRQoL had a negative association (β − 0.31, 95% CI ‐0.45, − 0.18). Participants told by their GP that they may need an operation were significantly more likely to consider surgery necessary (OR 31.41, 95% CI 11.30, 87.35), while older people were less likely (OR 0.94, 95% CI 0.90, 0.98).ConclusionsMore than one‐third of the participants had not accessed allied‐health care prior to specialist orthopaedic referral. Participants may consider their GPs opinion on the necessity of surgery compelling, and most expected to undergo surgery, but many couldn't report their diagnosis. The discordance between the expectation of surgery and historically low surgical conversion rates suggests more work is necessary to improve the management of this group.