bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-Generation Sequencing Identifies Gene Mutations That Are Predictive of Malignancy in Residual Needle Rinses Collected From Fine-Needle Aspirations of Thyroid Nodules
Authors: Fuller Maren Y. , Mody Dina , Hull April , Pepper Kristi , Hendrickson Heather , Olsen Randall 
Published: May 2017

Context.—
Thyroid nodules have a prevalence of approximately 70% in adults. Fine-needle aspiration (FNA) is a minimally invasive, cost-effective, standard method to collect tissue from thyroid nodules for cytologic examination. However, approximately 15% of thyroid FNA specimens cannot be unambiguously diagnosed as benign or malignant.

Objective.—
To investigate whether clinically actionable data can be obtained using next-generation sequencing of residual needle rinse material.

Design.—
A total of 24 residual needle rinse specimens with malignant (n = 6), indeterminate (n = 9), or benign (n = 9) thyroid FNA diagnoses were analyzed in our clinical molecular diagnostics laboratory using next-generation sequencing assays designed to detect gene mutations and translocations that commonly occur in thyroid cancer. Results were correlated with surgical diagnoses and clinical outcomes.

Results.—
Interpretable data were generated from 23 of 24 residual needle rinse specimens. Consistent with its well-known role in thyroid malignancy, BRAF V600E mutations were detected in 4 malignant cases. An NRAS mutation was detected in 1 benign case. No mutations were detected from specimens with indeterminate diagnoses.

Conclusions.—
Our data demonstrate that residual thyroid FNA needle rinses are an adequate source of material for molecular diagnostic testing. Importantly, detection of a mutation implicated in thyroid malignancy was predictive of the final surgical diagnosis and clinical outcome. Our strategy to triage thyroid nodules with indeterminate cytology with molecular testing eliminates the need to perform additional FNA passes into dedicated media or to schedule additional invasive procedures. Further investigation with a larger sample size to confirm the clinical utility of our proposed strategy is underway.
Eumelanin and pheomelanin are predominant pigments in bumblebee (Apidae:Bombus) pubescence
Authors: Polidori Carlo , Jorge Alberto , Ornosa Concepción 
Published: May 2017

BackgroundBumblebees (Hymenoptera: Apidae:Bombus) are well known for their important inter- and intra-specific variation in hair (or pubescence) color patterns, but the chemical nature of the pigments associated with these patterns is not fully understood. For example, though melanization is believed to provide darker colors, it still unknown which types of melanin are responsible for each color, and no conclusive data are available for the lighter colors, including white.MethodsBy using dispersive Raman spectroscopy analysis on 12 species/subspecies of bumblebees from seven subgenera, we tested the hypothesis that eumelanin and pheomelanin, the two main melanin types occurring in animals, are largely responsible for bumblebee pubescence coloration.ResultsEumelanin and pheomelanin occur in bumblebee pubescence. Black pigmentation is due to prevalent eumelanin, with visible signals of additional pheomelanin, while the yellow, orange, red and brown hairs clearly include pheomelanin. On the other hand, white hairs reward very weak Raman signals, suggesting that they are depigmented. Additional non-melanic pigments in yellow hair cannot be excluded but need other techniques to be detected. Raman spectra were more similar across similarly colored hairs, with no apparent effect of phylogeny and both melanin types appeared to be already used at the beginning of bumblebee radiation.DiscussionWe suggest that the two main melanin forms, at variable amounts and/or vibrational states, are sufficient in giving almost the whole color range of bumblebee pubescence, allowing these insects to use a single precursor instead of synthesizing a variety of chemically different pigments. This would agree with commonly seen color interchanges between body segments acrossBombusspecies.
The impact of a pressurized regional sea or global ocean on stresses on Enceladus
Authors: Johnston Stephanie A. , Montési Laurent G. J. 
Published: May 2017

AbstractLiquid water is likely present in the interior of Enceladus, but it is still debated whether this water forms a global ocean or a regional sea and whether the present‐day situation is stable. As the heat flux of Enceladus exceeds most heat source estimates, the liquid water is likely cooling and crystallizing, which results in expansion and pressurization of the sea or ocean. We determine, using an axisymmetric Finite Element Model, the tectonic patterns that pressurization of a regional sea or global ocean might produce at the surface of Enceladus. Tension is always predicted above where the ice is thinnest and generates cracks that might be at the origin of the Tiger Stripes. Tectonic activity is also expected in an annulus around the sea if the ice shell is in contact with but slips freely along the rocky core of the satellite. Cracks at the north pole are expected if the shell slips along the core or if there is a global ocean with thin ice at the pole. Water is likely injected along the base of the ice when the shell is grounded, which may lead to cycles of tectonic activity with the shell alternating between floating and grounded states and midlatitude faulting occurring at the transition from a grounded to a floating state.
Approach for estimating the dynamic physical thresholds of phytoplankton production and biomass in the tropical‐subtropical Pacific Ocean
Authors: Gómez‐Ocampo E. , Gaxiola‐Castro G. , Durazo Reginaldo 
Published: May 2017

AbstractThreshold is defined as the point where small changes in an environmental driver produce large responses in the ecosystem. Generalized additive models (GAMs) were used to estimate the thresholds and contribution of key dynamic physical variables in terms of phytoplankton production and variations in biomass in the tropical‐subtropical Pacific Ocean off Mexico. The statistical approach used here showed that thresholds were shallower for primary production than for phytoplankton biomass (pycnocline < 68 m and mixed layer < 30 m versus pycnocline < 45 m and mixed layer < 80 m) but were similar for absolute dynamic topography and Ekman pumping (ADT < 59 cm and EkP > 0 cm d−1 versus ADT < 60 cm and EkP > 4 cm d−1). The relatively high productivity on seasonal (spring) and interannual (La Niña 2008) scales was linked to low ADT (45–60 cm) and shallow pycnocline depth (9–68 m) and mixed layer (8–40 m). Statistical estimations from satellite data indicated that the contributions of ocean circulation to phytoplankton variability were 18% (for phytoplankton biomass) and 46% (for phytoplankton production). Although the statistical contribution of models constructed with in situ integrated chlorophyll a and primary production data was lower than the one obtained with satellite data (11%), the fits were better for the former, based on the residual distribution. The results reported here suggest that estimated thresholds may reliably explain the spatial‐temporal variations of phytoplankton in the tropical‐subtropical Pacific Ocean off the coast of Mexico.
New capillary number definition for displacement of residual nonwetting phase in natural fractures
Authors: AlQuaimi B. I. , Rossen W. R. 
Published: May 2017

AbstractWe propose a new capillary number for flow in fractures starting with a force balance on a trapped ganglion in a fracture. The new definition is validated with laboratory experiments using five distinctive model fractures. Capillary desaturation curves were generated experimentally using water‐air forced imbibition. The residual saturation‐capillary number relationship obtained from different fractures, which vary in aperture and roughness, can be represented approximately by a single curve in terms of the new definition of the capillary number. They do not fit a single trend using the conventional definition of the capillary number.
New insights into saline water evaporation from porous media: Complex interaction between evaporation rates, precipitation, and surface temperature
Authors: Shokri‐Kuehni Salomé M. S. , Vetter Thomas , Webb Colin , Shokri Nima 
Published: May 2017

AbstractUnderstanding salt transport and deposition patterns during evaporation from porous media is important in many engineering and hydrological processes such as soil salinization, ecosystem functioning, and land‐atmosphere interaction. As evaporation proceeds, salt concentration increases until it exceeds solubility limits, locally, and crystals precipitate. The interplay between transport processes, crystallization, and evaporation influences where crystallization occurs. During early stages, the precipitated salt creates an evolving porous structure affecting the evaporation kinetics. We conducted a comprehensive series of experiments to investigate how the salt concentration and precipitation influence evaporation dynamics. Our results illustrate the contribution of the evolving salt crust to the evaporative mass losses. High‐resolution thermal imaging enabled us to investigate the complex temperature dynamics at the surface of precipitated salt, providing further confirmation of salt crust contribution to the evaporation. We identify different phases of saline water evaporation from porous media with the corresponding dominant mechanisms in each phase and extend the physical understanding of such processes.
Decoding ice sheet behavior using englacial layer slopes
Authors: Holschuh Nicholas , Parizek Byron R. , Alley Richard B. , Anandakrishnan Sridhar 
Published: May 2017

AbstractThe complex flow fields of the Antarctic and Greenland ice sheets deform layers deposited as snow at the ice sheet surface, leaving a record of the regional flow history and/or local transitions in basal boundary conditions within the geometry of ice sheet layers. Ice‐penetrating radar reveals these layers, but radar data interpretations are limited by the challenges of quantitatively and reproducibly comparing observations with model output. We present a conceptual framework that relates along‐track reflector slope to gradients in the steady state velocity field of ice sheets. This method makes effective use of englacial reflectors in regions where it is challenging to image continuous layers and avoids the error propagation inherent to tracer‐transport methods, developing the potential for formal radar data assimilation in future modeling studies. We apply our method to radar data collected at the grounding line of Whillans Ice Stream, where enhanced bed friction produces characteristic reflector slopes reproducible using a higher‐order ice flow model.
Depth dependence of the frictional behavior of montmorillonite fault gouge: Implications for seismicity along a décollement zone
Authors: Mizutani Tomoyo , Hirauchi Ken‐ichi , Lin Weiren , Sawai Michiyo 
Published: May 2017

AbstractTo understand the seismogenic potential of shallow plate‐boundary thrust faults (décollements) in relatively warm subduction zones, water‐saturated Na‐montmorillonite gouges were sheared at a pore fluid pressure of 10 MPa, effective normal stresses (σneff) of 10–70 MPa, temperatures (T) of 25–150°C, and axial displacement rates of 0.03–3 μm/s. The Na‐montmorillonite gouges were frictionally very weak at all conditions tested (steady state friction coefficient μss = 0.05–0.09). At T ≤ 60°C, Na‐montmorillonite showed a transition from velocity‐strengthening to velocity‐weakening behavior with increasing σneff, whereas at T ≥ 90°C it was largely velocity neutral or velocity strengthening, irrespective of σneff. The rates of frictional healing (β) showed extremely low values (mostly <0.001) at all temperatures. Our results suggest that the existence of Na‐montmorillonite in the décollement zone at Costa Rica and Nankai promotes aseismic slip, particularly at shallow depths, forming weakly coupled regions.
Intense deformation field at oceanic front inferred from directional sea surface roughness observations
Authors: Rascle Nicolas , Molemaker Jeroen , Marié Louis , Nouguier Frédéric , Chapron Bertrand , Lund Björn , Mouche Alexis 
Published: May 2017

AbstractFine‐scale current gradients at the ocean surface can be observed by sea surface roughness. More specifically, directional surface roughness anomalies are related to the different horizontal current gradient components. This paper reports results from a dedicated experiment during the Lagrangian Submesoscale Experiment (LASER) drifter deployment. A very sharp front, 50 m wide, is detected simultaneously in drifter trajectories, sea surface temperature, and sea surface roughness. A new observational method is applied, using Sun glitter reflections during multiple airplane passes to reconstruct the multiangle roughness anomaly. This multiangle anomaly is consistent with wave‐current interactions over a front, including both cross‐front convergence and along‐front shear with cyclonic vorticity. Qualitatively, results agree with drifters and X‐band radar observations. Quantitatively, the sharpness of roughness anomaly suggests intense current gradients, 0.3 m s−1 over the 50 m wide front. This work opens new perspectives for monitoring intense oceanic fronts using drones or satellite constellations.
Seasonally transported aerosol layers over southeast Atlantic are closer to underlying clouds than previously reported
Authors: Rajapakshe Chamara , Zhang Zhibo , Yorks John E. , Yu Hongbin , Tan Qian , Meyer Kerry , Platnick Steven , Winker David M. 
Published: May 2017

AbstractFrom June to October, low‐level clouds in the southeast (SE) Atlantic often underlie seasonal aerosol layers transported from African continent. Previously, the Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) 532 nm lidar observations have been used to estimate the relative vertical location of the above‐cloud aerosols (ACA) to the underlying clouds. Here we show new observations from NASA's Cloud‐Aerosol Transport System (CATS) lidar. Two seasons of CATS 1064 nm observations reveal that the bottom of the ACA layer is much lower than previously estimated based on CALIPSO 532 nm observations. For about 60% of CATS nighttime ACA scenes, the aerosol layer base is within 360 m distance to the top of the underlying cloud. Our results are important for future studies of the microphysical indirect and semidirect effects of ACA in the SE Atlantic region.
On the asymmetry of the urban daily air temperature cycle
Authors: Wang Kai , Li Yuguo , Wang Yi , Yang Xinyan 
Published: May 2017

AbstractThe asymmetry phenomenon in daily temperature cycle refers to the smaller and decreasing diurnal temperature range, which resulted from much faster rise of the daily minimum temperature than that of the maximum temperature. The asymmetry is known to have occurred in greater magnitude in cities than rural sites. Spatially, the diurnal temperature range is much smaller in urban areas than in the surrounding rural areas. Temporally, the urban diurnal temperature range decreases much faster than that in the rural areas. Here, we demonstrate a new approach in understanding the spatial and temporal asymmetries in the urban daily air temperature cycle. Both asymmetries can be explained by a simple combination of a reduction in amplitudes with a rise in mean temperature, which are governed by difference factors. Our study provides new insights that increase our understanding of the mechanisms of urban warming.
Lags in hydrologic recovery following an extreme drought: Assessing the roles of climate and catchment characteristics
Authors: Yang Yuting , McVicar Tim R. , Donohue Randall J. , Zhang Yongqiang , Roderick Michael L. , Chiew Francis H.S. , Zhang Lu , Zhang Junlong 
Published: May 2017

AbstractDrought, generally characterized by below‐average water supply, propagates through the hydrologic system with consequent ecological and societal impacts. Compared with other drought aspects, the recovery of drought especially in the hydrological components, which directly relates to the recovery of water resources for agricultural, ecological and human needs, is less‐understood. Here, taking the Millennium drought in southeast Australia (∼1997–2009) as an illustrating case, we comprehensively examined multiple aspects of the meteorological (i.e., precipitation) and hydrological (i.e., streamflow and base flow) droughts across 130 unimpaired catchments using long‐term hydro‐meteorological observations. Results show that the duration and intensity of the meteorological drought are both lengthened and amplified in the hydrological drought, suggesting a nonstationarity in the rainfall‐runoff relationship during a prolonged drought. Additionally, we find a time lag commonly exists between the end of the meteorological droughts and the end of the hydrological drought, with the recovery of base flow showing a longer lag than the recovery of streamflow. The recovery rate of precipitation after drought was found to be the dominant factor that controls the recovery of hydrological droughts while catchment landscape (i.e., valley bottom flatness) plays an important but secondary role in controlling the lags in the hydrological recovery. Other hydro‐climatic factors and catchment properties appear to have only minor influences governing hydrological drought recovery. Our findings highlight a delayed response in the terrestrial components of the hydrological cycle to precipitation after prolonged drought, and provide valuable scientific guidance to water resources management and water security assessment in regions facing future droughts.
Delays to Care in Pediatric Lupus Patients: Data From the Childhood Arthritis and Rheumatology Research Alliance Legacy Registry
Authors: Rubinstein Tamar B. , Mowrey Wenzhu B. , Ilowite Norman T. , Wahezi Dawn M. ,   the Childhood Arthritis and Rheumatology Research Alliance INVESTIGATORS
Published: May 2017

ObjectivePrompt treatment for lupus is important to prevent morbidity. A potential barrier to early treatment of pediatric lupus is delayed presentation to a pediatric rheumatologist. To better understand factors contributing to delayed presentation among pediatric lupus patients, we examined differences in demographic and clinical characteristics of lupus patients within the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Legacy Registry with regard to time between symptom onset and presentation to a pediatric rheumatologist.MethodsWe analyzed data from 598 CARRA Legacy Registry participants for differences between those who presented early (within <1 month of symptom onset), between 1–3 months (typical presentation), with moderate delays (3–12 months), and with severe delays (≥1 year). Factors associated with early presentation, moderate delay, and severe delay were determined by multinomial logistic regression.ResultsForty‐four percent of patients presented early, while 23% had moderate delays and 9% had severe delays. Family history of lupus, absence of discoid rash, and location in a state with a higher density of pediatric rheumatologists were associated with earlier presentation. Younger age, low household income (<$25,000 per year), and a family history of lupus were associated with severe delay.ConclusionDelays to care ≥1 year exist in a notable minority of pediatric lupus patients from the CARRA Legacy Registry. In this large and diverse sample of patients, access to care and family resources played an important role in predicting time to presentation to a pediatric rheumatologist.
Association Between Metabolic Syndrome and Radiographic Hand Osteoarthritis: Data From a Community‐Based Longitudinal Cohort Study
Authors: Strand Mette P. , Neogi Tuhina , Niu Jingbo , Felson David T. , Haugen Ida K. 
Published: May 2017

ObjectiveTo explore whether metabolic syndrome and its components are associated with hand osteoarthritis (OA) using longitudinal data from the Framingham Study.MethodsOur cross‐sectional analyses included 1,089 persons (ages 50–75 years), of whom 785 had longitudinal radiographs obtained 7 years apart. Of these, 586 with no hand OA at baseline were included in analyses of hand OA incidence. We explored associations between metabolic syndrome and its components (central obesity, hypertension, diabetes mellitus, triglyceridemia, and low high‐density lipoprotein) and radiographic hand OA (defined as ≥2 interphalangeal joints with a Kellgren/Lawrence [K/L] grade of ≥2) using logistic regression analyses with adjustment for age, sex, and body mass index. In longitudinal analyses, metabolic syndrome was used as a predictor for change in K/L sum score and incident hand OA.ResultsMetabolic syndrome was not associated with the presence of hand OA (odds ratio [OR] 1.11 [95% confidence interval (95% CI) 0.78–1.59]), change in K/L sum score (OR 0.83 [95% CI 0.59–1.17]), or incidence of hand OA (OR 0.91 [95% CI 0.58–1.44]). Hypertension was borderline significantly associated with the presence of hand OA (OR 1.25 [95% CI 0.90–1.74]), and a significant association was found between hypertension and change in K/L sum score (OR 1.47 [95% CI 1.08–1.99]). Consistent dose‐response relationships were not demonstrated (data not shown). Furthermore, hypertension was not significantly associated with hand OA incidence (OR 1.23 [95% CI 0.82–1.83]). No significant associations were found between metabolic syndrome and erosive hand OA.ConclusionWe found no association between metabolic syndrome and hand OA. The role of hypertension in hand OA pathogenesis warrants further investigation.
Performance of Antinuclear Antibodies for Classifying Systemic Lupus Erythematosus: A Systematic Literature Review and Meta‐Regression of Diagnostic Data
Authors: Leuchten Nicolai , Hoyer Annika , Brinks Ralph , Schoels Monika , Schneider Matthias , Smolen Josef , Johnson Sindhu R. , Daikh David , Dörner Thomas , Aringer Martin , Bertsias George ,   the Systemic Lupus Erythematosus Classification Criteria Steering Committee
Published: May 2017

ObjectiveTo review the published literature on the performance of indirect immunofluorescence (IIF)–HEp‐2 antinuclear antibody (ANA) testing for classification of systemic lupus erythematosus (SLE).MethodsA systematic literature search was conducted in the Medline, Embase, and Cochrane databases for articles published between January 1990 and October 2015. The research question was structured according to Population, Intervention, Comparator, Outcome (PICO) format rules, and Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) recommendations were followed where appropriate. Meta‐regression analysis for diagnostic tests was performed, using the ANA titer as independent variable, while sensitivity and specificity were dependent variables.ResultsOf 4,483 publications screened, 62 matched the eligibility criteria, and another 2 articles were identified through reference analysis. The included studies comprised 13,080 SLE patients in total, of whom 12,542 (95.9%) were reported to be IIF‐ANA positive at various titers. For ANA at titers of 1:40, 1:80, 1:160, and 1:320, meta‐regression gave sensitivity values of 98.4% (95% confidence interval [95% CI] 97.6–99.0%), 97.8% (95% CI 96.8–98.5%), 95.8% (95% CI 94.1–97.1%), and 86.0% (95% CI 77.0–91.9%), respectively. The corresponding specificities were 66.9% (95% CI 57.8–74.9%), 74.7% (95% CI 66.7–81.3%), 86.2% (95% CI 80.4–90.5%), and 96.6% (95% CI 93.9–98.1%), respectively.ConclusionThe results of this systematic literature review and meta‐regression confirm that IIF‐ANAs have high sensitivity for SLE. ANAs at a titer of 1:80 have sufficiently high sensitivity to be considered as an entry criterion for SLE classification criteria, i.e., formally test other classification criteria for SLE only if ANAs of at least 1:80 have been found.