bluuebunny/crossref_metadata_2025_split huggingface dataset:
TSNAdb: A Database for Tumor-Specific Neoantigens from Immunogenomics Data Analysis
Authors: Wu Jingcheng , Zhao Wenyi , Zhou Binbin , Su Zhixi , Gu Xun , Zhou Zhan , Chen Shuqing 
Published: September 2018

Abstract
Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.
Why Is Impaired Sexual Function Distressing to Men? Consequences of Impaired Male Sexual Function and Their Associations With Sexual Well-Being
Authors: Stephenson Kyle R. , Truong Lina , Shimazu Lyndsey 
Published: September 2018

Abstract

Introduction
According to theoretical models of sexual dysfunction, the complex association between male sexual function and subjective sexual well-being (ie, sexual satisfaction and distress) may be partially mediated by specific “consequences” of impaired function, but little research has assessed the frequency of specific consequences or their association with well-being.

Aim
To pilot a scale assessing consequences of impaired male sexual function, and test whether specific consequences (eg, disruption of sexual activity, negative partner responses) mediated the association between sexual function and well-being.

Methods
166 men in sexually active heterosexual relationships completed self-report measures. A majority of men self-identified as experiencing impaired sexual function in the past month.

Main Outcome Measure
Sexual Satisfaction Scale, International Index of Erectile Function, and Measure of Sexual Consequences.

Results
17 specific consequences were reported with at least moderate frequency and were rated at least somewhat distressing. A factor analysis suggested 3 distinct categories of consequences: barrier to sex and pleasure, negative partner emotional responses, and impaired partner sexual function. These factors and the overall scale exhibited acceptable internal and test-retest reliability and each was significantly associated with multiple facets of sexual function and well-being. Frequency of sexual consequences significantly mediated the association between sexual function and well-being, with the strongest and most consistent indirect effects being found for the barrier to sex and pleasure factor.

Clinical Implications
Consequences of impaired sexual function on one’s sexual experiences may be an important maintaining factor of sexual dysfunction and reduction in these consequences may represent a mechanism of action for psychological treatments.

Strength and Limitations
Strengths included a relatively large sample with a diverse range of sexual function and well-being, as well as modern statistical analyses to assess factor structure and mediation effects. Limitations included the use of self-report scales with limited independent evidence of validity and reliability for use with male samples, as well as the cross-sectional methods that preclude strong conclusions regarding causal relationships.

Conclusion
Sexual consequences represent potential maintaining factors of male sexual dysfunction and may represent key targets of cognitive behavioral treatments.
Behind the Scenes: Mechanisms Regulating Climatic Patterns of Dissolved Organic Carbon Uptake in Headwater Streams
Authors: Catalán N. , Casas‐Ruiz J. P. , Arce M. I. , Abril M. , Bravo A. G. , del Campo R. , Estévez E. , Freixa A. , Giménez‐Grau P. , González‐Ferreras A. M. , Gómez‐Gener Ll. , Lupon A. , Martínez A. , Palacin‐Lizarbe C. , Poblador S. , Rasines‐Ladero R. , Reyes M. , Rodríguez‐Castillo T. , Rodríguez‐Lozano P. , Sanpera‐Calbet I. , Tornero I. , Pastor A. 
Published: September 2018

AbstractLarge variability in dissolved organic carbon (DOC) uptake rates has been reported for headwater streams, but the causes of this variability are still not well understood. Here we assessed acetate uptake rates across 11 European streams comprising different ecoregions by using whole‐reach pulse acetate additions. We evaluated the main climatic and biogeochemical drivers of acetate uptake during two seasonal periods. Our results show a minor influence of sampling periods but a strong effect of climate and dissolved organic matter (DOM) composition on acetate uptake. In particular, mean annual precipitation explained half of the variability of the acetate uptake velocities (VfAcetate) across streams. Temperate streams presented the lowestVfAcetate, together with humic‐like DOM and the highest stream respiration rates. In contrast, higherVfAcetatewere found in semiarid streams, with protein‐like DOM, indicating a dominance of reactive, labile compounds. This, together with lower stream respiration rates and molar ratios of DOC to nitrate, suggests a strong C limitation in semiarid streams, likely due to reduced inputs from the catchment. Overall, this study highlights the interplay of climate and DOM composition and its relevance to understand the biogeochemical mechanisms controlling DOC uptake in streams.
Soil Texture Effects on Surface Resistance to Bare‐Soil Evaporation
Authors: Lehmann P. , Merlin O. , Gentine P. , Or D. 
Published: September 2018

AbstractModeling of surface energy balance and the separation of evapotranspiration to its component fluxes require quantification of evaporation from land surfaces. The nonlinear relationship between surface heat fluxes and the hydration state of soil surfaces present a challenge to remote estimation of surface evaporation rates. We study the often‐overlooked role of soil properties in determining surface evaporation resistance. We present a framework for quantifying how the ratio of actual to potential evaporation rates varies with changes in surface water content for different soil textures. The model uses the evaporative characteristic length (a soil‐dependent active depth of evaporation) and soil resistance to capillary flow across that region. Predictions were in good agreement with flux tower measurements of bare‐soil evaporation from 10 soil textural classes. The study offers a simple and physically based method for incorporating surface evaporation resistance into land‐surface models considering soil type and surface water content.
Asymmetric Cloud‐Shortwave Radiation‐Sea Surface Temperature Feedback of Ningaloo Niño/Niña
Authors: Tozuka Tomoki , Oettli Pascal 
Published: September 2018

AbstractUsing observational and reanalysis data, the cloud‐shortwave radiation‐sea surface temperature (SST) feedback in the Ningaloo Niño/Niña region off the west coast of Australia is examined. It is found that this feedback operates as a negative feedback for positive SST anomalies and as a positive feedback for negative SST anomalies. This asymmetry is due to variation in the dominant cloud amount with SST. For positive SST anomalies, a decrease in the shortwave radiation resulting from an increase in high cloud amount associated with deep convection prevails, because SSTs in this region are relatively high compared to other eastern boundary regions and close to the convective threshold. Conversely, the region is under the influence of the subtropical high, and a decrease in the surface shortwave radiation associated with an increase in low cloud amount is dominant for negative SST anomalies.
CO2 Thermal Infrared Signature Following a Sprite Event in the Mesosphere
Authors: Romand Frédéric , Vialatte Anne , Croizé Laurence , Payan Sébastien , Barthélémy Mathieu 
Published: September 2018

AbstractSprites are a potential thermal infrared radiation source in the stratosphere and mesosphere through molecular vibrational excitation. We developed a plasma‐chemical model to compute the vibrational kinetics induced by a sprite streamer in the 40‐ to 70‐km altitude range until several tens of seconds after the visible flash is over. Then, we computed the consecutive time‐dependent thermal infrared spectra that could be observed from the stratosphere (from a balloon platform), high troposphere (from an aircraft), and low troposphere (aircraft or altitude observatory) using a nonlocal thermodynamic equilibrium radiative transfer model. Our simulations predict a strong production of CO2 in the (001) vibrational level which lasts at least 40 s before falling to background concentrations. This leads to enhanced emissions in the long‐wavelength infrared, around 1,000 cm−1, and midwavelength infrared, around 2,300 cm−1. The maximum sprite infrared signatures (sprite spectra minus background spectra) reach several 10−7 W/sr/cm2/cm−1 after propagation through the mesosphere and stratosphere, to an observer located at 20–40 km of altitude. This maximum signal is about 1 order of magnitude lower if propagated until the troposphere. From the two spectral bands, the 1,000‐cm−1 one could be detected more easily than the 2,300‐cm−1 one, which is more affected by atmospheric absorption (CO2 self‐trapping at all altitudes and H2O mostly in the troposphere). With a sufficiently sensitive instrumentation, mounted in an open stratospheric balloon platform for example, the 1,000‐cm−1 band could be detected from 20–40 km of altitude.
Implications of Seismic Velocity Structure at the Junction of Kuril‐Northeastern Japan Arcs on Active Shallow Seismicity and Deep Low‐Frequency Earthquakes
Authors: Shiina Takahiro , Takahashi Hiroaki , Okada Tomomi , Matsuzawa Toru 
Published: September 2018

AbstractWe estimate the velocity structures ofP(Vp) andSwaves (Vs) in southern Hokkaido, Japan, where a large number of crustal low‐frequency earthquakes (LFEs) have occurred. To investigate the relationship between structure and crustal seismicity, we compare the obtained velocity heterogeneity between the crustal LFE regions, which are characterized by active volcanoes, Quaternary volcanoes, and seismic swarms. The tomographic results show that low‐velocity zones (LVZs) with high Vp/Vs are located around the Moho discontinuity beneath active volcanoes, and the LVZs extend horizontally from beneath the active volcanoes to other LFE regions. In southern Hokkaido, crustal LFEs also appear inside and below the upper crust as well as around the Moho discontinuity. These intermediate‐depth and deep LFEs are located around the LVZs with a high Vp/Vs ratio, indicating the contribution of partial melt to the LFEs genesis, even at a distance from the active volcanoes. At intermediate depths of the crust, LFEs are distributed even in the high‐velocity zones, adjacent to the LVZs. This indicates that the partial melt migrations within the crust affect the activity of LFE at the intermediate depths. Below the seismic swarms in the upper crust, LVZs with crustal LFEs are distributed, probably owing to upward migrations of fluid originating from the solidification of the partial melt; this indicates a link between the shallow and deep crustal seismicity in southern Hokkaido.
Injection‐Induced Shear Slip and Permeability Enhancement in Granite Fractures
Authors: Ye Zhi , Ghassemi Ahmad 
Published: September 2018

AbstractShear stimulation, so‐called hydroshearing, is believed to reactivate critical or near‐critical preexisting fractures by pressurized fluid injection, causing them to slip and dilate for economic production from geothermal and unconventional petroleum reservoirs. However, little or no experiments have been conducted to directly probe the coupled hydromechanical responses and permeability evolution during fracture shearing. In this paper, we present the results of novel injection‐induced shear tests on cylindrical granite samples each containing a single tensile or saw cut fracture. The shear test on rough fractures demonstrates that retainable permeability enhancement can be achieved through dilatant shear slip. The characteristic stick‐slip behavior of the fracture during shearing is also observed. Fracture aperture controlled by effective normal stress dominates the fluid flow in stick state, while in slip state, the major contributor to production increase is the irreversible normal dilation caused by fracture shear slip. The experimental data show that depending on the fracture roughness, the fracture slip process includes two quasi‐static slip intervals with a slip velocity of ~10−9 to ~10−6 m/s and a dynamic slip interval with a slip velocity of ~10−7 to ~10−5 m/s. The fracture slip correlates well with the associated stress relaxation: a faster fracture slip induces a quicker stress relaxation, and vice versa. The influence of surface roughness on the hydromechanical responses during fracture shearing and the shear‐induced asperity degradation are also studied. The various experimental observations on rough and smooth fractures clearly indicate that the key component to shear stimulation is fracture self‐propping by asperities.
Induced Earthquake Families Reveal Distinctive Evolutionary Patterns Near Disposal Wells
Authors: Cochran Elizabeth S. , Ross Zachary E. , Harrington Rebecca M. , Dougherty Sara L. , Rubinstein Justin L. 
Published: September 2018

AbstractThe timing of events in seismic sequences can provide insights into the physical processes controlling fault slip. In southern Kansas, the rate of earthquakes rose rapidly starting in 2013 following expansion of energy production into the area, demanding the disposal of large volumes of wastewater into deep wells. Seismicity catalogs that are complete to low magnitudes can provide insights into the physical processes that induce seismicity near wastewater disposal. We develop a catalog of over 130,000 earthquakes recorded in southern Kansas from mid‐March 2014 through December 2017 by applying a matched filter algorithm to an original catalog of 5,831 template earthquakes. Detections have nearly identical waveforms to their associated template event and represent slip on nearly co‐located sections of a fault. We select template events with at least 100 associated detections and examine the characteristics of these prolific families of earthquakes. We find that families located close (<10 km) to areas with significant volumes of injected fluids have near‐Poissonian interevent times and the families remain active over longer durations. Families farther from high‐volume injection wells show strong clustering of interevent times and shorter sequence durations. We conclude that increasing pore fluid pressures from nearby disposal of large volumes of wastewater is the primary driver of these long duration episodes, with earthquake‐earthquake interactions driving sequences at greater distance from the wells.
Evaluation of Parameterized Convective Transport of Trace Gases in Simulation of Storms Observed During the DC3 Field Campaign
Authors: Li Y. , Pickering K. E. , Barth M. C. , Bela M. M. , Cummings K. A. , Allen D. J. 
Published: September 2018

AbstractDeep convective transport of surface moisture and pollution from the planetary boundary layer to the upper troposphere and lower stratosphere affects the radiation budget and climate. This study uses cloud‐parameterized Weather Research and Forecasting model coupled with Chemistry simulations to analyze the subgrid deep convective transport of CO at 12‐ and 36‐km horizontal resolution in supercell and mesoscale convective systems observed during the 2012 Deep Convective Clouds and Chemistry field campaign and compares the simulation results with aircraft measurements and cloud‐resolved simulations. The best Weather Research and Forecasting simulation of these storms was obtained with the use of the Grell‐Freitas convective scheme. The default Weather Research and Forecasting model coupled with Chemistry subgrid convective transport scheme was replaced with a scheme to compute convective transport within the Grell‐Freitas subgrid cumulus parameterization, which resulted in improved transport simulations. We examined the CO tendencies due to subgrid‐ and grid‐scale convective transport. Results showed that the subgrid convective transport started earlier than the grid‐scale convective transport. The subgrid‐scale convective transport reached its maximum during the hour prior to the formation of the grid‐scale constant‐altitude detrainment layer. After that, both the subgrid‐ and grid‐scale convective transport began to decrease. The subgrid‐scale convective transport played a more significant role in the supercell case than the mesoscale convective system case. Subgrid contribution reached ~90% at the beginning of the storm and decreased to ~30% (17%) for the 36‐km (12‐km) domain 4 hr later.
Space Weathering Induced Via Microparticle Impacts: 2. Dust Impact Simulation and Meteorite Target Analysis
Authors: Fiege K. , Guglielmino M. , Altobelli N. , Trieloff M. , Srama R. , Orlando T. M. 
Published: September 2018

AbstractThe role of micrometeorite bombardment in space weathering on asteroid surfaces was studied using a 2 MV Van de Graaff accelerator. About 90,000‐ to 100,000‐micron‐ to submicron‐sized copper particles with a mass and velocity distribution similar to the interplanetary dust population were fired onto the surfaces of polished Allende CV3 chondrite and eucrite NWA 6966 samples at speeds between 1 to 70 kilometers per second. We find a clear relationship between microparticle bombardment, infrared reflectance decrease, and overall spectral reddening. Differences in impact effects due to variable particle speed, size, and structure are observed. Some Cu particles form large clusters that break up upon impact and disperse. Other impactors leave imprints on the surface, and implant or generate typical craters with rims and spallation features. Very small, fast particles generate small craters without spallation or significant crater rim. Mid‐infrared (IR) spectra (bulk and microscopic measurements of individual components), 3‐D laser microscopic images and XRD spectra from the processed and unprocessed samples were collected. Mid‐IR spectra (700–6,000 cm−1) over the entire sample surface show overall darkening of features. Microscopic IR spectra show the damage seen as reflectance decrease and spectral reddening, which is variable in the micrometer range, depending on impact density and target properties (mineralogic composition). The fine‐grained Allende matrix with predominantly Fe‐rich olivine seems less affected than coarse‐grained chondrules with Mg‐rich silicates, where darkening can reach 60%. X‐ray diffraction analysis also suggests chemical and crystallographical differences in the bombarded sample, due to impact shock.
The Global Oscillation Network Group Facility—An Example of Research to Operations in Space Weather
Authors: Hill Frank 
Published: September 2018

AbstractThe Global Oscillation Network Group (GONG) is a system of ground‐based solar observing stations distributed geographically so that the Sun is visible nearly continuously at all times. Originally developed to provide data for research into the solar interior via helioseismology, GONG is now also providing data for operational space weather forecasting as a cost‐effective and reliable alternative to space missions. The data comprise full‐disk magnetograms, H‐α intensity images, and helioseismic maps of activity on the solar far side. These data are provided in near real time to the NOAA Space Weather Prediction Center, the US Air Force, and NASA. GONG is a successful example of transitioning a research facility funded by the NSF into an operational asset.
Higher HbA1c Measurement Quality Standards are Needed for Follow-Up and Diagnosis: Experience and Analyses from Germany
Authors: Heinemann Lutz , Kaiser Patricia , Freckmann Guido , Grote-Koska Denis , Kerner Wolfgang , Landgraf Rüdiger , Merker Ludwig , Müller Ulrich , Müller-Wieland Dirk , Roth Johannes , Spannagl Michael , Wallaschofski Henri , Nauck Matthias 
Published: September 2018

AbstractMeasurement of HbA1c is an essential laboratory measure for the follow-up and therapy decision-making in patients with diabetes. HbA1c is one of the measurands in laboratory medicine that have to be successfully checked according to the criteria of the guidelines of the German Medical Association (Rili-BAEK) in external quality assurance using the reference method value concept, when applied in patient care. The allowed deviation of ±18% in external quality assessment (EQA) and ± 10% in internal quality control has been ultimately met by virtually all the different manufacturers and methods. However, such broad limits for permissible deviations are not suitable in view of medical requirements in patient care. The low-level acceptance criteria also depends on the previously used EQA materials used in Germany. In fact, HbA1c measurement results that are imprecisely measured or come from incorrectly calibrated devices are difficult to identify. With implementation of unprocessed fresh EDTA blood, the situation has changed. Until now systems with unit use reagents for point-of-care testing (POCT) of HbA1c are not mandatory to participate in EQA schemes in Germany. This paper outlines why there was a need to narrow the acceptance limits listed within the Rili-BAEK for HbA1c’s internal (to ± 3%) and external (to ± 8%) quality controls in EQA schemes for Germany, which will take place after a transition period in the next years. Higher quality in HbA1c measurements will help to avoid misdiagnosis of diabetes as well as potential over- or undertreatment of patients at risk for diabetes.
A Novel Approach to Serial Amnioinfusion in a Case of Premature Rupture of Membranes Near the Limit of Viability
Authors: Kohari Katherine , Mehlhaff Krista , Merriam Audrey , Abdel-Razeq Sonya , Grechukhina Olga , Leon-Martinez Daisy , Bahtiyar Mert 
Published: September 2018

AbstractPrelabor rupture of the membranes (PROM) near the limit of viability is associated with significant risks for both mother and fetus. Preterm labor, intra-amniotic infection, and placental abruption are the immediate risks to the pregnancy; however, the fetus incurs additional risks related to the sequela of persistent oligohydramnios. Transabdominal intra-amniotic infusions have been studied. Results, suggesting that this intervention may prolong the latency period, and potentially, decrease pulmonary hypoplasia in surviving neonates without evidence of increasing risk of intra-amniotic infection. To our knowledge, the use of antibiotic-infused fluid has not been reported in this clinical scenario. Therefore, we present a case of a patient with PROM before the limit of viability who underwent serial transabdominal amnioinfusions with oxacillin-containing normal saline, which resulted in membrane resealing and neonatal survival with no additional maternal morbidity.