bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local Finite-Amplitude Wave Activity as a Diagnostic of Anomalous Weather Events
Authors: Huang Clare S. Y. , Nakamura Noboru 
Published: September 2015

Abstract
Finite-amplitude Rossby wave activity (FAWA) proposed by Nakamura and Zhu measures the waviness of quasigeostrophic potential vorticity (PV) contours and the associated modification of the zonal-mean zonal circulation, but it does not distinguish longitudinally localized weather anomalies, such as atmospheric blocking. In this article, FAWA is generalized to local wave activity (LWA) to diagnose eddy–mean flow interaction on the regional scale. LWA quantifies longitude-by-longitude contributions to FAWA following the meridional displacement of PV from the circle of equivalent latitude. The zonal average of LWA recovers FAWA. The budget of LWA is governed by the zonal advection of LWA and the radiation stress of Rossby waves. The utility of the diagnostic is tested with a barotropic vorticity equation on a sphere and meteorological reanalysis data. Compared with the previously derived Eulerian impulse-Casimir wave activity, LWA tends to be less filamentary and emphasizes large isolated vortices involving reversals of meridional gradient of potential vorticity. A pronounced Northern Hemisphere blocking episode in late October 2012 is well captured by a high-amplitude, near-stationary LWA. These analyses reveal that the nonacceleration relation holds approximately over regional scales: the growth of phase-averaged LWA and the deceleration of local zonal wind are highly correlated. However, marked departure from the exact nonacceleration relation is also observed during the analyzed blocking event, suggesting that the contributions from nonadiabatic processes to the blocking development are significant.
Reexamining the Relationship between Climate Sensitivity and the Southern Hemisphere Radiation Budget in CMIP Models
Authors: Grise Kevin M. , Polvani Lorenzo M. , Fasullo John T. 
Published: September 2015

Abstract
Recent efforts to narrow the spread in equilibrium climate sensitivity (ECS) across global climate models have focused on identifying observationally based constraints, which are rooted in empirical correlations between ECS and biases in the models’ present-day climate. This study reexamines one such constraint identified from CMIP3 models: the linkage between ECS and net top-of-the-atmosphere radiation biases in the Southern Hemisphere (SH).
As previously documented, the intermodel spread in the ECS of CMIP3 models is linked to present-day cloud and net radiation biases over the midlatitude Southern Ocean, where higher cloud fraction in the present-day climate is associated with larger values of ECS. However, in this study, no physical explanation is found to support this relationship. Furthermore, it is shown here that this relationship disappears in CMIP5 models and is unique to a subset of CMIP models characterized by unrealistically bright present-day clouds in the SH subtropics. In view of this evidence, Southern Ocean cloud and net radiation biases appear inappropriate for providing observationally based constraints on ECS.
Instead of the Southern Ocean, this study points to the stratocumulus-to-cumulus transition regions of the SH subtropical oceans as key to explaining the intermodel spread in the ECS of both CMIP3 and CMIP5 models. In these regions, ECS is linked to present-day cloud and net radiation biases with a plausible physical mechanism: models with brighter subtropical clouds in the present-day climate show greater ECS because 1) subtropical clouds dissipate with increasing CO2 concentrations in many models and 2) the dissipation of brighter clouds contributes to greater solar warming of the surface.
Response of the Equatorial Pacific Seasonal Cycle to Orbital Forcing
Authors: Erb Michael P. , Broccoli Anthony J. , Graham Neal T. , Clement Amy C. , Wittenberg Andrew T. , Vecchi Gabriel A. 
Published: September 2015

Abstract
The response of the equatorial Pacific Ocean’s seasonal cycle to orbital forcing is explored using idealized simulations with a coupled atmosphere–ocean GCM in which eccentricity, obliquity, and the longitude of perihelion are altered while other boundary conditions are maintained at preindustrial levels. The importance of ocean dynamics in the climate response is investigated using additional simulations with a slab ocean version of the model. Precession is found to substantially influence the equatorial Pacific seasonal cycle through both thermodynamic and dynamic mechanisms, while changes in obliquity have only a small effect. In the precession experiments, western equatorial Pacific SSTs respond in a direct thermodynamic manner to changes in insolation, while the eastern equatorial Pacific is first affected by the propagation of thermocline temperature anomalies from the west. These thermocline signals result from zonal wind anomalies associated with changes in the strength of subtropical anticyclones and shifts in the regions of convection in the western equatorial Pacific. The redistribution of heat from these thermocline signals, aided by the direct thermodynamic effect of insolation anomalies, results in large changes to the strength and timing of the eastern equatorial Pacific seasonal cycle. A comparison of 10 CMIP5 mid-Holocene experiments, in which the primary forcing is due to precession, shows that this response is relatively robust across models. Because equatorial Pacific SST anomalies have local climate impacts as well as nonlocal impacts through teleconnections, these results may be important to understanding paleoclimate variations both inside and outside of the tropical Pacific.
Near-Ground Rotation in Simulated Supercells: On the Robustness of the Baroclinic Mechanism*
Authors: Dahl Johannes M. L. 
Published: September 2015

Abstract
This study addresses the robustness of the baroclinic mechanism that facilitates the onset of surface rotation in supercells by using two idealized simulations with different microphysics parameterizations and by considering previous results. In particular, the importance of ambient crosswise vorticity relative to baroclinically generated vorticity in the development of near-ground cyclonic vorticity is analyzed. The storms were simulated using the CM1 model in a kinematic base state characterized by a straight-line hodograph. A trajectory analysis spanning about 30 min was performed for a large number of parcels that contribute to near-surface vertical-vorticity maxima. The vorticity along these trajectories was decomposed into barotropic and nonbarotropic parts, where the barotropic vorticity represents the effects of the preexisting, substantially crosswise horizontal storm-relative vorticity. The nonbarotropic part represents the vorticity produced baroclinically within the storm. It was found that the imported barotropic vorticity attains a downward component near the surface, while the baroclinic vorticity points upward and dominates. This dominance of the baroclinic vorticity is independent of whether a single-moment or double-moment microphysics parameterization is used. A scaling argument is offered as explanation, predicting that the baroclinic vertical vorticity becomes increasingly dominant as downdraft strength increases.
Early mobilisation in intensive care units in Australia and Scotland: a prospective, observational cohort study examining mobilisation practises and barriers
Authors: Harrold Meg E. , Salisbury Lisa G. , Webb Steve A. , Allison Garry T. ,   on behalf of the Australia and Scotland ICU Physiotherapy Collaboration
Published: September 2015

Abstract
Introduction
Mobilisation of patients in the intensive care unit (ICU) is an area of growing research. Currently, there is little data on baseline mobilisation practises and the barriers to them for patients of all admission diagnoses.

Methods
The objectives of the study were to (1) quantify and benchmark baseline levels of mobilisation in Australian and Scottish ICUs, (2) compare mobilisation practises between Australian and Scottish ICUs and (3) identify barriers to mobilisation in Australian and Scottish ICUs. We conducted a prospective, observational, cohort study with a 4-week inception period. Patients were censored for follow-up upon ICU discharge or after 28 days, whichever occurred first. Patients were included if they were >18 years of age, admitted to an ICU and received mechanical ventilation in the ICU.

Results
Ten tertiary ICUs in Australia and nine in Scotland participated in the study. The Australian cohort had a large proportion of patients admitted for cardiothoracic surgery (43.3 %), whereas the Scottish cohort had none. Therefore, comparison analysis was done after exclusion of patients admitted for cardiothoracic surgery. In total, 60.2 % of the 347 patients across 10 Australian ICUs and 40.1 % of the 167 patients across 9 Scottish ICUs mobilised during their ICU stay (p < 0.001). Patients in the Australian cohort were more likely to mobilise than patients in the Scottish cohort (hazard ratio 1.83, 95 % confidence interval 1.38–2.42). However, the percentage of episodes of mobilisation where patients were receiving mechanical ventilation was higher in the Scottish cohort (41.1 % vs 16.3 %, p < 0.001). Sedation was the most commonly reported barrier to mobilisation in both the Australian and Scottish cohorts. Physiological instability and the presence of an endotracheal tube were also frequently reported barriers.

Conclusions
This is the first study to benchmark baseline practise of early mobilisation internationally, and it demonstrates variation in early mobilisation practises between Australia and Scotland.
THAM reduces CO2-associated increase in pulmonary vascular resistance – an experimental study in lung-injured piglets
Authors: Höstman Staffan , Borges João Batista , Suarez-Sipmann Fernando , Ahlgren Kerstin M. , Engström Joakim , Hedenstierna Göran , Larsson Anders 
Published: September 2015

Abstract
Introduction
Low tidal volume (VT) ventilation is recommended in patients with acute respiratory distress syndrome (ARDS). This may increase arterial carbon dioxide tension (PaCO2), decrease pH, and augment pulmonary vascular resistance (PVR). We hypothesized that Tris(hydroxymethyl)aminomethane (THAM), a pure proton acceptor, would dampen these effects, preventing the increase in PVR.

Methods
A one-hit injury ARDS model was established by repeated lung lavages in 18 piglets. After ventilation with VT of 6 ml/kg to maintain normocapnia, VT was reduced to 3 ml/kg to induce hypercapnia. Six animals received THAM for 1 h, six for 3 h, and six serving as controls received no THAM. In all, the experiment continued for 6 h. The THAM dosage was calculated to normalize pH and exhibit a lasting effect. Gas exchange, pulmonary, and systemic hemodynamics were tracked. Inflammatory markers were obtained at the end of the experiment.

Results
In the controls, the decrease in VT from 6 to 3 ml/kg increased PaCO2 from 6.0±0.5 to 13.8±1.5 kPa and lowered pH from 7.40±0.01 to 7.12±0.06, whereas base excess (BE) remained stable at 2.7±2.3 mEq/L to 3.4±3.2 mEq/L. In the THAM groups, PaCO2 decreased and pH increased above 7.4 during the infusions. After discontinuing the infusions, PaCO2 increased above the corresponding level of the controls (15.2±1.7 kPa and 22.6±3.3 kPa for 1-h and 3-h THAM infusions, respectively). Despite a marked increase in BE (13.8±3.5 and 31.2±2.2 for 1-h and 3-h THAM infusions, respectively), pH became similar to the corresponding levels of the controls. PVR was lower in the THAM groups (at 6 h, 329±77 dyn∙s/m5 and 255±43 dyn∙s/m5 in the 1-h and 3-h groups, respectively, compared with 450±141 dyn∙s/m5 in the controls), as were pulmonary arterial pressures.

Conclusions
The pH in the THAM groups was similar to pH in the controls at 6 h, despite a marked increase in BE. This was due to an increase in PaCO2 after stopping the THAM infusion, possibly by intracellular release of CO2. Pulmonary arterial pressure and PVR were lower in the THAM-treated animals, indicating that THAM may be an option to reduce PVR in acute hypercapnia.
Inhaled nitric oxide improves transpulmonary blood flow and clinical outcomes after prolonged cardiac arrest: a large animal study
Authors: Derwall Matthias , Ebeling Andreas , Nolte Kay Wilhelm , Weis Joachim , Rossaint Rolf , Ichinose Fumito , Nix Christoph , Fries Michael , Brücken Anne 
Published: September 2015

Abstract
Introduction
The probability to achieve a return of spontaneous circulation (ROSC) after cardiac arrest can be improved by optimizing circulation during cardiopulomonary resuscitation using a percutaneous left ventricular assist device (iCPR). Inhaled nitric oxide may facilitate transpulmonary blood flow during iCPR and may therefore improve organ perfusion and outcome.

Methods
Ventricular fibrillation was electrically induced in 20 anesthetized male pigs. Animals were left untreated for 10 minutes before iCPR was attempted. Subjects received either 20 ppm of inhaled nitric oxide (iNO, n = 10) or 0 ppm iNO (Control, n = 10), simultaneously started with iCPR until 5 hours following ROSC. Animals were weaned from the respirator and followed up for five days using overall performance categories (OPC) and a spatial memory task. On day six, all animals were anesthetized again, and brains were harvested for neurohistopathologic evaluation.

Results
All animals in both groups achieved ROSC. Administration of iNO markedly increased iCPR flow during CPR (iNO: 1.81 ± 0.30 vs Control: 1.64 ± 0.51 L/min, p < 0.001), leading to significantly higher coronary perfusion pressure (CPP) during the 6 minutes of CPR (25 ± 13 vs 16 ± 6 mmHg, p = 0.002). iNO-treated animals showed significantly lower S-100 serum levels thirty minutes post ROSC (0.26 ± 0.09 vs 0.38 ± 0.15 ng/mL, p = 0.048), as well as lower blood glucose levels 120–360 minutes following ROSC. Lower S-100 serum levels were reflected by superior clinical outcome of iNO-treated animals as estimated with OPC (3 ± 2 vs. 5 ± 1, p = 0.036 on days 3 to 5). Three out of ten iNO-treated, but none of the Control animals were able to successfully participate in the spatial memory task. Neurohistopathological examination of vulnerable cerebral structures revealed a trend towards less cerebral lesions in neocortex, archicortex, and striatum in iNO-treated animals compared to Controls.

Conclusions
In pigs resuscitated with mechanically-assisted CPR from prolonged cardiac arrest, the administration of 20 ppm iNO during and following iCPR improved transpulmonary blood flow, leading to improved clinical neurological outcomes.
Clinical classification of tissue perfusion based on the central venous oxygen saturation and the peripheral perfusion index
Authors: He Huaiwu , Long Yun , Liu Dawei , Wang Xiaoting , Zhou Xiang 
Published: September 2015

Abstract
Introduction
We investigated whether combining the peripheral perfusion index (PI) and central venous oxygen saturation(ScvO2) would identify subsets of patients for assessing the tissue perfusion and predicting outcome during the resuscitation in critically ill patients.

Methods
A total of 202 patients with central venous catheters for resuscitation were enrolled in this prospective observational study. The arterial, central venous blood gas and the PI were measured simultaneously at the enrollment (T0) and 8 h (T8) after early resuscitation. Based on the distribution of the PI in healthy population, a cutoff of PI ≥1.4 was defined as a normal PI. Moreover, the critical value of PI was defined as the best cutoff value related to the mortality in the study population. The PI impairment stratification is defined as follows: a normal PI(≥1.4), mild PI impairment (critical value < PI < 1.4) and critical PI impairment (PI ≤ critical value).

Results
The PI at T8 was with the greatest AUC for prediction the 30-day mortality and PI is an independent risk factor for 30-day mortality. Moreover, a cutoff of PI < 0.6 is related to poor outcomes following resuscitation. So, based on cutoffs of ScvO2 (70 %) and critical PI (0.6) at T8, we assigned the patients to four categories: group 1 (PI ≤ 0.6 on ScvO2 < 70 %), group 2 (PI ≤ 0.6 on ScvO2 ≥ 70 %), group 3 (PI > 0.6 on ScvO2 < 70 %), and group 4 (PI > 0.6 on ScvO2 ≥ 70 %). The combination of low ScvO2(<70 %) and PI(≤0.6) was associated with the lowest survival rates at 30 days [log rank (Mantel–Cox) = 87.518, p < 0.0001]. The sub-group patients who had high ScvO2(>80 %) at T8 were with low mortality and high PI. Moreover, the normal PI (≥1.4) did not show a better outcome than mild impaired PI (0.6-1.4) patients who had a normalized ScvO2(>70 %) after resuscitation. The PI was correlated with the lactate, P(v-a)CO2, and ScvO2 in all the measurements (n = 404). These relationships are strengthened with abnormal PI (PI < 1.4) but not with normal PI (PI ≥ 1.4).

Conclusion
Complementing ScvO2 assessment with PI can better identify endpoints of resuscitation and adverse outcomes. Pursuing a normalized PI (≥1.4) may not result in better outcomes for a mild impaired PI after ScvO2 is normalized.
A close look at protein function prediction evaluation protocols
Authors: Kahanda Indika , Funk Christopher S , Ullah Fahad , Verspoor Karin M , Ben-Hur Asa 
Published: September 2015

Abstract

Background
The recently held Critical Assessment of Function Annotation challenge (CAFA2) required its participants to submit predictions for a large number of target proteins regardless of whether they have previous annotations or not. This is in contrast to the original CAFA challenge in which participants were asked to submit predictions for proteins with no existing annotations. The CAFA2 task is more realistic, in that it more closely mimics the accumulation of annotations over time. In this study we compare these tasks in terms of their difficulty, and determine whether cross-validation provides a good estimate of performance.

Results
The CAFA2 task is a combination of two subtasks: making predictions on annotated proteins and making predictions on previously unannotated proteins. In this study we analyze the performance of several function prediction methods in these two scenarios. Our results show that several methods (structured support vector machine, binary support vector machines and guilt-by-association methods) do not usually achieve the same level of accuracy on these two tasks as that achieved by cross-validation, and that predicting novel annotations for previously annotated proteins is a harder problem than predicting annotations for uncharacterized proteins. We also find that different methods have different performance characteristics in these tasks, and that cross-validation is not adequate at estimating performance and ranking methods.

Conclusions
These results have implications for the design of computational experiments in the area of automated function prediction and can provide useful insight for the understanding and design of future CAFA competitions.
The Impact of Demand Uncertainty on Consumer Subsidies for Green Technology Adoption
Authors: Cohen Maxime C. , Lobel Ruben , Perakis Georgia 
Published: September 2015

This paper studies government subsidies for green technology adoption while considering the manufacturing industry’s response. Government subsidies offered directly to consumers impact the supplier’s production and pricing decisions. Our analysis expands the current understanding of the price-setting newsvendor model, incorporating the external influence from the government, who is now an additional player in the system. We quantify how demand uncertainty impacts the various players (government, industry, and consumers) when designing policies. We further show that, for convex demand functions, an increase in demand uncertainty leads to higher production quantities and lower prices, resulting in lower profits for the supplier. With this in mind, one could expect consumer surplus to increase with uncertainty. In fact, we show that this is not always the case and that the uncertainty impact on consumer surplus depends on the trade-off between lower prices and the possibility of underserving customers with high valuations. We also show that when policy makers such as governments ignore demand uncertainty when designing consumer subsidies, they can significantly miss the desired adoption target level. From a coordination perspective, we demonstrate that the decentralized decisions are also optimal for a central planner managing jointly the supplier and the government. As a result, subsidies provide a coordination mechanism.This paper was accepted by Yossi Aviv, operations management.
Tandem Mass Spectrometry Has a Larger Analytical Range than Fluorescence Assays of Lysosomal Enzymes: Application to Newborn Screening and Diagnosis of Mucopolysaccharidoses Types II, IVA, and VI
Authors: Kumar Arun Babu , Masi Sophia , Ghomashchi Farideh , Chennamaneni Naveen Kumar , Ito Makoto , Scott C Ronald , Turecek Frantisek , Gelb Michael H , Spacil Zdenek 
Published: September 2015

Abstract

BACKGROUND
There is interest in newborn screening and diagnosis of lysosomal storage diseases because of the development of treatment options that improve clinical outcome. Assays of lysosomal enzymes with high analytical range (ratio of assay response from the enzymatic reaction divided by the assay response due to nonenzymatic processes) are desirable because they are predicted to lead to a lower rate of false positives in population screening and to more accurate diagnoses.

METHODS
We designed new tandem mass spectrometry (MS/MS) assays that give the largest analytical ranges reported to date for the use of dried blood spots (DBS) for detection of mucopolysaccharidoses type II (MPS-II), MPS-IVA, and MPS-VI. For comparison, we carried out fluorometric assays of 6 lysosomal enzymes using 4-methylumbelliferyl (4MU)-substrate conjugates.

RESULTS
The MS/MS assays for MPS-II, -IVA, and -VI displayed analytical ranges that are 1–2 orders of magnitude higher than those for the corresponding fluorometric assays. The relatively small analytical ranges of the 4MU assays are due to the intrinsic fluorescence of the 4MU substrates, which cause high background in the assay response.

CONCLUSIONS
These highly reproducible MS/MS assays for MPS-II, -IVA, and -VI can support multiplex newborn screening of these lysosomal storage diseases. MS/MS assays of lysosomal enzymes outperform 4MU fluorometric assays in terms of analytical range. Ongoing pilot studies will allow us to gauge the impact of the increased analytical range on newborn screening performance.
M-convolutions of products and ratios, statistical distributions and fractional calculus
Authors: Mathai Arakaparampil M. 
Published: September 2015

Abstract
It is shown that Mellin convolutions of products and ratios in the real scalar variable case can be considered as densities of products and ratios of two independently distributed real scalar positive random variables. It is also shown that these are also connected to Krätzel integrals and to the Krätzel transform in applied analysis, to reaction-rate probability integrals in astrophysics and to other related aspects when the random variables have gamma or generalized gamma densities, and to fractional calculus when one of the variables has a type-1 beta density and the other variable has an arbitrary density. Matrix-variate analogues are also discussed. In the matrix-variate case, the M-convolutions introduced by the author are shown to be directly connected to densities of products and ratios of statistically independently distributed positive definite matrix random variables in the real case and to Hermitian positive definite matrices in the complex domain. These M-convolutions reduce to Mellin convolutions in the scalar variable case.