bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anesthetic techniques to facilitate lung lavage for pulmonary alveolar proteinosis in children—new airway techniques and a review of the literature
Authors: Wilson Caroline A. , Wilmshurst Sally L. , Black Ann E. 
Published: February 2015

SummaryPediatric patients with pulmonary alveolar proteinosis require whole lung lavage to clear the accumulation of lipoproteinaceous material within the alveoli, to maintain respiratory function. Anesthesia for this presents a challenge due to preexisting respiratory failure, and the small diameter and length of the pediatric airway, which is often unable to accommodate existing one‐lung isolation and ventilation equipment. Novel techniques to facilitate lung lavage on seven occasions are described and placed in the context of the existing literature to date.
Contextual valence modulates the neural dynamics of risk processing
Authors: Zheng Ya , Li Qi , Wang Kai , Wu Haiyan , Liu Xun 
Published: February 2015

AbstractA well‐known bias in risky decision making is that most people tend to be risk averse when gains are salient but risk seeking when losses are salient. The present study addressed the neural dynamics of this process by recording ERPs during a gambling task in a gain and a loss context. Behaviorally, participants were found to be risk averse in the gain context but risk neutral in the loss context. During the anticipation stage, an increased stimulus‐preceding negativity was elicited by high‐ versus low‐risk choices in the gain but not the loss context. During the outcome‐appraisal stage, the feedback‐related negativity was larger after high‐ versus low‐risk choices in the gain instead of the loss context. For the P300, an outcome valence effect (a larger P300 for gain vs. loss outcomes) emerged following the high‐ versus low‐risk decisions in the gain but not the loss context. Our findings suggest that risk processing can be modulated by the context of valence during the anticipation stage and by both the contextual valence and the outcome valence during the outcome‐appraisal stage, which may be driven by the motivational salience imposed by the context of valence.
Quantifying and mapping topsoil inorganic carbon concentrations and stocks: approaches tested in France
Authors: Marchant B. P. , Villanneau E. J. , Arrouays D. , Saby N. P. A. , Rawlins B. G. 
Published: February 2015

AbstractSoils act as a sink or a source of atmospheric carbon, and great efforts are made to monitor soil organic carbon stocks, but soil inorganic carbon (SIC) stocks are not measured by many national‐ and continental‐scale soil monitoring networks. Topsoil (0–30 cm)SICconcentrations were determined for > 2000 sites on a regular 16‐km grid as part of the French, Réseau de Mesures de la Qualité des Sols (RMQS). We used design‐based statistical methods to calculate unbiased estimates of the meanSICconcentration and total stocks across France. Model‐based methods were used to determine the uncertainty of these estimates and to map the spatial distribution of these quantities. Observations of inorganic carbon were highly skewed and did not conform to standard statistical models. Data were normalized using a nonparametric transformation. The estimates and predictions of inorganic carbon are baselines against which the results of future phases of the network can be compared. We found that the total topsoil inorganic carbon stocks in France amount to 1070 ± 61 Tg, ca. one‐third of the corresponding organic carbon stocks. Spatial distribution ofSICwas strongly linked to the underlying geology. We tested the reliability of estimatingSICconcentrations and stocks from the French Soil Test Database, which contains the results of 280 000 soil analyses requested by farmers between 1990 and 2004. A biased estimate of soil inorganic carbon concentrations resulted, presumably because soil samples were selected according to concerns of farmers rather than by a statistical design.
Symbiodinium transcriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions
Authors: Xiang Tingting , Nelson William , Rodriguez Jesse , Tolleter Dimitri , Grossman Arthur R. 
Published: February 2015

SummarySymbiosis between unicellular dinoflagellates (genus Symbiodinium) and their cnidarian hosts (e.g. corals, sea anemones) is the foundation of coral reef ecosystems. Dysfunction of this symbiosis under changing environmental conditions has led to global reef decline. Little information is known about Symbiodinium gene expression and mechanisms by which light impacts host–symbiont associations. To address these issues, we generated a transcriptome from axenic Symbiodinium strain SSB01. Here we report features of the transcriptome, including occurrence and length distribution of spliced leader sequences, the functional landscape of encoded proteins and the impact of light on gene expression. Expression of many Symbiodinium genes appears to be significantly impacted by light. Transcript encoding cryptochrome 2 declined in high light while some transcripts for Regulators of Chromatin Condensation (RCC1) declined in the dark. We also identified a transcript encoding a light harvesting AcpPC protein with homology to Chlamydomonas LHCSR2. The level of this transcript increased in high light autotrophic conditions, suggesting that it is involved in photo‐protection and the dissipation of excess absorbed light energy. The most extensive changes in transcript abundances occurred when the algae were transferred from low light to darkness. Interestingly, transcripts encoding several cell adhesion proteins rapidly declined following movement of cultures to the dark, which correlated with a dramatic change in cell surface morphology, likely reflecting the complexity of the extracellular matrix. Thus, light‐sensitive cell adhesion proteins may play a role in establishing surface architecture, which may in turn alter interactions between the endosymbiont and its host.
Trade Costs in Bilateral Trade Flows: Heterogeneity and Zeroes in Structural Gravity Models
Authors: Bernardini Papalia Rosa , Bertarelli Silvia 
Published: February 2015

AbstractThis paper contributes to the explanation of international trade flows with structural gravity models taking heterogeneity and excess zeroes into account. We introduce a more general hypothesis on the structure of trade costs in Helpman et al. (The Quarterly Journal of Economics, 2008; 123, 2, 441) theoretical model that is capable of explaining over‐dispersion in trade data. Zero‐inflated negative binomial models are considered to analyse the impact of trade costs, measured in terms of geographical distance and contiguity effects. An analysis related to a sample of 37 countries' trade flows, with heterogeneous effects across sectors and trade‐integrated areas, such as APEC and EU, is presented. The size of exporting and destination economies and cultural and institutional factors are considered as influencing both the extensive and the intensive margin of trade.
Resveratrol protects against doxorubicin‐induced cardiotoxicity in aged hearts through the SIRT1‐USP7 axis
Authors: Sin Thomas K. , Tam Bjorn T. , Yung Benjamin Y. , Yip Shea P. , Chan Lawrence W. , Wong Cesar S. , Ying Michael , Rudd John A. , Siu Parco M. 
Published: February 2015

Key points
Doxorubicin induced functional deteriorations and elevations of USP7‐related apoptotic/catabolic signalling in the senescent heart
Resveratrol protects against doxorubicin‐induced alterations through the restoration of SIRT1 deacetylase activity
AbstractA compromised cardiac function is often seen in elderly cancer patients receiving doxorubicin therapy. The present study tested the hypothesis that acute intervention with resveratrol, a natural anti‐oxidant found in grapes and red wine, reduces the cardiotoxicity of doxorubicin through restoration of sirtuin 1 (SIRT1) deacetylase activity, and attenuation of the catabolic/apoptotic pathways orchestrated by USP7, a p53 deubiquitinating protein, using young (aged 2 months) and old (aged 10 months) senescence‐accelerated mice prone 8 (SAMP8). Animals were randomised to receive saline, doxorubicin, and doxorubicin in combination with resveratrol, in the presence or absence of SIRT1 inhibitors, sirtinol or EX527. Resveratrol alone, but not in combination with either of the SIRT1 inhibitors, suppressed the doxorubicin‐induced impairment of cardiac systolic function in aged animals. Doxorubicin reduced SIRT1 deacetylase activity, and elevated proteasomal activity and USP7; it also increased the protein level of p300 and ubiquitinated proteins in hearts from aged SAMP8. These doxorubicin‐induced alterations were prevented by resveratrol, whereas the protective action of resveratrol was antagonised by sirtinol and EX527. In young SAMP8 hearts, resveratrol attenuated the doxorubicin‐induced increases in acetylation of Foxo1 and transactivation of MuRF‐1, whereas these mitigations were not found after treatment with SIRT1 inhibitors. However, the protein contents of acetylated Foxo1 and MuRF‐1 were not affected by any of the drugs studied in aged SAMP8 hearts. Resveratrol also ameliorated the augmentation of pro‐apoptotic markers including p53, Bax, caspase 3 activity and apoptotic DNA fragmentation induced by doxorubicin in hearts from aged animals, whereas these reductions were diminished by combined treatment with SIRT1 inhibitors. These data demonstrate that resveratrol ameliorates doxorubicin‐induced cardiotoxicity in aged hearts through the restoration of SIRT1 activity to attenuate USP7‐related catabolic/pro‐apoptotic signalling.
Transient Tropical Diabatic Heating and the Seasonal-Mean Response to ENSO
Authors: Swenson Erik T. , Straus David M. 
Published: February 2015

Abstract
Boreal winter simulations of the Community Atmospheric Model, version 4.0, were carried out using observed sea surface temperature (SST) fields from the three El Niño events of 1982/83, 1991/92, and 1997/98 [control (CTL) runs] and from observed climatology (CLIM run). In each case, 50 ensemble members were run (1 November–31 March). The diabatic heating Q at every grid point, level, and day of the CTL runs in the Indo-Pacific region was stored and used in four additional suites of experiments, each of which parallels the appropriate CTL suite. In each suite, Q generated by the model is replaced by a specified subset of Q at every time step, grid point, and level spanning the Indo-Pacific. The Q subsets consist of the seasonal ensemble-CTL-mean Q for each ensemble member (suite FIX), the seasonal-mean Q from the appropriate ensemble member of the CTL (suite EFIX), the seasonal mean plus low-frequency component of Q (suite ESUBFIX), and the daily means of Q (suite DAYFIX).
The midlatitude ENSO anomalies of the seasonal-mean upper-level height field and time-filtered meridional wind variance are enhanced in the FIX, EFIX, and ESUBFIX suites, with little change in patterns, compared to CTL anomalies. The enhancements have a smaller magnitude in ESUBFIX and especially in DAYFIX; qualitative differences are seen in DAYFIX. These differences are due to (i) the required setup time for midlatitude response, (ii) the altered relationship between vertical structure and vertically integrated heating, and (iii) the lack of midlatitude interactive influence on tropical heating in the experiments.
Systematic Comparison of Four-Dimensional Data Assimilation Methods With and Without the Tangent Linear Model Using Hybrid Background Error Covariance: E4DVar versus 4DEnVar
Authors: Poterjoy Jonathan , Zhang Fuqing 
Published: February 2015

Abstract
Two ensemble formulations of the four-dimensional variational (4DVar) data assimilation technique are examined for a low-dimensional dynamical system. The first method, denoted E4DVar, uses tangent linear and adjoint model operators to minimize a cost function in the same manner as the traditional 4DVar data assimilation system. The second method, denoted 4DEnVar, uses an ensemble of nonlinear model trajectories to replace the function of linearized models in 4DVar, thus improving the parallelization of the data assimilation. Background errors for each algorithm are represented using a hybrid error covariance, which includes climatological errors as well as ensemble-estimated errors from an ensemble Kalman filter (EnKF). Numerical experiments performed over a range of scenarios suggest that both methods provide similar analysis accuracy for dense observation networks, and in perfect model experiments with large ensembles. Nevertheless, E4DVar has clear benefits over 4DEnVar when substantial covariance localization is required to treat sampling error. The greatest advantage of the tangent-linear approach is that it implicitly propagates a localized, full-rank ensemble covariance in time, thus avoiding the need to localize a time-dependent ensemble covariance. The tangent linear and adjoint model operators also provide a means of evolving flow-dependent information from the climate-based error component, which is found to be beneficial for treating model error. Challenges that need to be overcome before adopting a pure ensemble framework are illustrated through experiments estimating time covariances with four-dimensional ensembles and comparing results with those estimated with a tangent linear model.
Social Workers’ Training Evaluated by a Cluster-Randomized Study
Authors: Malmberg-Heimonen Ira Elena 
Published: February 2015

Objective: Using a cluster-randomized design, this study evaluates whether a skill training program for social workers increases reemployment among welfare recipients. The program focuses on systematizing follow-up work within the areas of encounters with users, system-oriented efforts, and administrative work. Methods: Data consist of baseline and 18-month follow-up questionnaires for welfare recipients ( N = 617) in the 18 participating labor and welfare offices randomized into experimental and control groups. Full-time employment, part-time employment, and participation in active labor market programs were assessed. Results: After adjusting for the clustered structure of data, the findings demonstrate that social workers’ skill training increased reemployment among welfare recipients. Although neutral effects on full-time employment, there was a highly significant effect on part-time employment ( p = .000). In contrast, recipients from the control group were significantly more often in activation programs at the follow-up ( p = .004). Conclusions: Close and comprehensive follow-ups to support reemployment among welfare recipients should be emphasized.
Perceptions of the appropriateness of care in California adult intensive care units
Authors: Anstey Matthew H , Adams John L , McGlynn Elizabeth A 
Published: February 2015

Abstract
Introduction
Increased demand for expensive intensive care unit (ICU) services may contribute to rising health-care costs. A focus on appropriate use may offer a clinically meaningful way of finding the balance. We aimed to determine the extent and characteristics of perceived inappropriate treatment among ICU doctors and nurses, defined as an imbalance between the amount or intensity of treatments being provided and the patient’s expected prognosis or wishes.

Methods
This was a cross-sectional study of doctors and nurses providing care to patients in 56 adult ICUs in California between May and August 2013. In total, 1,363 doctors and nurses completed an anonymous electronic survey.

Results
Thirty-eight percent of 1,169 respondents (95% confidence interval (CI) 35% to 41%, 51.1% of physicians and 35.8% of nurses) identified at least one patient as receiving inappropriate treatment. Respondents most commonly reported that the amount of treatment provided was disproportionate to the patient’s expected prognosis or wishes—325 out of 429 (76%, 95% CI 72% to 80%)—and that treatment was ‘too much’ in 93% of cases. Factors associated with perceived inappropriateness of treatment were the belief that death in their ICU is seen as a failure (odds ratio (OR) 5.75, 95% CI 2.28 to 14.53, P = 0.000), profession (doctors more than nurses) (OR 2.50, 95% CI 1.58 to 3.97, P = 0.000), lack of collaboration between doctors and nurses (OR 1.84, 95% CI 1.21 to 2.80, P = 0.004), intent to leave their job (OR 1.73, 95% CI 1.18 to 2.55, P = 0.005), and the perceived responsibility to control health-care costs (OR 1.57, 95% CI 1.05 to 2.33, P = 0.026). Providers supported formal communication training (90%, 95% CI 88% to 92%) and mandatory family meetings (89%, 95% CI 87% to 91%) as potential solutions to reduce the provision of inappropriate treatment.

Conclusions
Doctors and nurses working in California ICUs frequently perceive treatment to be inappropriate. They also identified measures that could reduce the provision of inappropriate treatment.
A new two-tier strength assessment approach to the diagnosis of weakness in intensive care: an observational study
Authors: Parry Selina M , Berney Sue , Granger Catherine L , Dunlop Danielle L , Murphy Laura , El-Ansary Doa , Koopman René , Denehy Linda 
Published: February 2015

Abstract
Introduction
Intensive care unit-acquired weakness (ICU-AW) is a significant problem. There is currently widespread variability in the methods used for manual muscle testing and handgrip dynamometry (HGD) to diagnose ICU-AW. This study was conducted in two parts. The aims of this study were: to determine the inter-rater reliability and agreement of manual muscle strength testing using both isometric and through-range techniques using the Medical Research Council sum score and a new four-point scale, and to examine the validity of HGD and determine a cutoff score for the diagnosis of ICU-AW for the new four-point scale.

Methods
Part one involved evaluation of muscle strength by two physical therapists in 29 patients ventilated >48 hours. Manual strength testing was performed by both physical therapists using two techniques: isometric and through range; and two scoring systems: traditional six-point Medical Research Council scale and a new collapsed four-point scale. Part two involved assessment of handgrip strength conducted on 60 patients. A cutoff score for ICU-AW was identified for the new four-point scoring system.

Results
The incidence of ICU-AW was 42% (n = 25/60) in this study (based on HGD). In part one the highest reliability and agreement was observed for the isometric technique using the four-point scale (intraclass correlation coefficient = 0.90: kappa = 0.72 respectively). Differences existed between isometric and through-range scores (mean difference = 1.76 points, P = 0.005). In part two, HGD had a sensitivity of 0.88 and specificity of 0.80 for diagnosing ICU-AW. A cutoff score of 24 out of 36 points was identified for the four-point scale.

Conclusions
The isometric technique is recommended with reporting on a collapsed four-point scale. Because HGD is easy to perform and sensitive, we recommend a new two-tier approach to diagnosing ICU-AW that first tests handgrip strength with follow-up strength assessment using the isometric technique for muscle strength testing if handgrip strength falls below cutoff scores. Whilst our results for the four-point scale are encouraging, further research is required to confirm the findings of this study and determine the validity of the four-point scoring system and cutoff score developed of less than 24 out of 36 before recommending adoption into clinical practice.
Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring
Authors: Case Laure K , Wall Emma H , Osmanski Erin E , Dragon Julie A , Saligrama Naresha , Zachary James F , Lemos Bernardo , Blankenhorn Elizabeth P , Teuscher Cory 
Published: February 2015

Abstract
Background
The prevalence of some autoimmune diseases is greater in females compared with males, although disease severity is often greater in males. The reason for this sexual dimorphism is unknown, but it may reflect negative selection of Y chromosome-bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the sexual dimorphism in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in Y chromosome multicopy genes. Here, we test the hypothesis that CNV in Y chromosome multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice.

Results
We show that C57BL/6 J consomic strains of mice possessing an identical X chromosome and CNV in Y chromosome multicopy genes exhibit sperm head abnormalities and female-biased sex ratio. This is consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous X:Y chromosome multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of microRNAs within the sperm nucleus. Furthermore, in humans, families of probands with multiple sclerosis similarly exhibit a female-biased sex ratio, whereas families of probands affected with non-sexually dimorphic autoimmune diseases exhibit unbiased sex ratios.

Conclusions
These findings provide evidence for a mechanism at the level of the male gamete that contributes to the sexual dimorphism in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the sexual dimorphism in multiple sclerosis.
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome
Authors: Pingault Lise , Choulet Frédéric , Alberti Adriana , Glover Natasha , Wincker Patrick , Feuillet Catherine , Paux Etienne 
Published: February 2015

Abstract
Background
Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before.

Results
By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level.

Conclusions
Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.