bluuebunny/crossref_metadata_2025_split huggingface dataset:
A-Train Observations of Maritime Midlatitude Storm-Track Cloud Systems: Comparing the Southern Ocean against the North Atlantic
Authors: Huang Yi , Protat Alain , Siems Steven T. , Manton Michael J. 
Published: December 2014

Abstract
Cloud and precipitation properties of the midlatitude storm-track regions over the Southern Ocean (SO) and North Atlantic (NA) are explored using reanalysis datasets and A-Train observations from 2007 to 2011. In addition to the high-level retrieval products, lower-level observed variables—CloudSat radar reflectivity and Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) lidar attenuated backscatter—are directly examined using both contoured frequency by altitude diagrams (CFADs) and contoured frequency by temperature diagrams (CFTDs) to provide direct insight into thermodynamic phase properties. While the wintertime temperature profiles are similar over the two regions, the summertime environment is warmer over the NA. The NA atmosphere is generally moister than the SO, while the SO boundary layer is moister during winter. The results herein suggest that although the two regions exhibit many similarities in the prevalence of boundary layer clouds (BLCs) and frontal systems, notable differences exist. The NA environment exhibits stronger seasonality in thermodynamic structure, cloud, and precipitation properties than the SO. The regional differences of cloud properties are dominated by microphysics in winter and thermodynamics in summer. Glaciated clouds with higher reflectivities are found at warmer temperatures over the NA. BLCs (primarily below 1.5 km) are a predominant component over the SO. The wintertime boundary layer is shallower over the SO. Midlevel clouds consisting of smaller hydrometeors in higher concentration (potentially supercooled liquid water) are more frequently observed over the SO. Cirrus clouds are more prevalent over the NA. Notable differences exist in both the frequencies of thermodynamic phases of precipitation and intensity of warm rain over the two regions.
Mechanism of Action of Levonorgestrel Emergency Contraception
Authors: Kahlenborn Chris , Peck Rebecca , Severs Walter B. 
Published: December 2014

There has been much debate regarding levonorgestrel emergency contraception's (LNG-EC's) method of action since 1999 when the Food and Drug Administration first approved its use. Proponents of LNG-EC have argued that they have moral certitude that LNG-EC works via a non-abortifacient mechanism of action, and claim that all the major scientific and medical data consistently support this hypothesis. However, newer medical data serve to undermine the consistency of the non-abortifacient hypothesis and instead support the hypothesis that preovulatory administration of LNG-EC has significant potential to work via abortion. The implications of the newer data have important ramifications for medical personnel, patients, and both Catholic and non-Catholic emergency room protocols. In the future, technology such as the use of early pregnancy factor may have the potential to quantify how frequently preovulatory LNG-EC works via abortion. Lay Summary: How Plan B (levonorgestrel emergency contraception) works has been vigorously debated ever since the Food and Drug Administration approved it in 1999. Many doctors and researchers claim that it has either no—or at most—an extremely small chance of working via abortion. However, the latest scientific and medical evidence now demonstrates that levonorgestrel emergency contraception theoretically works via abortion quite often. The implications of the newer data have important ramifications for medical personnel, patients, and both Catholic and non-Catholic emergency room rape protocols.
Five hematologic tests and treatments to question
Authors: Hicks Lisa K. , Bering Harriet , Carson Kenneth R. , Haynes Adam E. , Kleinerman Judith , Kukreti Vishal , Ma Alice , Mueller Brigitta U. , O'Brien Sarah H. , Panepinto Julie A. , Pasquini Marcelo C. , Rajasekhar Anita , Sarode Ravi , Wood William A. 
Published: December 2014

AbstractChoosing Wisely® is a medical stewardship initiative led by the American Board of Internal Medicine Foundation in collaboration with professional medical societies in the United States. The American Society of Hematology (ASH) released its first Choosing Wisely® list in 2013. Using the same evidence-based methodology as in 2013, ASH has identified 5 additional tests and treatments that should be questioned by clinicians and patients under specific, indicated circumstances. The ASH 2014 Choosing Wisely® recommendations include: (1) do not anticoagulate for more than 3 months in patients experiencing a first venous thromboembolic event in the setting of major, transient risk factors for venous thromboembolism; (2) do not routinely transfuse for chronic anemia or uncomplicated pain crises in patients with sickle cell disease; (3) do not perform baseline or surveillance computed tomography scans in patients with asymptomatic, early-stage chronic lymphocytic leukemia; (4) do not test or treat for heparin-induced thrombocytopenia if the clinical pretest probability of heparin-induced thrombocytopenia is low; and (5) do not treat patients with immune thrombocytopenia unless they are bleeding or have very low platelet counts.
An implicit method for finding a common fixed point of a representation of nonexpansive mappings in Banach spaces
Authors: Hussain Nawab , Lashkarizadeh Bami Mahmood , Soori Ebrahim 
Published: December 2014

Abstract
We introduce an implicit method for finding an element of the set of common fixed points of a representation of nonexpansive mappings. Then we prove the strong convergence of the proposed implicit scheme to the common fixed point of a representation of nonexpansive mappings.

MSC:90C33, 47H10.
Current practices and barriers impairing physicians’ and nurses’ adherence to analgo-sedation recommendations in the intensive care unit - a national survey
Authors: Sneyers Barbara , Laterre Pierre-François , Perreault Marc M , Wouters Dominique , Spinewine Anne 
Published: December 2014

Abstract
Introduction
Appropriate management of analgo-sedation in the intensive care unit (ICU) is associated with improved patient outcomes. Our objectives were: a) to describe utilization of analgo-sedation regimens and strategies (assessment using scales, protocolized analgo-sedation and daily sedation interruption (DSI)) and b) to describe and compare perceptions challenging utilization of these strategies, amongst physicians and nurses.

Methods
In the 101 adult ICUs in Belgium, we surveyed all physicians and a sample of seven nurses per ICU. A multidisciplinary team designed a survey tool based on a previous qualitative study and a literature review. The latter was available in paper (for nurses essentially) and web based (for physicians). Topics addressed included: practices, perceptions regarding recommended strategies and demographics. Pre-testing involved respondents’ debriefings and test re-test reliability. Four reminders were sent.

Results
Response rate was 60% (898/1,491 participants) representing 94% (95/101) of all hospitals. Protocols were available to 31% of respondents. Validated scales to monitor pain in patients unable to self-report and to monitor sedation were available to 11% and 75% of respondents, respectively. Frequency of use of sedation scales varied (never to hourly). More physicians than nurses agreed with statements reporting benefits of sedation scales, including: increased autonomy for nurses (82% versus 68%, P <0.001), enhancement of their role (84% versus 66%, P <0.001), aid in monitoring administration of sedatives (83% versus 68%, P <0.001), and cost control (54% versus 29%, P <0.001). DSI was used in less than 25% of patients for 75% of respondents. More nurses than physicians indicated DSI is contra-indicated in hemodynamic instability (66% versus 53%, P <0.001) and complicated weaning from mechanical ventilation (47% versus 29%, P <0.001). Conversely, more physicians than nurses indicated contra-indications including: seizures (56% versus 40%, P <0.001) and refractory intracranial hypertension (90% versus 83%, P <0.001). More nurses than physicians agreed with statements reporting DSI impairs patient comfort (60% versus 37%, P <0.001) and increases complications such as self-extubation (82% versus 69%, P <0.001).

Conclusions
Current analgo-sedation practices leave room for improvement. Physicians and nurses meet different challenges in using appropriate analgo-sedation strategies. Implementational interventions must be tailored according to profession.
Expert consensus and recommendations on safety criteria for active mobilization of mechanically ventilated critically ill adults
Authors: Hodgson Carol L , Stiller Kathy , Needham Dale M , Tipping Claire J , Harrold Megan , Baldwin Claire E , Bradley Scott , Berney Sue , Caruana Lawrence R , Elliott Doug , Green Margot , Haines Kimberley , Higgins Alisa M , Kaukonen Kirsi-Maija , Leditschke Isabel Anne , Nickels Marc R , Paratz Jennifer , Patman Shane , Skinner Elizabeth H , Young Paul J , Zanni Jennifer M , Denehy Linda , Webb Steven A 
Published: December 2014

Abstract
Introduction
The aim of this study was to develop consensus recommendations on safety parameters for mobilizing adult, mechanically ventilated, intensive care unit (ICU) patients.

Methods
A systematic literature review was followed by a meeting of 23 multidisciplinary ICU experts to seek consensus regarding the safe mobilization of mechanically ventilated patients.

Results
Safety considerations were summarized in four categories: respiratory, cardiovascular, neurological and other. Consensus was achieved on all criteria for safe mobilization, with the exception being levels of vasoactive agents. Intubation via an endotracheal tube was not a contraindication to early mobilization and a fraction of inspired oxygen less than 0.6 with a percutaneous oxygen saturation more than 90% and a respiratory rate less than 30 breaths/minute were considered safe criteria for in- and out-of-bed mobilization if there were no other contraindications. At an international meeting, 94 multidisciplinary ICU clinicians concurred with the proposed recommendations.

Conclusion
Consensus recommendations regarding safety criteria for mobilization of adult, mechanically ventilated patients in the ICU have the potential to guide ICU rehabilitation whilst minimizing the risk of adverse events.
Vitamin D deficiency as a risk factor for infection, sepsis and mortality in the critically ill: systematic review and meta-analysis
Authors: de Haan Kim , Groeneveld AB Johan , de Geus Hilde RH , Egal Mohamud , Struijs Ard 
Published: December 2014

Abstract
Introduction
In Europe, vitamin D deficiency is highly prevalent varying between 40% and 60% in the healthy general adult population. The consequences of vitamin D deficiency for sepsis and outcome in critically ill patients remain controversial. We therefore systematically reviewed observational cohort studies on vitamin D deficiency in the intensive care unit.

Methods
Fourteen observational reports published from January 2000 to March 2014, retrieved from Pubmed and Embase, involving 9,715 critically ill patients and serum 25-hydroxyvitamin D3 (25 (OH)-D) concentrations, were meta-analysed.

Results
Levels of 25 (OH)-D less than 50 nmol/L were associated with increased rates of infection (risk ratio (RR) 1.49, 95% (confidence interval (CI) 1.12 to 1.99), P = 0.007), sepsis (RR 1.46, 95% (CI 1.27 to 1.68), P <0.001), 30-day mortality (RR 1.42, 95% (CI 1.00 to 2.02), P = 0.05), and in-hospital mortality (RR 1.79, 95% (CI 1.49 to 2.16), P <0.001). In a subgroup analysis of adjusted data including vitamin D deficiency as a risk factor for 30-day mortality the pooled RR was 1.76 (95% CI 1.37 to 2.26, P <0.001).

Conclusions
This meta-analysis suggests that vitamin D deficiency increases susceptibility for severe infections and mortality of the critically ill.
Clinical neurophysiological assessment of sepsis-associated brain dysfunction: a systematic review
Authors: Hosokawa Koji , Gaspard Nicolas , Su Fuhong , Oddo Mauro , Vincent Jean-Louis , Taccone Fabio Silvio 
Published: December 2014

Abstract
Introduction
Several studies have reported the presence of electroencephalography (EEG) abnormalities or altered evoked potentials (EPs) during sepsis. However, the role of these tests in the diagnosis and prognostic assessment of sepsis-associated encephalopathy remains unclear.

Methods
We performed a systematic search for studies evaluating EEG and/or EPs in adult (≥18 years) patients with sepsis-associated encephalopathy. The following outcomes were extracted: a) incidence of EEG/EP abnormalities; b) diagnosis of sepsis-associated delirium or encephalopathy with EEG/EP; c) outcome.

Results
Among 1976 citations, 17 articles met the inclusion criteria. The incidence of EEG abnormalities during sepsis ranged from 12% to 100% for background abnormality and 6% to 12% for presence of triphasic waves. Two studies found that epileptiform discharges and electrographic seizures were more common in critically ill patients with than without sepsis. In one study, EEG background abnormalities were related to the presence and the severity of encephalopathy. Background slowing or suppression and the presence of triphasic waves were also associated with higher mortality. A few studies demonstrated that quantitative EEG analysis and EP could show significant differences in patients with sepsis compared to controls but their association with encephalopathy and outcome was not evaluated.

Conclusions
Abnormalities in EEG and EPs are present in the majority of septic patients. There is some evidence to support EEG use in the detection and prognostication of sepsis-associated encephalopathy, but further clinical investigation is needed to confirm this suggestion.
Plasma glutamine concentration after intensive care unit discharge: an observational study
Authors: Smedberg Marie , Grass Johanna Nordmark , Pettersson Linn , Norberg Åke , Rooyackers Olav , Wernerman Jan 
Published: December 2014

Abstract
Introduction
Low plasma glutamine concentration at ICU admission is associated with unfavorable outcomes. The prediction of plasma glutamine concentration after ICU discharge on outcomes has not been characterized. In the recent Scandinavian Glutamine Trial, a survival advantage was seen with glutamine supplementation as long as patients stayed in the ICU. It was therefore hypothesized that the glutamine level may drop at ICU discharge, indicative of a sustained glutamine deficiency, which may be related to outcome.

Methods
Fully fed ICU patients intravenously supplemented with glutamine for >3 days were studied at ICU discharge and post ICU. In study A, plasma glutamine level was followed every 5 to 7 days post ICU of the remaining hospital stay and compared to the level on the day of ICU discharge (n = 63). In study B, plasma glutamine level 24 to 72 hours after ICU discharge was related to 12-month all-cause mortality (n = 100).

Results
Post-ICU plasma glutamine levels were within normal range and were not found to be predictive for mortality outcome. Plasma glutamine level at discharge, on the other hand, was within normal limits but higher in nonsurvivors. In addition, it was adding prediction value to discharge SOFA scores for post-ICU mortality.

Conclusions
Post-ICU glutamine levels are not indicative of glutamine depletion. The relation between plasma glutamine concentration and glutamine availability during critical illness is not well understood, and needs to be studied further to define the possible role for glutamine supplementation.
The thermodynamic brain
Authors: Donnelly Joseph , Czosnyka Marek 
Published: December 2014

AbstractApart from its complex functionality, the brain is a robust thermodynamic machine; the tissue metabolic rate is high and it is thermally shielded by a skull. Therefore, if there is no high-volume blood flow to cool and stabilize the brain temperature, the possibility of unstable behavior seems to be high. Inflowing arterial blood is normally cooler than the brain tissue temperature, and outflowing venous blood is normally warmer than arterial blood but cooler than the brain tissue. Brain blood flow can thus be understood as a cooler for the brain. Pros and cons of clinical measurement, with clear indication for a multimodal monitoring approach, are discussed along with a brief review of basic facts known about temperature, cerebral blood flow and volume, intracranial pressure, and compartmental compliances of the brain.
Discovery of genes affecting resistance of barley to adapted and non-adapted powdery mildew fungi
Authors: Douchkov Dimitar , Lück Stefanie , Johrde Annika , Nowara Daniela , Himmelbach Axel , Rajaraman Jeyaraman , Stein Nils , Sharma Rajiv , Kilian Benjamin , Schweizer Patrick 
Published: December 2014

Abstract
Background
Non-host resistance, NHR, to non-adapted pathogens and quantitative host resistance, QR, confer durable protection to plants and are important for securing yield in a longer perspective. However, a more targeted exploitation of the trait usually possessing a complex mode of inheritance by many quantitative trait loci, QTLs, will require a better understanding of the most important genes and alleles.

Results
Here we present results from a transient-induced gene silencing, TIGS, approach of candidate genes for NHR and QR in barley against the powdery mildew fungus Blumeria graminis. Genes were selected based on transcript regulation, multigene-family membership or genetic map position. Out of 1,144 tested RNAi-target genes, 96 significantly affected resistance to the non-adapted wheat- or the compatible barley powdery mildew fungus, with an overlap of four genes. TIGS results for QR were combined with transcript regulation data, allele-trait associations, QTL co-localization and copy number variation resulting in a meta-dataset of 51 strong candidate genes with convergent evidence for a role in QR.

Conclusions
This study represents an initial, functional inventory of approximately 3% of the barley transcriptome for a role in NHR or QR against the powdery mildew pathogen. The discovered candidate genes support the idea that QR in this Triticeae host is primarily based on pathogen-associated molecular pattern-triggered immunity, which is compromised by effector molecules produced by the compatible pathogen. The overlap of four genes with significant TIGS effects both in the NHR and QR screens also indicates shared components for both forms of durable pathogen resistance.
Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse
Authors: Auclair Ghislain , Guibert Sylvain , Bender Ambre , Weber Michael 
Published: December 2014

Abstract
Background
In the mouse, the patterns of DNA methylation are established during early embryonic development in the epiblast. We quantified the targets and kinetics of DNA methylation acquisition in epiblast cells, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process.

Results
We generated single-base maps of DNA methylation from the blastocyst to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity. DNA methylation is established within two days of implantation between embryonic days 4.5 and 6.5. The kinetics of de novo methylation are uniform throughout the genome, suggesting a random mechanism of deposition. In contrast, many CpG islands acquire methylation slowly in late epiblast cells. Five percent of CpG islands gain methylation and are found in the promoters of germline genes and in exons of important developmental genes. The onset of global methylation correlates with the upregulation of Dnmt3a/b genes in the early epiblast. DNMT3A and DNMT3B act redundantly to methylate the bulk genome and repetitive elements, whereas DNMT3B has a prominent role in the methylation of CpG islands on autosomes and the X chromosome. Reduced CpG island methylation in Dnmt3b-deficient embryos correlates with gene reactivation in promoters but reduced transcript abundance in gene bodies. Finally, DNMT3B establishes secondary methylation marks at imprinted loci, which distinguishes bona fide germline from somatic methylation imprints.

Conclusions
We reveal that the DNMT3 de novo methyltransferases play both redundant and specific functions in the establishment of DNA methylation in the mouse embryo.
Organization and evolution of transposable elements along the bread wheat chromosome 3B
Authors: Daron Josquin , Glover Natasha , Pingault Lise , Theil Sébastien , Jamilloux Véronique , Paux Etienne , Barbe Valérie , Mangenot Sophie , Alberti Adriana , Wincker Patrick , Quesneville Hadi , Feuillet Catherine , Choulet Frédéric 
Published: December 2014

Abstract
Background
The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far.

Results
We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.

Conclusion
Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
Transcriptome-wide modulation of splicing by the exon junction complex
Authors: Wang Zhen , Murigneux Valentine , Le Hir Hervé 
Published: December 2014

Abstract
Background
The exon junction complex (EJC) is a dynamic multi-protein complex deposited onto nuclear spliced mRNAs upstream of exon-exon junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells.

Results
Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates.

Conclusion
Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition.