bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical Prediction of Integrated Kinetic Energy in North Atlantic Tropical Cyclones
Authors: Kozar Michael E. , Misra Vasubandhu 
Published: October 2014

Abstract
Integrated kinetic energy (IKE) is a useful quantity that measures the size and strength of a tropical cyclone wind field. As a result, it is inherently related to the destructive potential of these powerful storms. In most current operational settings, there are limited resources designed to assess the IKE of a tropical cyclone because storm track and maximum intensity are typically prioritized. Therefore, to complement existing forecasting tools, a statistical scheme is created to project fluctuations of IKE in North Atlantic tropical cyclones for several forecast intervals out to 72 h. The resulting scheme, named Statistical Prediction of Integrated Kinetic Energy (SPIKE), utilizes multivariate normal regression models trained on environmental and storm-related predictors from all North Atlantic tropical cyclones occurring from 1990 to 2011. During this training interval, SPIKE outperforms persistence and is capable of explaining more than 80% of observed variance in total IKE values at a forecast interval of 12 h, trailing down to just below 60% explained variance at an interval of 72 h. The skill of the SPIKE model is evaluated further using bootstrapping exercises in order to gauge the predictive abilities of the statistical scheme. In addition, the performance of the SPIKE model is also evaluated for the 2012 Atlantic hurricane season, which notably falls outside of the training interval. Ultimately, the validation exercises return shared variance scores similar to those found in the training exercises, serving as a proof of concept that the SPIKE model can be used to project IKE values when given accurate predictor data.
Observations of Wall Cloud Formation in Supercell Thunderstorms during VORTEX2
Authors: Atkins Nolan T. , Glidden Eva M. , Nicholson Timothy M. 
Published: October 2014

Abstract
This study presents an integrated analysis of dual-Doppler, cloud photogrammetry, surface mobile mesonet, and sounding data to examine wall cloud formation in two supercells observed during the Verification of the Origins of Rotation in Tornadoes Experiment II (VORTEX2). One of the wall clouds contained significant rotation and spawned an (enhanced Fujita) EF2 tornado, while the other was clearly displaced horizontally from the mesocyclone and exhibited little rotation at the time of data collection. Backward parcel trajectories show that the majority of the air entering the wall cloud base originates in the forward-flank region. A small fraction of the parcels enter the wall cloud base from the inflow. Some rear-flank downdraft parcels descend into the strongly rotating wall cloud. For both wall clouds, much of the observed wall cloud lowering is attributed to evaporatively cooled parcels in the forward-flank region being ingested into the low-level updraft. Additional wall cloud-base lowering is observed near the circulation center of the strongly rotating wall cloud. This localized lowering is created by the pressure deficit and associated cooling. The observational results presented herein are compared to long-standing wall cloud formation conceptual models published in the refereed literature.
Implementation of a Stochastic Eddy-Diffusivity/Mass-Flux Parameterization into the Navy Global Environmental Model
Authors: Sušelj Kay , Hogan Timothy F. , Teixeira João 
Published: October 2014

Abstract
A unified boundary layer and shallow convection parameterization based on a stochastic eddy-diffusivity/mass-flux (EDMF) approach is implemented and tested in the Navy Global Environmental Model (NAVGEM). The primary goals of this work are to improve the representation of convectively driven boundary layers and the coupling between the boundary layer and cumulus regions. Within the EDMF framework the subgrid vertical fluxes are calculated as a sum of an eddy-diffusivity part, which in the current implementation is based on the approach developed by Louis in the late 1970s, and a stochastic mass-flux parameterization. The mass-flux parameterization is a model for both dry and moist convective thermals. Dry thermals, which represent surface-forced coherent structures in a flow, provide countergradient mixing in the boundary layer and, if conditions permit, are the roots for moist thermals. Moist thermals represent shallow convective clouds. The new parameterization implemented in a single-column model (SCM) version of NAVGEM is shown to be able to realistically simulate a variety of dry and moist convective cases. The NAVGEM SCM results are validated against large-eddy-simulation results. The skill of NAVGEM as a global weather forecasting model is considerably improved with the new EDMF parameterization. The EDMF parameterization became part of the operational NAVGEM in November 2013.
The electronic structure and optical properties of Mn and B, C, N co-doped MoS2 monolayers
Authors: Xu Wei-bin , Huang Bao-jun , Li Ping , Li Feng , Zhang Chang-wen , Wang Pei-ji 
Published: October 2014

Abstract
The electronic structure and optical properties of Mn and B, C, N co-doped molybdenum disulfide (MoS2) monolayers have been investigated through first-principles calculations. It is shown that the MoS2 monolayer reflects magnetism with a magnetic moment of 0.87 μB when co-doped with Mn-C. However, the systems co-doped with Mn-B and Mn-N atoms exhibit semiconducting behavior and their energy bandgaps are 1.03 and 0.81 eV, respectively. The bandgaps of the co-doped systems are smaller than those of the corresponding pristine forms, due to effective charge compensation between Mn and B (N) atoms. The optical properties of Mn-B (C, N) co-doped systems all reflect the redshift phenomenon. The absorption edge of the pure molybdenum disulfide monolayer is 0.8 eV, while the absorption edges of the Mn-B, Mn-C, and Mn-N co-doped systems become 0.45, 0.5, and 0 eV, respectively. As a potential material, MoS2 is widely used in many fields such as the production of optoelectronic devices, military devices, and civil devices.
Measuring pain in non-verbal critically ill patients: which pain instrument?
Authors: Payen Jean-Francois , Gélinas Céline 
Published: October 2014

AbstractPain is experienced by many critically ill patients. Although the patient’s self-report represents the gold-standard measure for pain, many patients are unable to communicate in the ICU. In this commentary, we discuss the study findings comparing three objective scales for the assessment of pain in non-verbal patients and the importance of the tool selection process.
How much oxygen in adult cardiac arrest?
Authors: Dell’Anna Antonio Maria , Lamanna Irene , Vincent Jean-Louis , Taccone Fabio Silvio 
Published: October 2014

AbstractAlthough experimental studies have suggested that a high arterial oxygen pressure (PaO2) might aggravate post-anoxic brain injury, clinical studies in patients resuscitated from cardiac arrest (CA) have given conflicting results. Some studies found that a PaO2 of more than 300 mm Hg (hyperoxemia) was an independent predictor of poor outcome, but others reported no association between blood oxygenation and neurological recovery in this setting. In this article, we review the potential mechanisms of oxygen toxicity after CA, animal data available in this field, and key human studies dealing with the impact of oxygen management in CA patients, highlighting some potential confounders and limitations and indicating future areas of research in this field. From the currently available literature, high oxygen concentrations during cardiopulmonary resuscitation seem preferable, whereas hyperoxemia should be avoided in the post-CA care. A specific threshold for oxygen toxicity has not yet been identified. The mechanisms of oxygen toxicity after CA, such as seizure development, reactive oxygen species production, and the development of organ dysfunction, need to be further evaluated in prospective studies.
Etomidate for anesthesia induction: friends or foe in major cardiac surgery?
Authors: De Jong Audrey , Jaber Samir 
Published: October 2014

AbstractUse of etomidate for anesthesia induction is still debated. In the previous issue of Critical Care, Heinrich and colleagues reported that etomidate for anesthesia induction had similar outcome in comparison with other drugs, in a specific population of 3,054 patients ahead of major cardiac surgery. For the authors, the similar outcomes for mortality and length of hospital stay add to the hemodynamic stability and the improved intubation conditions to support keeping etomidate in the emergency drugs armamentarium for induction of anesthesia in patients at risk of hemodynamic failure. This commentary reviews the results and implications of their study.
DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival
Authors: Conway Kathleen , Edmiston Sharon N , May Ryan , Kuan Pei Fen , Chu Haitao , Bryant Christopher , Tse Chiu-Kit , Swift-Scanlan Theresa , Geradts Joseph , Troester Melissa A , Millikan Robert C 
Published: October 2014

Abstract
Introduction
Breast cancer is a heterogeneous disease, with several intrinsic subtypes differing by hormone receptor (HR) status, molecular profiles, and prognosis. However, the role of DNA methylation in breast cancer development and progression and its relationship with the intrinsic tumor subtypes are not fully understood.

Methods
A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 breast tumors from the Carolina Breast Cancer Study, a population-based study of invasive breast cancer.

Results
Consensus clustering using methylation (β) values for the 167 most variant CpG loci defined four clusters differing most distinctly in HR status, intrinsic subtype (luminal versus basal-like), and p53 mutation status. Supervised analyses for HR status, subtype, and p53 status identified 266 differentially methylated CpG loci with considerable overlap. Genes relatively hypermethylated in HR+, luminal A, or p53 wild-type breast cancers included FABP3, FGF2, FZD9, GAS7, HDAC9, HOXA11, MME, PAX6, POMC, PTGS2, RASSF1, RBP1, and SCGB3A1, whereas those more highly methylated in HR-, basal-like, or p53 mutant tumors included BCR, C4B, DAB2IP, MEST, RARA, SEPT5, TFF1, THY1, and SERPINA5. Clustering also defined a hypermethylated luminal-enriched tumor cluster 3 that gene ontology analysis revealed to be enriched for homeobox and other developmental genes (ASCL2, DLK1, EYA4, GAS7, HOXA5, HOXA9, HOXB13, IHH, IPF1, ISL1, PAX6, TBX1, SOX1, and SOX17). Although basal-enriched cluster 2 showed worse short-term survival, the luminal-enriched cluster 3 showed worse long-term survival but was not independently prognostic in multivariate Cox proportional hazard analysis, likely due to the mostly early stage cases in this dataset.

Conclusions
This study demonstrates that epigenetic patterns are strongly associated with HR status, subtype, and p53 mutation status and may show heterogeneity within tumor subclass. Among HR+ breast tumors, a subset exhibiting a gene signature characterized by hypermethylation of developmental genes and poorer clinicopathologic features may have prognostic value and requires further study. Genes differentially methylated between clinically important tumor subsets have roles in differentiation, development, and tumor growth and may be critical to establishing and maintaining tumor phenotypes and clinical outcomes.
Sequence specificity incompletely defines the genome-wide occupancy of Myc
Authors: Guo Jiannan , Li Tiandao , Schipper Joshua , Nilson Kyle A , Fordjour Francis K , Cooper Jeffrey J , Gordân Raluca , Price David H 
Published: October 2014

Abstract
Background
The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.

Results
By analyzing ChIP-Seq datasets, we demonstrate that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II, Pol II, transcription machinery significantly better than with E-boxes. Metagene analyses show that in promoter regions, Myc is uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 15 bp upstream of Myc. We re-evaluate the DNA binding properties of full length Myc-Max proteins. Electrophoretic mobility shift assay results demonstrate Myc-Max heterodimers display significant sequence preference, but have high affinity for any DNA. Quantification of the relative affinities of Myc-Max for all possible 8-mers using universal protein-binding microarray assays shows that sequences surrounding core 6-mers significantly affect binding. Compared to the in vitro sequence preferences, Myc-Max genomic occupancy measured by ChIP-Seq is largely, although not completely, independent of sequence specificity.

Conclusions
We quantified the affinity of Myc-Max to all possible 8-mers and compared this with the sites of Myc binding across the human genome. Our results indicate that the genomic occupancy of Myc cannot be explained by its intrinsic DNA specificity and suggest that the transcription machinery and associated promoter accessibility play a predominant role in Myc recruitment.
Subchondral bone influences chondrogenic differentiation and collagen production of human bone marrow-derived mesenchymal stem cells and articular chondrocytes
Authors: Leyh Michaela , Seitz Andreas , Dürselen Lutz , Schaumburger Jens , Ignatius Anita , Grifka Joachim , Grässel Susanne 
Published: October 2014

Abstract
Introduction
Osteoarthritis (OA) is characterized by an imbalance in cartilage and underlying subchondral bone homeostasis. We hypothesized that signals from the subchondral bone may modulate production of matrix components, alter chondrogenic differentiation potential of cocultured bone marrow-derived mesenchymal stem cells (BMSC) and induce a phenotypic shift in differentiated OA chondrocytes.

Methods
We established a novel coculture model between BMSC, mixed cultures (BMSC and chondrocytes) and chondrocytes embedded in fibrin gel with OA and normal subchondral bone explants (OAB and NB). Tissues and cells were either derived from OA or trauma patients. In addition, we used adipose-derived stem cells (ASC) from liposuction. With gene expression analysis, biochemical assays, immunofluorescence and biomechanical tests we characterized the properties of newly generated extracellular matrix (ECM) from chondrocytes and chondrogenically differentiating BMSC cocultured with OAB or NB in comparison with monocultures (cultures without bone explants).

Results
Overall, gene expression of collagens of OAB and NB cocultured cells was reduced compared to monocultures. Concomitantly, we observed significantly lower collagen I, II and III and glycosaminoglycan (GAG) production in OAB cocultured cell lysates. In parallel, we detected increased concentrations of soluble GAGs and basic fibroblast growth factor (bFGF), interleukin (IL)-6 and IL-8 in supernatants of OAB and NB cocultures mainly at early time points. IL-1ß concentration was increased in supernatants of OAB cocultures, but not in NB cocultures. Cell-free NB or OAB explants released different amounts of IL-1ß, bFGF and soluble GAG into cell culture supernatants. In comparison to cocultures, monocultures exhibited higher Young’s modulus and equilibrium modulus. Stimulation of monocultures with IL-1ß led to a downregulation of aggrecan (ACAN) gene expression and in general to induced matrix metalloprotease (MMP)2, MMP3 and MMP-13 gene expression while IL-6 and IL-8 stimulation partly reduced ACAN, MMP3 and MMP-13 gene expression.

Conclusions
Our results suggest an alteration of molecular composition and mechanical properties of the newly formed ECM in subchondral bone cocultures. We suggest that soluble factors, that is interleukins and bFGF, released in cocultures exert inhibitory effects on collagen and temporary effects on proteoglycan production, which finally results in a reduction of mechanical strength of newly formed fibrillar networks.
Study protocol: Randomised controlled trial to evaluate the impact of an educational programme on Alzheimer’s disease patients’ quality of life
Authors: Villars Hélène , Gardette Virginie , Perrin Amélie , Hein Christophe , Elmalem Sophie , de Peretti Eva , Zueras Audrey , Vellas Bruno , Nourhashémi Fati 
Published: October 2014

Abstract
Introduction
Therapeutic education is expanding in the management of Alzheimer’s disease (AD) patients. Several studies have revealed a positive impact of therapeutic educational programmes on the caregiver’s burden and/or quality of life. However, to date, no study has evaluated its impact on the quality of life of the AD patient.

Methods
The THERAD study (THerapeutic Education in Alzheimer’s Disease) is a 12-month randomised controlled trial that started in January 2013. This paper describes the study protocol. THERAD plans to enroll 170 dyads (AD patient and caregiver) on the basis of the following criteria: patient at a mild to moderately severe stage of AD, living at home, receiving support from a family caregiver. The main outcome is the patient’s quality of life assessed by the Logsdon QoL-AD scale at 2 months, reported by the caregiver. The study is being led by geriatricians trained in therapeutic education at Toulouse University Hospital in France. To date, 107 caregiver/patient dyads have been recruited.

Conclusion
This is the first trial designed to assess the specific impact of a therapeutic educational programme on the AD patient’s quality of life. The final results will be available in 2015.

Trial registration
[ClinicalTrials.gov: NCT01796314] Registered 19 February 2013
Biological and clinical significance of cancer stem cell plasticity
Authors: Zhu Yongyou , Luo Ming , Brooks Michael , Clouthier Shawn G , Wicha Max S 
Published: October 2014

AbstractIn the past decade, the traditional view of cancers as a homogeneous collection of malignant cells is being replaced by a model of ever increasing complexity suggesting that cancers are complex tissues composed of multiple cell types. This complex model of tumorigenesis has been well supported by a growing body of evidence indicating that most cancers including those derived from blood and solid tissues display a hierarchical organization of tumor cells with phenotypic and functional heterogeneity and at the apex of this hierarchy are cells capable of self‐renewal. These “tumor imitating cells” or “cancer stem cells” drive tumorigenesis and contribute to metastasis, treatment resistance and tumor relapse. Although tumor stem cells themselves may display both genetic and phenotypic heterogeneity, recent studies have demonstrated that cancer stem cells maintain plasticity to transition between mesenchymal‐like (EMT) and epithelial‐like (MET) states, which may be regulated by the tumor microenvironment. These stem cell state transitions may play a fundamental role in tumor progression and treatment resistance. In this review, we discuss the emerging knowledge regarding the plasticity of cancer stem cells with an emphasis on the signaling pathways and noncoding RNAs including microRNAs (miRNA) and long non‐coding RNAs (lncRNAs) in regulation of this plasticity during tumor growth and metastasis. Lastly, we point out the importance of targeting both the EMT and MET states of CSCs in order to eliminate these lethal seeds of cancers.
A randomized controlled trial of gonadotropin-releasing hormone agonist versus gonadotropin-releasing hormone antagonist in Iranian infertile couples: oocyte gene expression
Authors: Hoseini Fatemeh Sadat , Noori Mugahi Seyed Mohammad Hossein , Akbari-Asbagh Firoozeh , Eftekhari-Yazdi Poopak , Aflatoonian Behrouz , Aghaee-Bakhtiari Seyed Hamid , Aflatoonian Reza , Salsabili Nasser 
Published: October 2014

Abstract

Background
The main objective of the present work was to compare the effects of the gonadotropin-releasing hormone agonist (GnRH-a) and GnRH antagonist (GnRH-ant) on the gene expression profiles of oocytes obtained from Iranian infertile couples undergoing in vitro fertilization (IVF).

Methods
Fifty infertile couples who underwent IVF between June 2012 and November 2013 at the Infertility Center of Tehran Women General Hospital, Tehran University of Medical Sciences, were included in this study. We included women that had undergone IVF treatment because of male factor, tubal factor, or unexplained infertility. The women randomly underwent controlled ovarian stimulation (COS) with either the GnRH-a (n = 26) or the GnRH-ant (n = 24). We obtained 50 germinal vesicle (GV) oocytes donated by women in each group. After the sampling, pool of 50 GV oocytes for each group was separately analyzed by quantitative polymerase chain reaction (qPCR).

Result
The expression levels of Adenosine triphosphatase 6 (ATPase 6), Bone morphogenetic protein 15 (BMP15), and Neuronal apoptosis inhibitory protein (NAIP) genes were significantly upregulated in the GnRH-ant group compared to the GnRH-a group, with the fold change of 3.990 (SD ± 1.325), 6.274 (SD ± 1.542), and 2.156 (SD ± 1.443), respectively, (P < 0.001). Growth differentiation factor 9 (GDF9) mRNA did not have any expression in the GnRH-a group; however, GDF9 mRNA was expressed in the GnRH-ant group. Finally, it was found that the genes involved in the DNA repairing and cell cycle checkpoint did not have any expression in either group.

Conclusion
The present study showed, for the first time, the expression levels of genes involved in the cytoplasmic maturity (BMP15, GDF9), adenosine triphosphate production (ATPase 6), and antiapoptotic process (NAIP), in human GV oocytes were significantly higher in the GnRH-anta group than in the GnRH-a group in COS. Higher expression level of these genes when GnRH-ant protocol is applied, this protocol seems to be a more appropriate choice for women with poly cystic ovarian syndrome, because it can probably improve the expression of the aforementioned genes.

Trial registration
Current Controlled Trials: IRCT 2014031112307 N3.