bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Approach to Generating Mutually Independent Initial Perturbations for Ensemble Forecasts: Orthogonal Conditional Nonlinear Optimal Perturbations
Authors: Duan Wansuo , Huo Zhenhua 
Published: December 2015

Abstract
Conditional nonlinear optimal perturbation (CNOP) is the initial perturbation that satisfies a certain physical constraint and causes the largest nonlinear evolution at prediction time. To yield mutually independent initial perturbations in ensemble forecasts, orthogonal CNOPs are developed. Orthogonal CNOPs are then applied to a Lorenz-96 model to generate initial perturbations for ensemble forecasting, as compared with orthogonal singular vectors (SVs). When the initial analysis errors are fast growing, the ensemble forecasts generated by orthogonal CNOPs of the control forecasts perform much more skillfully. Nevertheless, for slow-growing initial analysis errors, the ensemble forecasts generated by orthogonal SVs achieve higher skill when the ensemble initial perturbations are large, whereas the ensemble forecasts generated by orthogonal CNOPs achieve almost the same forecast skill as those generated by orthogonal SVs when the ensemble initial perturbations are sufficiently small. The initial analysis errors that possess much faster growth behavior are easily influenced by nonlinearity, and extreme events (extreme here refers to strong), because of strong nonlinear instability, may be much more likely to cause fast growth of initial analysis errors. Therefore, the ensemble forecasts generated by orthogonal CNOPs may have higher skill than those generated by orthogonal SVs for extreme events; in particular, the ensemble forecasts generated by orthogonal CNOPs, compared with those generated by orthogonal SVs, require a much smaller number of ensemble members to achieve high skill. Therefore, orthogonal CNOPs may provide another useful technique to generate initial perturbations for ensemble forecasting.
Tropical Atmospheric Forcing of the Wintertime North Atlantic Oscillation
Authors: Yu Bin , Lin Hai 
Published: December 2015

Abstract
The relationship between the interannual wintertime variability of the North Atlantic Oscillation (NAO) and tropical heating anomalies is examined using the NCEP–NCAR reanalysis and observation-based sea surface temperature (SST) and precipitation data for the period from 1980 to 2011. The NAO is found to be significantly correlated with the precipitation anomalies in the tropical Indian Ocean and tropical American–Atlantic region, but not with the underlying SST anomalies. The tropical heating impact on the NAO is examined and the evolution process of the influence is explored by numerical experiments using a primitive equation atmospheric model forced by atmospheric heating perturbations. Results from the reanalysis data and numerical experiments suggest that the atmospheric heating in the tropical Indian Ocean appears to be a driving force for the NAO variability. The atmospheric response to the tropical heating involves the combined effects of Rossby wave dispersion, normal mode instability, and transient eddy feedback. The remote forcing influence on the NAO tends to be organized and achieved by the circumglobal teleconnection pattern. By contrast, the influence of the tropical American–Atlantic heating on the NAO is weak. The linkage between the NAO and the tropical American–Atlantic heating is likely through the anomalously meridional atmospheric circulation over the Atlantic Ocean.
Mid- to Inner-Shelf Coupled ROMS–SWAN Model–Data Comparison of Currents and Temperature: Diurnal and Semidiurnal Variability
Authors: Kumar Nirnimesh , Feddersen Falk , Suanda Sutara , Uchiyama Yusuke , McWilliams James 
Published: December 2015

AbstractAccurately representing diurnal and semidiurnal internal variability is necessary to investigate inner-shelf to midshelf exchange processes. Here, a coupled Regional Ocean Model System (ROMS)–Simulating Waves Nearshore (SWAN) model is compared to observed diurnal and semidiurnal internal tidal variability on the mid and inner shelf (26–8 m water depth) near San Pedro Bay, California. Modeled mean stratification is about one-half of that observed. Modeled and observed baroclinic velocity rotary spectra are similar in the diurnal and semidiurnal band. Modeled and observed temperature spectra have similar diurnal and semidiurnal band structure, although the modeled is weaker. The observed and modeled diurnal and semidiurnal baroclinic velocity- and temperature-dominant vertical structures are similar and consistent with mode-one internal motions. Both observed and modeled diurnal baroclinic kinetic energy are strongly correlated to diurnal wind forcing and enhanced by subtidal vorticity-induced reduction in the inertial frequency. The mid- and inner-shelf modeled diurnal depth-integrated heat budget is a balance between advective heat flux divergence and temperature time derivative. Temperature–velocity phase indicates progressive semidiurnal internal tide on the midshelf and largely standing internal tide on the inner shelf in both observed and modeled. The ratio of observed to modeled inferred phase speed is consistent with the observed to modeled stratification. The San Pedro Bay modeled semidiurnal internal tide has significant spatial variability, variable incident wave angles, and multiple local generation sites. Overall, the coupled ROMS–SWAN model represents well the complex diurnal and semidiurnal internal variability from the mid to the inner shelf.
Reducing Correlation Sampling Error in Ensemble Kalman Filter Data Assimilation
Authors: Anderson Jeffrey L. 
Published: December 2015

Abstract
Ensemble Kalman filters are widely used for data assimilation in large geophysical models. Good results with affordable ensemble sizes require enhancements to the basic algorithms to deal with insufficient ensemble variance and spurious ensemble correlations between observations and state variables. These challenges are often dealt with by using inflation and localization algorithms. A new method for understanding and reducing some ensemble filter errors is introduced and tested. The method assumes that sampling error due to small ensemble size is the primary source of error. Sampling error in the ensemble correlations between observations and state variables is reduced by estimating the distribution of correlations as part of the ensemble filter algorithm. This correlation error reduction (CER) algorithm can produce high-quality ensemble assimilations in low-order models without using any a priori localization like a specified localization function. The method is also applied in an observing system simulation experiment with a very coarse resolution dry atmospheric general circulation model. This demonstrates that the algorithm provides insight into the need for localization in large geophysical applications, suggesting that sampling error may be a primary cause in some cases.
Alemtuzumab levels impact acute GVHD, mixed chimerism, and lymphocyte recovery following alemtuzumab, fludarabine, and melphalan RIC HCT
Authors: Marsh Rebecca A. , Lane Adam , Mehta Parinda A. , Neumeier Lisa , Jodele Sonata , Davies Stella M. , Filipovich Alexandra H. 
Published: December 2015

Key Points
Alemtuzumab levels impact acute GVHD, mixed chimerism, and lymphocyte recovery after alemtuzumab, fludarabine, and melphalan RIC HCT. An in vivo lytic threshold appears to lie near 0.1 to 0.16 μg/mL; targeted dose trials are warranted to optimize outcomes.
Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose
Authors: Van der Nest M. A. , Steenkamp E. T. , McTaggart A. R. , Trollip C. , Godlonton T. , Sauerman E. , Roodt D. , Naidoo K. , Coetzee M. P. A. , Wilken P. M. , Wingfield M. J. , Wingfield B. D. 
Published: December 2015

Abstract
Background
Proteins in the Glycoside Hydrolase family 32 (GH32) are carbohydrate-active enzymes known as invertases that hydrolyse the glycosidic bonds of complex saccharides. Fungi rely on these enzymes to gain access to and utilize plant-derived sucrose. In fungi, GH32 invertase genes are found in higher copy numbers in the genomes of pathogens when compared to closely related saprophytes, suggesting an association between invertases and ecological strategy. The aim of this study was to investigate the distribution and evolution of GH32 invertases in the Ceratocystidaceae using a comparative genomics approach. This fungal family provides an interesting model to study the evolution of these genes, because it includes economically important pathogenic species such as Ceratocystis fimbriata, C. manginecans and C. albifundus, as well as saprophytic species such as Huntiella moniliformis, H. omanensis and H. savannae.

Results
The publicly available Ceratocystidaceae genome sequences, as well as the H. savannae genome sequenced here, allowed for the identification of novel GH32-like sequences. The de novo assembly of the H. savannae draft genome consisted of 28.54 megabases that coded for 7 687 putative genes of which one represented a GH32 family member. The number of GH32 gene family members appeared to be related to the ecological adaptations of these fungi. The pathogenic Ceratocystis species all contained two GH32 family genes (a putative cell wall and a putative vacuolar invertase), while the saprophytic Huntiella species had only one of these genes (a putative cell wall invertase). Further analysis showed that the evolution of the GH32 gene family in the Ceratocystidaceae involved transposable element-based retro-transposition and translocation. As an example, the activity of a Fot5-like element likely facilitated the assembly of the genomic regions harbouring the GH32 family genes in Ceratocystis.

Conclusions
This study provides insight into the evolutionary history of the GH32 gene family in Ceratocystidaceae. Our findings suggest that transposable elements shaped the evolution of the GH32 gene family, which in turn determines the sucrolytic activities and related ecological strategies of the Ceratocystidaceae species that harbour them. The study also provides insights into the role of carbohydrate-active enzymes in plant-fungal interactions and adds to our understanding of the evolution of these enzymes and their role in the life style of these fungi.
Cellular and molecular mechanisms in graft-versus-host disease
Authors: Zhang Lingling , Chu Jianhong , Yu Jianhua , Wei Wei 
Published: December 2015

AbstractGraft-versus-host disease is a complication in patients undergoing hematopoietic stem cell transplantation. Graft-versus-host disease includes acute graft-versus-host disease and chronic graft-versus-host disease. Host APCs (e.g., dendritic cells and macrophages), effector T cells (e.g., Th1, Th17, and abnormal Th17:regulatory T cell ratio), B cells, and NK cells are implicated in graft-versus-host disease physiopathology. Proinflammation cytokines (e.g., IL-17, IL-1β, and TNF-α) are increased in graft-versus-host disease. Costimulatory molecules play an important role in inducing graft-versus-host disease. Pattern-recognition receptors, such as TLRs and nucleotide-binding oligomerization domain-like receptors, are critically involved in the pathogenesis of graft-versus-host disease. Complement system C3 mediates Th1/Th17 polarization in human T cell activation and skin graft-versus-host disease. Accumulation of CD26 T cells in graft-versus-host disease target organs was found. As a therapeutic target, soluble CD83 molecules or antibodies have been demonstrated to have therapeutic effects against graft-versus-host disease, and signaling molecules promote the inflammatory and immune process of graft-versus-host disease. These immune cells and molecules could be the predictors of graft-versus-host disease development and the drug targets of the treatments for graft-versus-host disease. This article focuses on major advances on cellular and molecular mechanisms in graft-versus-host disease.
Financial Hardship Associated With Cancer in the United States: Findings From a Population-Based Sample of Adult Cancer Survivors
Authors: Yabroff K. Robin , Dowling Emily C. , Guy Gery P. , Banegas Matthew P. , Davidoff Amy , Han Xuesong , Virgo Katherine S. , McNeel Timothy S. , Chawla Neetu , Blanch-Hartigan Danielle , Kent Erin E. , Li Chunyu , Rodriguez Juan L. , de Moor Janet S. , Zheng Zhiyuan , Jemal Ahmedin , Ekwueme Donatus U. 
Published: December 2015

Purpose To estimate the prevalence of financial hardship associated with cancer in the United States and identify characteristics of cancer survivors associated with financial hardship. Methods We identified 1,202 adult cancer survivors diagnosed or treated at ≥ 18 years of age from the 2011 Medical Expenditure Panel Survey Experiences With Cancer questionnaire. Material financial hardship was measured by ever (1) borrowing money or going into debt, (2) filing for bankruptcy, (3) being unable to cover one’s share of medical care costs, or (4) making other financial sacrifices because of cancer, its treatment, and lasting effects of treatment. Psychological financial hardship was measured as ever worrying about paying large medical bills. We examined factors associated with any material or psychological financial hardship using separate multivariable logistic regression models stratified by age group (18 to 64 and ≥ 65 years). Results Material financial hardship was more common in cancer survivors age 18 to 64 years than in those ≥ 65 years of age (28.4% v 13.8%; P < .001), as was psychological financial hardship (31.9% v 14.7%, P < .001). In adjusted analyses, cancer survivors age 18 to 64 years who were younger, female, nonwhite, and treated more recently and who had changed employment because of cancer were significantly more likely to report any material financial hardship. Cancer survivors who were uninsured, had lower family income, and were treated more recently were more likely to report psychological financial hardship. Among cancer survivors ≥ 65 years of age, those who were younger were more likely to report any financial hardship. Conclusion Cancer survivors, especially the working-age population, commonly experience material and psychological financial hardship.
Symptom Monitoring With Patient-Reported Outcomes During Routine Cancer Treatment: A Randomized Controlled Trial
Authors: Basch Ethan , Deal Allison M. , Kris Mark G. , Scher Howard I. , Hudis Clifford A. , Sabbatini Paul , Rogak Lauren , Bennett Antonia V. , Dueck Amylou C. , Atkinson Thomas M. , Chou Joanne F. , Dulko Dorothy , Sit Laura , Barz Allison , Novotny Paul , Fruscione Michael , Sloan Jeff A. , Schrag Deborah 
Published: December 2015

Purpose There is growing interest to enhance symptom monitoring during routine cancer care using patient-reported outcomes, but evidence of impact on clinical outcomes is limited. Methods We randomly assigned patients receiving routine outpatient chemotherapy for advanced solid tumors at Memorial Sloan Kettering Cancer Center to report 12 common symptoms via tablet computers or to receive usual care consisting of symptom monitoring at the discretion of clinicians. Those with home computers received weekly e-mail prompts to report between visits. Treating physicians received symptom printouts at visits, and nurses received e-mail alerts when participants reported severe or worsening symptoms. The primary outcome was change in health-related quality of life (HRQL) at 6 months compared with baseline, measured by the EuroQol EQ-5D Index. Secondary endpoints included emergency room (ER) visits, hospitalizations, and survival. Results Among 766 patients allocated, HRQL improved among more participants in the intervention group than usual care (34% v 18%) and worsened among fewer (38% v 53%; P < .001). Overall, mean HRQL declined by less in the intervention group than usual care (1.4- v 7.1-point drop; P < .001). Patients receiving intervention were less frequently admitted to the ER (34% v 41%; P = .02) or hospitalized (45% v 49%; P = .08) and remained on chemotherapy longer (mean, 8.2 v 6.3 months; P = .002). Although 75% of the intervention group was alive at 1 year, 69% with usual care survived the year (P = .05), with differences also seen in quality-adjusted survival (mean of 8.7 v. 8.0 months; P = .004). Benefits were greater for participants lacking prior computer experience. Most patients receiving intervention (63%) reported severe symptoms during the study. Nurses frequently initiated clinical actions in response to e-mail alerts. Conclusion Clinical benefits were associated with symptom self-reporting during cancer care.
Androgen Deprivation Therapy and Future Alzheimer’s Disease Risk
Authors: Nead Kevin T. , Gaskin Greg , Chester Cariad , Swisher-McClure Samuel , Dudley Joel T. , Leeper Nicholas J. , Shah Nigam H. 
Published: December 2015

Purpose To test the association of androgen deprivation therapy (ADT) in the treatment of prostate cancer with subsequent Alzheimer’s disease risk. Methods We used a previously validated and implemented text-processing pipeline to analyze electronic medical record data in a retrospective cohort of patients at Stanford University and Mt. Sinai hospitals. Specifically, we extracted International Classification of Diseases-9th revision diagnosis and Current Procedural Terminology codes, medication lists, and positive-present mentions of drug and disease concepts from all clinical notes. We then tested the effect of ADT on risk of Alzheimer’s disease using 1:5 propensity score–matched and traditional multivariable-adjusted Cox proportional hazards models. The duration of ADT use was also tested for association with Alzheimer’s disease risk. Results There were 16,888 individuals with prostate cancer meeting all inclusion and exclusion criteria, with 2,397 (14.2%) receiving ADT during a median follow-up period of 2.7 years (interquartile range, 1.0-5.4 years). Propensity score–matched analysis (hazard ratio, 1.88; 95% CI, 1.10 to 3.20; P = .021) and traditional multivariable-adjusted Cox regression analysis (hazard ratio, 1.66; 95% CI, 1.05 to 2.64; P = .031) both supported a statistically significant association between ADT use and Alzheimer’s disease risk. We also observed a statistically significant increased risk of Alzheimer’s disease with increasing duration of ADT (P = .016). Conclusion Our results support an association between the use of ADT in the treatment of prostate cancer and an increased risk of Alzheimer’s disease in a general population cohort. This study demonstrates the utility of novel methods to analyze electronic medical record data to generate practice-based evidence.
Adjuvant Imatinib for GI Stromal Tumors: When and For How Long?
Authors: Benjamin Robert S. , Casali Paolo Giovanni 
Published: December 2015

The Oncology Grand Rounds series is designed to place original reports published in the Journal into clinical context. A case presentation is followed by a description of diagnostic and management challenges, a review of the relevant literature, and a summary of the authors' suggested management approaches. The goal of this series is to help readers better understand how to apply the results of key studies, including those published in Journal of Clinical Oncology, to patients seen in their own clinical practice. A 45-year-old woman presented with syncope. She was severely anemic, with a hemoglobin level of 6 g/dL, and was found to have lower GI bleeding. A diagnostic colonoscopy was negative. A subsequent computed tomography scan of the abdomen and pelvis was performed, revealing a 3.2 × 3 × 2.9–cm contrast-enhancing right lower-quadrant mass arising from the wall of the ileum. There was no evidence of metastatic disease. The patient underwent laparotomy, and a 3.5-cm mass was resected with negative margins. Pathology revealed a GI stromal tumor with mixed spindle and epithelioid features involving the mucosa and submucosa ( Fig 1A ). The tumor cells were positive for CD117 (c-kit) ( Fig 1B ) and DOG-1( Fig 1C ). There were eight to 10 mitoses per 50 high-power fields ( Fig 1D ). Molecular studies showed a 42-base pair deletion in exon 11 of the KIT gene that would delete all or part of codons 558 to 572 (V559_D572del) and would change the 558-encoding amino acid from Lys to Asn (K558N).
Genesis of Theoretical Ideas of Career As Basis of Formation of the Theory of Management
Authors: Сотникова  , Sotnikova Svetlana 
Published: December 2015

Formation of market philosophy of managing causes the necessity of allocation of management of career as special independent function of human resource
management in a control system of the organization. And for the Russian management it is rather new tendency. Due to the increasing need of formation of
the complete, reliable, systematically developed knowledge of essential communications and regularities of career there were separate works of research and
scientific and methodical character on this problem. Of course, they are very valuable, but the used conceptual and categorial device far isn’t worked yet; often
in them contradictory interpretation of career are given. All this quite often results in distinctions in a statement of the same questions in scientific discussions,
in the course of teaching economic and administrative disciplines. Disorder of terms complicates in many cases transfer and interpretation of foreign literature
[7–14]. Consecutive consideration in article of research tools of career allowed to create harmonous system of knowledge of career from a heap of interpretation,
to gain a complex impression about its social and economic essence and the contents. Author’s understanding of career is presented from positions of substantial,
structural, functional, morphological, institutional, substantsionalny, system approaches in the article. The essence and the maintenance of basic elements of
system of career are allocated: career purposes, career space, career vector, resource base, career bases, norm, dynamics of career. Author’s interpretation of
elements of system of career is offered.
Agency Selling or Reselling? Channel Structures in Electronic Retailing
Authors: Abhishek Vibhanshu , Jerath Kinshuk , Zhang Z. John 
Published: December 2015

In recent years, online retailers (also called e-tailers) have started allowing manufacturers direct access to their customers while charging a fee for providing this access, a format commonly referred to as agency selling. In this paper, we use a stylized theoretical model to answer a key question that e-tailers are facing: When should they use an agency selling format instead of using the more conventional reselling format? We find that agency selling is more efficient than reselling and leads to lower retail prices; however, the e-tailers end up giving control over retail prices to the manufacturer. Therefore, the reaction by the manufacturer, who makes electronic channel pricing decisions based on their impact on demand in the traditional channel (brick-and-mortar retailing), is an important factor for e-tailers to consider. We find that when sales in the electronic channel lead to a negative effect on demand in the traditional channel, e-tailers prefer agency selling, whereas when sales in the electronic channel lead to substantial stimulation of demand in the traditional channel, e-tailers prefer reselling. This preference is mediated by competition between e-tailers—as competition between them increases, e-tailers prefer to use agency selling. We also find that when e-tailers benefit from positive externalities from the sales of the focal product (such as additional profits from sales of associated products), retail prices may be lower under reselling than under agency selling, and the e-tailers prefer reselling under some conditions for which they would prefer agency selling without the positive externalities. This paper was accepted by Chris Forman, information systems.