bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance Assessment of a New Stationarity-Based Parameter Estimation Method with a Simplified Land Surface Model Using In Situ and Remotely Sensed Surface States
Authors: Sun Jian , Salvucci Guido D. 
Published: August 2013

Abstract
This study evaluates the performance of a new stationarity-based method for parameter estimation of a simple coupled water and energy balance model using in situ and remotely sensed surface soil moisture [from Advanced Microwave Scanning Radiometer for Earth Observing System (EOS; AMSR-E)] and surface temperature [from a combined Moderate Resolution Imaging Spectroradiometer (MODIS) and AMSR-E product]. Parameter estimation is carried out using both direct calibration to measured surface fluxes (latent, sensible, and ground heat) and a recently published method based on enforcing stationarity of model-predicted surface state tendency terms. The latter stationarity-based method was developed for parameter estimation without knowledge of observed fluxes—that is, it requires only forcing terms (e.g., radiation, wind speed, air temperature) and surface states (moisture and temperature). In addition, the stationarity-based method can easily handle gaps in atmospheric forcing and surface state data, as it does not integrate over time to simulate fluxes. The evaluation is conducted at three AmeriFlux sites. Changing the data sources of surface states (in situ measured and remotely sensed data) leads to little degradation in estimating turbulent fluxes despite the relatively poor quality of satellite data at some sites. In all cases, direct calibration yields marginally better predictions than the stationarity-based method, with site-averaged root-mean-square errors for daily total energy fluxes approximately 5–6 W m−2 lower. However, direct calibration requires observed fluxes in the objective function, which imposes a strong limit on its application.
Assessing Groundwater Storage Changes Using Remote Sensing–Based Evapotranspiration and Precipitation at a Large Semiarid Basin Scale
Authors: Gokmen Mustafa , Vekerdy Zoltan , Lubczynski Maciek W. , Timmermans Joris , Batelaan Okke , Verhoef Wouter 
Published: August 2013

Abstract
A method is presented that uses remote sensing (RS)-based evapotranspiration (ET) and precipitation estimates with improved accuracies under semiarid conditions to quantify a spatially distributed water balance, for analyzing groundwater storage changes due to supplementary water uses. The method is tested for the semiarid Konya basin (Turkey), one of the largest endorheic basins in the world. Based on the spatially distributed water balance estimation, the mean irrigation for croplands was 308 mm yr−1, which corresponds to a total reduction of 2270 million cubic meters per year (106 m3 yr−1, or MCM yr−1) in the groundwater storage during the study period 2005–09. The storage change estimated as the residual of the spatially distributed water balance was confirmed by the volume change calculated from groundwater table observations. To obtain an improved precipitation distribution, the monthly Tropical Rainfall Measuring Mission (TRMM) rainfall product was assessed. After a bias removal, TRMM data were combined with the snow water equivalent estimated by a multivariate analysis using snow gauge observations, the Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover product, and the digital elevation model. With respect to the distribution of ET, the standard SEBS and the soil moisture integrated SEBS-SM models were compared; SEBS-SM proved to better reflect the water-limited evapotranspiration regime of semiarid regions. The RS-based distributed water balance calculation as presented in this study can be applied in other large basins, especially in semiarid and arid regions. It is capable of estimating spatially distributed water balances and storage changes, which otherwise, by ground-based point measurements, would not be feasible.
Aerodynamic Resistance and Penman–Monteith Evapotranspiration over a Seasonally Two-Layered Canopy in Semiarid Central Australia
Authors: Cleverly James , Chen Chao , Boulain Nicolas , Villalobos-Vega Randol , Faux Ralph , Grant Nicole , Yu Qiang , Eamus Derek 
Published: August 2013

Abstract
Accurate prediction of evapotranspiration E depends upon representative characterization of meteorological conditions in the boundary layer. Drag and bulk transfer coefficient schemes for estimating aerodynamic resistance to vapor transfer were compared over a semiarid natural woodland ecosystem in central Australia. Aerodynamic resistance was overestimated from the drag coefficient, resulting in limited E at intermediate values of vapor pressure deficit. Large vertical humidity gradients were present during the summer, causing divergence between momentum and vapor transport within and above the canopy surface. Because of intermittency in growth of the summer-active, rain-dependent understory and physiological responses of the canopy, leaf resistance varied from less than 50 s m−1 to greater than 106 s m−1, in which the particularly large values were obtained from inversion of drag coefficient resistance. Soil moisture limitations further contributed to divergence between actual and reference E. Unsurprisingly, inclusion of site-specific meteorological (e.g., vertical humidity gradients) and hydrological (e.g., soil moisture content) information improved the accuracy of predicting E when applying Penman–Monteith analysis. These results apply regardless of canopy layering (i.e., even when the understory was not present) wherever atmospheric humidity gradients develop and are thus not restricted to two-layer canopies in semiarid regions.
Inclusion of Linearized Moist Physics in NASA’s Goddard Earth Observing System Data Assimilation Tools
Authors: Holdaway Daniel , Errico Ronald , Gelaro Ronald , Kim Jong G. 
Published: August 2013

Abstract
Inclusion of moist physics in the linearized version of a weather forecast model is beneficial in terms of variational data assimilation. Further, it improves the capability of important tools, such as adjoint-based observation impacts and sensitivity studies. A linearized version of the relaxed Arakawa–Schubert (RAS) convection scheme has been developed and tested in NASA’s Goddard Earth Observing System data assimilation tools. A previous study of the RAS scheme showed it to exhibit reasonable linearity and stability. This motivates the development of a linearization of a near-exact version of the RAS scheme. Linearized large-scale condensation is included through simple conversion of supersaturation into precipitation. The linearization of moist physics is validated against the full nonlinear model for 6- and 24-h intervals, relevant to variational data assimilation and observation impacts, respectively. For a small number of profiles, sudden large growth in the perturbation trajectory is encountered. Efficient filtering of these profiles is achieved by diagnosis of steep gradients in a reduced version of the operator of the tangent linear model. With filtering turned on, the inclusion of linearized moist physics increases the correlation between the nonlinear perturbation trajectory and the linear approximation of the perturbation trajectory. A month-long observation impact experiment is performed and the effect of including moist physics on the impacts is discussed. Impacts from moist-sensitive instruments and channels are increased. The effect of including moist physics is examined for adjoint sensitivity studies. A case study examining an intensifying Northern Hemisphere Atlantic storm is presented. The results show a significant sensitivity with respect to moisture.
Human Performance Consequences of Stages and Levels of Automation
Authors: Onnasch Linda , Wickens Christopher D. , Li Huiyang , Manzey Dietrich 
Published: August 2013

Objective: We investigated how automation-induced human performance consequences depended on the degree of automation (DOA). Background: Function allocation between human and automation can be represented in terms of the stages and levels taxonomy proposed by Parasuraman, Sheridan, and Wickens. Higher DOAs are achieved both by later stages and higher levels within stages. Method: A meta-analysis based on data of 18 experiments examines the mediating effects of DOA on routine system performance, performance when the automation fails, workload, and situation awareness (SA). The effects of DOA on these measures are summarized by level of statistical significance. Results: We found (a) a clear automation benefit for routine system performance with increasing DOA, (b) a similar but weaker pattern for workload when automation functioned properly, and (c) a negative impact of higher DOA on failure system performance and SA. Most interesting was the finding that negative consequences of automation seem to be most likely when DOA moved across a critical boundary, which was identified between automation supporting information analysis and automation supporting action selection. Conclusion: Results support the proposed cost–benefit trade-off with regard to DOA. It seems that routine performance and workload on one hand, and the potential loss of SA and manual skills on the other hand, directly trade off and that appropriate function allocation can serve only one of the two aspects. Application: Findings contribute to the body of research on adequate function allocation by providing an overall picture through quantitatively combining data from a variety of studies across varying domains.
The prevalence of lymph node metastases in clinically N0 necks with oral cavity squamous cell carcinoma: is CT good enough for nodal staging?
Authors: Furukawa Matakazu , Dillon Jasjit K , Futran Neal D , Anzai Yoshimi 
Published: August 2013

Background Nodal metastases and extracapsular extension (ECE) are important prognostic indicators. However, the diagnostic accuracy of CT is still limited for patients with clinically N0 neck. Purpose To determine the prevalence of lymph node (LN) metastases and ECE for oral cavity squamous cell carcinoma (SCC) patients with clinical and CT negative preoperative neck. Material and Methods Thirty-two patients with N0 oral cavity SCC who underwent neck dissection were included in this retrospective analysis. The size of LN was measured on transverse CT images, and radiological size criterion was based upon a minimal axial diameter of 10 mm. Pathology was used as the standard reference. Imaging and histopathological correlation was done for 132 LN levels in the 32 patients. Results Fourteen of 32 patients (44%) had metastatic nodes and six patients had ECE. Among 132 LN levels, 22 levels (17%) had metastatic LNs (level I 5/37, level II 8/39, level III 7/35, level IV 2/18), and eight of 22 levels with metastases had ECE. Poorly differentiated histology was a predictive factor for LN metastases or ECE (poorly versus well and moderately differentiated SCC: P = 0.07 for LN metastases and P = 0.08 for ECE, respectively). T-classification was also an important predictor for occult nodal metastases (2 of 10 patients in T1, 12 of 22 patients in T2–4), although it did not reach statistical significance ( P = 0.11). Conclusion Diagnostic accuracy of CT is limited among N0 oral cavity SCC patients. Neck dissection should be performed, particularly for patients with poorly differentiated SCC or higher T-classification.
Serum microRNA-92 expression in patients with ovarian epithelial carcinoma
Authors: Guo Fengjun , Tian Jingyan , Lin Yang , Jin Yuemei , Wang Ling , Cui Manhua 
Published: August 2013

Objectives Studies have reported the significance of circulating microRNAs (miRNAs) as biochemical markers of cancer. Few reports demonstrate the significance of miRNAs in the serum of patients with ovarian epithelial carcinoma (EOC). The present study prospectively investigated the status of miRNA-92 (miR-92) in the serum of EOC patients and healthy controls, and examined the potential usefulness of this molecule as a biomarker for EOC diagnosis. Methods Levels of miR-92 in serum samples from EOC patients and controls were measured by quantitative real time reverse transcription–polymerase chain reaction (RT–PCR). Associations between serum miR-92 concentrations and clinical parameters were assessed by Fisher’s exact probability test. Results The serum concentration of miR-92 in EOC patients ( n = 50) was significantly higher than in controls ( n = 50). There were significant correlations between miR-92 expression and regional lymph node involvement and clinical stage of the tumour. There was no significant association between expression of miR-92 and age. Conclusion The detection of miR-92 levels in the serum might serve as a new tumour biomarker in the diagnosis and assessment of prognosis of EOC.
Vascular endothelial growth factor C expression is closely correlated with lymph node recurrence and poor prognosis in patients with early stage cervical cancer
Authors: DeMei Ma , XiangXin Li , YongPing Xu , YongXia Yang , YunHai Yu , Lin Zhu 
Published: August 2013

Objectives To detect vascular endothelial growth factor (VEGF)-C mRNA expression in surgically resected tissues of ‘pathologic N0’ (pN0) cervical cancer; to investigate the relevance of VEGF-C mRNA expression to clinicopathological factors, lymph node recurrence and prognosis in early stage cervical cancer. Methods Patients with pN0 cervical cancer who successfully underwent radical hysterectomy with bilateral adnexectomy and bilateral pelvic lymphadenectomy were enrolled sequentially into this retrospective study. Reverse transcriptase–polymerase chain reaction (RT–PCR) was performed to detect VEGF-C mRNA. Results Seventy-eight patients entered the study. VEGF-C mRNA was detected in 35 (44.87%) patients and was significantly correlated with tumour differentiation. VEGF-C mRNA expression was significantly associated with lymph node recurrence and poor overall survival 5 years after surgery. Multivariate analysis confirmed that VEGF-C mRNA expression was an independent predictor for lymph node recurrence and unfavourable overall survival. Conclusions These findings indicate that detection of VEGF-C mRNA has clinical potential as a predictor for identifying patients with pN0 cervical cancer at high risk of lymph node recurrence and poor prognosis.
Interleukin-7 is produced by afferent lymphatic vessels and supports lymphatic drainage
Authors: Iolyeva Maria , Aebischer David , Proulx Steven T. , Willrodt Ann-Helen , Ecoiffier Tatiana , Häner Simone , Bouchaud Grégory , Krieg Carsten , Onder Lucas , Ludewig Burkhard , Santambrogio Laura , Boyman Onur , Chen Lu , Finke Daniela , Halin Cornelia 
Published: August 2013

Key Points
Afferent lymphatic vessels express interleukin-7. Interleukin-7 supports lymphatic drainage.
Caloric restriction modulates Mcl-1 expression and sensitizes lymphomas to BH3 mimetic in mice
Authors: Meynet Ophélie , Zunino Barbara , Happo Lina , Pradelli Ludivine A. , Chiche Johanna , Jacquin Marie A. , Mondragón Laura , Tanti Jean-François , Taillan Bruno , Garnier Georges , Reverso-Meinietti Julie , Mounier Nicolas , Michiels Jean-François , Michalak Ewa M. , Carles Michel , Scott Clare L. , Ricci Jean-Ehrland 
Published: August 2013

Key Points
Caloric restriction reduces Mcl-1 expression and sensitizes lymphoma cells to ABT-737 in vivo. Caloric restriction mimetics can sensitize lymphomas to ABT-737–induced death independently of p53 and of the main BH3-only proteins.
Platelets in tissue repair: control of apoptosis and interactions with regenerative cells
Authors: Gawaz Meinrad , Vogel Sebastian 
Published: August 2013

AbstractBesides mediating primary hemostasis and thrombosis, platelets play a critical role in tissue repair and regeneration. They regulate fundamental mechanisms involved in the healing process including cellular migration, proliferation, and angiogenesis. Control of apoptosis/cell survival and interaction with progenitor cells, which are clinically relevant but poorly understood aspects of platelets in tissue repair, will be highlighted in this review. Gaining deeper insight into the less well-characterized molecular mechanisms is necessary to develop new therapeutic platelet-based options.
How I treat CNS lymphomas
Authors: Rubenstein James L. , Gupta Neel K. , Mannis Gabriel N. , LaMarre Amanda K. , Treseler Patrick 
Published: August 2013

AbstractThe pathogenesis of primary and secondary central nervous system (CNS) lymphoma poses a unique set of diagnostic, prognostic, and therapeutic challenges. During the past 10 years, there has been significant progress in the elucidation of the molecular properties of CNS lymphomas and their microenvironment, as well as evolution in the development of novel treatment strategies. Although a CNS lymphoma diagnosis was once assumed to be uniformly associated with a dismal prognosis, it is now reasonable to anticipate long-term survival, and possibly a cure, for a significant fraction of CNS lymphoma patients. The pathogenesis of CNS lymphomas affects multiple compartments within the neuroaxis, and proper treatment of the CNS lymphoma patient requires a multidisciplinary team with expertise not only in hematology/oncology but also in neurology, neuroradiology, neurosurgery, clinical neuropsychology, ophthalmology, pathology, and radiation oncology. Given the evolving principles of management and the evidence for improvements in survival, our goal is to provide an overview of current knowledge regarding the pathogenesis of CNS lymphomas and to highlight promising strategies that we believe to be most effective in establishing diagnosis, staging, and therapeutic management.
WholeCellViz: data visualization for whole-cell models
Authors: Lee Ruby , Karr Jonathan R , Covert Markus W 
Published: August 2013

Abstract

Background
Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dimensional data.

Results
We developed WholeCellViz, a web-based software program for visually exploring and analyzing whole-cell simulations. WholeCellViz provides 14 animated visualizations, including metabolic and chromosome maps. These visualizations help researchers analyze model predictions by displaying predictions in their biological context. Furthermore, WholeCellViz enables researchers to compare predictions within and across simulations by allowing users to simultaneously display multiple visualizations.

Conclusion
WholeCellViz was designed to facilitate exploration, analysis, and communication of whole-cell model data. Taken together, WholeCellViz helps researchers use whole-cell model simulations to drive advances in biology and bioengineering.
Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo
Authors: He Cai-yun , Cui Kai , Zhang Jian-guo , Duan Ai-guo , Zeng Yan-fei 
Published: August 2013

AbstractBackgroundAs one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocyclacv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.ResultsOur anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.ConclusionsThis is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.
Education is associated with lower levels of abdominal obesity in women with a non-agricultural occupation: an interaction study using China’s four provinces survey
Authors: Aitsi-Selmi Amina , Chen Ruoling , Shipley Martin J , Marmot Michael G 
Published: August 2013

Abstract

Background
The prevalence of obesity is increasing rapidly in low- and middle-income countries (LMICs) as their populations become exposed to obesogenic environments. The transition from an agrarian to an industrial and service-based economy results in important lifestyle changes. Yet different socioeconomic groups may experience and respond to these changes differently. Investigating the socioeconomic distribution of obesity in LMICs is key to understanding the causes of obesity but the field is limited by the scarcity of data and a uni-dimensional approach to socioeconomic status (SES). This study splits socioeconomic status into two dimensions to investigate how educated women may have lower levels of obesity in a context where labour market opportunities have shifted away from agriculture to other forms of employment.

Methods
The Four Provinces Study in China 2008/09 is a household-based community survey of 4,314 people aged ≥60 years (2,465 women). It was used to investigate an interaction between education (none/any) and occupation (agricultural/non-agricultural) on high-risk central obesity defined as a waist circumference ≥80 cm. An interaction term between education and occupation was incorporated in a multivariate logistic regression model, and the estimates adjusted for age, parity, urban/rural residence and health behaviours (smoking, alcohol, meat and fruit & vegetable consumption). Complete case analyses were undertaken and results confirmed using multiple imputation to impute missing data.

Results
An interaction between occupation and education was present (P = 0.02). In the group with no education, the odds of central obesity in the sedentary occupation group were more than double those of the agricultural occupation group even after taking age group and parity into account (OR; 95%CI: 2.21; 1.52, 3.21), while in the group with any education there was no evidence of such a relationship (OR; 95%CI: 1.25; 0.92, 1.70). Health behaviours appeared to account for some of the association.

Conclusion
These findings suggest that education may have a protective role in women against the higher odds of obesity associated with occupational shifts in middle-income countries, and that investment in women’s education may present an important long term investment in obesity prevention. Further research could elucidate the mechanisms behind this association.