bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis
Authors: Obertello Mariana , Krouk Gabriel , Katari Manpreet S , Runko Suzan J , Coruzzi Gloria M 
Published: September 2010

Abstract

Background
Nitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of nitrogen (N) and light (L) treatment conditions and performing transcriptome analysis. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide.

Results
This transcriptome analysis demonstrates that a mutation in the bZIP1 gene can alter the L and/or N-regulation of several gene clusters. More surprisingly, the bZIP1 mutation can also trigger N and/or L regulation of genes that are not normally controlled by these signals in WT plants. This analysis also reveals that bZIP1 can, to a large extent, invert gene regulation (e.g., several genes induced by N in WT plants are repressed by N in the bZIP1 mutant).

Conclusion
These findings demonstrate that the bZIP1 mutation triggers a genome-wide de-regulation in response to L and/or N signals that range from i) a reduction of the L signal effect, to ii) unlocking gene regulation in response to L and N combinations. This systems biology approach demonstrates that bZIP1 tunes L and N signaling relationships genome-wide, and can suppress regulatory mechanisms hypothesized to be needed at different developmental stages and/or environmental conditions.
An algorithm to discover gene signatures with predictive potential
Authors: Hallett Robin M , Dvorkin Anna , Gabardo Christine M , Hassell John A 
Published: September 2010

Abstract

Background
The advent of global gene expression profiling has generated unprecedented insight into our molecular understanding of cancer, including breast cancer. For example, human breast cancer patients display significant diversity in terms of their survival, recurrence, metastasis as well as response to treatment. These patient outcomes can be predicted by the transcriptional programs of their individual breast tumors. Predictive gene signatures allow us to correctly classify human breast tumors into various risk groups as well as to more accurately target therapy to ensure more durable cancer treatment.

Results
Here we present a novel algorithm to generate gene signatures with predictive potential. The method first classifies the expression intensity for each gene as determined by global gene expression profiling as low, average or high. The matrix containing the classified data for each gene is then used to score the expression of each gene based its individual ability to predict the patient characteristic of interest. Finally, all examined genes are ranked based on their predictive ability and the most highly ranked genes are included in the master gene signature, which is then ready for use as a predictor. This method was used to accurately predict the survival outcomes in a cohort of human breast cancer patients.

Conclusions
We confirmed the capacity of our algorithm to generate gene signatures with bona fide predictive ability. The simplicity of our algorithm will enable biological researchers to quickly generate valuable gene signatures without specialized software or extensive bioinformatics training.
Predictors of interstitial lung disease in early systemic sclerosis: a prospective longitudinal study of the GENISOS cohort
Authors: Assassi Shervin , Sharif Roozbeh , Lasky Robert E , McNearney Terry A , Estrada-Y-Martin Rosa M , Draeger Hilda , Nair Deepthi K , Fritzler Marvin J , Reveille John D , Arnett Frank C , Mayes Maureen D ,   the GENISOS Study Group
Published: September 2010

Abstract
Introduction
The objective of the present study was to examine the association of baseline demographic and clinical characteristics with sequentially obtained measurements of forced vital capacity (FVC), expressed as a percentage of the predicted value, and to identify predictors of the decline rate in FVC over time in the Genetics versus Environment in Scleroderma Outcome Study (GENISOS).

Methods
To date, 266 patients have been enrolled in GENISOS, a prospective, observational cohort of patients with early systemic sclerosis. In addition to pulmonary function tests (PFTs), clinical and laboratory data were obtained from each patient. We analyzed 926 FVC measurements utilizing generalized linear mixed models. The predictive significance of baseline variables for the decline rate in FVC was investigated by the interaction term between the variable and the follow-up time within the first 3 years after enrollment as well as throughout the entire follow-up time.

Results
The cohort consisted of 125 white, 54 African American, and 77 Hispanic patients with average disease duration of 2.5 years at enrollment. The mean follow-up time was 3.8 years, ranging up to 11.4 years. A number of baseline variables, including antibody status, African American ethnicity, disease type, baseline PFT values, modified Rodnan Skin Score, fibrosis on chest radiograph, and lung and skin subscores of the Severity Index, were associated with serially measured FVC levels. However, only the presence of anti-topoisomerase I antibodies (ATA) was associated with lower FVC levels (P < 0.001) as well as accelerated decline rate in FVC within the first 3 years of follow-up (P = 0.02). None of the baseline variables predicted the rate of decline in FVC on long-term follow-up. Patients with rapidly progressive ILD, however, were under-represented in the long-term follow-up group because the accelerated rate of decline in FVC was associated with poor survival (P = 0.001).

Conclusions
Presence of ATA was the only baseline variable associated with differential FVC levels, predicting the rate of decline in FVC within the first 3 years of follow-up. The association of faster decline in FVC with poor survival further emphasizes the need for identification of predictive biomarkers by collection of genetic information and serial blood samples in cohort studies.
Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer
Authors: Prat Aleix , Parker Joel S , Karginova Olga , Fan Cheng , Livasy Chad , Herschkowitz Jason I , He Xiaping , Perou Charles M 
Published: September 2010

Abstract
Introduction
In breast cancer, gene expression analyses have defined five tumor subtypes (luminal A, luminal B, HER2-enriched, basal-like and claudin-low), each of which has unique biologic and prognostic features. Here, we comprehensively characterize the recently identified claudin-low tumor subtype.

Methods
The clinical, pathological and biological features of claudin-low tumors were compared to the other tumor subtypes using an updated human tumor database and multiple independent data sets. These main features of claudin-low tumors were also evaluated in a panel of breast cancer cell lines and genetically engineered mouse models.

Results
Claudin-low tumors are characterized by the low to absent expression of luminal differentiation markers, high enrichment for epithelial-to-mesenchymal transition markers, immune response genes and cancer stem cell-like features. Clinically, the majority of claudin-low tumors are poor prognosis estrogen receptor (ER)-negative, progesterone receptor (PR)-negative, and epidermal growth factor receptor 2 (HER2)-negative (triple negative) invasive ductal carcinomas with a high frequency of metaplastic and medullary differentiation. They also have a response rate to standard preoperative chemotherapy that is intermediate between that of basal-like and luminal tumors. Interestingly, we show that a group of highly utilized breast cancer cell lines, and several genetically engineered mouse models, express the claudin-low phenotype. Finally, we confirm that a prognostically relevant differentiation hierarchy exists across all breast cancers in which the claudin-low subtype most closely resembles the mammary epithelial stem cell.

Conclusions
These results should help to improve our understanding of the biologic heterogeneity of breast cancer and provide tools for the further evaluation of the unique biology of claudin-low tumors and cell lines.
Studies on production of high specific activity 99Mo and 90Y by Szilard Chalmers reaction
Authors: Tomar Bhupendra S. , Steinebach Olav M. , Terpstra B.E. , Bode P. , Wolterbeek H. Th. 
Published: September 2010

Abstract
Attempts have been made to use Szilard Chalmers reaction to prepare 99Mo and 90Y in high specific activity. Experiments were carried out using irradiation of freshly prepared oxinate complexes of molybdenum and yttrium in the HOR reactor of Reactor Institute at TU Delft. The irradiated target was dissolved in dichloromethane and the radionuclides were separated by solvent extraction into aqueous phase. Detailed investigations on the effect of pH of aqueous solution, irradiation time and target amount was also carried out to optimize the enrichment factor and yield. The highest enrichment factor for 99Mo was found to be around 200 with a yield close to 30%. In the case of 90Y, solvent extraction method did not yield high enrichment factors. Slightly higher enrichment factors were achieved with ion exchange method. Studies were also carried out with yttrium oxide nano-powder. Speciation study of 99Mo in the separated aqueous fraction showed it to be present as 99MoO4
2− ion. The results appear to be quite promising for large scale production of 99Mo for medical applications.
Study of the role of sulfur functionalities in humic acids for uranium(VI) complexation
Authors: Sachs Susanne , Reich T. , Bernhard Gert 
Published: September 2010

AbstractSulfur containing humic acid model substances have been synthesized to study the role of sulfur functionalities for the complexation behavior of humic acids towards U(VI). Humic acids type M1-S with different sulfur contents (1.9, 3.9, 6.9 wt.%) were synthesized and characterized. The identity of the sulfur species was determined by X-ray photoelectron spectroscopy (XPS). Reduced sulfur species, such as thiols, dialkylsulfides and/or disulfides, were determined as the dominating sulfur functionalities in the used humic acids. The U(VI) complexation of humic acids with different sulfur contents has been studied by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and TRLFS with ultrashort femtosecond laser pulses (fs-TRLFS) in comparison to a sulfur-free humic acid type M1 (pH 3.80±0.02;I=0.1 M NaClO4;pCO2=10−3.5 atm). For all studied humic acids, similar complexation constants were determined. However, with increasing sulfur contents of the humic acids (>2 wt.%) an increase of the number of humic acid binding sites for U(VI) was determined which is reflected in increasing U(VI) loading capacities and increasing total humic acid ligand concentrations for U(VI) measured by TRLFS and fs-TRLFS, respectively. This increase of the fraction of humic acid binding sites for U(VI) points to an involvement of reduced sulfur functionalities, such as thiol groups, in the complexation between U(VI) and humic acid. However, for environmentally relevant sulfur contents of humic acids (<2 wt.%) it can be concluded that, compared to oxygen functionalities, especially carboxylic groups, reduced sulfur functionalities play only a subordinate role for the U(VI) complexation by humic acids in the acidic pH range.
Selective caesium transport using hollow fibre-supported liquid membrane containing calix[4]arene-bis-naphthocrown-6 as the carrier extractant
Authors: Kandwal Pankaj , Mohapatra P. K. , Ansari S. A. , Manchanda V. K. 
Published: September 2010

Abstract
Polypropylene hollow fibre-based supported liquid membrane (HFSLM) containing calix[4]-bis-2,3-naphtho-crown-6 in 20% (v/v) n-dodecane+80% (v/v) 2-nitrophenyl octyl ether (NPOE) as the carrier solvent was employed for the first time to investigate the transport behaviour of radio-caesium. The carrier solution was 1 mM calix[4]-bis-2,3-naphtho-crown-6 in 20% (v/v) dodecane+80% (v/v) NPOE+0.4% alamine 336 and the feed was 3 M HNO3 while distilled water was used as the receiver phase. In spite of high viscosity of the carrier solvent, quantitative (>99%) transport was possible in about 6 h. Significant amount of acid transport was also noticed which was ascribed to a co-transport mechanism involving encapsulated hydronium ion. Selectivity studies were carried out by taking a mixture of radiotracers, viz.
51Cr, 59Fe, 85,89Sr, 137Cs, 152,154Eu and 241Am, which represent some of the elements present in the high level waste, in the feed solution. The decontamination factors for various metal ions were found to be in the range 540–890. High decontamination factors as well as possibility of working over several days without deterioration of the liquid membrane suggested possible application of the system for the recovery of radio-caesium from high level waste. Studies on the membrane stability indicated reproducible transport data over 40 h.
Mikrowellengestützte Aufklärung elektrochemischer Vorgänge in Katalysatoren und verwandten Systemen
Authors: Fischerauer Gerhard , Spörl Matthias , Reiß Sebasian , Moos Ralf 
Published: September 2010

Zusammenfassung
Technisch bedeutsame elektrochemische Reaktionen laufen oftmals bei hohen Temperaturen und im Volumen von Festkörpern ab. Die mit ihrer direkten Überwachung zusammenhängenden Probleme werden meist durch indirekte Messverfahren umgangen. Der vorliegende Beitrag berichtet über ein mikrowellenbasiertes direktes Messverfahren und die damit erzielten Ergebnisse bei Anwendung auf Messobjekte wie Dreiwegekatalysatoren (three-way catalysts, TWC), NOx-Speicherkatalysatoren (NSK, lean NOx traps, LNT) und Dieselpartikelfilter (DPF).
Simulation of Copper Phthalocyanine (CuPc)/Fullerene (C60) Heterojunction. photovoltaic cell with and without electron transport layer (ETL)
Authors: Satyala Nikhil T , Wondmagegn Wudyalew T , Pieper Ron J , Korn Michael R 
Published: September 2010

AbstractA two-dimensional finite element simulation model for the bi-layer heterostructure organic photovoltaic (PV) cell, based on copper phthalocyanine (CuPc) and fullerene (C60) in the presence and absence of electron transport layers (ETLs) is presented. The effect of bathocuproine (BCP), tris(8-hydroxyquinolinato)aluminum (Alq3), and copper phthalocyanine (CuPc) as ETLs on short-circuit current (Jsc), open-circuit voltage (Voc), and power conversion efficiency (PCE) is investigated. The Frenkel-Poole mobility model was employed in describing the conduction mechanisms in the active layers. Singlet exciton and Langevin recombination techniques were employed to describe excitonic generation and recombination, respectively. The obtained simulation results demonstrate that the efficiency of PV cells is primarily dependent on the short-circuit current, the absorption capability of the active layers, and the charge collection efficiency at the electrodes. In addition, significant reduction in power conversion efficiency is observed with increasing thickness of the ETL layer. From among the modeled device designs, PV cells containing a 50Å BCP layer result in the best power conversion efficiencies of 2.05%.
Proton Conduction Through Interface Phase of CPAA/KDP Composites
Authors: Zakharyevich Dmitry , Neustroev Aleksey 
Published: September 2010

AbstractIn this paper we present the results of the studies on proton conduction in composites polyantimonic acid (PAA)-potassium dihydrophosphate (KDP) obtained by precipitation technique as well as mechanical mixing. The highest conductivity (~10-2 Sm/sm at 300 K) is achieved in the precipitated samples with volume fraction of KDP close to f = 13 %. The results of X-ray diffraction showed the absence of reflections from KDP for the samples with f < 20% and slight change in the intensities of odd and even reflections from PAA, which is explained by the ion exchange between the phases through the interface. These indicate that conduction is occurred through the interface regions of the composite. The value of interface conductivity is estimated from the dependence of the composite conductivity on the volume fraction of KDP based according to the model by Uvarov et al. This gives σs ≈ 5 Sm/sm, however the equation derived in this model doesn't represent the experimental data properly. Probably the maximum of the dependence simply corresponds to the percolation through the interface's continuous cluster – it is close to the classical percolation threshold.
Catalyst formation and growth of Sn- and In-catalyzed silicon nanowires
Authors: Ngo Irene , O'Donnell Benedict , Alvarez José , Gueunier-Farret Marie , Kleider Jean-Paul , Yu Linwei , Roca i Cabarrocas Pere 
Published: September 2010

AbstractSilicon nanowires (Si NWs) were grown directly on transparent conductive oxide layers using a single pump down process in a plasma enhanced chemical vapour deposition (PECVD) system. Layers of ITO and SnO2 on glass substrates were exposed to a hydrogen plasma leading to the reduction of the oxide and to the agglomeration of the metal into catalyst droplets of a few tens of nanometers diameter. The diameter and the density of the nanowires depend on the catalysts droplets size and density, we studied step by step the evolution of the surface prior to and at the initial stage of the nanowire growth. The catalyst droplets size and distribution were essentially investigated through Scanning Electron Microscopy (SEM).
Adjoint Multiscale Mixed Finite Elements
Authors: Krogstad S.. , Hauge V.L.. L. , Gulbransen A.F.. F. 
Published: September 2010

Summary
We develop an adjoint model for a simulator consisting of a multiscale pressure solver and a saturation solver that works on flow-adapted grids. The multiscale method solves the pressure on a coarse grid that is close to uniform in index space and incorporates fine-grid effects through numerically computed basis functions. The transport solver works on a coarse grid adapted by a fine-grid velocity field obtained by the multiscale solver. Both the multiscale solver for pressure and the flow-based coarsening approach for transport have shown earlier the ability to produce accurate results for a high degree of coarsening. We present results for a complex realistic model to demonstrate that control settings based on optimization of our multiscale flow-based model closely match or even outperform those found by using a fine-grid model. For additional speed-up, we develop mappings used for rapid system updates during the timestepping procedure. As a result, no fine-grid quantities are required during simulations and all fine-grid computations (multiscale basis functions, generation of coarse transport grid, and coarse mappings) become a preprocessing step. The combined methodology enables optimization of waterflooding on a complex model with 45,000 grid cells in a few minutes.
Case History: Successful Wellbore Strengthening Approach in a Depleted and Highly Unconsolidated Sand in Deepwater Gulf of Mexico
Authors: Fett Darryl , Martin Frederic , Dardeau Claude , Rignol Joel , Benaissa Saddok , Adachi Jose , Pastor Jorge 
Published: September 2010

Summary
In early 2008, Total E&P USA sidetracked the Mississippi Canyon 243 #A2 well on its "Matterhorn" tension-leg platform (TLP) in the deepwater Gulf of Mexico. A preproject geomechanics study identified that the mud-weight/fracture-pressure window in the depleted and highly unconsolidated "A" reservoir was very narrow, creating a strong potential for mud losses during drilling and cementing of the 7-in. liner. The risk of losses was a primary concern because the well would be frac packed, and if a competent cement column did not reach a sufficient height, the ability to fracture the reservoir would have been compromised. To mitigate this risk, the decision was made to drill through the depleted reservoir using a flat-rheology synthetic-based fluid, engineered with a high concentration of bridging particles to impart a strengthening effect on the formation.
The designer fluid allowed the reservoir to be drilled through successfully and the 7-in. liner to be run and cemented with full returns. Analysis of the frac-pack data showed that the formation-breakdown pressure was lower than the wellbore pressures experienced while drilling and cementing the liner, suggesting that the designer fluid improved the fracture resistance of the formation. The results imply that using such a designer fluid can have a strengthening effect on depleted/unconsolidated formations, in which some operators have had limited success applying wellbore-strengthening techniques.
The implication for the industry is that this technique can and should be considered on wells with challenges and risks similar to those of the Matterhorn A2 well. This paper will describe the approach taken in the laboratory for the fluid design, as well as operational practices to apply the treatment on location. A postmortem analysis will compare formation-breakdown pressures taken from the fracturing operations to actual wellbore pressures experienced while drilling and cementing, to demonstrate that a strengthening effect was realized.
Antipatterns: A Tool for Continuous Improvement
Authors: Feineman David R. 
Published: September 2010

Summary
Process design patterns are fragments of business processes used as a solution to commonly encountered problems. A process design antipattern is a special form of pattern that is ineffective or has negative consequences, but it may also be routinely followed. The objective in studying process antipatterns is to identify suboptimal performance and replace it with better practices. This paper describes some antipatterns in the implementation of digital-oilfield projects, refactored solutions that enable recovery from those antipatterns, and the root causes that create them. It concludes with a description of how continuous improvement enabled by antipatterns differs from more traditional approaches to project lessons learned and why antipatterns represent a better way to capture and reuse experience-based learning.
Stochastic reconstruction of the microstructure of equilibrium form snow and computation of effective elastic properties
Authors: Yuan Hongyan , Lee Jonah H. , Guilkey James E. 
Published: September 2010

AbstractThree-dimensional geometric descriptions of microstructure are indispensable to obtain the structure–property relationships of snow. Because snow is a random heterogeneous material, it is often helpful to construct stochastic geometric models that can be used to model physical and mechanical properties of snow. In the present study, the Gaussian random field-based stochastic reconstruction of the sieved and sintered dry-snow sample with grain size less than 1 mm is investigated. The one- and two-point correlation functions of the snow samples are used as input for the stochastic snow model. Several statistical descriptors not used as input to the stochastic reconstruction are computed for the real and reconstructed snow to assess the quality of the reconstructed images. For the snow samples and the reconstructed snow microstructure, we also estimate the mechanical properties and the size of the associated representative volume element using numerical simulations as additional assessment of the quality of the reconstructed images. The results indicate that the stochastic reconstruction technique used in this paper is reasonably accurate, robust and highly efficient in numerical computations for the high-density snow samples we consider.