bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis
Authors: Gregis Veronica , Andrés Fernando , Sessa Alice , Guerra Rosalinda F , Simonini Sara , Mateos Julieta L , Torti Stefano , Zambelli Federico , Prazzoli Gian Marco , Bjerkan Katrine N , Grini Paul E , Pavesi Giulio , Colombo Lucia , Coupland George , Kater Martin M 
Published: June 2013

Abstract
Background
MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism.

Results
To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively.

Conclusions
Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them.
Patient Preference and Contraindications in Measuring Quality of Care: What Do Administrative Data Miss?
Authors: Ryoo Joan J. , Ordin Diana L. , Antonio Anna Liza M. , Oishi Sabine M. , Gould Michael K. , Asch Steven M. , Malin Jennifer L. 
Published: June 2013

PurposePrior studies report that half of patients with lung cancer do not receive guideline-concordant care. With data from a national Veterans Health Administration (VHA) study on quality of care, we sought to determine what proportion of patients refused or had a contraindication to recommended lung cancer therapy.Patients and MethodsThrough medical record abstraction, we evaluated adherence to six quality indicators addressing lung cancer–directed therapy for patients diagnosed within the VHA during 2007 and calculated the proportion of patients receiving, refusing, or having contraindications to recommended treatment.ResultsMean age of the predominantly male population was 67.7 years (standard deviation, 9.4 years), and 15% were black. Adherence to quality indicators ranged from 81% for adjuvant chemotherapy to 98% for curative resection; however, many patients met quality indicator criteria without actually receiving recommended therapy by having a refusal (0% to 14%) or contraindication (1% to 30%) documented. Less than 1% of patients refused palliative chemotherapy. Black patients were more likely to refuse or bear a contraindication to surgery even when controlling for comorbidity; race was not associated with refusals or contraindications to other treatments.ConclusionRefusals and contraindications are common and may account for previously demonstrated low rates of recommended lung cancer therapy performance at the VHA. Racial disparities in treatment may be explained, in part, by such factors. These results sound a cautionary note for quality measurement that depends on data that do not reflect patient preference or contraindications in conditions where such considerations are important.
Adrenocortical Carcinoma Is a Lynch Syndrome–Associated Cancer
Authors: Raymond Victoria M. , Everett Jessica N. , Furtado Larissa V. , Gustafson Shanna L. , Jungbluth Chelsy R. , Gruber Stephen B. , Hammer Gary D. , Stoffel Elena M. , Greenson Joel K. , Giordano Thomas J. , Else Tobias 
Published: June 2013

Purpose Adrenocortical carcinoma (ACC) is an endocrine malignancy with a poor prognosis. The association of adult-onset ACC with inherited cancer predisposition syndromes is poorly understood. Our study sought to define the prevalence of Lynch syndrome (LS) among patients with ACC. Patients and Methods One hundred fourteen patients with ACC were evaluated in a specialized endocrine oncology clinic and were prospectively offered genetic counseling and clinical genetics risk assessment (group 1). In addition, families with known mismatch repair (MMR) gene mutations that were recorded in the University of Michigan Cancer Genetics Registry were retrospectively reviewed for the presence of ACC (group 2). ACC tumors from patients with LS were tested for microsatellite instability and immunohistochemistry (IHC) to evaluate for MMR deficiency. Results Ninety-four (82.5%) of 114 patients with ACC underwent genetic counseling (group 1). Three individuals (3.2%) had family histories suggestive of LS. All three families were found to have MMR gene mutations. Retrospective review of an additional 135 MMR gene–positive probands identified two with ACC (group 2). Four ACC tumors were available (group 1, 3; group 2, 1). All four tumors were microsatellite stable; three had IHC staining patterns consistent with germline mutation status. Conclusion The prevalence of LS among patients with ACC is 3.2%, which is comparable to the prevalence of LS in colorectal and endometrial cancer. Patients with ACC and a personal or family history of LS tumors should be strongly considered for genetic risk assessment. IHC screening of all ACC tumors may be an effective strategy for identifying patients with LS.
METHODICAL APPROACH TO FORMATION OF AN EFFECTIVE PORTFOLIO OF INNOVATIVE AND INVESTMENT PROJECTS IN THE CONDITIONS OF RESOURCE RESTRICTIONS
Authors: Мыльник Владимир , Mylnik Vladimir , Зубеева Елена , Zubeeva Elena 
Published: June 2013

This article is devoted to the development of the methodological approach to the formation of an effective portfolio of innovative-investment projects at the industrial enterprise in the conditions of resource constraints. In the article the main goals, objectives,
algorithm of formation of a portfolio are described, as well as methodological framework for the analysis of socio-economic and synergetic effects.
Diagnostic inconsistency of faecal immunochemical tests for haemoglobin in population screening of colorectal cancer
Authors: Huang Yanqin , Ge Weiting , London Viktoriya , Li Qilong , Cai Shanrong , Zhang Suzhan , Zheng Shu 
Published: June 2013

AbstractBackground:There is currently very little data available on the consistency of quantitative and qualitative faecal immunochemical test (FIT) for colorectal cancer screening.Methods:A representative random population (n=1889, 40–74 year olds) in Jiashan, China was invited for FIT screening in 2012. Faecal samples were collected by a single specimen collection device and simultaneously tested by a quantitative FIT (OC-SENSOR, OC) and two qualitative FITs (FIT A and FIT B with intrinsic positive haemoglobin cut-off concentrations of 20 μg Hb/g faeces and 40 μg Hb/g faeces, respectively). The observational criteria for a positive result of the qualitative FIT were set according to the density of the colour appearing in the test strip. The results produced by the quantitative and qualitative FIT for each sample were compared. κ coefficient was used to measure consistency.Results:A total of 1368 (72.4%) individuals returned faecal samples. Both FIT A and FIT B precisely identified all faecal samples with haemoglobin concentration above 100 μg Hb/g faeces, but the overall consistency was poor for OC & FIT A (κ=0.32, 95% CI 0.20–0.44) and was moderate for OC & FIT B (κ=0.74, 95% CI 0.64–0.85). A more favourable consistency (κ=0.64, 95% CI 0.57–0.72) was achieved when a different positive criterion was employed for FIT A.Conclusions:The diagnostic inconsistency between quantitative and qualitative FITs mainly exists in the faecal samples with low haemoglobin concentrations. Refining the criterion for a positive result may be a feasible way to improve the accuracy of qualitative FIT.
Experimental and finite element study of the effect of temperature and moisture on the tangential tensile strength and fracture behavior in timber logs
Authors: Larsen Finn , Ormarsson Sigurdur 
Published: June 2013

Abstract
Timber is normally dried by kiln drying, in the course of which moisture-induced stresses and fractures can occur. Cracks occur primarily in the radial direction due to tangential tensile strength (TSt) that exceeds the strength of the material. The present article reports on experiments and numerical simulations by finite element modeling (FEM) concerning the TSt and fracture behavior of Norway spruce under various climatic conditions. Thin log disc specimens were studied to simplify the description of the moisture flow in the samples. The specimens designed for TS were acclimatized to a moisture content (MC) of 18% before TSt tests at 20°C, 60°C, and 90°C were carried out. The maximum stress results of the disc simulations by FEM were compared with the experimental strength results at the same temperature levels. There is a rather good agreement between the results of modeling and experiments. The results also illustrate the strong decrease of TSt with increasing temperature at a constant MC level.
Evaluating Recycled Concrete Aggregate as Hot Mix Asphalt Aggregate
Authors: Bhusal Sushanta , Wen Haifang 
Published: June 2013

Abstract
The use of recycled concrete aggregate (RCA) in asphalt mix is a sustainable construction practice, provided that the addition of RCA does not adversely affect the performance of the asphalt mix. In this study, the effects of RCA on the performance behavior of hot mix asphalt (HMA) were examined. The mixes were produced by blending RCA with virgin aggregate at six different percentages (0 %, 20 %, 40 %, 60 %, 80 %, and 100 %). The mix design results indicate that the RCA is highly absorptive, and that as the percentage of RCA in the mix increases, the optimum asphalt content increases significantly. In terms of performance behavior, the addition of RCA to the HMA mix reduced the modulus, resistance to rutting, fatigue, thermal cracking, and resistance to moisture damage of the asphalt mix. Considering the performance behavior and the need for a higher asphalt content, the use of RCA as HMA aggregate is not recommended, even though all the RCA mixes met the volumetric requirements. More important, the findings in this study indicate that the absorbed asphalt might play a significant role at high temperatures, likely because of expansion of the asphalt.
Outcomes of an Early Feeding Practices Intervention to Prevent Childhood Obesity
Authors: Daniels Lynne Allison , Mallan Kimberley Margaret , Nicholson Jan Maree , Battistutta Diana , Magarey Anthea 
Published: June 2013

OBJECTIVE:
The goal of this study was to evaluate outcomes of a universal intervention to promote protective feeding practices that commenced in infancy and aimed to prevent childhood obesity.

METHODS:
The NOURISH randomized controlled trial enrolled 698 first-time mothers (mean ± SD age: 30.1 ± 5.3 years) with healthy term infants (51% female) aged 4.3 ± 1.0 months at baseline. Mothers were randomly allocated to self-directed access to usual care or to attend two 6-session interactive group education modules that provided anticipatory guidance on early feeding practices. Outcomes were assessed 6 months after completion of the second information module, 20 months from baseline and when the children were 2 years old. Maternal feeding practices were self-reported by using validated questionnaires and study-developed items. Study-measured child height and weight were used to calculate BMI z scores.

RESULTS:
Retention at follow-up was 78%. Mothers in the intervention group reported using responsive feeding more frequently on 6 of 9 subscales and 8 of 8 items (all, P ≤ .03) and overall less controlling feeding practices (P &lt; .001). They also more frequently used feeding practices (3 of 4 items; all, P &lt; .01) likely to enhance food acceptance. No statistically significant differences were noted in anthropometric outcomes (BMI z score: P = .10) nor in prevalence of overweight/obesity (control 17.9% vs intervention 13.8%; P = .23).

CONCLUSIONS:
Evaluation of NOURISH data at child age 2 years found that anticipatory guidance on complementary feeding, tailored to developmental stage, increased use by first-time mothers of “protective” feeding practices that potentially support the development of healthy eating and growth patterns in young children.
Systematic Review of Community-Based Childhood Obesity Prevention Studies
Authors: Bleich Sara N. , Segal Jodi , Wu Yang , Wilson Renee , Wang Youfa 
Published: June 2013

OBJECTIVE:
This study systematically reviewed community-based childhood obesity prevention programs in the United States and high-income countries.

METHODS:
We searched Medline, Embase, PsychInfo, CINAHL, clinicaltrials.gov, and the Cochrane Library for relevant English-language studies. Studies were eligible if the intervention was primarily implemented in the community setting; had at least 1 year of follow-up after baseline; and compared results from an intervention to a comparison group. Two independent reviewers conducted title scans and abstract reviews and reviewed the full articles to assess eligibility. Each article received a double review for data abstraction. The second reviewer confirmed the first reviewer’s data abstraction for completeness and accuracy.

RESULTS:
Nine community-based studies were included; 5 randomized controlled trials and 4 non–randomized controlled trials. One study was conducted only in the community setting, 3 were conducted in the community and school setting, and 5 were conducted in the community setting in combination with at least 1 other setting such as the home. Desirable changes in BMI or BMI z-score were found in 4 of the 9 studies. Two studies reported significant improvements in behavioral outcomes (1 in physical activity and 1 in vegetable intake).

CONCLUSIONS:
The strength of evidence is moderate that a combined diet and physical activity intervention conducted in the community with a school component is more effective at preventing obesity or overweight. More research and consistent methods are needed to understand the comparative effectiveness of childhood obesity prevention programs in the community setting.
Wireline Formation Testers Unlock Potential in a Deepwater Gas Condensate Reservoir
Authors: Zope Dinesh , Saxena Kamlesh Raj , Gupta Akshat , Jha Subhash , Tellapaneni Prasanna K. , Ojha Aditya , Shukla Sourabh , Jackson Richard , Jadhav Madhavi Vitthal 
Published: June 2013

Abstract
Reservoir-fluid properties play a key role in exploration and field development planning as accurate fluid characterization is important for designing reservoir development strategy, optimizing well completion, optimizingthe production system and efficient reservoir management. Characterization of reservoir fluids with more complex behaviors, such as gas condensates and near-critical fluids can be technically challenging, especially in a deepwater environment as reservoir development planning and production facility design is contingent on getting an accurate description of the reservoir fluid. Fluid characterization begins with the collection of representative formation fluid samples during initial wireline formation testing, bottomhole sampling and during conventional well testing operations. Traditionally these fluid samples are sent to offsite laboratories for sample analysis. However, characterizing a gas condensate fluid system based on a single sample set can be potentially misleading since PVT properties of samples acquired across a reservoir may be different due to spatial variation in their components and compositional grading. In this technical contribution we present a case study to demonstrate that characterizing gas and gas-condensate systems using only a basic set of measurements and from analysis of pressure gradients alone; could lead to potentially ambiguous results, an inappropriate fluid model or misinterpretation. In our study, we describe the practical application of advanced wireline formation sampling and testing techniques in combination with downhole fluid analysis, and their integration with laboratory PVT studies and equation-of-state (EOS) models. We describe the importance of a comprehensive data collection and fluid analysis plan early in the exploration/ appraisal process, and illustrate how high-quality fluid sample data and property measurements from advanced formation sampling and testing tools in combination with conventional well testing techniques can add significant value by helping to reduce uncertainty and aiding better technical decision making.
Hydrocarbon Production and Microseismic Monitoring – Treatment Optimization in the Marcellus Shale
Authors: Neuhaus Carl W. , Telker Cherie , Ellison Mary , Blair Keith 
Published: June 2013

Abstract
An integrated analysis of hydraulic fracturing treatments in the Marcellus Shale monitored by a permanently installed array of buried geophones was conducted to investigate the relationship between reservoir geology, wellbore completion and stimulation design, and microseismic data. Available data from other sources (such as well logs and well cores, information on reservoir properties, regional and local geology, and other sub-surface structural information) was utilized to determine how factors related to the specific geology in the Marcellus and to the variability of hydraulic fracture treatments impacted the microseismic response of the formation. These findings were then used to evaluate the correlation between hydrocarbon production and microseismic results relative to changes in geology and variability of the stimulation approach. The observed variability in the microseismic response under the footprint of the array was used to derive and extrapolate regional trends to optimize field development. The initial production was compared to reservoir and engineering parameters, such as treatment pressures, sequence of treatments (toe-to-heel vs. zipper-frac), net pressures, and stage spacing, to determine if the variability in the microseismic results is due to engineering differences or to spatially-varying reservoir properties.
A stress inversion based on focal mechanisms was used to explain the asymmetry of the microseismicity about the wellbore and calculate the magnitudes and directions of the three principal stresses. Fracture orientations defined by failure planes from source mechanisms were used to build a discrete fracture network (DFN) representing the existing unstimulated fracture network in the Marcellus Shale. Simulations then calculated where failure is likely to occur in the DFN during the stimulation using data obtained from the stress inversion comparing the results to the microseismic event locations. Finally, a calibrated model was used to determine the effect of changes in treatment parameters, such as flow rate, treatment pressure, and volume of fluid pumped as well as completion parameters such as stage length, number of perforations, and perforation cluster spacing, in order to optimize the hydraulic fracturing design.
Short-Term Production Prediction in Real Time Using Intelligent Techniques
Authors: Al-Jasmi A. , Goel H. K. , Nasr H. , Querales M. , Rebeschini J. , Villamizar M. A. , Carvajal G. A. , Knabe S. , Rivas Francklin , Saputelli L. 
Published: June 2013

Abstract
Intelligent digital oilfield operations collect real-time data from an operating asset and transform that raw data into information through intelligent, automated work processes, which assist engineers with key well operations and monitoring, improving their productivity and decision-making. A major oil and gas operator in the Middle East is developing a set of intelligent workflows for key activities and processes for its production operations, with the ultimate goal of improved asset performance.
Real-time surveillance and monitoring of production operation processes have proven to be operationally and economically important for managing complex, high-cost reservoirs. However, predicting short-term production and production interruptions—for example, related to pump settings—has posed a tremendous challenge. While operators routinely forecast production for the next 60 to 90 days, sophisticated tools such as full-field numerical simulation models are of limited use in predicting short-term production of 30 days. Similarly, while nodal analysis can estimate current operating conditions, it cannot be used for prediction. Because of its simplicity, rapid training, and demonstrated results, a prediction technique using neural networks (NN) has emerged as a solution that can predict short-term well production behavior with acceptable accuracy.
This paper presents a case study using NNs to predict liquid rate and water cut performance in a mature reservoir with more than 20% water cut. The NN was trained using available surface and down-hole, real-time production data, time-dependent data, and completion design data. The time-dependent data are included as time series configured to let users generate scenarios by changing well operations. This approach not only provides a base-case prediction but also simulates results after making adjustments in control variables, such as tubing head pressure (THP) and pump frequency. Changing THP and frequency lets users model production to predict and circumvent negative well pump events.
This project was implemented in a mature carbonate oil reservoir under waterflood in the Middle East. Despite limited reservoir data, the results show that the NN is a powerful and rapid tool that predicts liquid rate and water cut with acceptable accuracy, helping engineers make prompt decisions to prevent and reduce downtime.