bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells
Authors: Albert Thomas K , Grote Korbinian , Boeing Stefan , Meisterernst Michael 
Published: March 2010

Abstract
Background
The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex levels. As yet, genome-scale promoter mapping of human TFIIB has not been reported. It thus remains elusive how human core promoters contribute to preinitiation complex formation in vivo.

Results
We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA elements, but not the previously in vitro defined TFIIB recognition elements, are enriched in some 4 to 5% of the genes. NC2 binds to a highly related target gene set. Nonetheless, subpopulations show strong variations in factor ratios: whereas high TFIIB/NC2 ratios select for promoters with focused start sites and conserved core elements, high NC2/TFIIB ratios correlate to multiple start-site promoters lacking defined core elements.

Conclusions
TFIIB and NC2 are global players that occupy active genes. Preinitiation complex formation is independent of core elements at the majority of genes. TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes. Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.
Predictors of Tumor Progression During Neoadjuvant Chemotherapy in Breast Cancer
Authors: Caudle Abigail S. , Gonzalez-Angulo Ana M. , Hunt Kelly K. , Liu Ping , Pusztai Lajos , Symmans W. Fraser , Kuerer Henry M. , Mittendorf Elizabeth A. , Hortobagyi Gabriel N. , Meric-Bernstam Funda 
Published: March 2010

Purpose Although most breast cancer patients who receive neoadjuvant chemotherapy (NCT) have a tumor response, a small proportion experience progressive disease (PD). Predictors of response have been reported, but predictors for progression have not been identified. We sought to identify predictors of tumor progression during NCT with the ultimate aim of identifying patients who might benefit from a first-line surgical approach or from novel targeted therapies. Patients and Methods Data were obtained from reviewing medical records of patients with stage I to III breast cancer who received NCT (anthracycline and/or taxane based). Statistical analysis was performed to compare patients with any response or stable disease with patients with PD. Results One thousand nine hundred twenty-eight patients received NCT; 1,762 patients (91%) had some response, 107 (6%) had stable disease, and 59 (3%) had PD at some point during NCT. Factors predictive of PD included African American race (P = .002), tumor (T) status (P = .002), and American Joint Committee on Cancer clinical stage (P = .02). Histopathologic features of PD were high tumor grade (P = .005), high Ki-67 score (P = .002), and negative estrogen receptor (ER)/progesterone receptor (PR) status (P < .001/P < .001). Pre-NCT T status, race, and ER status were independent predictors of progression in multivariate analysis. Disease progression was a negative predictor of distant disease–free survival and overall survival in multivariate analysis (P < .001). Conclusion Factors predictive of PD include race, advanced tumor stage, high nuclear grade, high Ki-67 score, and ER/PR negativity. Because many of these variables are also associated with response to NCT, novel molecular predictors are needed to identify patients at risk for progression on standard NCT.
Predicting Adverse Events in Children With Fever and Chemotherapy-Induced Neutropenia: The Prospective Multicenter SPOG 2003 FN Study
Authors: Ammann Roland A. , Bodmer Nicole , Hirt Andreas , Niggli Felix K. , Nadal David , Simon Arne , Ozsahin Hulya , Kontny Udo , Kühne Thomas , Popovic Maja Beck , Lüthy Annette Ridolfi , Aebi Christoph 
Published: March 2010

PurposeTo develop a score predicting the risk of adverse events (AEs) in pediatric patients with cancer who experience fever and neutropenia (FN) and to evaluate its performance.Patients and MethodsPediatric patients with cancer presenting with FN induced by nonmyeloablative chemotherapy were observed in a prospective multicenter study. A score predicting the risk of future AEs (ie, serious medical complication, microbiologically defined infection, radiologically confirmed pneumonia) was developed from a multivariate mixed logistic regression model. Its cross-validated predictive performance was compared with that of published risk prediction rules.ResultsAn AE was reported in 122 (29%) of 423 FN episodes. In 57 episodes (13%), the first AE was known only after reassessment after 8 to 24 hours of inpatient management. Predicting AE at reassessment was better than prediction at presentation with FN. A differential leukocyte count did not increase the predictive performance. The score predicting future AE in 358 episodes without known AE at reassessment used the following four variables: preceding chemotherapy more intensive than acute lymphoblastic leukemia maintenance (weight = 4), hemoglobin ≥ 90 g/L (weight = 5), leukocyte count less than 0.3 G/L (weight = 3), and platelet count less than 50 G/L (weight = 3). A score (sum of weights) ≥ 9 predicted future AEs. The cross-validated performance of this score exceeded the performance of published risk prediction rules. At an overall sensitivity of 92%, 35% of the episodes were classified as low risk, with a specificity of 45% and a negative predictive value of 93%.ConclusionThis score, based on four routinely accessible characteristics, accurately identifies pediatric patients with cancer with FN at risk for AEs after reassessment.
Surgery With or Without Preoperative Paclitaxel and Carboplatin in Early-Stage Non–Small-Cell Lung Cancer: Southwest Oncology Group Trial S9900, an Intergroup, Randomized, Phase III Trial
Authors: Pisters Katherine M.W. , Vallières Eric , Crowley John J. , Franklin Wilbur A. , Bunn Paul A. , Ginsberg Robert J. , Putnam Joe B. , Chansky Kari , Gandara David 
Published: March 2010

Purpose Patients with early-stage non–small-cell lung cancer (NSCLC) have a poor prognosis even after complete resection. Earlier studies of preoperative (induction) chemotherapy in resectable NSCLC demonstrated feasibility and encouraging survival data. This randomized phase III trial compared overall survival (OS) for preoperative paclitaxel and carboplatin followed by surgery with surgery alone in patients with early-stage NSCLC. Patients and Methods Patients with clinical stage IB-IIIA NSCLC (excluding superior sulcus tumors and N2 disease) were eligible. Patients were randomly assigned to surgery alone or to three cycles of paclitaxel (225 mg/m2) and carboplatin (area under curve, 6) followed by surgical resection. The primary end point was OS; secondary end points were progression-free survival (PFS), chemotherapy response, and toxicity. Results The trial closed early with 354 patients after reports of a survival benefit for postoperative chemotherapy in other studies. The median OS was 41 months in the surgery-only arm and 62 months in the preoperative chemotherapy arm (hazard ratio, 0.79; 95% CI, 0.60 to 1.06; P = .11.) The median PFS was 20 months for surgery alone and 33 months for preoperative chemotherapy (hazard ratio, 0.80; 95% CI, 0.61 to 1.04; P = .10.) Major response to chemotherapy was seen in 41% of patients; no unexpected toxicity was observed. Conclusion This trial closed prematurely after compelling evidence supporting postoperative chemotherapy emerged. Although OS and PFS were higher with preoperative chemotherapy, the differences did not reach statistical significance. At present, stronger evidence exists for postoperative chemotherapy in early-stage NSCLC.
Multiplex Enzyme Assay for Galactosemia Using Ultraperformance Liquid Chromatography–Tandem Mass Spectrometry
Authors: Ko Dae-Hyun , Jun Sun-Hee , Park Hyung-Doo , Song Sang Hoon , Park Kyoung Un , Kim Jin Q , Song Young-Han , Song Junghan 
Published: March 2010

AbstractBackground: Galactosemia is one of the most important inherited disorders detected by newborn screening tests. Abnormal results in screening tests should be confirmed by enzyme activity assays, but existing methods are time and labor intensive. We developed a novel multiplex enzyme assay for galactosemia using ultraperformance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS).Methods: [13C6]-galactose, [13C2]-galactose-1-phosphate, and UDP-glucose were used as substrates for 3 galactose-metabolizing enzymes. The end products from the combined reaction mixtures, [13C6]-galactose-1-phosphate, UDP-[13C2]-galactose, and UDP-galactose, were simultaneously measured using UPLC-MS/MS. Linearity, imprecision, ion suppression, and the effects of substrate were evaluated to determine assay performance. Enzyme activities from 35 healthy individuals, 8 patients with enzyme deficiency, and 18 mutant cells were analyzed.Results: Substrates, products, and internal standards from the mixture of 3 enzyme reactions were clearly separated by using UPLC-MS/MS, with an injection cycle time of 10 min. Ion suppression was 0.1%–2.5%, the interassay imprecision of UPLC-MS/MS was 3.3%–10.6% CV, and the linearity of each system was good (R2 = 0.994–0.999). Patient samples and mutated cells showed consistently low enzyme activities compared with those of normal individuals and wild-type cells.Conclusions: This method allows for a high-throughput and reproducible multiplex enzyme assay for galactosemia in erythrocytes.
Species composition and distribution of macroalgae on Atol das Rocas, Brazil, SW Atlantic
Authors: Villaça Roberto , Carvalhal Fonseca Adriana , Jensen Viviane Köppe , Knoppers Bastiaan 
Published: March 2010

Abstract
This study, performed over the years 1999–2003, analyzed the species composition, spatial distribution and ecological aspects of macroalgal assemblages on Atol das Rocas reef, located 266 km off northeastern Brazil. It is the sole atoll in the South Atlantic and is almost completely built of coralline algae. Forty-seven new occurrences of macroalgae were recorded. Adding these to the previous studies, 143 taxa are now known for the local marine flora, with the Rhodophyta as the dominant group. New finds were mainly on the fore reef and in reef pools. The inner habitats (the reef flat, internal ridge and inner pools) harbored fewer macroalgal species than the outer habitats (the reef front, reef crest crevices and outer pools). Inner habitats are subject to prolonged desiccation and solar irradiation stress together with abrupt changes in temperature and salinity controlled by the water oscillations of the mesotidal regime within the atoll; the outer habitats are less affected by these short temporal impacts and are mainly governed by oceanic forcing. Atol das Rocas harbors some species unknown in other Brazilian waters, but these are common in Caribbean reef waters.
Open Energy Gateway Architecture for Customers in the Distribution GridArchitektur eines offenen Gateways für Energiemanagement und Energieeffizienz für Verteilnetzkunden
Authors: Nestle David , Ringelstein Jan , Waldschmidt Heiko 
Published: March 2010

Abstract
Energy management and energy efficiency for small electricity customers as part of a Smart Grid strategy are gaining significance with increasing share of renewable and distributed generation. The concept presented provides a single Gateway between the customer and the grid on top of which a variety of applications shall be executable, which access costumer devices, user displays, smart meters, measuring data, pricing data etc.
Renewable Generation and Reliability in the Electric Power NetworkZuverlässigkeit elektrischer Netze mit Energieerzeugung aus erneuerbaren Energien
Authors: Styczynski Zbigniew A. , Heyde Chris O. , Rohrig Kurt , Rudion Krzysztof 
Published: March 2010

AbstractPresent day electric power systems in developed countries are characterised by very high reliability. In Germany the mean supply interruption time per year for the end customers is 23 minutes. How will this high quality of supply change with the increase of decentralised and renewable generation? Which measures are necessary to keep on this high reliability standard? This is one of the investigation goals in the E-Energy project Regenerative Modellregion Harz (RegModHarz). From a power system planning point of view it is possible to calculate some reliability indexes to evaluate the network structure. This methodology and some calculation examples will be given in part one of this paper. Further, taking into account the current experiences with power system operation, some necessary measures to support the secure power system operation with a high share of renewable generation, will be presented. The expected level of reliability in the future distribution power system will be analysed.
Simulations in the Smart Grid Field Study MeRegioSimulationen im MeRegio Smart Grid Feldtest
Authors: Hirsch Christian , Hillemacher Lutz , Block Carsten , Schuller Alexander , Möst Dominik 
Published: March 2010

Abstract
The aim of the research project MeRegio is to meet the claim for more efficient decentralized energy systems by integrating advanced information and communication technologies (ICT) into all stages of the energy supply chain. Several marketplaces — in particular for power and for ancillary services — which are coupled to the technical energy infrastructure through a powerful and lawful ICT infrastructure should serve as a basis for an efficient and transparent coordination of energy supply, energy demand, and services. The developed concepts will be both validated by simulations and tested within a model region.
Innovative Retail Laboratory — Investigating Future Shopping TechnologiesInnovative Retail Laboratory — Erforschung von Technologien für das Einkaufen von morgen
Authors: Krüger Antonio , Spassova Lübomira , Jung Ralf 
Published: March 2010

Abstract
The Innovative Retail Laboratory (IRL) is an application-oriented research laboratory of the German Research Center for Artificial Intelligence (DFKI) run in collaboration with the German retailer GLOBUS SB-Warenhaus Holding in St. Wendel. In this living lab, we conduct research in a wide range of different domains all connected to intelligent shopping consultants, which range from a virtual assistant responsible for matters of dieting and allergies, over a digital sommelier, to personalized cross and up selling, smart items with digital product memories as a further development of the RFID technology, indoor positioning and navigation as well as new logistics concepts, to see if they are suitable for everyday life and useful for customers. New ways of customer interaction are developed and tested for implementation. The range varies from personalized shopping assistants to “talking” products and intelligent shopping carts, which plan and show the way through the store according to your shopping list. Furthermore they can give advice on what to buy for the recipes you have in mind, they compare products, point out special offers in a personalized way and give additional information about the products. However, the concepts and technologies that regard the self-service store of the future as a place for shopping are not IRL´s only focus. The relation between the store and its customers begins way before the shopping trip itself takes place. It starts with an individual shopping preparation and a personalized presentation of offers at home and will be continued afterwards through advice that is given about purchased goods and information about their use.
Approach to the patient with secondary osteoporosis
Authors: Hofbauer Lorenz C , Hamann Christine , Ebeling Peter R 
Published: March 2010

AbstractSecondary osteoporosis is characterized by low bone mass with microarchitectural alterations in bone leading to fragility fractures in the presence of an underlying disease or medication. Scenarios that are highly suspicious for secondary osteoporosis include fragility fractures in younger men or premenopausal women, very low bone mineral density (BMD) values, and fractures despite anti-osteoporotic therapy. An open-minded approach with a detailed history and physical examination combined with first-line laboratory tests are aimed at identifying clinical risk factors for fractures, osteoporosis-inducing drugs, and underlying endocrine, gastrointestinal, hematologic, or rheumatic diseases, which then need to be confirmed by specific and/or more invasive tests. BMD should be assessed with bone densitometry at the hip and spine. Lateral X-rays of the thoracic and lumbar spine should be performed to identify or exclude prevalent vertebral fractures which may be clinically silent. Management of secondary osteoporosis includes treatment of the underlying disease, modification of medications known to affect the skeleton, and specific anti-osteoporotic therapy. Calcium and vitamin D supplementation should be initiated with doses that result in normocalcemia and serum 25-hydroxyvitamin D concentrations of at least 30 ng/ml. Oral and i.v. bisphosphonates are effective and safe drugs for most forms of secondary osteoporosis. Severe osteoporosis may require the use of teriparatide.
A Cost-effectiveness Analysis of Screening Urine Dipsticks in Well-Child Care
Authors: Sekhar Deepa L. , Wang Li , Hollenbeak Christopher S. , Widome Mark D. , Paul Ian M. 
Published: March 2010

OBJECTIVE:
Despite data suggesting that routine urine screening for chronic kidney disease (CKD) has low diagnostic yield and the American Academy of Pediatrics 2007 recommendation to discontinue this screening, pediatricians may not have recognized this change. Because the new recommendation marks a major alteration in the practice guidelines, we sought to evaluate the cost-effectiveness of dipstick urinalysis for detection of CKD from the primary care practitioner's perspective.

METHODS:
Decision analysis was used to model a screening dipstick urinalysis strategy relative to a no-screening strategy. Data on the incidence of hematuria and proteinuria in children were derived from published reports of large cohorts of school-aged children. Direct costs were estimated from the perspective of the primary care practitioner. The measure of effectiveness was the rate of diagnoses of CKD. Cost-effectiveness was evaluated by using an incremental cost-effectiveness ratio.

RESULTS:
Expected costs and effectiveness for the no-screening strategy were $0 because no resources were used and no cases of CKD were diagnosed. The screening strategy involved a cost per dipstick of $3.05. Accounting for both true-positive and false-positive initial screens, 14.2% of the patients required a second dipstick as per typical clinical care, bringing the expected cost of the screening strategy to $3.47 per patient. In the screening strategy, 1 case of CKD was diagnosed per 800 screened, and the incremental cost-effectiveness ratio was $2779.50 per case diagnosed.

CONCLUSIONS:
Urine dipstick is inexpensive, but it is a poor screening test for CKD and a cost-ineffective procedure for the primary care provider. These data support the change in the American Academy of Pediatrics guidelines on the use of screening dipstick urinalysis. Clinicians must consider the cost-effectiveness of preventive care procedures to make better use of available resources.
Catheter Duration and Risk of CLA-BSI in Neonates With PICCs
Authors: Sengupta Arnab , Lehmann Christoph , Diener-West Marie , Perl Trish M. , Milstone Aaron M. 
Published: March 2010

OBJECTIVE:
To determine whether the risk of central line-associated bloodstream infections (CLA-BSIs) remained constant over the duration of peripherally inserted central venous catheters (PICCs) in high-risk neonates.

PATIENT AND METHODS:
We performed a retrospective cohort study of NICU patients who had a PICC inserted between January 1, 2006, and December 31, 2008. A Poisson regression model with linear spline terms to model time since PICC insertion was used to evaluate potential changes in the risk of CLA-BSI while adjusting for other variables.

RESULTS:
Six hundred eighty-three neonates were eligible for analysis. There were 21 CLA-BSIs within a follow-up period of 10 470 catheter-days. The incidence of PICC-associated CLA-BSI was 2.01 per 1 000 catheter-days (95% confidence interval [CI]: 1.24–3.06). The incidence rate of CLA-BSIs increased by 14% per day during the first 18 days after PICC insertion (incidence rate ratio [IRR]: 1.14 [95% CI: 1.04–1.25]). From days 19 through 35 after PICC insertion, the trend reversed (IRR: 0.8 [95% CI: 0.66–0.96]). From days 36 through 60 after PICC insertion, the incidence rate of CLA-BSI again increased by 33% per day (IRR: 1.33 [95% CI: 1.12–1.57]). There was no statistically significant association between the risk of CLA-BSI and gestational age groups, birth weight groups, or chronological age groups.

CONCLUSIONS:
Our data suggest that catheter duration is an important risk factor for PICC-associated CLA-BSI in the NICU. A significant daily increase in the risk of CLA-BSI after 35 days may warrant PICC replacement if intravascular access is necessary beyond that period.
Phosphorus Availability in Low-Phytate Mutant Varieties of Barley: Digestibility Studies with Channel Catfish and Red Drum
Authors: Buentello J Alejandro , Gatlin Delbert M 
Published: March 2010

Abstract
About 70% of the phosphorus in plant feedstuffs is typically in the form of organic phytates, but molecular phytogenetic techniques allow the development of variant seed forms that are capable of storing most of it in an inorganic form. In response to concerns over excessive phosphorus discharges from uneaten or unassimilated aquaculture feeds, two independent digestibility trials were conducted to evaluate the suitability of single-gene, low-phytic-acid mutations of barley Hordeum vulgare as feedstuffs for channel catfish Ictalurus punctatus and red drum Sciaenops ocellatus. Five isonitrogenous and isocaloric diets containing five different barley variants plus one reference diet (RD) were independently evaluated with each species. The RD for catfish contained 30% menhaden Brevoortia tyranus fish meal and 30% soybean meal, whereas the red drum RD included 48% lyophilized red drum muscle meal as the sole protein source. Each experimental diet was formulated so that a barley mutant replaced 30% of the RD. The diets were fed for 3 weeks to triplicate groups of juvenile channel catfish weighing 200 ± 10 g/fish (mean ± SD) and red drum weighing 400 ± 17 g/fish. Fecal samples were collected 8–12 h postfeeding. Apparent phosphorus, crude protein, and organic matter digestibility coefficients were determined by using chromic oxide as an inert marker. For catfish, the apparent digestibility coefficients for organic matter, phosphorus, and protein ranged from 28% to 62%, 47% to 98%, and 66% to 75%, respectively, for the different barley varieties. The same coefficients for red drum ranged from 69% to 93%, 54% to 86%, and 71% to 84%, respectively. Barley variant 955 resulted in the lowest fecal phosphorus content for both species. These results indicate that a considerable reduction of phosphorus excretion by fish could be achieved solely by substituting ordinary barley (or other plant ingredients) with low-phytate mutant grains. This information may lead to reductions in the amount of unavailable phosphorus added to commercial fish diets, with concomitant reductions in discharges of waste phosphorus.