bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solving Noisy, Large-Scale Fixed-Point Problems and Systems of Nonlinear Equations
Authors: Bierlaire Michel , Crittin Frank 
Published: February 2006

Many complex transportation models can be formulated as fixed-point problems. Typical examples are the “equilibrium-like” models, motivated by the need to capture the interaction between the transport supply (that is, the infrastructure) and transport demand (that is, travelers’ behavior) in various ways. In this paper, we propose a new approach for solving fixed-point problems and, equivalently, systems of nonlinear equations. It is a generalization of secant methods, and uses several previous iterates to generate a linear approximation of the nonlinear function. Although it belongs to the quasi-Newton family of methods, our algorithm is matrix free, allowing it to solve large-scale systems of equations without derivative and without any particular assumption about the structure of the problem or its Jacobian. Computational experiments on standard problems show that this algorithm outperforms classical, large-scale quasi-Newton methods in terms of efficiency and robustness. Its numerical performances are similar to Newton-Krylov methods currently considered as the best algorithms to solve large-scale nonlinear systems of equations. Furthermore, our approach, using multiple previous iterates to build a linear approximation of the nonlinear function, exhibits robust behavior in the presence of noise in the equations, which makes it particularly well adapted to transportation problems. We run our algorithm on a simple origin-destination (OD) matrix estimation problem and on some instances of the consistent anticipatory route guidance (CARG) problem, to illustrate the applicability of the proposed method and to show its significant superiority to the classical method of successive averages (MSA). Regarding size, we were able to solve a CARG problem with more than 120,000 variables. We were also able to solve classical problems with up to two million variables.
Slot Trading Opportunities in Collaborative Ground Delay Programs
Authors: Vossen Thomas W. M. , Ball Michael O. 
Published: February 2006

The Federal Aviation Administration (FAA) and the major airlines in the United States have embraced a new initiative to improve air traffic flow management. This initiative, called collaborative decision making (CDM), is based on the recognition that improved data exchange and communication between the FAA and the airlines will lead to better decision making. In particular, the CDM philosophy emphasizes that decisions with a potential economic impact on airlines should be decentralized and made in collaboration with the airlines whenever possible. The CDM paradigm has led to fundamental changes in the implementation of ground delay programs. A key component has been the introduction of the compression procedure, which allows for the exchange of arrival slots between airlines. In this paper, we consider opportunities for increased airline control by interpreting the compression procedure as a mediated slot trading mechanism. Based on this interpretation, we propose an extension that allows airlines to submit so-called at-least, at-most offers. We develop an efficient integer programming model to solve the mediator’s problem, and show that the resulting mechanism can substantially improve the ability of airlines to optimize their internal cost functions.
Planning for Robust Airline Operations: Optimizing Aircraft Routings and Flight Departure Times to Minimize Passenger Disruptions
Authors: Lan Shan , Clarke John-Paul , Barnhart Cynthia 
Published: February 2006

Airlines typically construct their schedules assuming that every flight leg will depart and arrive as planned. Because this optimistic scenario rarely occurs, these plans are frequently disrupted and airlines often incur significant costs in addition to those originally planned. Flight delays and schedule disruptions also cause passenger delays and disruptions. A more robust plan can reduce the occurrence and impact of these delays, thereby reducing costs. In this paper, we present two new approaches to minimize passenger disruptions and achieve robust airline schedule plans. The first approach involves routing aircraft, and the second involves retiming flight departure times. Because each airplane usually flies a sequence of flight legs, delay of one flight leg might propagate along the aircraft route to downstream flight legs and cause further delays and disruptions. We propose a new approach to reduce delay propagation by intelligently routing aircraft. We formulate this problem as a mixed-integer programming problem with stochastically generated inputs. An algorithmic solution approach is presented. Computational results obtained using data from a major U.S. airline show that our approach can reduce delay propagation significantly, thus improving on-time performance and reducing the numbers of passengers disrupted. Our second area of research considers passengers who miss their flight legs due to insufficient connection time. We develop a new approach to minimize the number of passenger misconnections by retiming the departure times of flight legs within a small time window. We formulate the problem and an algorithmic solution approach is presented. Computational results obtained using data from a major U.S. airline show that this approach can substantially reduce the number of passenger misconnections without significantly increasing operational costs.
Quantification of mRNA in Whole Blood by Assessing Recovery of RNA and Efficiency of cDNA Synthesis
Authors: Mitsuhashi Masato , Tomozawa Shigeru , Endo Katsuya , Shinagawa Atsushi 
Published: February 2006

AbstractBackground: Current gene expression analysis relies on the assumption that the isolated RNA represents all species of mRNA in proportions equal to those in the original materials. No system is available for absolute quantification of mRNA.Methods: We applied whole blood to 96-well filterplates to trap leukocytes. Lysis buffer containing cocktails of specific reverse primers and known concentrations of synthetic external control RNA (RNA34) was added to filterplates, and cell lysates were transferred to oligo(dT)-immobilized microplates for hybridization. We then synthesized the cDNA in the oligo(dT)-immobilized microplates from these primer sites and used the cDNA for real-time PCR. RNA34 acted as a universal control, and gene amplification results were converted to quantities of mRNA per microliter of whole blood after the recovery of RNA34 in each sample was determined.Results: Under fully optimized conditions, both added RNA34 and native mRNA species exhibited ∼10% recovery from whole blood to real-time PCR. When whole blood was stimulated ex vivo, changes in gene expression as low as 30%–40% were detected with statistical significance, and the experimental CVs were low (10%–20%).Conclusion: This new system to estimate mRNA copies per microliter of whole blood may allow standardization of gene-expression–based molecular diagnostics.
Variations in Porphobilinogen and 5-Aminolevulinic Acid Concentrations in Plasma and Urine from Asymptomatic Carriers of the Acute Intermittent Porphyria Gene with Increased Porphyrin Precursor Excretion
Authors: Floderus Ylva , Sardh Eliane , Möller Christer , Andersson Claes , Rejkjaer Lillan , Andersson Dan EH , Harper Pauline 
Published: February 2006

AbstractBackground: The heme precursors porphobilinogen (PBG) and 5-aminolevulinic acid (ALA) accumulate during overt crises of acute intermittent porphyria (AIP), and high excretion of these metabolites often continues in the asymptomatic phase.Methods: We measured concentrations of PBG and ALA and investigated the correlation between these metabolites in plasma and urine in 10 asymptomatic AIP carriers with high excretion and in 5 healthy individuals. We quantified plasma concentrations with an HPLC–mass spectrometric method and urine concentrations with ion-exchange chromatography.Results: The mean (SD) plasma concentrations of PBG and ALA in the AIP carriers were 3.1 (1.0) and 1.7 (0.7) μmol/L, respectively. The mean 8-h urinary excretion amounts of PBG and ALA in the AIP carriers were 102 (25) and 56 (18) μmol, respectively, whereas the corresponding values for healthy individuals were 2.9 (0.7) and 9.3 (1.2) μmol. The correlations between PBG and ALA values in plasma and urine of the AIP carriers were 0.678 and 0.856, respectively. The mean PBG/ALA ratio was ∼2.0 in both plasma and urine for the AIP carriers and 0.3 in urine for the healthy individuals. The renal clearance rates for PBG and ALA were 71 (15) and 70 (13) mL/min, respectively.Conclusions: The described HPLC-mass spectrometric method enabled characterization of variations in plasma PBG and ALA in AIP carriers during an 8-h period. The renal clearances were similar for both metabolites. This method could be used to monitor AIP patients during treatment.
B-Type Natriuretic Peptide (BNP) and N-Terminal Pro-BNP in Obese Patients without Heart Failure: Relationship to Body Mass Index and Gastric Bypass Surgery
Authors: St. Peter John V , Hartley Guilford G , Murakami MaryAnn M , Apple Fred S 
Published: February 2006

Abstract
Background: Further investigations are warranted to better characterize variables that may confound the clinical interpretation of plasma natriuretic peptide measurements, which are increasingly recognized to have diagnostic and predictive importance.
Methods: Blood samples (EDTA plasma) from patients (n = 206) attending clinics for the medical treatment and follow-up of obesity were analyzed for B-type natriuretic peptide (BNP; Bayer assay) and the N-terminal segment of its prohormone (NT-proBNP; Roche assay). Natriuretic peptide concentration ranges were evaluated in those without diagnosis of congestive heart failure (CHF) or chronic kidney disease (CKD).
Results: BNP and NT-proBNP were directly correlated (r = 0.87; P = 0.01), with NT-proBNP concentrations higher relative to BNP. Of obese patients without CHF or CKD, 21.6% (40 of 185) had NT-proBNP concentrations greater than the published assay upper reference limit. Concentrations of both natriuretic peptides were higher in patients currently exposed to beta blockers, patients with the diagnosis of hypertension or type 2 diabetes, and patients with a history of gastric bypass surgery. An inverse relationship between body mass index (BMI) and both BNP and NT-proBNP was evident. According to the National Institutes of Health, National Heart, Lung, and Blood Institute classification, more than 95% of the participants sampled in this study were either obesity class 2 (35 kg/m2 &lt; BMI &lt; 39.9 kg/m2) or class 3 (BMI ≥40 kg/m2)
Conclusions: A substantial proportion of obese patients without CHF or CKD have concentrations greater than the upper reference limit for NT-proBNP but not for simultaneously measured BNP. A history of gastric bypass surgery appeared to be a significant predictor of increased natriuretic peptide concentrations when assessed in a population of patients with class 2 or 3 obesity.
Mechanisms in Protein O-Glycan Biosynthesis and Clinical and Molecular Aspects of Protein O-Glycan Biosynthesis Defects: A Review
Authors: Wopereis Suzan , Lefeber Dirk J , Morava Éva , Wevers Ron A 
Published: February 2006

AbstractBackground: Genetic diseases that affect the biosynthesis of protein O-glycans are a rapidly growing group of disorders. Because this group of disorders does not have a collective name, it is difficult to get an overview of O-glycosylation in relation to human health and disease. Many patients with an unsolved defect in N-glycosylation are found to have an abnormal O-glycosylation as well. It is becoming increasingly evident that the primary defect of these disorders is not necessarily localized in one of the glycan-specific transferases, but can likewise be found in the biosynthesis of nucleotide sugars, their transport to the endoplasmic reticulum (ER)/Golgi, and in Golgi trafficking. Already, disorders in O-glycan biosynthesis form a substantial group of genetic diseases. In view of the number of genes involved in O-glycosylation processes and the increasing scientific interest in congenital disorders of glycosylation, it is expected that the number of identified diseases in this group will grow rapidly over the coming years.Content: We first discuss the biosynthesis of protein O-glycans from their building blocks to their secretion from the Golgi. Subsequently, we review 24 different genetic disorders in O-glycosylation and 10 different genetic disorders that affect both N- and O-glycosylation. The key clinical, metabolic, chemical, diagnostic, and genetic features are described. Additionally, we describe methods that can be used in clinical laboratory screening for protein O-glycosylation biosynthesis defects and their pitfalls. Finally, we introduce existing methods that might be useful for unraveling O-glycosylation defects in the future.
Stochastische, rekursive Weichenklassifikation zur gleisselektiven Ortung von Schienenfahrzeugen (Stochastic, Recursive Turnout Classification for Track-selective Location of Rail Vehicles)
Authors: Geistler Alexander , Böhringer Frank 
Published: February 2006

Abstract
Bei der sicherheitstechnisch relevanten Anwendung bordautonomer Ortungssysteme im Eisenbahnwesen ist die gleisgenaue Ortung, z. B. in Bahnhöfen oder auf zwei- und mehrgleisigen Strecken, eine elementare Forderung. Mit Wirbelstrom-Sensoren können Eisenbahnweichen detektiert und klassifiziert werden, um diese Forderung zu erfüllen. Die statistische Bewertung der Klassifikation geschieht mit dem Modell eines Bayes-Klassifikators. Die Zuordnung der geschätzten Position zu einem Gleis erfolgt dann mittels eines Markov-Modells. Erste erfolgversprechende Versuchsergebnisse zeigen die Robustheit der propagierten Methode.
Innovative Dämpferkonzepte für moderne Hochleistungslokomotiven (Innovative Damper Concepts for Modern High-performance Locomotives)
Authors: Breuer Werner 
Published: February 2006

Abstract
Die Achslasten moderner Hochleistungslokomotiven nähern sich immer mehr den Grenzwerten. Dies zieht Einschränkungen bei der Zulassung und im Betrieb nach sich. Siemens Transportation Systems hat daher zwei neuartige Dämpferkonzepte entwickelt: Den aktiven Drehdämpfer, der die Zulassungsfähigkeit garantiert, und den frequenzgeregelten Vertikaldämpfer, der die Oberbaubelastung nachhaltig reduziert.
Potenziale aktiver und semiaktiver Skyhook-Regelgesetze in der Sekundärfederstufe von Schienenfahrzeugen (Potentials of Active and Semiactive Skyhook Control Laws applied to the Secondary Suspensions of Railway Vehicles)
Authors: Hohenbichler Norbert , Six Klaus 
Published: February 2006

Abstract
Im vorliegenden Beitrag wird das Potenzial nach dem Skyhook-Gesetz hochdynamisch geregelter aktiver und semiaktiver Fahrwerksregelungen in der Sekundärfederstufe von Schienenfahrzeugen hinsichtlich Fahrkomfort und unter Berücksichtigung der resultierenden Federwege untersucht. Es wird eine systematische Vorgehensweise vorgestellt, die es ermöglicht, einen sinnvollen Vergleich zwischen passiven und aktiven Systemen zu führen. Die Untersuchungen zeigen, dass der Komfortgewinn der untersuchten Skyhook-Konzepte auf dem betrachteten Fahrweg bei idealer Sensorik, Aktorik und Signalverarbeitung aufgrund der deterministischen Trassierung nicht mehr als 10% beträgt.
Prevalence of Necrotizing Hepatopancreatitis in Female Broodstock of White Shrimp Penaeus vannamei with Unilateral Eyestalk Ablation and Hormone Injection
Authors: Morales Covarrubias M. S. , Osuna-Duarte A. G. , Garcia-Gasca A. , Lightner D. V. , Mota-Urbina J. C. 
Published: February 2006

Abstract
The present study analyzed the relationship between unilateral eyestalk ablation and steroid hormone injection in female white shrimp Penaeus vannamei, the prevalence of necrotizing hepatopancreatitis (NHP) caused by the intracellular rickettsia-like bacterium NHP-B. Two simultaneous bioassays determined the onset and development of NHP in broodstock. Wet-mount analysis, conventional histopathology, and in situ hybridization with an NHP-B-specific DNA probe were used to assess the prevalence and degree of severity of NHP and to confirm NHP-B infection. Wet-mount and histopathological results showed that females with unilateral eyestalk ablation had a 64% prevalence of NHP at grades 2 and 4, while females receiving the hormone injection showed a 23% prevalence of NHP at grades 3 and 4; control shrimp injected with phosphate-buffered saline (PBS) displayed a 9% prevalence of NHP at grade 3, whereas nonablated controls showed no signs of disease. The rickettsia-like specific DNA probe demonstrated a positive hybridization signal in NHP-B, and the hepatopancreas, the target tissue for the bacterium, showed a strong positive signal. Significant differences (P &lt; 0.05) were found in females with unilateral eyestalk ablation compared with nonablated controls, in hormone-injected females compared with PBS-injected controls, and in females with unilateral eyestalk ablation compared with the hormone injection group. We conclude that unilateral eyestalk ablation enhances NHP disease prevalence in broodstock reared under maturation conditions.
Susceptibility of Koi Carp, Common Carp, Goldfish, and Goldfish × Common Carp Hybrids to Cyprinid Herpesvirus-2 and Herpesvirus-3
Authors: Hedrick Ronald P. , Waltzek Thomas B. , McDowell Terry S. 
Published: February 2006

Abstract
Hybrid goldfish (male goldfish Carassius auratus × female common carp Cyprinus carpio) were completely resistant to mortality following experimental infections with cyprinid herpesvirus-2 (CyHV-2) and moderately resistant to cyprinid herpesvirus-3 (CyHV-3). In contrast, examination of the parental species demonstrated that goldfish were highly susceptible to CyHV-2 infections and that both common carp and koi (a variant of common carp) were highly susceptible to CyHV-3. Approximately 50% of the hybrids examined at 25 d after intraperitoneal injection with either CyHV-2 or CyHV-3 possessed viral genomic DNA, as detected by polymerase chain reaction assays. These initial trials suggest that hybrid goldfish have a natural resistance to mortality following experimental challenge with CyHV-2 and CyHV-3. However, additional studies that examine virus replication, including the potential for the development of a carrier state in hybrids, are needed. The production of hybrids for the food fish market may represent one means of avoiding the severe and negative impacts of the disease associated with CyHV-3.
Successful Stem Cell Therapy Using Umbilical Cord Blood-Derived Multipotent Stem Cells for Buerger's Disease and Ischemic Limb Disease Animal Model
Authors: Kim Sung-Whan , Han Hoon , Chae Gue-Tae , Lee Sung-Hoon , Bo Sun , Yoon Jung-Hee , Lee Yong-Soon , Lee Kwang-Soo , Park Hwon-Kyum , Kang Kyung-Sun 
Published: February 2006

Abstract
Buerger's disease, also known as thromboangiitis obliterans, is a nonatherosclerotic, inflammatory, vasoocclusive disease. It is characterized pathologically as a panangiitis of medium and small blood vessels, including both arteries and adjacent veins, especially the distal extremities (the feet and the hands). There is no curative medication or surgery for this disease. In the present study, we transplanted human leukocyte antigen-matched human umbilical cord blood (UCB)-derived mesenchymal stem cells (MSCs) into four men with Buerger's disease who had already received medical treatment and surgical therapies. After the stem cell transplantation, ischemic rest pain suddenly disappeared from their affected extremities. The necrotic skin lesions were healed within 4 weeks. In the follow-up angiography, digital capillaries were increased in number and size. In addition, vascular resistance in the affected extremities, compared with the preoperative examination, was markedly decreased due to improvement of the peripheral circulation. Because an animal model of Buerger's disease is absent and also to understand human results, we transplanted human UCB-derived MSCs to athymic nude mice with hind limb ischemia by femoral artery ligation. Up to 60% of the hind limbs were salvaged in the femoral artery-ligated animals. By in situ hybridization, the human UCB-derived MSCs were detected in the arterial walls of the ischemic hind limb in the treated group. Therefore, it is suggested that human UCB-derived MSC transplantation may be a new and useful therapeutic armament for Buerger's disease and similar ischemic diseases.
In Vitro Culture During Retroviral Transduction Improves Thymic Repopulation and Output After Total Body Irradiation and Autologous Peripheral Blood Progenitor Cell Transplantation in Rhesus Macaques
Authors: Loré Karin , Seggewiss Ruth , Guenaga F. Javier , Pittaluga Stefania , Donahue Robert E. , Krouse Allen , Metzger Mark E. , Koup Richard A. , Reilly Cavan , Douek Daniel C. , Dunbar Cynthia E. 
Published: February 2006

AbstractImmunodeficiency after peripheral blood progenitor cell (PBPC) transplantation may be influenced by graft composition, underlying disease, and/or pre-treatment. These factors are difficult to study independently in humans. Ex vivo culture and genetic manipulation of PBPC grafts may also affect immune reconstitution, with relevance to gene therapy applications. We directly compared the effects of three clinically relevant autologous graft compositions on immune reconstitution after myeloblative total body irradiation in rhesus macaques, the first time these studies have been performed in a large animal model with direct clinical relevance. Animals received CD34+ cell dose-matched grafts of either peripheral blood mononuclear cells, purified CD34+ PBPCs, or purified CD34+ PBPCs expanded in vitro and retrovirally transduced. We evaluated the reconstitution of T, B, natural killer, dendritic cells, and monocytes in blood and lymph nodes for up to 1 year post-transplantation. Animals receiving selected-transduced CD34+ cells had the fastest recovery of T-cell numbers, along with the highest T-cell-receptor gene rearrangement excision circles levels, the fewest proliferating Ki-67+ T-cells in the blood, and the best-preserved thymic architecture. Selected-transduced CD34+ cells may therefore repopulate the thymus more efficiently and promote a higher output of naïve T-cells. These results have implications for the design of gene therapy trials, as well as for the use of expanded PBPCs for improved T-cell immune reconstitution after transplantation.
The Impact of Delivery Synergies on Bidding in the Georgia School Milk Market
Authors: Marshall Robert C. , Raiff Matthew E. , Richard Jean-Francois , Schulenberg Steven P. 
Published: February 2006

Abstract
Each summer milk processors around the country participate in sealed bid procurements for the right to provide public schools with milk throughout the subsequent academic year. School district contracts are an important part of vehicle routing problems that milk processors solve on an ongoing basis. There are allegedly substantial cost savings for a milk processor from servicing a district that is directly adjacent to one they already service. In this paper, following the work of Krishna and Rosenthal (1996), we construct a procurement model allowing for cost synergies. The equilibrium bid function maps directly into an empirical specification. Using data from a time period when bidders were allegedly acting non-cooperatively, our structural parametric estimation results give significant support for the presence of cost synergies in the bidding.