bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global dynamic optimization approach to predict activation in metabolic pathways
Authors: de Hijas-Liste Gundián M , Klipp Edda , Balsa-Canto Eva , Banga Julio R 
Published: January 2014

Abstract

Background
During the last decade, a number of authors have shown that the genetic regulation of metabolic networks may follow optimality principles. Optimal control theory has been succesfully used to compute optimal enzyme profiles considering simple metabolic pathways. However, applying this optimal control framework to more general networks (e.g. branched networks, or networks incorporating enzyme production dynamics) yields problems that are analytically intractable and/or numerically very challenging. Further, these previous studies have only considered a single-objective framework.

Results
In this work we consider a more general multi-objective formulation and we present solutions based on recent developments in global dynamic optimization techniques. We illustrate the performance and capabilities of these techniques considering two sets of problems. First, we consider a set of single-objective examples of increasing complexity taken from the recent literature. We analyze the multimodal character of the associated non linear optimization problems, and we also evaluate different global optimization approaches in terms of numerical robustness, efficiency and scalability. Second, we consider generalized multi-objective formulations for several examples, and we show how this framework results in more biologically meaningful results.

Conclusions
The proposed strategy was used to solve a set of single-objective case studies related to unbranched and branched metabolic networks of different levels of complexity. All problems were successfully solved in reasonable computation times with our global dynamic optimization approach, reaching solutions which were comparable or better than those reported in previous literature. Further, we considered, for the first time, multi-objective formulations, illustrating how activation in metabolic pathways can be explained in terms of the best trade-offs between conflicting objectives. This new methodology can be applied to metabolic networks with arbitrary topologies, non-linear dynamics and constraints.
Expressions and clinical significances of c-MET, p-MET and E2f-1 in human gastric carcinoma
Authors: Wu Ju-gang , Yu Ji-wei , Wu Hong-biao , Zheng Lin-hai , Ni Xiao-chun , Li Xiao-qiang , Du Guang-ye , Jiang Bo-jian 
Published: January 2014

Abstract

Background
To investigate on the expressions and the clinical significances of hepatocyte growth factor receptor (c-MET), phosphorylated c-MET (p-MET) and e2f-1 transcription factor in primary lesion of gastric adenocarcinoma (GC).

Method
Tissue samples from the primary lesion of GC in patients who accepted D2/D3 radical gastrectomy with R0/R1 resection were stained by immunohistochemistry of c-MET, p-MET, e2f-1 and Ki-67. The univariate and the multivariate analyses involving in clinicopathological parameters and prognostic factors were evaluated.

Results
The positivity rates for c-MET (66.12%, 80 cases/121 cases), p-MET (59.50%, 72 cases/121 cases), e2f-1 (38.84%, 47 cases/121 cases) and Ki-67 (72.73%, 88 cases/121 cases) in primary lesion of GC was significantly higher than that in non-cancerous tissue at 5 cm places far from the margin of primary lesion (P < 0.05, respectively). The deeper tumor invasion, the severer lymph node metastasis, the later stage of TNM and the higher expression of Ki-67 was respectively an independent risk factor for the higher expression of c-MET or p-MET, but the younger age and the shorter survival time was an independent risk factor for the higher expression of e2f-1 respectively. Survival analysis showed that the worse prognosis could be observed in the patients with the combination of both c-MET-positive and e2f-1-negative (P = 0.038) or both p-MET-positive and e2f-1-negative (P = 0.042). Cox analysis demonstrated that the severer lymphatic node metastasis and the higher positivity rate of c-MET, p-MET or e2f-1 were an independent prognosis factor respectively. The higher expression of e2f-1 was identified in patients with Stage I-II, which correlated with a shorter survival time. Survival analysis also revealed that the prognosis of patients with positive expression of e2f-1 at Stage I-II was significantly worse than that in patients with negative expression of e2f-1 (χ
2 = 13.437, P = 0.001). However, in the cases with Stage III-IV, no significant difference could be identified in the prognostic comparison between positive and negative expressions of e2f-1.

Conclusions
The expression of c-MET or p-MET is an independent prognosis factor. It has been observed that the higher expression of e2f-1 occurred in the early stages while the lower expression of it in the later stages in GC.
Removal of boron from aqueous solution using magnetic carbon nanotube improved with tartaric acid
Authors: Zohdi Nima , Mahdavi Fariba , Abdullah Luqman Chuah , Choong Thomas SY 
Published: January 2014

Abstract
Boron removal capacity of multi-walled carbon nanotubes (MWCNTs) modified with tartaric acid was investigated in this study. Modification of MWCNTs with tartaric acid was confirmed by Boehm surface chemistry method and fourier transform infra-red (FT-IR) spectroscopy. Experiments were performed to determine the adsorption isotherm and adsorption thermodynamic parameters of boron adsorption on tartaric acid modified MWCNTs (TA-MWCNTs). The effect of variables including initial pH, dosage of adsorbent, contact time and temperature was investigated. Analysis of data showed that adsorption equilibrium could be better described by Freundlich isotherm and the maximum adsorption capacities obtained at the pH of 6.0 was 1.97 mg/g. The estimated thermodynamic values of free energy (ΔG°), entropy (ΔS°) and enthalpy (ΔH°) indicated a spontaneous and an endothermic process. Furthermore, the TA-MWCNTs was magnetized for separation of boron-contaminated adsorbent from aqueous solution by applying magnetic field. The results showed that magnetic TA-MWCNTs particles were separated effectively after adsorption from contaminated water.
A Branch and Bound Algorithm for a Class of Biobjective Mixed Integer Programs
Authors: Stidsen Thomas , Andersen Kim Allan , Dammann Bernd 
Published: January 2014

Most real-world optimization problems are multiobjective by nature, involving noncomparable objectives. Many of these problems can be formulated in terms of a set of linear objective functions that should be simultaneously optimized over a class of linear constraints. Often there is the complicating factor that some of the variables are required to be integral. The resulting class of problems is named multiobjective mixed integer programming (MOMIP) problems. Solving these kinds of optimization problems exactly requires a method that can generate the whole set of nondominated points (the Pareto-optimal front). In this paper, we first give a survey of the newly developed branch and bound methods for solving MOMIP problems. After that, we propose a new branch and bound method for solving a subclass of MOMIP problems, where only two objectives are allowed, the integer variables are binary, and one of the two objectives has only integer variables. The proposed method is able to find the full set of nondominated points. It is tested on a large number of problem instances, from six different classes of MOMIP problems. The results reveal that the developed biobjective branch and bound method performs better on five of the six test problems, compared with a generic two-phase method. At this time, the two-phase method is the most preferred exact method for solving MOMIP problems with two criteria and binary variables. This paper was accepted by Dimitris Bertsimas, optimization.
Analysis of Product Rollover Strategies in the Presence of Strategic Customers
Authors: Liang Chao , Çakanyıldırım Metin , Sethi Suresh P. 
Published: January 2014

Frequent product introductions emphasize the importance of product rollover strategies. With single rollover, when a new product is introduced, the old product is phased out from the market. With dual rollover, the old product remains in the market along with the new product. Anticipating the introduction of the new product and the potential markdown of the old product, strategic customers may delay their purchases. We study the interaction between product rollover strategies and strategic customer purchasing behavior and find that single rollover is more valuable when the new product's innovation is low and the number of strategic customers is high. Interestingly and counter to intuition, the firm may have to charge a lower price for the old product as well as receive a lower profit with a higher value disposal (outside) option for the old product under single rollover. Facing a market composed of both strategic and myopic customers, the firm does not necessarily reduce the stocking level as more myopic customers become strategic. This paper was accepted by Yossi Aviv, operations management.
Raised levels of metal ions in the blood in patients who have undergone uncemented metal-on-polyethylene Trident–Accolade total hip replacement
Authors: Craig P. , Bancroft G. , Burton A. , Collier S. , Shaylor P. , Sinha A. 
Published: January 2014

The issues surrounding raised levels of metal ions in the blood following large head metal-on-metal total hip replacement (THR), such as cobalt and chromium, have been well documented. Despite the national popularity of uncemented metal-on-polyethylene (MoP) THR using a large-diameter femoral head, few papers have reported the levels of metal ions in the blood following this combination. Following an isolated failure of a 44 mm Trident–Accolade uncemented THR associated with severe wear between the femoral head and the trunnion in the presence of markedly elevated levels of cobalt ions in the blood, we investigated the relationship between modular femoral head diameter and the levels of cobalt and chromium ions in the blood following this THR. A total of 69 patients received an uncemented Trident–Accolade MoP THR in 2009. Of these, 43 patients (23 men and 20 women, mean age 67.0 years) were recruited and had levels of cobalt and chromium ions in the blood measured between May and June 2012. The patients were then divided into three groups according to the diameter of the femoral head used: 12 patients in the 28 mm group (controls), 18 patients in the 36 mm group and 13 patients in the 40 mm group. A total of four patients had identical bilateral prostheses in situ at phlebotomy: one each in the 28 mm and 36 mm groups and two in the 40 mm group. There was a significant increase in the mean levels of cobalt ions in the blood in those with a 36 mm diameter femoral head compared with those with a 28 mm diameter head (p = 0.013). The levels of cobalt ions in the blood were raised in those with a 40 mm diameter head but there was no statistically significant difference between this group and the control group (p = 0.152). The levels of chromium ions in the blood were normal in all patients. The clinical significance of this finding is unclear, but we have stopped using femoral heads with a diameter of ≤ 36 mm, and await further larger studies to clarify whether, for instance, this issue particularly affects this combination of components. Cite this article: Bone Joint J 2014;96-B:43–7.
The economics of using prophylactic antibiotic-loaded bone cement in total knee replacement
Authors: Gutowski C. J. , Zmistowski B. M. , Clyde C. T. , Parvizi J. 
Published: January 2014

The rate of peri-prosthetic infection following total joint replacement continues to rise, and attempts to curb this trend have included the use of antibiotic-loaded bone cement at the time of primary surgery. We have investigated the clinical- and cost-effectiveness of the use of antibiotic-loaded cement for primary total knee replacement (TKR) by comparing the rate of infection in 3048 TKRs performed without loaded cement over a three-year period versus the incidence of infection after 4830 TKRs performed with tobramycin-loaded cement over a later period of time of a similar duration. In order to adjust for confounding factors, the rate of infection in 3347 and 4702 uncemented total hip replacements (THR) performed during the same time periods, respectively, was also examined. There were no significant differences in the characteristics of the patients in the different cohorts.The absolute rate of infection increased when antibiotic-loaded cement was used in TKR. However, this rate of increase was less than the rate of increase in infection following uncemented THR during the same period. If the rise in the rate of infection observed in THR were extrapolated to the TKR cohort, 18 additional cases of infection would have been expected to occur in the cohort receiving antibiotic-loaded cement, compared with the number observed. Depending on the type of antibiotic-loaded cement that is used, its cost in all primary TKRs ranges between USD $2112.72 and USD $112 606.67 per case of infection that is prevented.Cite this article: Bone Joint J 2014;96-B:65–9.
The influence of femoral offset on health-related quality of life after total hip replacement
Authors: Liebs T. R.  , Nasser L. , Herzberg W. , Rüther W. , Hassenpflug J. 
Published: January 2014

Several factors have been implicated in unsatisfactory results after total hip replacement (THR). We examined whether femoral offset, as measured on digitised post-operative radiographs, was associated with pain after THR. The routine post-operative radiographs of 362 patients (230 women and 132 men, mean age 70.0 years (35.2 to 90.5)) who received primary unilateral THRs of varying designs were measured after calibration. The femoral offset was calculated using the known dimensions of the implants to control for femoral rotation. Femoral offset was categorised into three groups: normal offset (within 5 mm of the height-adjusted femoral offset), low offset and high offset. We determined the associations to the absolute final score and the improvement in the mean Western Ontario and McMaster Universities osteoarthritis index (WOMAC) pain subscale scores at three, six, 12 and 24 months, adjusting for confounding variables. The amount of femoral offset was associated with the mean WOMAC pain subscale score at all points of follow-up, with the low-offset group reporting less WOMAC pain than the normal or high-offset groups (six months: 7.01 (sd 11.69) vs 12.26 (sd 15.10) vs 13.10 (sd 16.20), p = 0.006; 12 months: 6.55 (sd 11.09) vs 9.73 (sd 13.76) vs 13.46 (sd 18.39), p = 0.010; 24 months: 5.84 (sd 10.23) vs 9.60 (sd 14.43) vs 13.12 (sd 17.43), p = 0.004). When adjusting for confounding variables, including age and gender, the greatest improvement was seen in the low-offset group, with the normal-offset group demonstrating more improvement than the high-offset group. Cite this article: Bone Joint J 2014;96-B:36–42.
Thromboprophylaxis with dabigatran leads to an increased incidence of wound leakage and an increased length of stay after total joint replacement
Authors: Bloch B. V. , Patel V. , Best A. J. 
Published: January 2014

Since the introduction of the National Institute for Health and Care Excellence (NICE) guidelines on thromboprophylaxis and the use of extended thromboprophylaxis with new oral agents, there have been reports of complications arising as a result of their use. We have looked at the incidence of wound complications after the introduction of dabigatran for thromboprophylaxis in our unit. We investigated the rate of venous thromboembolism and wound leakage in 1728 patients undergoing primary joint replacement, both before and after the introduction of dabigatran, and following its subsequent withdrawal from our unit. We found that the use of dabigatran led to a significant increase in post-operative wound leakage (20% with dabigatran, 5% with a multimodal regimen; p < 0.001), which also resulted in an increased duration of hospital stay. The rate of thromboembolism in patients receiving dabigatran was higher (1.3%) than in those receiving the multimodal thromboprophylaxis regimen, including low molecular weight heparin as an inpatient and the extended use of aspirin (0.3%, p = 0.047). We have ceased the use of dabigatran for thromboprophylaxis in these patients. Cite this article: Bone Joint J 2014;96-B:122–6.
Giant cell tumour of the proximal femur
Authors: Wijsbek A. E. , Vazquez-Garcia B. L. , Grimer R. J. , Carter S. R. , Abudu A. A. , Tillman R. M. , Jeys L. 
Published: January 2014

The purpose of this study was to assess whether the use of a joint-sparing technique such as curettage and grafting was successful in eradicating giant cell tumours of the proximal femur, or whether an alternative strategy was more appropriate.Between 1974 and 2012, 24 patients with a giant cell tumour of the proximal femur were treated primarily at our hospital. Treatment was either joint sparing or joint replacing. Joint-sparing treatment was undertaken in ten patients by curettage with or without adjunctive bone graft. Joint replacement was by total hip replacement in nine patients and endoprosthetic replacement in five. All 11 patients who presented with a pathological fracture were treated by replacement.Local recurrence occurred in five patients (21%): two were treated by hip replacement, three by curettage and none with an endoprosthesis. Of the ten patients treated initially by curettage, six had a successful outcome without local recurrence and required no further surgery. Three eventually needed a hip replacement for local recurrence and one an endoprosthetic replacement for mechanical failure. Thus 18 patients had the affected joint replaced and only six (25%) retained their native joint. Overall, 60% of patients without a pathological fracture who were treated with curettage had a successful outcome.Cite this article: Bone Joint J 2014;96-B:127–31.
Progression of spinal deformity in wheelchair-dependent patients with Duchenne muscular dystrophy who are not treated with steroids
Authors: Shapiro F. , Zurakowski D. , Bui T. , Darras B. T. 
Published: January 2014

We determined the frequency, rate and extent of development of scoliosis (coronal plane deformity) in wheelchair-dependent patients with Duchenne muscular dystrophy (DMD) who were not receiving steroid treatment. We also assessed kyphosis and lordosis (sagittal plane deformity). The extent of scoliosis was assessed on sitting anteroposterior (AP) spinal radiographs in 88 consecutive non-ambulatory patients with DMD. Radiographs were studied from the time the patients became wheelchair-dependent until the time of spinal fusion, or the latest assessment if surgery was not undertaken. Progression was estimated using a longitudinal mixed-model regression analysis to handle repeated measurements. Scoliosis ≥ 10° occurred in 85 of 88 patients (97%), ≥ 20° in 78 of 88 (89%) and ≥ 30° in 66 of 88 patients (75%). The fitted longitudinal model revealed that time in a wheelchair was a highly significant predictor of the magnitude of the curve, independent of the age of the patient (p < 0.001). Scoliosis developed in virtually all DMD patients not receiving steroids once they became wheelchair-dependent, and the degree of deformity deteriorated over time. In general, scoliosis increased at a constant rate, beginning at the time of wheelchair-dependency (p < 0.001). In some there was no scoliosis for as long as three years after dependency, but scoliosis then developed and increased at a constant rate. Some patients showed a rapid increase in the rate of progression of the curve after a few years – the clinical phenomenon of a rapidly collapsing curve over a few months. A sagittal plane kyphotic deformity was seen in 37 of 60 patients (62%) with appropriate radiographs, with 23 (38%) showing lumbar lordosis (16 (27%) abnormal and seven (11%) normal). This study provides a baseline to assess the effects of steroids and other forms of treatment on the natural history of scoliosis in patients with DMD, and an approach to assessing spinal deformity in the coronal and sagittal planes in wheelchair-dependent patients with other neuromuscular disorders. Cite this article: Bone Joint J 2014;96-B:100–5.
The evolution and concepts of joint-preserving surgery of the hip
Authors: Leunig M. , Ganz R. 
Published: January 2014

The use of joint-preserving surgery of the hip has been largely abandoned since the introduction of total hip replacement. However, with the modification of such techniques as pelvic osteotomy, and the introduction of intracapsular procedures such as surgical hip dislocation and arthroscopy, previously unexpected options for the surgical treatment of sequelae of childhood conditions, including developmental dysplasia of the hip, slipped upper femoral epiphysis and Perthes’ disease, have become available. Moreover, femoroacetabular impingement has been identified as a significant aetiological factor in the development of osteoarthritis in many hips previously considered to suffer from primary osteoarthritis.As mechanical causes of degenerative joint disease are now recognised earlier in the disease process, these techniques may be used to decelerate or even prevent progression to osteoarthritis. We review the recent development of these concepts and the associated surgical techniques.Cite this article: Bone Joint J 2014;96-B:5–18.
Assessing the Supply Chain Efficiency of Hardwood Sawmills in New York State through Case Study Analysis and Data Envelopment Analysis Modeling
Authors: Penfield Patrick C. , Germain René , Smith William 
Published: January 2014

Abstract
Hardwood sawmills throughout the United States were under severe financial pressures during the 2007 to 2009 recession. This was attributed to demand weakness, profitability challenges, and supply chain inefficiencies. The focus of our study was on hardwood sawmills in New York State. A supply chain assessment tool was created to evaluate the supply chain processes of 15 sawmills that had the capability to produce from 3 to 20 million board feet of lumber per year and accounted for 31 percent of the hardwood lumber produced in New York. We collected data that allowed us to rate each sawmill's supply chain and computed their relative efficiency using a mathematical modeling technique called Data Envelopment Analysis. We then used a Pearson correlation analysis to compare our sawmill assessment scores and the relative efficiency score from each sawmill and found a significant correlation of 0.716. The assessment tool we developed can help hardwood sawmills find opportunities to improve their supply chains, allowing their business to save money and improve profit margins.
Economic Benefits Coming from the Absence of Labels Proliferation
Authors: Marette Stéphan 
Published: January 2014

Abstract
In a lab experiment, two milk bottles with different levels of omega-3 were offered to participants for eliciting willingness to pay. We find that a simple message on the difference regarding the omega-3 content between bottles significantly impacts the participants’ willingness to pay for these bottles. The exit questionnaire also shows that participants would prefer the exclusive use of the omega-3 label posted on the bottle with the highest content in omega-3. From an interpretation of questionnaires and elicited willingness to pay, simulations show that the exclusive use of one label signaling omega-3 would have a positive impact on both profits and consumers’ surpluses.