bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory
Authors: Nogales Juan , Palsson Bernhard Ø , Thiele Ines 
Published: September 2008

Abstract

Background

Pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions.

Results
We present a genome-scale reconstruction of P. putida KT2440's metabolism, i JN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. i JN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of i JN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected.

Conclusion
Here we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of i JN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.
Biliary peritonitis caused by a leaking T-tube fistula disconnected at the point of contact with the anterior abdominal wall: a case report
Authors: Nikolić Marko , Karthikesalingam Alan , Nachimuthu Senthil , Tang Tjun Y , Harris Adrian M 
Published: September 2008

Abstract

Introduction
Operations on the common bile duct may lead to potentially serious complications such as biliary peritonitis. T-tube insertion is performed to reduce the risk of this occurring postoperatively. Biliary leakage at the point of insertion into the common bile duct, or along the fistula, can sometimes occur after T-tube removal and this has been reported extensively in the literature. We report a case where the site at which the T-tube fistula leaked proved to be the point of contact between the fistula and the anterior abdominal wall, a previously unreported complication.

Case presentation
A 36-year-old sub-Saharan African woman presented with gallstone-induced pancreatitis and, once her symptoms settled, laparoscopic cholecystectomy was performed, common bile duct stones were removed and a T-tube was inserted. Three weeks later, T-tube removal led to biliary peritonitis due to the disconnection of the T-tube fistula which was recannulated laparoscopically using a Latex drain.

Conclusion
This case highlights a previously unreported mechanism for bile leak following T-tube removal caused by detachment of a fistula tract at its contact point with the anterior abdominal wall. Hepatobiliary surgeons should be aware of this mechanism of biliary leakage and the use of laparoscopy to recannulate the fistula.
Acral lentiginous melanoma of the foot and ankle: A case series and review of the literature
Authors: Bristow Ivan R , Acland Katharine 
Published: September 2008

AbstractBackgroundAcral lentiginous melanoma (ALM) is an uncommon, cutaneous malignant tumour which may arise on the foot. Its relative rarity, atypical appearance and late presentation frequently serve as poor prognostic indicators.MethodsAt a tertiary skin tumour centre, a retrospective review was undertaken of all patients diagnosed with the tumour at the level of ankle or below.ResultsOver a six year period, 27 cases (20 female, 7 male) were identified with positive histology confirming the disease. The age ranged from 35–96 years of age (mean 62.7 years). The majority of the cohort were white (59%) with plantar lesions (62%). 33% of patients were initially were diagnosed incorrectly. The average time taken from the point of recognition, by the patient, to the lesion being correctly diagnosed was around 13.5 months.ConclusionEarlier diagnosis of ALM requires education at both a patient and practitioner level.
Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
Authors: Staaf Johan , Lindgren David , Vallon-Christersson Johan , Isaksson Anders , Göransson Hanna , Juliusson Gunnar , Rosenquist Richard , Höglund Mattias , Borg Åke , Ringnér Markus 
Published: September 2008

AbstractWe present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell line mixed with its paired normal cell line and data generated on Affymetrix and Illumina platforms, including paired tumor-normal samples and tumors characterized by fluorescent in situ hybridization, we demonstrate a high sensitivity and specificity of the strategy for detecting both minute and gross allelic imbalances in heterogeneous tumor samples.
Leukotriene modifiers in the treatment of cardiovascular diseases
Authors: Riccioni Graziano , Capra Valerie , D’Orazio Nicolantonio , Bucciarelli Tonino , Bazzano Lydia A 
Published: September 2008

AbstractCysteinyl-leukotrienes (Cys-LTs) and LTB4 are potent proinflammatory mediators derived from arachidonic acid through the 5-lipoxygenase (5-LO) pathway, which exerts important pharmacological effects through their interaction with specific receptors: Cys-LT receptors (CysLT1 and CysLT2) and LTB4 receptors (BLT1 and BLT2). Published evidence justifies a broader role for LT receptor antagonists (LTRAs), in particular, montelukast, in the treatment of bronchial asthma, allergic rhinitis, and recently, in cardiocerebrovascular disease. The actions of Cys-LTs on the cardiovascular (CV) system are well-documented and include a broad array of activities with promising therapeutic targets in animal models exploring the use of selective 5-LO (or 5-LO-activating protein) inhibitors or dual LO-cycloxygenase-blocking agents in experimentally induced acute myocardial infarction. The picture that emerges from studies with LTRAs is more controversial at the moment, and some findings suggest a role for Cys-LTs in the extension of ischemic damage and in cardiac dysfunction during reperfusion; others do not. The aim of this short review is to summarize the state of present research about LT modifier treatment in CV disease.
Prognostic Significance of Disseminated Tumor Cells in the Bone Marrow of Prostate Cancer Patients Treated With Neoadjuvant Hormone Treatment
Authors: Köllermann Jens , Weikert Steffen , Schostak Martin , Kempkensteffen Carsten , Kleinschmidt Klaus , Rau Thomas , Pantel Klaus 
Published: September 2008

Purpose To explore whether the presence of occult disseminated tumor cells (DTCs) in the bone marrow before neoadjuvant hormone therapy influences the prognosis of patients with organ confined prostate cancer treated by radical prostatectomy. Patients and Methods Pretreatment bone marrow aspirates from 193 cT (1-4) pN0M0 prostate cancer patients submitted to neoadjuvant hormone therapy (mean, 8 months) followed by radical prostatectomy were immunohistochemically evaluated by anticytokeratin antibody A45-B/B3 previously validated for the detection of DTCs. Bone marrow status was compared with established clinical and histopathologic risk parameters. Patients’ outcome was evaluated using prostate-specific antigen (PSA) blood serum measurements as surrogate marker for recurrence over a median follow-up of 44 months. Results DTCs were detected in 44.6% of patients. Bone marrow status neither correlated with tumor grade and stage, nor with the pretreatment PSA risk category (all P values > .05). In the univariate Kaplan-Meier analysis, the presence of DTCs was a significant prognostic factor with respect to poor PSA progression-free survival (log-rank test P = .0035). Using a multivariable piecewise Cox regression model, the presence of DTCs was an independent predictor of PSA relapse (relative risk 1.82; P = .014). Conclusion The presence of DTCs in the bone marrow of patients with prostate cancer before neoadjuvant hormone therapy and subsequent surgery represents an independent prognostic parameter, suggesting that DTCs may contribute to the failure of current neoadjuvant hormone therapy regimens.
Pediatric Phase I and Pharmacokinetic Study of Erlotinib Followed by the Combination of Erlotinib and Temozolomide: A Children's Oncology Group Phase I Consortium Study
Authors: Jakacki Regina I. , Hamilton Marta , Gilbertson Richard J. , Blaney Susan M. , Tersak Jean , Krailo Mark D. , Ingle Ashish M. , Voss Stephan D. , Dancey Janet E. , Adamson Peter C. 
Published: September 2008

PurposeWe conducted a phase I and pharmacokinetic study of the epidermal growth factor receptor (EGFR) inhibitor erlotinib as a single agent and in combination with temozolomide in children with refractory solid tumors.Patients and MethodsErlotinib was administered orally once daily to cohorts of three to six children for a single 28-day course. Patients then received the combination of daily erlotinib and temozolomide daily for 5 days for all subsequent 28-day courses. An oral erlotinib solution was administered during the dose-finding phase and a tablet formulation was subsequently studied at the maximum-tolerated dose (MTD). Pharmacokinetic studies and ERBB-receptor expression and signaling studies were performed.ResultsForty-six patients, median age 11.5 years, received erlotinib at doses of 35, 50, 65, 85, or 110 mg/m2/d. At 110 mg/m2/d, two of four patients had dose-limiting toxicity (DLT) consisting of rash and hyperbilirubinemia, whereas one of six patients developed dose-limiting rash at 85 mg/m2/d. The most frequent non-DLTs included diarrhea, rash, and hyperbilirubinemia. The combination of erlotinib and temozolomide was well tolerated. The median apparent erlotinib clearance was 3.1 L/h/m2and the median terminal half-life was 8.7 hours. One patient with a neurocytoma had stable disease for 19 months, two patients with neuroblastoma remained on study for 23 and 24 months, and one patient with myoepithelioma had a mixed response.ConclusionThe recommended phase II dose of erlotinib in recurrent pediatric solid tumors is 85 mg/m2/d, either alone or in combination with temozolomide.
Treatment and Survival Differences in Older Medicare Patients With Lung Cancer as Compared With Those Who Are Dually Eligible for Medicare and Medicaid
Authors: Bradley Cathy J. , Dahman Bassam , Given Charles W. 
Published: September 2008

Purpose This study compares non–small-cell lung cancer (NSCLC) treatments provided to older patients (age ≥ 66 years) who are dually eligible for Medicare and Medicaid with treatments provided to similar patients who are insured by Medicare. We extend the analysis to include a comparison of survival rates between Medicare and dually eligible patients. Dual eligibility is associated with low socioeconomic status. However, Medicaid coverage in addition to Medicare removes many financial barriers to care. Patients and Methods The sample included 2,626 older patients with local and regional stage NSCLC diagnosed between 1997 and 2000. Four outcomes were studied: the likelihood of receiving resection, chemotherapy, radiation therapy, and survival (perioperative and longer-term). Logistic regression was used to predict the likelihood of treatment, and stratified and multivariate analyses were used to evaluate differences in survival. Results Dually eligible patients were half as likely to undergo resection as Medicare patients (P < .001) and were more likely to receive radiation than Medicare patients. Stratified and multivariate analyses showed that surgically treated dually eligible patients had slightly inferior survival as compared with that of Medicare patients. Survival was equivalent among patients who did not undergo resection, regardless of insurance coverage. Conclusion Older dually eligible patients with NSCLC had a lower likelihood of undergoing resection despite controls for socioeconomic factors and comorbidities. However, if such patients were surgically treated, survival improved substantially, but it remained inferior to the survival of Medicare patients. Additional research is needed to understand why resection rates were substantially lower among dually eligible patients.
Adjuvant Chemotherapy After Potentially Curative Resection of Metastases From Colorectal Cancer: A Pooled Analysis of Two Randomized Trials
Authors: Mitry Emmanuel , Fields Anthony L.A. , Bleiberg Harry , Labianca Roberto , Portier Guillaume , Tu Dongsheng , Nitti Donato , Torri Valter , Elias Dominique , O'Callaghan Chris , Langer Bernard , Martignoni Giancarlo , Bouché Olivier , Lazorthes Franck , Van Cutsem Eric , Bedenne Laurent , Moore Malcolm J. , Rougier Philippe 
Published: September 2008

Purpose Adjuvant systemic chemotherapy administered after surgical resection of colorectal cancer metastases may reduce the risk of recurrence and improve survival, but its benefit has never been demonstrated. Two phase III trials (Fédération Francophone de Cancérologie Digestive [FFCD] Trial 9002 and the European Organisation for Research and Treatment of Cancer/National Cancer Institute of Canada Clinical Trials Group/Gruppo Italiano di Valutazione Interventi in Oncologia [ENG] trial) used a similar design and showed a trend favoring adjuvant chemotherapy, but both had to close prematurely because of slow accrual, thus lacking the statistical power to demonstrate the predefined difference in survival. We report here a pooled analysis based on individual data from these two trials. Patients and Methods After complete resection of colorectal liver or lung metastases, patients were randomly assigned to chemotherapy (CT arm; fluorouracil [FU] 400 mg/m2 administered intravenously [IV] once daily plus dl-leucovorin 200 mg/m2 [FFCD] × 5 days or FU 370 mg/m2 plus l-leucovorin 100 mg/m2 IV × 5 days [ENG] for six cycles at 28-day intervals) or to surgery alone (S arm). Results A total of 278 patients (CT, n = 138; S, n = 140) were included in the pooled analysis. Median progression-free survival was 27.9 months in the CT arm as compared with 18.8 months in the S arm (hazard ratio = 1.32; 95% CI, 1.00 to 1.76; P = .058). Median overall survival was 62.2 months in the CT arm compared with 47.3 months in the S arm (hazard ratio = 1.32; 95% CI, 0.95 to 1.82; P = .095). Adjuvant chemotherapy was independently associated with both progression-free survival and overall survival in multivariable analysis. Conclusion This pooled analysis shows a marginal statistical significance in favor of adjuvant chemotherapy with an FU bolus–based regimen after complete resection of colorectal cancer metastases.
Metronomic Cyclophosphamide and Capecitabine Combined With Bevacizumab in Advanced Breast Cancer
Authors: Dellapasqua Silvia , Bertolini Francesco , Bagnardi Vincenzo , Campagnoli Elisabetta , Scarano Eloise , Torrisi Rosalba , Shaked Yuval , Mancuso Patrizia , Goldhirsch Aron , Rocca Andrea , Pietri Elisabetta , Colleoni Marco 
Published: September 2008

Purpose Metronomic chemotherapy has shown efficacy in patients with metastatic breast cancer. When used in association with targeted antiangiogenic drugs, it was more active than metronomic therapy alone in preclinical and clinical studies. Patients and Methods Patients with advanced breast cancer were candidates to receive metronomic oral capecitabine (500 mg thrice daily) and cyclophosphamide (50 mg daily) plus bevacizumab (10 mg/kg every 2 weeks). Results In 46 assessable patients, we observed one complete response (CR; 2%), 21 partial responses (PR; 46%), 19 patients (41%) with stable disease (SD), and five patients (11%) with progressive disease, for an overall response rate of 48% (95% CI, 33% to 63%). Additional long-term disease stabilization (SD ≥ 24 weeks) occurred in eight patients, for an overall clinical benefit (CR + PR + SD ≥ 24 weeks) of 68% (95% CI, 51% to 81%). Median time to progression was 42 weeks (95% CI, 26 to 72 weeks). Toxicity was generally mild. Grade 3 or 4 nonhematologic adverse effects included hypertension (n = 8), transaminitis (n = 2), and nausea/vomiting (n = 2). Higher baseline circulating endothelial cells (CECs) were correlated with overall response (P = .02), clinical benefit (P = .01), and improved progression-free survival (P = .04). Conclusion Treatment with metronomic capecitabine and cyclophosphamide in combination with bevacizumab was effective in advanced breast cancer and was minimally toxic. The number of baseline CECs significantly correlated with response and outcome, therefore supporting further studies on this surrogate marker for the selection of patients to be candidates for antiangiogenic treatments.
Microfluidic Distillation Utilizing Micro–Nano Combined Structure
Authors: Hibara Akihide , Toshin Kunihiko , Tsukahara Takehiko , Mawatari Kazuma , Kitamori Takehiko 
Published: September 2008

Abstract
This paper reports a novel distillation method in microchannels. For the gas–liquid separator in the evaporator, hydrophilic–hydrophobic patterned microchannel structure was utilized. In order to control condensation of the vapor, nanopillar structures having a capillary radius of 270 nm were fabricated after the separator. In the nanopillars, vapor pressure is lower than that at a flat liquid surface. An aqueous solution of 9.0 wt % ethanol was used as a model sample, and concentration of the condensed liquid in the nanopillar was estimated as 19 wt %.
Synthesis of Macrocycles Comprising 2,7-Disubstituted Naphthalene and Polyamine Moieties via Pd-catalyzed Amination
Authors: Averin Alexei D , Uglov Alexei N , Beletskaya Irina P 
Published: September 2008

Abstract
The Pd-catalyzed reaction of equimolar amounts of 2,7-dibromonaphthalene and various polyamines led to the formation of the macrocycles comprising one naphthalene and one polyamine moieties. The same reaction also gave cyclodimers and cyclotrimers as by-products. Application of excess 2,7-dibromonaphthalene provided N,N′-bis(7-bromonaphth-2-yl)oxadiamine which was used for the synthesis of macrocycles with two naphthalene and two oxadiamine fragments.
An Efficient Method for the Transformation of High Fatty Acid Containing Vegetable Oils to Biodiesel Fuels
Authors: Kótai László , Gömöry Ágnes , Gács István , Holly late Sándor , Sajó István E , Tamics Ernö , Aradi Tamás , Bihátsi László 
Published: September 2008

Abstract
Transesterification of fatty acid containing used or nonfood type vegetable oils with methanol in the presence of partially hydrated calcium oxide has been performed. The calcium soaps formed are treated with sulfuric acid without separation from the ester phase, and the free acids formed are immediately converted to ester with the excess of methanol and the sulfuric acid (as catalyst).
Saint Elsewhere: German and English Reactions to Mendelssohn's Paulus
Authors: Sposato Jeffrey S. 
Published: September 2008

Abstract
This article examines German and English reactions to Felix Mendelssohn's 1836 oratorio, Paulus. German Protestant audiences recognized Paulus's devotional, or spiritual, quality, which derived from its incorporation of well-known Lutheran chorales. In using chorales and reflective arias and choruses, Mendelssohn followed the model established by Johann Sebastian Bach in his St. Matthew Passion, a work that Mendelssohn had reintroduced to German audiences in 1829. When Paulus was premiered for English audiences in a translation called St. Paul, it was enthusiastically received. But these audiences misunderstood St. Paul's devotional elements, for several reasons. Not only were English audiences unfamiliar with both Bach's music and the Lutheran chorale, they also expected oratorios to follow the model established by Handel. As such, English audiences were confused by those places in St. Paul where the present-day audience is called to reflect and attempted to attribute these numbers to characters in the drama. Mendelssohn responded to this confusion when writing his next oratorio, Elias (or Elijah), in which he hewed more closely to the Handelian model.
The Case Against Routine Electroencephalography in Specific Language Impairment
Authors: Venkateswaran Sunita , Shevell Michael 
Published: September 2008

BACKGROUND. Specific language impairment is a primary developmental language disorder in which language is impaired disproportionately to other developmental domains. Electroencephalography is often conducted in the medical investigation of a child with specific language impairment; however, at present, there is uncertainty regarding necessary testing using electroencephalography.METHODS. The cases of 111 children with the diagnosis of specific language impairment over a 10-year interval, who also underwent electroencephalography, were systematically reviewed in a retrospective manner. Children with a history of previous afebrile seizures, acquired language delay, or documented language regression, developmental delay, hearing loss, coexisting autistic features, and known central nervous system disorders were excluded.RESULTS. The majority (76%) of the children were boys. Thirty-five (31.5%) children had abnormal electroencephalography results, including 7 (6.3%) children with epileptiform activity. This is higher than the prevalence rate of epileptiform activity in a historical cohort of 3726 (3.54%) children but not statistically significant. The epileptiform activity was deemed active in only 3 of 7 patients and was not related to the specific type of language delay observed.CONCLUSIONS. Although abnormal electroencephalographic activity is seen frequently in children with specific language impairment, epileptiform activity is rare and without apparent impact on clinical care. Awake electroencephalography does not seem to be useful in the routine diagnostic evaluation of young children with specific language impairment, although further investigations of both wake and sleep electroencephalography in this homogenous population must be conducted before definitive recommendations can be made.
One in Five Cancer Clinical Trials Is Published: A Terrible Symptom—What's the Diagnosis?
Authors: Curt Gregory A. , Chabner Bruce A. 
Published: September 2008

Abstract
This editorial invites readers to weigh in on whether The Oncologist should expend the considerable effort and expense to produce a peer-reviewed, searchable venue for publishing the results of all well-executed cancer trials that fail to meet positive endpoints.