bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biocatalytic polyester acrylation—process optimization and enzyme stability
Authors: Hagström Anna E.V. , Nordblad Mathias , Adlercreutz Patrick 
Published: September 2008

AbstractAn OH‐functional polyester has been acrylated via transesterification of ethyl acrylate, catalyzed by Candida antarctica lipase B (CalB) in two different preparations: Novozym® 435 and immobilized on Accurel® MP1000. The batch process resulted in incomplete acrylation as well as severe degradation of the polyester. A high degree of acrylation was achieved by optimization through the application of low pressure (15 kPa), continuous inflow of ethyl acrylate and continuous distillation to evaporate the by‐product, ethanol. The enzyme preparations displayed good stability with half‐lives of 180 and 324 h for Novozym® 435 and CalB/MP1000, respectively. This translates into product yields of 3600 and 6200 times the weight of the catalyst, indicating that the enzyme will have a marginal impact on the total process cost. Biotechnol. Bioeng. 2009; 102: 693–699. © 2008 Wiley Periodicals, Inc.
Enrichment of fermentation media and optimization of expression conditions for the production of EAK16 peptide as fusions with SUMO
Authors: Satakarni Makkapati , Koutinas Apostolis A. , Webb Colin , Curtis Robin 
Published: September 2008

AbstractEAK16 (AEAEAKAKAEAKAEAK) belongs to a novel class of self‐assembling peptides, which is being investigated in research and industry. SUMO belongs to the ubiquitin class of proteins and is a promising fusion partner currently in use. In this study, EAK16 peptide fusions with hexa‐histidine tagged SUMO have been constructed using Escherichia coli based pET expression vector. Intracellular expression of the SUMO–EAK16 fusion using LB media has been optimized. Low‐cost complex media (fungal autolysates, wheat and gluten hydrolysates) produced via a novel wheat‐based biorefinery have been used as alternative fermentation media to LB. Shake flask cultures using either enriched LB or complex wheat‐derived media containing 2 g/L of glucose resulted in intracellular SUMO–EAK16 fusion protein production of approximately 250 mg/L fermentation volume which corresponded to 30–35% of the total bacterial protein expressed being the fusion protein. Fusion protein productivities up to five times higher were achieved when using a bioreactor. Biotechnol. Bioeng. 2009; 102: 725–735. © 2008 Wiley Periodicals, Inc.
High‐throughput lensfree imaging and characterization of a heterogeneous cell solution on a chip
Authors: Su Ting‐Wei , Seo Sungkyu , Erlinger Anthony , Ozcan Aydogan 
Published: September 2008

AbstractA high‐throughput on‐chip imaging platform that can rapidly monitor and characterize various cell types within a heterogeneous solution over a depth‐of‐field of ∼4 mm and a field‐of‐view of ∼10 cm2 is introduced. This powerful system can rapidly image/monitor multiple layers of cells, within a volume of ∼4 mL all in parallel without the need for any lenses, microscope‐objectives or any mechanical scanning. In this high‐throughput lensless imaging scheme, the classical diffraction pattern (i.e., the shadow) of each micro‐particle within the entire sample volume is detected in less than a second using an opto‐electronic sensor chip. The acquired shadow image is then digitally processed using a custom developed “decision algorithm” to enable both the identification of the particle location in 3D and the characterization of each micro‐particle type within the sample volume. Through experimental results, we show that different cell types (e.g., red blood cells, fibroblasts, etc.) or other micro‐particles all exhibit uniquely different shadow patterns and therefore can be rapidly identified without any ambiguity using the developed decision algorithm, enabling high‐throughput characterization of a heterogeneous solution. This lensfree on chip cell imaging platform shows a significant promise especially for medical diagnostic applications relevant to global health problems, where compact and cost‐effective diagnostic tools are urgently needed in resource limited settings. Biotechnol. Bioeng. 2009; 102: 856–868. © 2008 Wiley Periodicals, Inc.
Rapid and quantitative quality control of microarrays using cationic nanoparticles
Authors: Sun Ye , Fan Wenhua , McCann Michael P. , Golovlev Val 
Published: September 2008

AbstractThe fabrication quality of microarrays significantly influences the accuracy and reproducibility of microarray experiments. In this report, we present a simple and fast quality control (QC) method for spotted oligonucleotide and cDNA microarrays. It employs a nonspecific electrostatic interaction of colloidal gold nanoparticles with the chemical groups of DNA molecules and other biomolecules immobilized on the microarray surface that bear positive or negative charges. An inexpensive flatbed scanner is used to visualize and quantify the binding of cationic gold particles to the anionic DNA probes on the microarray surface. An image analysis software was designed to assess the various parameters of the array spots including spot intensity, shape and array homogeneity, calculate the overall array quality score, and save the detailed array quality report in an Excel file. The gold staining technique is fast and sensitive. It can be completed in 10 min and detect less than 1% of the probe amount commonly recommended for microarrays. Compared to the current microarray QC method that utilizes the hybridization of probes with short random sequence oligonucleotides labeled with fluorophore, our gold staining method requires less time for the analysis, reduces the reagent cost, and eliminates the need for the expensive laser scanner. Biotechnol. Bioeng. 2009; 102: 960–964. © 2008 Wiley Periodicals, Inc.
A model of Agrobacterium tumefaciens vacuum infiltration into harvested leaf tissue and subsequent in planta transgene transient expression
Authors: Simmons Christopher W. , VanderGheynst Jean S. , Upadhyaya Shrinivasa K. 
Published: September 2008

AbstractAgrobacterium‐mediated gene transfer, or agroinfiltration, can be a highly efficient method for transforming and inducing transient transgene expression in plant tissue. The technique uses the innate DNA secretion pathway of Agrobacterium tumefaciens to vector a particular plasmid‐encoded segment of DNA from the bacteria to plant cells. Vacuum is often applied to plant tissue submerged in a suspension of A. tumefaciens to improve agroinfiltration. However, the effects of vacuum application on agroinfiltration and in planta transient transgene expression have not been well quantified. Here we show that vacuum application and release act to drive A. tumefaciens suspension into the interior of leaf tissue. Moreover, the amount of suspension that enters leaves can be predicted based on the vacuum intensity and duration. Furthermore, we show that transient expression levels of an agroinfiltrated reporter gene vary in response to the amount of A. tumefaciens vacuum infiltrated into leaf tissue, suggesting that vacuum infiltration conditions can be tailored to achieve optimal transient transgene expression levels after agroinfiltration. Biotechnol. Bioeng. 2009; 102: 965–970. © 2008 Wiley Periodicals, Inc.
Determination of rank by median absolute deviation (DRMAD): a simple method for determining the number of principal factors responsible for a data matrix
Authors: Malinowski Edmund R. 
Published: September 2008

AbstractMedian absolute deviation (MAD) is a well‐established statistical method for determining outliers. This simple statistic can be used to determine the number of principal factors responsible for a data matrix by direct application to the residual standard deviation (RSD) obtained from principal component analysis (PCA). Unlike many other popular methods the proposed method, called determination of rank by MAD (DRMAD), does not involve the use of pseudo degrees of freedom, pseudo F‐tests, extensive calibration tables, time‐consuming iterations, nor empirical procedures. The method does not require strict adherence to normal distributions of experimental uncertainties. The computations are direct, simple to use and extremely fast, ideally suitable for online data processing. The results obtained using various sets of chemical data previously reported in the chemical literature agree with the early work. Limitations of the method, determined from model data, are discussed. An algorithm, written in MATLAB format, is presented in the Appendix. Copyright © 2008 John Wiley & Sons, Ltd.
Use of cluster separation indices and the influence of outliers: application of two new separation indices, the modified silhouette index and the overlap coefficient to simulated data and mouse urine metabolomic profiles
Authors: Dixon Sarah J. , Heinrich Nina , Holmboe Maria , Schaefer Michele L. , Reed Randall R. , Trevejo Jose , Brereton Richard G. 
Published: September 2008

AbstractTo quantify separate classes, four indices are compared namely the Davies Bouldin index, the silhouette width and two new approaches described in this paper, the modified silhouette width index based on the proportion of objects with a positive silhouette width and the Overlap Coefficient. Four sets of simulated datasets are described, each in turn, consisting of 15 sets of data of varying degrees of overlap, and differing in the nature of outliers. Three experimental datasets consisting of the gas chromatography mass spectrometry of extracts from mouse urine obtained to study the effect of different environmental (stress), physiological (diet) and developmental (age) factors on their metabolic profiles are also described. The paper discusses the robustness of each approach to outliers, and to allow assessment of class separation for each index. The two modifications protect against outliers. Copyright © 2008 John Wiley & Sons, Ltd.
Accuracy of magnetic resonance imaging in predicting residual disease in patients treated for stage IB2/II cervical carcinoma with chemoradiation therapy
Authors: Vincens Etienne , Balleyguier Corinne , Rey Annie , Uzan Catherine , Zareski Elise , Gouy Sebastien , Pautier Patricia , Duvillard Pierre , Haie‐Meder Christine , Morice Philippe 
Published: September 2008

AbstractBACKGROUNDThe evaluation of residual disease (RD) after chemoradiation therapy (CRT) in stage IB2/II cervical carcinoma conventionally is based on a clinical examination and magnetic resonance imaging (MRI) performed 3 to 8 weeks after the end of treatment. Very few studies have correlated MRI and histologic findings specifically in cervix cancer. This was the objective of the current study.METHODSA retrospective review was undertaken of patients who fulfilled the following inclusion criteria: 1) stage IB2/II cervical cancer, 2) external radiotherapy (45 grays [Gy]) was given with concomitant chemotherapy followed by uterovaginal brachytherapy (15 Gy), 3) MRI studies were obtained between 3 weeks and 8 weeks after brachytherapy, and 4) completion surgery included at least a hysterectomy. Postsurgical histologic findings and MRI results were compared.RESULTSForty‐four patients who were treated between 2003 and 2006 fulfilled all inclusion criteria. Twelve patients (27%) had achieved a radiologic complete response, 16 patients (36.5%) had unclassified lesions (RD or ‘fibrosis’), and 16 patients (36.5%) had radiologic residual tumor. According to the histologic results, 19 patients (43%) had no RD, 10 patients (23%) had inframillimeter RD, 2 patients (5%) had RD that measured <1 cm, and 13 patients (29%) had RD that measured >1 cm. The sensitivity and specificity of MRI in evaluating RD were 80% and 55%, respectively.CONCLUSIONSThe current results indicated that the evaluation of RD 3 to 8 weeks after CRT with MRI is difficult, and the risk of false‐positive results is high. Another radiologic procedure or a more technologically advanced MRI technique, such as diffusion‐weighted MRI, should be evaluated. Cancer 2008. © 2008 American Cancer Society.
Multidisciplinary treatment of brain metastases derived from clear cell renal cancer incorporating stereotactic radiosurgery
Authors: Samlowski Wolfram E. , Majer Martin , Boucher Kenneth M. , Shrieve Annabelle F. , Dechet Christopher , Jensen Randy L. , Shrieve Dennis C. 
Published: September 2008

AbstractBACKGROUNDBrain metastases are a frequent complication in patients with metastatic clear cell renal cancer. Survival after whole‐brain radiotherapy (WBRT) is disappointing. A retrospective analysis of multimodality treatment was performed in patients who had received linear accelerator (LINAC)‐based stereotactic radiosurgery (SRS).METHODSThirty‐two patients underwent SRS‐based treatment for 71 metastatic foci between 2000 and 2006. All patients had a Karnofsky performance status ≥70 and all 32 patients had extracranial metastatic disease (Radiation Therapy Oncology Group recursive partitioning analysis [RPA] Class 2). Survival was calculated from the time of diagnosis of brain metastases. The minimum potential follow‐up was 1 year after SRS. Univariate and multivariate analysis of potential prognostic factors affecting survival was performed.RESULTSTwenty‐six patients required only 1 SRS treatment (84%) to achieve central nervous system (CNS) control, whereas 5 patients received 2 to 3 treatments (16%). The median survival of renal cancer patients from the diagnosis of brain metastases was 10.1 months (95% confidence interval, 6.4‐14.8 months). One‐year and 3‐year survival rates were 43% and 16%, respectively. The addition of surgery or WBRT did not appear to prolong survival. Immunotherapy after control of brain metastases with SRS appeared to result in significantly improved survival. Survival was also found to be strongly influenced by prognostic stratification of metastatic disease using Motzer or modified risk criteria.CONCLUSIONSThe results of the current study demonstrated that SRS‐based treatment of patients with up to 5 brain metastases from clear cell renal cancer is feasible and results in excellent CNS control. Survival beyond 3 years from the time of diagnosis of brain metastases was achievable in 16% of patients and was associated with the use of systemic immunotherapy with interleukin‐2 and interferon but not antiangiogenic agents. Cancer 2008. © 2008 American Cancer Society.
Surgical resection of the primary tumor, chest wall control, and survival in women with metastatic breast cancer
Authors: Hazard Hannah W. , Gorla Seema R. , Scholtens Denise , Kiel Krystyna , Gradishar William J. , Khan Seema A. 
Published: September 2008

AbstractBACKGROUNDAmong women presenting with de novo stage IV breast cancer, 35% to 60% undergo local therapy, presumably to avoid uncontrolled chest wall disease. Several studies suggest that resection of the primary tumor may prolong survival, but chest wall outcome data are notably lacking. The authors reviewed chest wall status, time to first progression (TTFP), and overall survival (OS) in this group of women.METHODSWomen presenting at the Lynn Sage Breast Center (1995‐2005) with an intact primary tumor and stage IV breast cancer or postoperative diagnosis of distant metastases were identified. Logistic regression and Cox proportional hazards models, adjusted for relevant covariates, were used to examine associations between surgical treatment and chest wall status, TTFP, and OS.RESULTSOf 111 eligible women, 47 (42%) underwent early resection of the primary tumor. Chest wall status was available for 103 women. Local control was maintained in 36 of 44 (82%) patients in the surgical group versus 20 of 59 (34%) patients without surgery (P = .001). TTFP was prolonged in the surgical group (adjusted hazards ratio [HR], 0.493; P = .015). The adjusted HR for OS in the surgical group was 0.798 (P = .520). Chest wall control was associated with improved OS regardless of whether surgical resection of the tumor was performed (HR, 0.415; P < .0002).CONCLUSIONSThese data support the notion that improved local control may play a role in improving outcomes in women with stage IV breast cancer, and resection of in‐breast tumors can help to achieve this. A randomized trial is needed to rule out selection bias as an explanation for these findings. Cancer 2008. © 2008 American Cancer Society.
Parallels between the development of therapeutic drugs and cancer health disparity programs
Authors: Chu Kenneth C. , Chen Moon S. , Dignan Mark B. , Taylor Emmanuel , Partridge Edward ,   Community Network Program Principal Investigators
Published: September 2008

AbstractBACKGROUNDThere are analogies between the development of therapeutic drugs for cancer and the development of interventions for reducing cancer health disparities. In both cases, it can take between 12 and 15 years for the benefits to become apparent.METHODSThe initial preclinical phase of drug development is analogous to the development of community partnerships and helping the community learn about cancer. The preclinical phase of in vitro and in vivo testing is analogous to identifying the disparities in the community. Then clinical testing begins with phase 1, toxicity, and dose‐establishing studies. Analogously, community‐based participatory research is used to develop disparities–reducing interventions (DRIs) within the community.RESULTSThe phase 2 clinical studies to determine whether the drug has activity are analogous to the DRI being implemented in the community to determine whether it can cause behavioral changes that will reduce cancer health disparities. If a drug passes phase 1 and 2 studies, phase 3 clinical trials are initiated. These are controlled studies to examine the efficacy of the drug. The similar activity for disparities research is to determine whether the DRI is better than the current standard/usual practice in controlled trials. If the drug is beneficial, the final phase is the dissemination and adoption of the drug. Analogously in disparities, if the DRI is beneficial, it is disseminated and is culturally adapted to other racial/ethnic groups and finally adopted as standard practice.CONCLUSIONSThe process of creating an effective DRI can be envisioned to have 4 stages, which can be used to aid in measuring the progress being made in reducing cancer health disparities. Cancer 2008. Published 2008 by the American Cancer Society.
Acute Renal Failure After Biopsy of a Transplant Kidney
Authors: Burhan Umber , Schleifer Charles R. 
Published: September 2008

AbstractPercutaneous biopsies of renal allografts are performed frequently, mostly for clinical indications and occasionally as protocol biopsies in some transplant centers. A rare complication of percutaneous needle biopsy is the development of a subcapsular hematoma, also known as Page kidney. The authors report such a case in a renal allograft following biopsy. What makes this case remarkable is the spontaneous resolution of the hematoma without surgical intervention, with reasonable recovery of allograft function, allowing cessation of dialysis.
Assessment of Potential Living Kidney Donors: Options for Increasing Donation
Authors: Akoh Jacob A. , Stacey Sarah 
Published: September 2008

AbstractOBJECTIVEThe aim of this study was to report the outcome of assessments of potential donors within a single center and to identify what factors can be modified to increase donation.METHODSBetween January 2003 and February 2008, 364 potential donors (237 related, 120 unrelated, and 7 altruistic) were referred to the stages assessment process for living kidney donation. Records of assessment and outcomes were entered prospectively into a spreadsheet maintained by the Living Donor Transplant Coordinator.RESULTSOf the 143 potential donors proceeding to stage 2 assessments, 25 were excluded for medical and other reasons, and 46 are currently being assessed. Sixty‐five donor nephrectomies were performed, with 7 awaiting surgery, giving a donation rate of 21.3% (65 of 305) and a potential donation rate of 24% (72 of 305) if all 7 successfully donate. The reasons for exclusion from stage 1 assessment included immunological considerations, multiple donors, and cadaveric transplantation of an intended recipient.DISCUSSIONIntroduction of paired exchange and non‐directed donation, ABO incompatible transplantation, or desensitization of potential recipients will improve living donation rates. Potential donors withdrawing either because of another more suitable donor or their recipient being transplanted could be made aware (no obligations) of the option of altruistic non‐directed donation.
Prevalence of Occult Hepatitis B Infection in Hemodialysis Patients
Authors: Ersoy Osman , Yilmaz Rahmi , Arici Mustafa , Turgan Cetin , Bayraktar Yusuf 
Published: September 2008

AbstractBACKGROUNDThe presence of low‐level hepatitis B virus (HBV) DNA has been demonstrated in some hepatitis B surface antigen (HBsAg)–negative patients. This HBsAg‐negative but HBV DNA–positive case has been named occult hepatitis B virus (OHBV) infection. The aim of this study was to determine the prevalence of OHBV in patients on maintenance hemodialysis.METHODSEighty patients who were on dialysis and were previously detected as HBsAg negative were recruited in the study. Thirty‐two patients (40%) were female, and the mean age was 51.56 ± 14.16 years (21–78 years). HBV DNA was searched for by the polymerase chain reaction method in the sera of all patients.RESULTSSixty‐eight patients (85%) positive for at least 1 of the serological markers used for hepatitis B, 3 patients (3.75%) positive for only antibody to hepatitis B core antigen, and 33 patients (41.25%) positive for only antibody to HBsAg were identified. The prevalence of OHBV infection was found to be 1.25%.CONCLUSIONSEven though the prevalence of OHBV infection was found to be low in patients undergoing dialysis, searching for HBV DNA, if possible, will be useful because there is contagiousness in OHBV infection, and activation of OHBV infection has been known to occur after immunosuppressive treatment.
Seismic design and response evaluation of unbonded post‐tensioned hybrid coupled wall structures
Authors: Kurama Yahya C. , Shen Qiang 
Published: September 2008

AbstractThis paper presents an analytical investigation on the seismic design and response of coupled wall structures that use unbonded post‐tensioned steel coupling beams. Both monolithic cast‐in‐place reinforced concrete wall piers and precast concrete wall piers are considered. Steel top and seat angles are used at the coupling beam ends for energy dissipation. The seismic design of prototype structures to achieve target displacement‐based performance objectives is evaluated based on nonlinear static and dynamic time history analyses. Additional recommendations are provided on shear design. Comparisons with ‘conventional’ structures that use embedded steel coupling beams as well as isolated walls with no coupling are provided. The results indicate that while the peak lateral displacements of unbonded post‐tensioned coupled wall structures are larger than the peak displacements of structures with embedded beams, the residual displacements are significantly reduced as a result of the restoring effect of the post‐tensioning steel. Copyright © 2008 John Wiley & Sons, Ltd.